Branching diagram of evolutionary relationships between organisms
POPULARITY
6 episodes with phylogeny
3 episodes with phylogeny
2 episodes with phylogeny
2 episodes with phylogeny
2 episodes with phylogeny
2 episodes with phylogeny
2 episodes with phylogeny
7 episodes with phylogeny
3 episodes with phylogeny
In this episode, we explore Oxytocin and Vasopressin's vast roles in Human Biology. We time travel to cover the evolution of the two molecules and learn about their functions with developing and socializing. Oxytocin and Vasopressin are dynamic molecules whereby they are Peptides and Hormones. In addition, we cover previously discussed brain regions and how the molecules work alongside key Neuromodulators like Serotonin and Dopamine.Social Reward https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214365/Social Reward Requires Oxytocin and Serotonin in Nucleus Accumbens (Parvo Path) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091761/Magnocellular and Parvocellular social Information Processing https://www.cell.com/neuron/fulltext/S0896-6273(20)30770-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627320307704%3Fshowall%3DtrueMagnocellular and Parvocellular https://onlinelibrary.wiley.com/doi/10.1111/jne.12284Meta-Analysis of Intranasal https://pubmed.ncbi.nlm.nih.gov/?term=intranasal+oxytocin+autism&sort=pubdate&filter=pubt.meta-analysishttps://pubmed.ncbi.nlm.nih.gov/33400920/Intranasal Review https://pubmed.ncbi.nlm.nih.gov/38579916/(0:00) Intro; Oxytocin and Vasopressin; Episode Objectives(2:46) Oxytocin and Vasopressin; 700 million year time travel (Phylogeny)(4:12) Peptides and Hormones; Modes of Transmission- Endocrine, Paracrine, Synaptic(6:35) Proteins and Peptides; Amino Acids and Aromatic Amino Acids and Light(8:58) Magnocellular and Parvocellular(12:33) Roles of Oxytocin and Vasopressin and connections to various Brain Regions(22:20) Scientific Literatures(27:12) Oxytocin and Serotonin; 1) Reward Processing, 2) Fear Response, 3) Social-Emotional Processing(30:07) Oxytocin and Dopamine(31:08) Dopamine Receptors(31:37) GABA(33:57) Intranasal Oxytocin(36:08) Take aways from Intranasal Literature(37:24) Biggest Take Away (Magnocellular versus Parvocellular and Intranasal Administration)email: info.fromthespectrum@gmail.com
Send us a textIn this episode I"m joined by Bahar Roohshad, an undergraduate student from one of my classes to talk about phylogenetics. What are they? what are they for and how might we use on?
For today's episode, we discussing transferring energy from the environment across our biology. We discuss a few quantum theories, atoms, molecules, water, DHA, and NF-kB. Life on Earth is driven by energy from the environment, and this could be missed with humans, and especially with developmental problems like Autism.Water Podcast 1: Rubin, Kruse, Huberman https://www.youtube.com/watch?v=0lBAcUMGIeI&t=43sWater Podcast 2: Gulhane and Kruse (Light changes the Physics of Water !) https://www.youtube.com/watch?v=l9UbguvfpysWater Podcast 3: Gulhane and Kruse https://www.youtube.com/watch?v=W5w0WainlMMhttps://www.plefa.com/article/S0952-3278(12)00147-0/abstracthttps://pmc.ncbi.nlm.nih.gov/articles/PMC5793004/#:~:text=Electrons%20exist%20in%20all%20matter,role%20in%20oxidation%2Dreduction%20reactions.Quantum-coherent energy transfer: implications for biology and new energy technologies https://pmc.ncbi.nlm.nih.gov/articles/PMC3385675/#:~:text=In%20the%20simplest%20picture%2C%20quantum,transport%20at%20the%20molecular%20scale.Quantum cognition: The possibility of processing with nuclear spins in the brain https://www.sciencedirect.com/science/article/abs/pii/S0003491615003243Role of semiconductivity and ion transport in the electrical conduction of melanin https://www.pnas.org/doi/10.1073/pnas.11199481090:00 Intro0:40 Quantum Biology, Coherence, Thermodynamics, Water, DHA, NF-kB, and transferring energy - Atoms & Molecules2:00 Oxygen and CCO; Mitochondria3:55 Quantum Biology; Environments influence Atoms & Molecules5:50 Coherence & States; Light guides Life on Earth; Light provides Energy after it hits Matter7:16 Modern Human Environments7:41 Quantum Thermodynamics; Melanin, Electrons; Rules9:03 Biophotons, Photons and Lux; Seasonal Impact11:15 Electrons & Mitochondria; Real sources of Energy12:00 Artificial Light versus 280nm-3100nm Light; Big Harma & GLP-1 sidebar14:16 Autism and Loss of Biological Energy; changes in Light15:43 Electrons in Biology; Water; Coherent Domains; Semiconductors17:15 DHA; Electron Efficiency; Cells; Photoreceptors and Converting Energy and Developing Nervous Systems (plural)19:20 Phylogeny of Oxytocin and DHA sidebar; pi-electons; DHA dictates DNA22:40 Jack Kruse Quote23:36 Cells, Tissues, & Synapses; Origins of Autism; DHA roles26:14 Autism and X, Y, Z comorbid conditions (plural); definitions of Autism (modern versus origins), Criteria29:23 DHA takeaways; efficiency31:41 NF-kB; creating the womb and nervous systems; Autism and Orbitofrontal Cortex (OFC)35:06 Reviews/Rating & Contact Info
Heute tauchen wir ab. Zu schwarzen Rauchern und mysteriösen Metallgebilden. Zu Seegurken und Borstenwürmern. Zu Anglerfischen und anderen leuchtenden Wesen. Wir reisen in die Tiefsee. Und so karg es dort auf den schummrigen Aufnahmen von Unterwasserrobotern aussehen mag: In der Dunkelheit wimmelt es nur so von Leben! Ging man bis zur Mitte des 21. Jahrhunderts davon aus, dass dort unten nur vereinzelte, zoologische Kuriositäten überleben können, weiß man heute: Die Artenvielfalt am Grund unserer Meere ist stellenweise mit der tropischer Regenwälder vergleichbar. Erforscht ist von dieser fremden Welt so gut wie nichts. Und doch wollen wir sie ausbeuten: Tiefseebergbau soll Metalle fördern. Mähdrescherartige Maschinen sollen über Jahrmillionen gewachsene Strukturen einsammeln. All das natürlich ohne eine Ahnung davon zu haben, welche Auswirkungen das auf das Ökosystem Tiefsee, aber auch auf unseren Planeten haben könnte.Aber bleiben wir doch lieber bei den schönen und faszinierenden Seiten dieser entlegenen Welt! Und übrigens: Wer jedes Mal, wenn die Worte“Seegurke” und “Manganknolle” fallen, einen Liegestütz macht, hat am Ende der Folge sein Workout absolviert!Weiterführende Links:alle Links zur Show und uns gibt's jetzt hier: linkt.ree/tierischpodcastAuf das Thema sind wir durch unsere Hörerin Elena gekommen, die uns diesen Artikel über Manganknollen schickte: https://www.scinexx.de/news/geowissen/tiefsee-erzeugt-dunklen-sauerstoff/Buch von Frauke: https://www.oekom.de/buch/wal-macht-wetter-9783962384197Mehr zu Bioluminiszenz bei Tierisch! #49 Die große Weichtierrevue: https://shows.acast.com/642c2103dcec3a00114ec45f/663962b955607b00121d92abMehr zum Anglerfisch bei Tierisch! #60 Fataler Sex: https://shows.acast.com/642c2103dcec3a00114ec45f/668c2fb32387098e0478fca9Interview mit Bioluminiszenz-Forscher: https://www.bundesregierung.de/breg-de/aktuelles/biolumineszenz-2019600Diversität an Wal Skeletten: https://www.researchgate.net/publication/279401832_Phylogeny_and_diversity_of_symbionts_from_whale_fall_invertebratesIhr könnt uns unterstützen: https://steadyhq.com/de/tierisch/ Hosted on Acast. See acast.com/privacy for more information.
-How did horror movies come to haunt us? Guest: Dr. Gary Rhodes, Professor of Media Production at Oklahoma Baptist University -Could BC's deep sea minerals offer cures for illness? Guest: Moronke Harris, Founder of The Imaginative Scientist -Are ghosts real? Guest: Dr. Christopher French, Professor of psychology and Head of the Anomalistic Psychology Research Unit at Goldsmiths, University of London -What are Canada's most genetically lonely animals? Guest: Arne Mooers, Professor of Biodiversity, Phylogeny and Evolution at Simon Fraser University -How prevalent is misinformation in Canada? Guest: Timothy Caulfield, Professor in the Faculty of Law and the School of Public Health and Research Director of the Health Law Institute at the University of Alberta -What is the origin story of Halloween? Guest: Nicole Kilburn, Professor of Anthropology at Camosun College Learn more about your ad choices. Visit megaphone.fm/adchoices
Matters Microbial #59: Some (Microbes) Like It Hot—Discussions with the Thermal Biology Institute October 3, 2024 Today is an unusual episode of the podcast. I am visiting four microbiologists in the Thermal Biology Institute at Montana State University of Bozeman, Montana. They discuss their work exploring the unusual microbes and environments to be found in Yellowstone National Park, ranging from the history of the park to opportunities for undergraduate students, as well as up-to-the-minute research done on the microbial denizens of this microbiological landmark. Host: Mark O. Martin Guests (in order of appearance:): Brent Peyton, Dana Skorupa, Zackary Jay, Anthony Kohtzy Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode A history and overview of Yellowstone National Park. An overview of microbiology in Yellowstone National Park. The story of Yellowstone National Park and PCR. Website for the Thermal Biology Institute. A prior podcast of #MattersMicrobial involving Dr. Roland Hatzenpichler and the research done by several of today's guests. Dr. Peyton's faculty website. Dr. Peyton's laboratory website. Dr. Skorupa's faculty website. A great article on the adventurous REU (Research Experience for Undergraduates) that Dr. Skorupa supervises. Dr. Jay's faculty website. A journal article describing some of Dr. Jay's (and Dr. Kohtz') work. A page including Dr. Kohtz An article describing some of Dr. Kohtz' (and Dr. Jay's) work. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com
Send us a textWhat happens when a dare to perform in a red Speedo turns into a legendary band memory? In this milestone 100th episode of Milk Crates and Turntables, we trip down memory lane, discussing junior high dances, the formation of early bands like Phylocinium and Phylogeny, and the wild escapades of Anthony, Todd, and Lou. Discover the hilarious origin stories, the brotherly bond between bandmates, and the iconic moments that have shaped their musical journey. With playful banter and amusing anecdotes, this episode is a celebration of camaraderie and the early days of live music.But that's not all—our episode is packed with engaging segments that are bound to keep you entertained. Join us as we debate the merits of guitar solos versus drum solos, and Southern rock versus glam rock, sparking a lively discussion about our favorite musical eras and genres. We get competitive with a music trivia game show, drawing classic vinyl records and reminiscing about hits from legendary labels like Arista and Atlantic. From the creative genius of bands like Blue Öyster Cult to the technical prowess of disco music, there's something for every music enthusiast.Finally, we dive into the melancholic yet powerful world of Nick Cave and the Bad Seeds, focusing on his recent album "Ghosteen" and the emotional depth of his music. We explore the intellectual richness of contemporary artists like PJ Harvey and Steven Wilson, reflecting on how their work adds a timeless layer to our musical landscape. Join us for an episode overflowing with nostalgia, laughter, and an unwavering love for music, as we celebrate our 100th episode with heartfelt appreciation for our loyal listeners and podcast family.
In this episode, we explore Oxytocin and Vasopressin's vast roles in Human Biology. We time travel to cover the evolution of the two molecules and learn about their functions with developing and socializing. Oxytocin and Vasopressin are dynamic molecules whereby they are Peptides and Hormones. In addition, we cover previously discussed brain regions and how the molecules work alongside key Neuromodulators like Serotonin and Dopamine.Social Reward https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214365/Social Reward Requires Oxytocin and Serotonin in Nucleus Accumbens (Parvo Path) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091761/Magnocellular and Parvocellular social Information Processing https://www.cell.com/neuron/fulltext/S0896-6273(20)30770-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627320307704%3Fshowall%3DtrueMagnocellular and Parvocellular https://onlinelibrary.wiley.com/doi/10.1111/jne.12284Meta-Analysis of Intranasal https://pubmed.ncbi.nlm.nih.gov/?term=intranasal+oxytocin+autism&sort=pubdate&filter=pubt.meta-analysishttps://pubmed.ncbi.nlm.nih.gov/33400920/Intranasal Review https://pubmed.ncbi.nlm.nih.gov/38579916/(0:00) Intro; Oxytocin and Vasopressin; Episode Objectives(2:46) Oxytocin and Vasopressin; 700 million year time travel (Phylogeny)(4:12) Peptides and Hormones; Modes of Transmission- Endocrine, Paracrine, Synaptic(6:35) Proteins and Peptides; Amino Acids and Aromatic Amino Acids and Light(8:58) Magnocellular and Parvocellular(12:33) Roles of Oxytocin and Vasopressin and connections to various Brain Regions(22:20) Scientific Literatures(27:12) Oxytocin and Serotonin; 1) Reward Processing, 2) Fear Response, 3) Social-Emotional Processing(30:07) Oxytocin and Dopamine(31:08) Dopamine Receptors(31:37) GABA(33:57) Intranasal Oxytocin(36:08) Take aways from Intranasal Literature(37:24) Biggest Take Away (Magnocellular versus Parvocellular and Intranasal Administration)email: info.fromthespectrum@gmail.com
Today, Dr. Todd Wood of the Core Academy of Science, summarizes his list of what I would presume is his best evidence against evolution...and it's not very good.Cards:Evidence for Evolution - Phylogenetics: https://www.youtube.com/watch?v=cf90hGT8ZeAIs it human? Ape? Both? Neither?:https://www.youtube.com/watch?v=G1KDnYlJrJ0Irreducible Complexity PROVES evolution?!?
Classifying organisms is an important function of biology. But if phylogenetics is ultimately based on a floundering theory of origins, how helpful is it to our understanding of living things? On this ID The Future, host Andrew McDiarmid and paleoentemologist Gunter Bechly unpack some of the major problems with arachnid phylogeny and its implications for the common descent hypothesis. Source
Make sure you celebrate International Plant Appreciation Day tomorrow! Music by James Milor from Pixabay Information provided by: Carnivorous plants: Phylogeny and structural evolution by Victor A. Albert, Stephen E. Williams, & Mark W. Chase (1992) https://doi.org/10.1126/science.1523408 Fluid physico-chemical properties influence capture and diet in Nepenthes pitcher plants by Vincent Bazile, et al. (2015) https://doi.org/10.1093/aob/mcu266 https://www.britannica.com/plant/pitcher-plant https://www.buffalo.edu/news/releases/2023/11/how-carnivorous-Asian-pitcher-plants-acquired-signature-insect-traps.html How a sticky fluid facilitates prey retention in a carnivorous pitcher plant (Nepenthes rafflesiana) by Victor Kang, et al. (2021) https://doi.org/10.1016/j.actbio.2021.04.002 Bait, not reward: CO2-enriched Nepenthes pitchers secrete toxic nectar by Chandni Chandran Lathika, et al. (2023) https://doi.org/10.1101/2023.11.25.568661 https://www.nationalgeographic.com/environment/article/carnivorous-pitcher-plants https://en.wikipedia.org/wiki/Pitcher_plant https://www.worldwildlife.org/magazine/issues/fall-2020/articles/tropical-pitcher-plants-are-beautiful-but-deadly
Brian Boyd is a Distinguished Professor in English and Drama at the University of Auckland. We talk mainly about Vladimir Nabokov: Brian wrote the defining biography on Nabokov (in addition to books on more specific aspects about Nabokov), so we discuss Nabokov's life & work, Brian's approachh to writing biographies, with some hints of the new biography Brian is writing about Karl Popper.BJKS Podcast is a podcast about neuroscience, psychology, and anything vaguely related, hosted by Benjamin James Kuper-Smith.Support the show: https://geni.us/bjks-patreonTimestamps0:00:00: Why this is a special episode for me0:07:02: Nabokov's family & childhood0:15:54: The Russian Revolution, starting in 19170:19:52: Nabokov's study years in Cambridge and emigre years in Berlin in the 1920s and 30s0:30:19: Nabokov's early American years: teaching and butterflies0:35:56: Nabokov's Russian vs English works, and the problem of translations0:41:48: Lolita0:50:13: Pale Fire1:02:46: Nabokov's writing process1:07:26: Nabokov's reception1:10:00: Writing Nabokov's biography: how it started, meeting Nabokov's family, researching and writing, and the responsibility of writing the defining work on someone1:28:26: Which Nabokov book should new readers read first?1:30:58: A book or paper more people should read1:35:03: Something Brian wishes he'd learnt sooner1:38:47: Advice for PhD students/postdocsPodcast linksWebsite: https://geni.us/bjks-podTwitter: https://geni.us/bjks-pod-twtBrian's linksWebsite: https://geni.us/boyd-webBen's linksWebsite: https://geni.us/bjks-webGoogle Scholar: https://geni.us/bjks-scholarTwitter: https://geni.us/bjks-twtReferences and linksThe estate Nabokov inherent and immediately lost in th revolution: https://en.wikipedia.org/wiki/Rozhdestveno_Memorial_EstateAda online, Brian's line-by-line annotations to Nabokov's Ada: https://www.ada.auckland.ac.nz/ Boyd (1985/2001). Nabokov's Ada: The Place of Consciousness. Boyd (1990). Vladimir Nabokov: The Russian Years. Boyd (1991). Vladimir Nabokov: The American Years.Boyd & Pyle (eds) (2000). Nabokov's Butterflies .Boyd (2001). Nabokov's Pale Fire: The Magic of Artistic Discovery.Grass (1959). Die Blechtrommel.James (1897). What Maisie Knew. Machado de Assis (1882). The Posthumous Memoirs of Brás Cubas. [The 2 new translations are by Thomson-DeVeaux (Penguin Classics), and by Jull Costa & Patterson (Liveright)]Nabokov (1929). The (Luzhin) Defense. Nabokov (1936). Invitation to a Beheading. Nabokov (1947). Bend Sinister. Nabokov (1955). Lolita. Nabokov (1957). Pnin. Nabokov (1962). Pale Fire. Nabokov (1967). Speak, Memory. Nabokov (1969). Ada or Ardor.Tarnowsky (1908). Les femmes homicides. [Nabokov's great-aunt; see also: Huff-Corzine & Toohy (2023). The life and scholarship of Pauline Tarnowsky: Criminology's mother. Journal of Criminal Justice]Vila, Bell, Macniven, Goldman-Huertas, Ree, Marshall, ... & Pierce (2011). Phylogeny and palaeoecology of Polyommatus blue butterflies show Beringia was a climate-regulated gateway to the New World. Proceedings of the Royal Society B: Biological Sciences.
Today on Mushroom Hour we have the pleasure of interviewing Dr. Francisco Kuhar. Dr. Kuhar is a Mycologist specialized in the fungal diversity of gasteroid and ectomycorrhizal fungi and biotechnological applications of fungal enzymes. He has a special interest in the evolutionary biology of sequestrate forms of fungi. Dr. Kuhar is an Associate researcher at CONICET in the Instituto Multidisciplinario de Biologia Vegetal (IMBIV - UNC), curator of Fungi at the CORD Herbarium and one of the leaders of Inommy Labs helping to pioneer a new fungi-based product platform. TOPICS: Freud, Linguistics and Life Sciences Hongos in Patagonia See the Future in a Spore Hypogeous & Sequestrate Fungi Pedomorphosis Mutations Happening too Fast in the Evolutionary Record Are We Too Obsessed with Adaptation in Evolutionary Biology? The Story of Rhizopogon and Suillis Alan Turing Equations Predicting Biological Forms Approaching Scientific Questions with an Open Mind Burning Questions on Underground Fungi Matching Genetics to Traits in Fungi Inommy Labs Fungal Bioprospecting LINKS: Francisco Kuhar IG: https://www.instagram.com/franfungi Innomy Labs: http://innomylabs.com/index.html Hongos De Argentina: https://hongos.ar/ "Ontogeny and Phylogeny": https://www.hup.harvard.edu/catalog.php?isbn=9780674639416 Turing pattern: https://en.wikipedia.org/wiki/Turing_pattern Geastrum genus: https://en.wikipedia.org/wiki/Geastrum
------------------Support the channel------------ Patreon: https://www.patreon.com/thedissenter PayPal: paypal.me/thedissenter PayPal Subscription 3 Dollars: https://tinyurl.com/ybn6bg9l PayPal Subscription 5 Dollars: https://tinyurl.com/ycmr9gpz PayPal Subscription 10 Dollars: https://tinyurl.com/y9r3fc9m PayPal Subscription 20 Dollars: https://tinyurl.com/y95uvkao ------------------Follow me on--------------------- Twitter: https://twitter.com/TheDissenterYT This show is sponsored by Enlites, Learning & Development done differently. Check the website here: http://enlites.com/ Dr. Carrie Mongle is Assistant Professor in the Department of Anthropology at Stony Brook University and the Turkana Basin Institute. She also heads the Mongle Lab. Her research aims to reconstruct the major trends and transitions that characterize hominin diversity and evolution. Her ongoing work toward that goal involves (1) the discovery and description of new hominin fossils from the Turkana Basin in Kenya; (2) quantification of morphological variation; and (3) comprehensive phylogenetic analyses founded on the careful character assessment of both craniodental and postcranial characters. In this episode, we talk about hominin phylogenetics. We first talk about work done in the Turkana Basin in Kenya. We talk about craniodental and postcranial features looked at when studying human phylogenetics, and changes in hominin dentition. We discuss what we know about hominin phylogeny, and the cases of Ardipithecus ramidus and Australopithecus sediba. We talk about studying microevolution and macroevolution, and how they interact. We talk about the example of primate molars. We discuss the relationship between development and evolution. We talk about how we can best model hominin evolution. Finally, we discuss some unanswered questions in human phylogenetics. -- A HUGE THANK YOU TO MY PATRONS/SUPPORTERS: PER HELGE LARSEN, JERRY MULLER, HANS FREDRIK SUNDE, BERNARDO SEIXAS, OLAF ALEX, ADAM KESSEL, MATTHEW WHITINGBIRD, ARNAUD WOLFF, TIM HOLLOSY, HENRIK AHLENIUS, JOHN CONNORS, FILIP FORS CONNOLLY, DAN DEMETRIOU, ROBERT WINDHAGER, RUI INACIO, ZOOP, MARCO NEVES, COLIN HOLBROOK, PHIL KAVANAGH, SAMUEL ANDREEFF, FRANCIS FORDE, TIAGO NUNES, FERGAL CUSSEN, HAL HERZOG, NUNO MACHADO, JONATHAN LEIBRANT, JOÃO LINHARES, STANTON T, SAMUEL CORREA, ERIK HAINES, MARK SMITH, JOÃO EIRA, TOM HUMMEL, SARDUS FRANCE, DAVID SLOAN WILSON, YACILA DEZA-ARAUJO, ROMAIN ROCH, DIEGO LONDOÑO CORREA, YANICK PUNTER, ADANER USMANI, CHARLOTTE BLEASE, NICOLE BARBARO, ADAM HUNT, PAWEL OSTASZEWSKI, NELLEKE BAK, GUY MADISON, GARY G HELLMANN, SAIMA AFZAL, ADRIAN JAEGGI, PAULO TOLENTINO, JOÃO BARBOSA, JULIAN PRICE, EDWARD HALL, HEDIN BRØNNER, DOUGLAS FRY, FRANCA BORTOLOTTI, GABRIEL PONS CORTÈS, URSULA LITZCKE, SCOTT, ZACHARY FISH, TIM DUFFY, SUNNY SMITH, JON WISMAN, DANIEL FRIEDMAN, WILLIAM BUCKNER, PAUL-GEORGE ARNAUD, LUKE GLOWACKI, GEORGIOS THEOPHANOUS, CHRIS WILLIAMSON, PETER WOLOSZYN, DAVID WILLIAMS, DIOGO COSTA, ANTON ERIKSSON, CHARLES MOREY, ALEX CHAU, AMAURI MARTÍNEZ, CORALIE CHEVALLIER, BANGALORE ATHEISTS, LARRY D. LEE JR., OLD HERRINGBONE, STARRY, MICHAEL BAILEY, DAN SPERBER, ROBERT GRESSIS, IGOR N, JEFF MCMAHAN, JAKE ZUEHL, BARNABAS RADICS, MARK CAMPBELL, TOMAS DAUBNER, LUKE NISSEN, CHRIS STORY, KIMBERLY JOHNSON, BENJAMIN GELBART, JESSICA NOWICKI, LINDA BRANDIN, NIKLAS CARLSSON, ISMAËL BENSLIMANE, GEORGE CHORIATIS, VALENTIN STEINMANN, PER KRAULIS, KATE VON GOELER, ALEXANDER HUBBARD, LIAM DUNAWAY, BR, MASOUD ALIMOHAMMADI, PURPENDICULAR, JONAS HERTNER, URSULA GOODENOUGH, GREGORY HASTINGS, DAVID PINSOF, SEAN NELSON, MIKE LAVIGNE, JOS KNECHT, ERIK ENGMAN, AND LUCY! A SPECIAL THANKS TO MY PRODUCERS, YZAR WEHBE, JIM FRANK, ŁUKASZ STAFINIAK, TOM VANEGDOM, BERNARD HUGUENEY, CURTIS DIXON, BENEDIKT MUELLER, THOMAS TRUMBLE, KATHRINE AND PATRICK TOBIN, JONCARLO MONTENEGRO, AL NICK ORTIZ, AND NICK GOLDEN! AND TO MY EXECUTIVE PRODUCERS, MATTHEW LAVENDER, SERGIU CODREANU, BOGDAN KANIVETS, AND ROSEY!
The physical solidity of books encourages notions of "the text" or "the canonical edition". The challenges to this view from post-modernist thought are well known. But there are other ways in which this model of a static text may fail. Our guest this week is Peter Robinson (my dad!) who takes us through his work on Chaucer's Canterbury Tales. This is a paradigmatic case of a work of literature that defies understanding as fixed text. Originally it would have been read, or performed. What exists now are fragments of transcripts of performances. And copies of those fragments. And copies of copies.Using techniques from phylogenetics, Peter has led efforts to piece together the relationships between these manuscripts. By tracing how transcription errors (or edits) appear to propagate, we can create a family tree of the texts, just as we can trace the propagation of biological traits through generations.Sounds simple? "After 30 years of working on this, we're really just beginning to understand what a representation of a textual tradition using these tools gives us" Peter's academic homepage Peter's article in Nature on The Canterbury Tales (there are not many articles in Nature about Chaucer!) Multiverses home
Several anti-creationists have made a hobby out of attacking creationists. Their best efforts, however, have generally failed. For example, see: Sanford 2013 Critic ignores reality of Genetic Entropy: the author of a landmark book on genomic decay responds to unsustainable criticisms creation.com 7 Mar 2013. Price, Carter, and Sanford 2020, Responding to supposed refutations of genetic entropy from the ‘experts', creation.com, 1 Dec 2020. Unperturbed, "Gutsick Gibbon" has recently tried to discredit Dr Jeffrey Tomkins and his work on human-chimp genetic similarities: "80% Chimpanzee" | The Bogus Creationism of Jeffery Tomkins" 26 May 2023 youtube.com/watch?v=QtTHlqhRQi0. In my analysis of her analysis, I note several flaws in her logic. Note, however, that I deliberately ignored several of her main objections. This was not because I do not have answers, mind you, but because I wanted to focus on the most salient questions. Ignored were questions about why God would have included all the chimp-like non-coding DNA when he made humans and questions about properly weighting samples. The most recent comparison I am aware of claimed 96.6% similarity between humans and chimps: Seaman and Buggs 2020 FluentDNA: nucleotide visualization of whole genomes, annotations, and alignments, Frontiers in Genetics 30;11:292. This comes from the laboratory of Richard Buggs. This is much higher than Tomkins' estimates, that, with one exception, are generally in the 80s. However, I know the first author on that paper, so I called him up to discuss his methods. Sure enough, he used entirely different methodology than earlier work from that same laboratory (which arrived at an estimate of ~85%). To reach the higher percentage similarity, they cut out everything humans and chimps do not share, including the centromeres, telomeres, copy number variations of many annotated genes, and hundreds of thousands of small insertions and deletions that must be included to align the two genomes. This "apples to apples" comparison is fine, as long as everybody acknowledges that the true similarity is necessarily less than 96.6%. Yet, if the percent similarity is much less than 99%, there is no way, mathematically, to explain how so many millions of difference arose in the (imagined) 6.5 million years since our last common ancestor. Additional links: The Waiting Time Problem, BiblicalGenetics.com, 8 Jun 2021. Hierachical clustering complicates baraminiological analysis Carter 2021 Robert Carter gets everything wrong? Responding to even more ridiculous aspersions, creation.com, 10 July 2021. “Dr. Rob Carter Gets Everything Wrong (with Gutsick Gibbon)” 20 May 2021. Sibley and Alquist. 1991. The Phylogeny and Classification of Birds. King and Wilson. 1975. Evolution at two levels in humans and chimpanzees, Science 188(4184):107–116. Moorjani et al. 2016. Variation in the molecular clock of primates, PNAS 113(38):10607–10612. Sibley and Ahlquist. 1984. The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization, J Mol Evol 20(1):2–15. Sibley, Comstock, and Ahlquist. 1990. DNA hybridization evidence of hominoid phylogeny: a reanalysis of the data, J Mol Evol 30(3):202–36. Wikipedia page on DNA reassociation kinetics. Bergman and Tomkins 2012 Is the human genome nearly identical to chimpanzee?—a reassessment of the literature, Journal of Creation 26(1):54–60, Tomkins and Bergman 2012 Genomic monkey business—estimates of nearly identical human–chimp DNA similarity re-evaluated using omitted data, Journal of Creation 26(1):94–100, Tomkins 2013 Comprehensive analysis of chimpanzee and human chromosomes reveals average DNA similarity of 70%. Answers Research Journal 8:379–390. The version of BLAST he used for this paper had a flaw in the algorithm that only manifested when using extremely large data sets. Tomkins corresponded with the bioinformatics group at the NIH to get the BLAST...
The Matt Slick Live daily radio show broadcast is a production of the Christian Apologetics Research Ministry -CARM-. During the show, Matt answers questions on the air, and offers insight on topics like The Bible, Apologetics, Theology, World Religions, Atheism, and other issues-- The show airs live on the Truth Network, Monday through Friday, 6-7 PM, EST -3-4 PM, PST--You can also email questions to Matt using- info-carm.org, Please put -Radio Show Question- in the Subject line--You can also watch a live stream during the live show on RUMBLE---Time stamps are approximate due to commercials being removed for PODCAST.--Topics include---04- Amillennialism, Revelation- 20- 1-3.-16- Assembly Of God Church, The AOG.-18- Is there a literal 1000 year Millennial reign.-24- Nazarene Church issues.-27- The Assyrian Church of the East, Nestorianism, Hypostatic Union.-35- Phylogeny.
The Matt Slick Live daily radio show broadcast is a production of the Christian Apologetics Research Ministry (CARM). During the show, Matt answers questions on the air, and offers insight on topics like The Bible, Apologetics, Theology, World Religions, Atheism, and other issues! The show airs live on the Truth Network, Monday through Friday, 6-7 PM, EST (3-4 PM, PST) You can also email questions to Matt using: info@carm.org, Please put "Radio Show Question" in the Subject line! You can also watch a live stream during the live show on RUMBLE! MSL: August, 3 2023 Time stamps are approximate due to commercials being removed for PODCAST. Topics include: 04- Amillennialism, Revelation: 20: 1-3. 16- Assembly Of God Church, The AOG. 18- Is there a literal 1000 year Millennial reign. 24- Nazarene Church issues. 27- The Assyrian Church of the East, Nestorianism, Hypostatic Union. 35- Phylogeny. MSL: August, 3 2023 CARM This show LIVE STREAMS on RUMBLE during the Radio Broadcast! Subscribe to the CARM YouTube Channel Subscribe to the Matt Slick YouTube Channel CARM on Facebook Visit the CARM Website Donate to CARM You can find our past podcast by clicking here!
The Matt Slick Live daily radio show broadcast is a production of the Christian Apologetics Research Ministry (CARM). During the show, Matt answers questions on the air, and offers insight on topics like The Bible, Apologetics, Theology, World Religions, Atheism, and other issues! The show airs live on the Truth Network, Monday through Friday, 6-7 PM, EST (3-4 PM, PST) You can also email questions to Matt using: info@carm.org, Please put "Radio Show Question" in the Subject line! You can also watch a live stream during the live show on RUMBLE! MSL: August, 3 2023 Time stamps are approximate due to commercials being removed for PODCAST. Topics include: 04- Amillennialism, Revelation: 20: 1-3. 16- Assembly Of God Church, The AOG. 18- Is there a literal 1000 year Millennial reign. 24- Nazarene Church issues. 27- The Assyrian Church of the East, Nestorianism, Hypostatic Union. 35- Phylogeny. MSL: August, 3 2023 CARM This show LIVE STREAMS on RUMBLE during the Radio Broadcast! Subscribe to the CARM YouTube Channel Subscribe to the Matt Slick YouTube Channel CARM on Facebook Visit the CARM Website Donate to CARM You can find our past podcast by clicking here!
These podcasts are linked to my blog Notes from a small scientist. In this episode, I provide a plain language summary of a paper we recently published, which explores how the differences in the genomes of the bacteria used to make the BCG vaccine, used for over 100 years to prevent tuberculosis, can change how effective it is at preventing disease. All my posts have links to online resources that you might find useful, and you can find the link to this particular post here.
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In this episode of Biodiversity Speaks, Dr. Jonathan Davies speaks about his work in phylogenetics and evolutionary biology. From underground trees to acknowledging the privilege that comes with doing fieldwork abroad, this episode has it all.
Happy 2023 everybody! On today's episode Max is going to tell us about a Fairy Princess who loves pot, and Janey is going re-tell John Wick but instead of Keanu Reeves, it's a goat. Enjoy!Max's Sources - The Potted Princess“Victorian Fairy Tales: The Revolt of the Fairies and Elves” by Jack Zipes Free text of Rudyard Kipling's “The Potted Princess” (with image of a grain pot) Janey's Sources - The Episode of the Mother Goat“Folktales from Syria” collected by Samir Tahhan Free PDF of “Folktales From Syria” “Such deep roots you have: How Little Red Riding Hood's tale evolved” by Alan Boyle, Science Editor (2013) The Wolf and the Seven Young Goats wikipedia The Phylogeny of Little Red Riding Hood by Jamshid J. Tehrani Check out our books (and support local bookstores!) on our Bookshop.org affiliate account!Starting your own podcast with your very cool best friend? Try hosting on Buzzsprout (and get a $20 Amazon gift card!)Want more??Visit our website!Join the Discord!Shop the merch at TeePublic!If you liked these stories, let us know on our various socials!InstagramTiktokGoodreadsAnd email us at sortofthestory@gmail.com And a huge thank you to our sound engineer, Keith! Y'know the thing about Keith, he's got... lifeless eyes, black eyes, like a doll's eyes. When he comes at ya, doesn't seem to be livin'... until he bites ya. And those black eyes roll over white, and then... oh, then you hear that terrible high-pitch screamin', the ocean turns red, and spite of all the poundin' and the hollerin', he comes in and he... rips you to pieces.
Mutations are known to occur at much higher rates than can be accounted for in evolutionary theory. Given measurable rates, Y Chromosome Adam and Mitochondrial Eve would have lived only a few thousand years ago. To answer this, evolutionists generally appeal to natural selection or genetic drift. Yet, selection can only remove 'selectable' mutations, and most mutations are necessarily selectively neutral. Also, drift fails to do anything at all in answering the dilemma. In the end, Adam and Eve are recent and there is little anyone can say about it. Notes and links: Carter 2019 A successful decade for Mendel's Accountant Robert Carter gets everything wrong? Rupe and Sanford 2008 USING NUMERICAL SIMULATION TO BETTER UNDERSTAND FIXATION RATES, AND ESTABLISHMENT OF A NEW PRINCIPLE: HALDANE'S RATCHET ReMine 2005 Cost theory and the cost of substitution—a clarification International Conference on Creationism
This was a wide-ranging and fun conversation that covered a lot of ground. We could have kept going for a lot longer. Professor Marchesi is an expert on the application of next-generation sequencing technology and novel analytical methods to study microbial ecologies. Our understanding of the microbiome and the genomic potential of the microorganisms within the microbiome has vastly increased due improvements to DNA sequencing technology and associated reductions in the cost of sequencing a genome. DNA sequencing has allowed us to create inventories of microbiomes based on the source of the sample collected: stool, sputum etc. These inventories allow us to understand datasets generated from research studies. However, Professor Marchesi describes there being microbial ‘dark matter' within the microbiome, in which dark matter is defined as a DNA sequence that has never been definitively linked to a strain of bacteria that has been cultured in a pure culture setting and phenotypically characterised. This is an inherent limitation to our understanding. There are a variety of technologies and approaches available to study the microbiome beyond using next-generation sequencing technology. They can be broadly described and categorised as ‘omics'. Each of the Omics describes a different technique e.g proteomics (study of proteins) metabolomics (study of metabolites) etc. Researchers combine these techniques to study microbes and ecosystems, but there is still a lot that we do not know. To exemplify this, Professor Marceshi referenced E.coli, the most well-studied microbe on the planet. Despite all of the research that has been conducted to date to characterise E.coli, only 40% of its genome has been mapped to particular functions. Professor Marchesi and colleagues at Imperial College have pioneered the application of intestinal microbiota transfer (IMT) to different diseases, including recurrent C.difficle infection and patients undergoing treatment for blood cancer. Looking into the future, Professor Marchesi believes that probiotics will be rationally described and selected based on specific microbiome profiles in the intended recipient (s). He also believes that donor screening for IMT will evolve and that robust analysis of the microbiome in patients before and after IMT procedures may reveal clues about the mechanism of action of IMT, which, in turn, may result in the discovery of new drug candidates. — Some facts from the conversation with Prof Marchesi : 50% of stool biomass is bacteria. It is for this reason that we alternate between being greater or less than 50% human/microbial. They're roughly 150 species in the gut of any person and 1000's different species. The microbiome has been shown to have an impact on drug metabolism and safety/tolerability/efficacy. There are bacteria that can cause uncontrolled growth in plants - there may be parallels between what happens in plants and what happens in human cells. There are distinct differences between the microbiomes in the small and large intestines, as well as significant differences in immunology. The differences in microbiome profile primarily relate to differences in food sources. Microbes can be described as factories that produce chemicals and proteins. We know more about chemicals then proteins such as short-chain fatty acids (an energy source for colonocytes acetate, proportionate, butyrate and valerate. Professor Marchesi describes them as anti-inflammatory, anti-proliferative and anti-carcinogenic - i.e they reduce the risk of cancer and help with your mental health. Every one bacteria has ten viruses trying to predate it in the gut. Viruses are the most abundant organism on the planet. There are more viruses on the planet than there are stars in the Universe. Timecodes: 00:00 Introduction 1:15 Silent retreats and isolation chambers 3:41 Artificial intelligence 6:10 Julian's journey into the microbiome 9:10 Phylogeny and morphology 12:18 Evolution of DNA sequencing 13:40 Personalised medicine 14:51 The human genome project 15:33 Finding your way as a scientist 16:05 Culture-independent approaches and culture approaches 22:08 Dark matter 26:24 Naming bacteria after people 27:30 Omics and gene profiling 30:22 Drug metabolism and microbes 34:51 Is the microbiome the passenger or the driver? 36.06 Colon cancer and cancer in plants 40:24 Intracellular bacteria 41:10 Probiotics including the segment relating to a generic probiotic and IBD drug 45:25 Single strain vs a complex ecosystem 46:26 Small intestine vs large intestine microbiomes 51:29 Probiotics 54:10 Post-antibiotic use microbial therapy 55:52 Donor screening for intestinal microbiota transfer good clip of EnteroBiotix 58:40 where I talk about scale, would be good to clip 1:00:52 Using metabolomics to screen donors 1:01:25 What is metabolomics? 1:03:50 Microbial metabolites 1:05:30 Reverse engineering FMT/IMT 1:06:35 Bariatric surgery 1:08:30 Obesity and food cravings 1:11:06 Maternal transmission and the early life microbiome , also good clip on short-chain fatty acids 1:13:00 Microbial proteins, 10% of world's biomass is below the sea floor and it's bacteria, good clip. Level of the adaptation is really good 1:15:30 Antimicrobial resistance 1:18:00 Fungi in the microbiome 1:19:10 Blastocystis hominis 1:20:50 Phage and fungi in the microbiome 1:29:22 Understanding how IMT / FMT works
The successive recapitulation of societal development (theoretically) remains a constant. If you know what to look for.
Today on the Mushroom Hour we are honored to be joined by Dr. Andrew Wilson - Assistant Curator of Mycology in the Sam Mitchel Herbarium of Fungi at Denver Botanic Gardens. For Dr. Wilson the discovery of mycology began back in the late 90's at San Francisco State University in taking classes from world renown mushroom taxonomist, Dr. Dennis Desjardin. Working with Dennis, Andrew earned a Masters degree studying the mushroom genus Gymnopus from Java and Bali. He later went on to earn a PhD in the lab of Dr. David Hibbett at Clark University. His project took him back to Southeast Asia, this time to study the ecology and evolution enigmatic puffball genus Calostoma and their relatives. In 2009, Andrew graduated and began a postdoc with Dr. Gregory Mueller at the Chicago Botanic Garden where he explored the systematic evolution of the Cantharellales and the model ectomycorrhizal mushroom genus Laccaria. He also did a one-year postdoc at Purdue University, in the lab of Dr. Cathie Aime, teasing apart the complex evolution of plant pathogenic rust fungi. At Denver Botanic Gardens, Dr. Wilson is working on a regional contribution to the Fungal Diversity Survey (FunDiS) that encompasses the state of Colorado, with a focus on the Southern Rockies. In this effort he is training students on how to study biodiversity using natural history collection and DNA sequence analysis. He is also working on new tools in DNA sequencing to better sample and study fungal diversity. TOPICS COVERED: Formed in a Family of Biologists Intellectual Explorations at San Francisco State University Genus Gymnopus Expeditions to Southeast Asia What are Systematics? Genus Calostoma Role of Isotopes in Understanding Fungal Ecologies Biogeographic Histories of Fungi Interpreting Ancestry and Evolution in Phylogenetic Data Gondwana Supercontinent Finding a Living, Ancient Ancestor on the Lacarria Family Tree Denver Botanic Gardens & Sam Mitchell Fungi Herbarium New Methods of High-Throughput DNA Sequencing Biodiversity & Evolutionary History of Southern Rocky Mountain Fungi EPISODE RESOURCES: Dr. Andrew Wilson - Denver Botanic Gardens: https://www.botanicgardens.org/team/profile/andrew-w-wilson-phd Dr. Dennis Desjardin (Mentor): https://biology.sfsu.edu/faculty/desjardin Dr. David Hibbet (Mentor): https://www2.clarku.edu/faculty/facultybio.cfm?id=355 Gymnopus (Genus): https://en.wikipedia.org/wiki/Gymnopus Calostoma (Genus): https://en.wikipedia.org/wiki/Calostoma Laccaria (Genus): https://en.wikipedia.org/wiki/Laccaria Calostoma cinnabarinum: https://en.wikipedia.org/wiki/Calostoma_cinnabarinum Colorado Mycological Society: https://cmsweb.org/ Colorado Mycoflora Project: https://coloradomycoflora.org/
Over the next couple of episodes we are going to be dipping into a different group of life than we usually do, the plants. Mike has been getting back into carnivorous plant rearing and wants to share all he knows about the world of plants that eat bugs. How the tables can turn! Darwin's drawings of the leaves and tentacles of a sundew (Drosera rotundifolia), Figures 1, 4, and 5 from "Insectivorous Plants" (1897), in the public domain. Aphids and other small insects caught in the sticky trichomes of Nicotiana insecticida, a newly described species of tobacco from Australia. Photograph by Maarten Christenhusz, Figure 1 in Chase & Lambkin (2021). Phylogeny angiosperm plants with carnivorous taxa indicated by numbered circles. Illustration by Andreas Fleischmann, in Fleischmann et al. (2017) "Evolution of carnivory in angiosperms" in Ellison & Adamec (eds) "Carnivorous Plants: Physiology, ecology, and evolution".A wetland in Loyalsock State Forest, Lycoming County, Pennsylvania that is home to temperate sundews. Photography by Nicholas_T via Flickr, used under a CC BY 2.0 license. Tropical swamp in New Caledonia, habitat for Drosera neocaledonica. Photograph by Boaz Ng via Flickr, used under a CC BY-NC-ND 2.0 license.Utricularia jamesoniana growing as an epiphyte on a tree. Photography by Dr. Alexey Yakovlev via Flickr, used under a CC BY-SA 2.0 licenseUtricularia corunta growing as a dense matt in an aquatic habitat. Photograph by peupleloup via Flickr, used under a CC BY-SA 2.0 license.Catopsis berteroniana in the Florida Everglades growing as an epiphyte in the upper branches of mangrove trees. Photograph by Scott Zona via Flickr, used under a CC BY-NC 2.0 license.Albany pitcher plant (Cephalotus follicularis) in culture. Photograph by Lucas Arrrrgh via Flickr, used under a CC BY-NC-ND 2.0 license.Wild Nepenthes mirabilis growing in Hong Kong. Photograph by Boaz Ng via Flickr, used under a CC BY-NC-ND 2.0 license.Nepenthes albomarginata growing from on a cliff side above a beach. This species has white trichomes around the rim of the pitcher that are attractive to foraging termites. Photograph by Bernard DUPONT via Flickr, used under a CC BY-SA 2.0 license.Nepenthes ampularia are a species that have adapted away from carnivory and instead capture leaves that fall from the canopy. Photograph by CIFOR via Flickr, used under a CC BY-NC-ND 2.0 license.A spoon-leaved sundew, Drosera spatulata. This species has a circumboreal distribution with an isolated population also found in the highlands of Borneo. Photograph by Boaz Ng via Flickr, used under a CC BY-NC-ND 2.0 license.Forked-leaf sundews (Drosera binata) in the wild. Photograph by Doug Beckers via Flickr, used under a CC BY-SA 2.0 license. Oblong-leaved sundews (Drosera intermedia), showing the semi-aquatic habitat of this species. Photograph by Ashley Basil via Flickr, used under a CC BY 2.0 license.Vining sundew showing the round sticky traps along the vine and flowers. Photograph by Jean and Fred Hort via Flickr, used under a CC BY 2.0 license.Wild Venus fly trap in a natural environment. Photograph by NC Wetlands via Flickr, in the public domain.Venus fly traps being sold commercially. Photograph by Mike Mozart via Flickr, used under a CC BY 2.0 license.A waterwheel plant (Aldrovanda vesiculosa), which have snap traps and are closely related to Venus fly traps. This species is at risk in their native range but have been introduced into North America, where they may be invasive. This specimen was photographed at Fort AP Hill in New York, USA. Photograph by the U.S. Government, in the public domain.Individual Aldrovanda nodes showing the whorl of leaves and snap traps. Photograph by David Short via Flickr, used under a CC BY 2.0 license.A young dewy pine (Drosophyllum lusitanicum) grown in culture. While this sticky-leaved plant may look like a sundew, they are only distantly related to one another. Photograph by incidencematrix via Flickr, used under a CC BY 2.0 license.Abundant prey captured by a dewy pine. Photograph by incidencematrix via Flickr, used under a CC BY 2.0 license.Young Triphyophylum plants showing the characteristic wavy primary leaves. Photograph by Carel Jongkind via iNaturalist, used under a CC BY-NC 4.0 license.Secondary carnivorous leaves of Triphyophylum. Photograph by Lotus-Salvinia.de via Flickr.Tertiary leaves of Triphyophylum, note the the apical hooks. Photograph by Carel Jongkind via iNaturalist, used under a CC BY-NC 4.0 license. Questions? Comments? Follow the show on Twitter @Arthro_PodshowFollow the hosts on Twitter @bugmanjon, @JodyBugsmeUNL, and @MSkvarla36Get the show through Apple Podcast, Stitcher, Spotify, or your favorite podcatching app!If you can spare a moment, we appreciate when you subscribe to the show on those apps or when you take time to leave a review!Subscribe to our feed on Feedburner! This episode is freely available on archive.org and is licensed under Creative Commons: By Attribution 3.0. http://creativecommons.org/licenses/by/3.0/
Long chat with AronRa.We talk about electric cars, science, Phylogeny, religion and many other things.Aron Ra's YouTubehttps://www.youtube.com/c/aronra
Casey looks at embryology's failure to provide significant support in favor of the theory of universal common ancestry.
The family Fabaceae is one of the most ecologically successful and diverse plant families in the world, especially in arid and subtropical regions. In this episode we talk Legumes - their ecology, floral morphology and evolution - with Marty Wojciechowski at ASU. We talk about the 50kb inversion, psychoactive and poisonous secondary chemistry, subfamily classifications elucidated by molecular phylogenetics, how mimosoids lack Rhizobium root affiliations (bummer) and a bunch more interesting sh#t. Plant in the thumbnail photo is Schotia afra.
85: Kirsten Lindsmith - Autism & Neurodiversty ✨ In today's podcast I am joined by Kirsten Lindsmith to talk about Autism and Neurodiversity. Kirsten Lindsmith is an author, artist, consultant, and autism advocate from New York City. After receiving an ASD diagnosis at the age of 19, she began co-hosting the online television show Autism Talk TV and speaking at conferences and events about her experience as a young woman on the spectrum. Kirsten has written columns for Wrong Planet and Autism After 16, and was profiled in The New York Times. Kirsten graduated from the University of Massachusetts Amherst with a degree in Vertebrate Ontogeny and Phylogeny. She currently works as a therapist in partnership with Melody of Autism, and as a consultant for behavioral and sensory needs. In the conversation Kirsten speaks about what Autism is and what it is not. The misconception and stereotypes of Autism. The division between Aspergers and Autism, and the divisions between ‘Low functioning' and ‘high functioning' and its implications. Kirsten also addresses why Autistic women are misdiagnosed with Bipolar, Borderline Personality Disorder, and Schizophrenia, Autism and Empathy and mistaking the autistic individual as sociopathic, masking, cognitive looping and how it refers to Autistics special interests, how autistic traits affect social and romantic relationships, sensory processing disorder, and more. Kirsten also address the overlap of ADHD, OCD, Bipolar and Autism. Kirsten Lindsmiths Blog: https://kirstenlindsmith.com Listen to Kirsten talk about Neurologically Mixed Relationships https://youtu.be/e7TqYkzGaUU If you enjoyed this episode, share on Instagram @amyletitia777 Don't forget if your listening on Apple Podcast, and your benefitting from this podcast in anyway, please leave a review and a 5 star rating (if you feel it's deserved
After a 40 minute opening rant, we explore the nuances of the Orchid Family - the most species-rich and diverse family of flowering plants, and we touch on a few of the things that make this family so ecologically successful. This is a good crash course for anybody interested in learning about this plant family and understanding the differences between the five subfamilies Apostasioideae, Vanilloideae, Cypripedioideae, Orchidoideae and the largest subfamily of them all - Epidendroideae.
Today on the Mushroom Hour Podcast we are honored to be joined by Else Vellinga. In her career as a mycologist, Else has described 22 new mushroom species in California. Her most recent work is at the University and Jepson Herbaria at UC Berkeley, and at UCSF, on the Microfungi Collections Digitization project. She received her training at the National Herbarium of the Netherlands, and earned her PhD at the University of Leiden (layden). Additionally, Else is a researcher and professor with the Bruns Laboratory at UC Berkeley. The main motivation for her taxonomic work is that it lays the basis for efforts to include mushroom species in nature management and conservation plans. She has proposed several species for the International Union for Conservation of Nature (IUCN), a global database of endangered species. She concentrates especially on Lepiotas, or Parasol mushrooms. Else is an avid knitter and uses mushroom dyed yarn for her creations. TOPICS COVERED: Growing up in Netherlands Wilderness What are Scientific Names Based On? Importance of Physical Features Impact of DNA Sequences on Taxonomy ITS, Multiple Gene Sequence and Whole Genome Phylogenetic Information Monophyletic vs Paraphyletic Genera What is Sufficient Difference to Make a New Taxonomic Grouping? Relationship Between Genera and Clades How are Names Selected? Does There Need to be a Consensus? Process of Naming a Species Potential Taxonomic Shakeups Fungal Conservation Fungal Diversity Survey Official State Mushrooms Education, Outreach and Awareness Central to Conservation Efforts EPISODE RESOURCES: Else Vellinga ResearchGate: https://www.researchgate.net/profile/Else-Vellinga University and Jepson Herbaria: https://ucjeps.berkeley.edu/ National Herbarium of the Netherlands: https://plants.jstor.org/partner/NHN Bruns Laboratory: https://nature.berkeley.edu/brunslab/ IUCN Fungi List: https://www.iucn.org/commissions/ssc-groups/plants-fungi/fungi Global Fungal Redlist Initiative: http://iucn.ekoo.se/en/iucn/welcome Fungal Diversity Survey (FunDiS): https://fundis.org/ Lepiota (Fungal Genus): https://en.wikipedia.org/wiki/Lepiota Entoloma (Fungal Genus): https://www.mushroomexpert.com/entoloma.html Cryptomarasmius (Fungal Genus): https://en.wikipedia.org/wiki/Cryptomarasmius
Today on Mushroom Hour we are joined by adventurer and mycologist Danny Haelewaters PhD. Danny Haelewaters holds a Bachelor's in Veterinary Sciences, a Master of Science in biology, and a PhD in Organismic and Evolutionary Biology. During his Masters program he developed a new technology to analyze forensic relevant fungi in casework at the Netherlands Forensic Institute. Between 2012 and 2018, he worked at the Farlow Herbarium of the Harvard University Herbaria (Cambridge, MA) as a PhD student. In 2018, he did a short postdoc at the University of South Bohemia in the Czech Republic, and from November 2018 until late 2020 he was a USDA-funded postdoctoral research assistant at Purdue University, where he worked on characterizing the fungal microbiota of Romaine lettuce. Currently he works at Ghent University as a junior postdoctoral fellow on a project dealing with Laboulbeniales associated with bat flies. In addition, he writes popular science articles for different sources. Since the very beginning of his student career at Ghent University (Belgium), he has has loved the interdisciplinary research in biology. It probably contributed to his choice to study the ecto-parasitic Laboulbeniales fungus. I'm excited to learn more about these unique organisms as well as the secrets of other little-known parasitic fungi. TOPICS COVERED:From Vet to MycologistFungal Inspiration at the University of GhentDiscovering LaboulbenialesUncovering Phylogeny of Rare, Microscopic FungiBat Fly Research in PanamaTripartite System of Bats, Bat Flies and FungiFuture of Laboulbeniales Research on Bat FliesOther Entomopathogens Including HerpomycesPhysiology of LaboubienialesInvasive Species & "Enemy Release” HypothesisImportance of Conserving Fungal PathogensExploring Laboubeniales as a BioControl AgentDiscovering new Clades of Cryptic Fungal OrganismsUnderstudied Habitats (Romaine Lettuce & Dead Bodies?!)EPISODE RESOURCES:Danny Haelewaters Website: http://www.dannyhaelewaters.com/Danny Haelewaters Twitter: https://twitter.com/dhaelewa/Laboulbeniales (Fungal Order): https://en.wikipedia.org/wiki/LaboulbenialesHerpomyces (Fungal Genus): https://en.wikipedia.org/wiki/HerpomycesBeauveria bassiana (Fungal Species): https://en.wikipedia.org/wiki/Beauveria_bassianaMetarhizium brunneum (Fungal Species Complex):https://en.wikipedia.org/wiki/Metarhizium_brunneumOphiocordyceps (Fungal Genus): https://en.wikipedia.org/wiki/Ophiocordyceps
Peter Daszak, Thea Kølsen Fischer, and Marion Koopmans, members of the WHO team investigating the origins of SARS-CoV-2 join TWiV to explain the work done by the committee during phase one, their conclusions, and the extent of work that remains to be done in phase two. Hosts: Vincent Racaniello, Rich Condit, and Kathy Spindler Guests: Peter Daszak, Thea Kølsen Fischer, and Marion Koopmans Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode Peter on TWiV 615, 623 Thea on TWiV 576 Marion on TWiV 413, 548 WHO report on origins of SARS-CoV-2 Timestamps by Jolene. Thanks! Weekly Picks Kathy – My Octopus Teacher Rich – John Wyndam classic Sci Fi: The Chrysalids, The Day of the Triffids Vincent – SARS-CoV-2 Phylogeny and Spatiotemporal Spread (paper) Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv
Peter Daszak, Thea Kølsen Fischer, and Marion Koopmans, members of the WHO team investigating the origins of SARS-CoV-2 join TWiV to explain the work done by the committee during phase one, their conclusions, and the extent of work that remains to be done in phase two. Hosts: Vincent Racaniello, Rich Condit, and Kathy Spindler Guests: Peter Daszak, Thea Kølsen Fischer, and Marion Koopmans Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode Peter on TWiV 615, 623 Thea on TWiV 576 Marion on TWiV 413, 548 WHO report on origins of SARS-CoV-2 Timestamps by Jolene. Thanks! Weekly Picks Kathy – My Octopus Teacher Rich – John Wyndam classic Sci Fi: The Chrysalids, The Day of the Triffids Vincent – SARS-CoV-2 Phylogeny and Spatiotemporal Spread (paper) Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv
In this episode, Stacy Krueger-Hadfield, Kelle Freel, and Rishi De-Kayne chat with Jeremy Yoder about a pandemic-focused Darwin Day symposium, the phylogenetic conservation of a bioluminescence symbiosis, and the online iteration of a venerable population genetics conference. Links to the things we discuss: The UAB Darwin Day event — and online video of the talks The phylogenetics of cardinalfishes, which host light-producing, environmentally acquired symbiotic bacteria Rishi's PopGroup conference interviews The music in this episode is Leroy Anderson's "The Syncopated Clock," performed on piano by Markus Staab and available under a Creative Commons license via Musopen. --- Send in a voice message: https://anchor.fm/molecular-ecologist/message
Join Melanie on a 5K in episode 73. Phylogeny studies the evolutionary history amongst groups of organisms. It tells the story of relatedness, the branches in the road. (1:37). Be careful - just because two organisms are physically adjacent on a diagram, does not mean they are more closely related (4:05). The episode concludes with unit connections and exam tips (5:34).The Question of the Day asks (6:50) Ernst Haeckel coined the phrase “ontogeny recapitulates phylogeny.” What is ontogeny?Thank you for listening to The APsolute RecAP: Biology Edition!(AP is a registered trademark of the College Board and is not affiliated with The APsolute RecAP. Copyright 2021 - The APsolute RecAP, LLC. All rights reserved.)Website:www.theapsoluterecap.comEMAIL:TheAPsoluteRecAP@gmail.comFollow Us:INSTAGRAMTWITTERFACEBOOKYOUTUBE
Today on Mushroom Hour we have the pleasure of learning from Jackie Shay. Jackie is a fungal evolutionary biologist and microbial ecologist fascinated with the intimate history and future significance of symbiotic relationships between plant hosts and their microbial communities. Her goal is to use integrative techniques to explore these interactions in the natural world and learn how we can apply these partnerships to promote conservation and resilience through climate change. Jackie received a master's in Ecology, Evolution, and Conservation Biology from the Desjardin lab at San Francisco State University studying the evolution of wood decaying mushrooms (Marasmius) from Madagascar. She is currently a Ph.D. student in the Sexton and Frank labs in the Quantitative and Systems Biology Program at the University of California, Merced. This interdisciplinary team has set out to uncover the mystery behind the Monkeyflower microbiome and discover whether these microbes influence their plant hosts across its range. Topics Covered: From Urban Dweller to Forest Lover Desjardin Lab at SFSU Marasmius Research in Madagascar Unseen Ecological Importance of Saprobic Fungi Fungal Genetics Importance of "ITS" Region in Fungal Gene Sequencing Discovering New Species of Marasmius Monkeyflower Microbiome Bioinformatics Endophytes Defined Endophytes and Climate Change Mysteries of "Dark" Endophytes We Need More Mycologists! New Pedagogic Career Path & Future Plans Episode Resources:Jackie Shay Website: https://www.jackieshay.com/ Castilleja miniata: https://en.wikipedia.org/wiki/Castilleja_miniataMarasmius (Fungi Genus): https://en.wikipedia.org/wiki/MarasmiusDesjardin Lab SFSU: http://biology.sfsu.edu/people/dennis-desjardin Mimulus "Monkeyflower" (Plant Genus): https://en.wikipedia.org/wiki/MimulusSexton and Frank labs UC Merced: http://sextonlab.ucmerced.edu/ Merced Center for Engaged Teaching and Learning: https://cetl.ucmerced.edu/Cordyceps (Fungi Genus): https://en.wikipedia.org/wiki/Cordyceps
Today on Mushroom Hour we have the pleasure of speaking with the distinguished Todd Osmundson PhD, Associate Professor of Biology at The University of Wisconsin Lacrosse. Todd is a faculty member in the Department of Biology and his research specialties include studying the ecology, genetic relationships, geographic distributions, and conservation biology of bacteria and especially fungi, using fieldwork, microscopy, and molecular genetic (DNA-based) tools. His professional mycology career really began during a fateful encounter with a local mushroom club in Montana. Todd has conducted mycological fieldwork in the U.S., French Polynesia, China, Mexico, Costa Rica, Guatemala, Svalbard, Thailand, and Australia. His varied research projects have seen him span alpine, arctic, tropical, and temperate habitats in search of fungi. There are few people more familiar with the process of finding, observing, extracting DNA, and genetically sequencing fungi. Let's learn more about where “we” are in cataloging fungal populations, what that means for mycology and how citizen scientists can be a part of this process. Topics Covered:Seizing Opportunity to Begin a Mycology CareerMorea & French PolynesiaModel Ecosystem Modeling with GeneticsPCR Analysis and SequencingInterpreting Genetic DataChallenges of Identifying Fungal SpeciesWhat are Clades and How Do We Use Them?165 Million Species of Fungi?!MicrosporidiansMysteries of Burn MorelsDifferentiating Individuals with GeneticsFungal Herbarium Collections as Genetic Vaults?Biogeography & Evolutionary HistoryDiversity Surveys & Fungi ConservationEpisode Resources:Todd Osmundson Website: https://www.uwlax.edu/profile/tosmundson/Larry Evans (Inspiration): http://www.montanamushrooms.com/tag/larry-evans/Dr Cathy Cripps (Inspiration): https://plantsciences.montana.edu/alpinemushrooms/investigators/principal.htmlMicrosporidians (fungi): https://en.wikipedia.org/wiki/MicrosporidiaAndy Bruce (student): https://andibruce.com/Alan Rockefeller (Inspiration): https://www.instagram.com/alan_rockefeller/Boletus separans (Mushroom): https://boletes.wpamushroomclub.org/product/xanthoconium-separans/Tylopilus (mushroom): https://en.wikipedia.org/wiki/Tylopilus
Ever feel the existential dread induced by the realization that you are just another corporate entity from the moment of your inception? Well you should, because you are. ALL OF US ARE! The show gets more philosophical and professional, as today we present you our brand new product: a huge episode, on a huge topic, for the huge fan willing to donate a huge portion of their daily attention, and risk having their brain reprogrammed forever! We will tell you not just the meaning of life, but the meaning of reality itself! And as all great philosophers..we will constantly repeat ourselves and never shut up :) ====================== Diagram 1 Diagram 2 Diagram 3 ====================== Send us suggestions and comments to darwinsdeviations@gmail.com Intro/outro sampled from "Sequence (Mystery and Terror) 3" by Francisco Sánchez (@fanchisanchez) at pixabay.com Sound effects obtained from https://www.zapsplat.com Image Credit Frank Fox, CC BY-SA 3.0 DE, via Wikimedia Commons (Episode image is heavily edited, the image owner reserves all rights to their image, and is not affiliated with our podcast) SOURCES: A LOT of Wikipedia articles I cannot possibly list AlgaeBase: Volvox Linnaeus, 1758 MicrobeWiki: Volvox carteri Umen, James. (2020). Volvox and volvocine green algae. EvoDevo. 11. 10.1186/s13227-020-00158-7. Herron, Matthew & Nedelcu, Aurora. (2015). Volvocine Algae: From Simple to Complex Multicellularity. 10.1007/978-94-017-9642-2_7. Szövényi, Péter & Waller, Manuel & Kirbis, Alexander. (2018). Evolution of the plant body plan. 10.1016/bs.ctdb.2018.11.005. Herron, Matthew & Michod, Richard. (2008). Evolution of Complexity in the Volvocine Algae: Transitions in Individuality Through Darwin's Eye. Evolution; international journal of organic evolution. 62. 436-51. 10.1111/j.1558-5646.2007.00304.x. Herron, Matthew & Hackett, Jeremiah & Aylward, Frank & Michod, Richard. (2009). Triassic origin and early radiation of multicellular volvocine algae. Proceedings of the National Academy of Sciences of the United States of America. 106. 3254-8. 10.1073/pnas.0811205106. Kirk DL. Evolution of multicellularity in the volvocine algae. Curr Opin Plant Biol. 1999;2(6):496-501. doi:10.1016/s1369-5266(99)00019-9 Kirk, David. (2000). Volvox as a Model System for Studying the Ontogeny and Phylogeny of Multicellularity and Cellular Differentiation. Journal of Plant Growth Regulation. 19. 265-274. 10.1007/s003440000039. Domozych, David & Domozych, Catherine. (2014). Multicellularity in green algae: Upsizing in a walled complex. Frontiers in plant science. 5. 649. 10.3389/fpls.2014.00649. Matt, Gavriel & Umen, James. (2016). Volvox: A simple algal model for embryogenesis, morphogenesis and cellular differentiation. Developmental Biology. 419. 10.1016/j.ydbio.2016.07.014. Starr, R.. “Colony Formation in Algae.” (1984).
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.10.334003v1?rss=1 Authors: Redelings, B. D. Abstract: BAli-Phy is a Markov chain Monte Carlo (MCMC) program that jointly estimates phylogeny, alignment, and other parameters from unaligned sequence data. Version 3 is substantially faster for large trees, and implements covarion models, RNA stem models, and other new models. It implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously. Availability: Software is available for download at http://www.bali-phy.org. C++ source code is freely available on Github under the GPL2 License. Copy rights belong to original authors. Visit the link for more info
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.07.329516v1?rss=1 Authors: Schulz, C., Almaas, E. Abstract: Approaches for systematizing information of relatedness between organisms is important in biology. Phylogenetic analyses based on sets of highly conserved genes are currently the basis for the Tree of Life. Genome-scale metabolic reconstructions contain high-quality information regarding the metabolic capability of an organism and are typically restricted to metabolically active enzyme-encoding genes. While there are many tools available to generate draft reconstructions, expert-level knowledge is still required to generate and manually curate high-quality genome-scale metabolic models and to fill gaps in their reaction networks. Here, we use the tool AutoKEGGRec to construct $975$ genome-scale metabolic draft reconstructions encoded in the KEGG database without further curation. The organisms are selected across all three domains, and their metabolic networks serve as basis for generating phylogenetic trees. We find that using all reactions encoded, these metabolism-based comparisons give rise to a phylogenetic tree with close similarity to the Tree of Life. While this tree is quite robust to reasonable levels of noise in the metabolic reaction content of an organism, we find a significant heterogeneity in how much noise an organism may tolerate before it is incorrectly placed in the tree. Furthermore, by using the protein sequences for particular metabolic functions and pathway sets, such as central carbon-, nitrogen-, and sulfur-metabolism, as basis for the organism comparisons, we generate highly specific phylogenetic trees. We believe the generation of phylogenetic trees based on metabolic reaction content, in particular when focused on specific functions and pathways, could aid the identification of functionally important metabolic enzymes and be of value for genome-scale metabolic modellers and enzyme-engineers. Copy rights belong to original authors. Visit the link for more info
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.22.216242v1?rss=1 Authors: Vitanyi, P. M. B., Cilibrasi, R. L. Abstract: We analyze the phylogeny and taxonomy of the SARS-CoV-2 virus using compression. This is a new alignment-free method called the "normalized compression distance" (NCD) method. It discovers all effective similarities based on Kolmogorov complexity. The latter being incomputable we approximate it by a good compressor such as the modern zpaq. The results comprise that the SARS-CoV-2 virus is closest to the RaTG13 virus and similar to two bat SARS-like coronaviruses bat-SL-CoVZXC21 and bat-SL-CoVZC4. The similarity is quantified and compared with the same quantified similarities among the mtDNA of certain species. We treat the question whether Pangolins are involved in the SARS-CoV-2 virus. Copy rights belong to original authors. Visit the link for more info
Charles Darwin's theory of evolution dramatically increased the arguments for racism according to Harvard's famed evolutionist Stephen Jay Gould, as The Origin of Species book is subtitled, "Preservation of Favoured Races". Darwin also wrote that "the negro" is closer to "the gorilla" than is the evolutionist's own "civilized" race. * Racist Darwin's Racist Writings: * Darwin Claimed Blacks Are Closer to Apes: Later editions of Darwin's Origin of Species dropped the phrase "Favored Races" from the book's title. But then in his second book, after asking whether man has given rise to races that "must be classed as doubtful species", Darwin ominously wrote: At some future period, not very distant as measured by centuries, the civilised races of man will almost certainly exterminate and replace throughout the world the savage races. At the same time the anthropomorphous apes, as Professor Schaaffhausen has remarked, will no doubt be exterminated. The break [between humans and animals] will then be rendered wider, for it will intervene between man in a more civilised state, as we may hope, than the Caucasian, and some ape as low as a baboon, instead of as at present between the negro... and the gorilla. -Charles Darwin, The Descent of Man, p. 156. * Darwin's Racism Spreads Fast and Furious: A famed 20th-century evolutionist, Harvard's Stephen Jay Gould, admitted: Biological arguments for racism may have been common before 1850, but they increased by orders of magnitude following the acceptance of evolutionary theory. * True White Privilege Given to Whites by Liberals: RSR hosts Bob Enyart and Fred Williams discuss the true white privilege, that our own white children are warned not to be racist while cruelly, black children are told by liberals that they are not able to be racist. That dehumanizing absurdity is a primary reason for the seething and unchecked systemic racism within the black community. Further, the epidemic of black violence is the main reason for tension between overwhelmingly non-racist police departments and the broadly racist black community. Black Lives Matter to the cops but not to Black Lives Matter. So the guys air audio from scholars Heather Mac Donald and Voddie Bacham but not before quoting God's Word, that God "has made from one blood every nation of men to dwell on all the face of the earth..." * Ballotopedia News: Bob was quoted this week by this news outlet in their article, Coloradans will decide a ballot initiative in November that would prohibit abortions after 22 weeks gestational age: Bob Enyart, a spokesman for Colorado Right to Life, told Rewire.News, "Our misguided pro-life allies have presided over decades of regulating child-killing. You don’t regulate crime; you deter crime." * Cops Save Black Lives: The police have saved tens of thousands of black lives which is far more than any other government program or department. "The Police" haven't killed a black man in living memory. "A police officer" or "officers" have rarely unjustifiably killed the innocent. The left's rage would be not one speck less if no police officer had killed any unarmed black over the last thirty years. See also our kgov.com/ways-to-reduce-crime. * See Also Scholar Voddie Baucham on Race:
Charles Darwin's theory of evolution dramatically increased the arguments for racism according to Harvard's famed evolutionist Stephen Jay Gould, as The Origin of Species book is subtitled, "Preservation of Favoured Races". Darwin also wrote that "the negro" is closer to "the gorilla" than is the evolutionist's own "civilized" race. * Racist Darwin's Racist Writings: * Darwin Claimed Blacks Are Closer to Apes: Later editions of Darwin's Origin of Species dropped the phrase "Favored Races" from the book's title. But then in his second book, after asking whether man has given rise to races that "must be classed as doubtful species", Darwin ominously wrote: At some future period, not very distant as measured by centuries, the civilised races of man will almost certainly exterminate and replace throughout the world the savage races. At the same time the anthropomorphous apes, as Professor Schaaffhausen has remarked, will no doubt be exterminated. The break [between humans and animals] will then be rendered wider, for it will intervene between man in a more civilised state, as we may hope, than the Caucasian, and some ape as low as a baboon, instead of as at present between the negro... and the gorilla. -Charles Darwin, The Descent of Man, p. 156. * Darwin's Racism Spreads Fast and Furious: A famed 20th-century evolutionist, Harvard's Stephen Jay Gould, admitted: Biological arguments for racism may have been common before 1850, but they increased by orders of magnitude following the acceptance of evolutionary theory. * True White Privilege Given to Whites by Liberals: RSR hosts Bob Enyart and Fred Williams discuss the true white privilege, that our own white children are warned not to be racist while cruelly, black children are told by liberals that they are not able to be racist. That dehumanizing absurdity is a primary reason for the seething and unchecked systemic racism within the black community. Further, the epidemic of black violence is the main reason for tension between overwhelmingly non-racist police departments and the broadly racist black community. Black Lives Matter to the cops but not to Black Lives Matter. So the guys air audio from scholars Heather Mac Donald and Voddie Bacham but not before quoting God's Word, that God "has made from one blood every nation of men to dwell on all the face of the earth..." * Ballotopedia News: Bob was quoted this week by this news outlet in their article, Coloradans will decide a ballot initiative in November that would prohibit abortions after 22 weeks gestational age: Bob Enyart, a spokesman for Colorado Right to Life, told Rewire.News, "Our misguided pro-life allies have presided over decades of regulating child-killing. You don’t regulate crime; you deter crime." * Cops Save Black Lives: The police have saved tens of thousands of black lives which is far more than any other government program or department. "The Police" haven't killed a black man in living memory. "A police officer" or "officers" have rarely unjustifiably killed the innocent. The left's rage would be not one speck less if no police officer had killed any unarmed black over the last thirty years. See also our kgov.com/ways-to-reduce-crime. * See Also Scholar Voddie Baucham on Race:
How can the intricate relationship between soil microbiota and plants be managed for improved plant health? Linda Kinkel discusses new insights into the plant rhizosphere and the ways that some Streptomyces isolates can protect agricultural crops against bacterial, fungal, oomycete, and nematode infections. Julie’s Biggest Takeaways: The soil microbiome is extremely dynamic, with boom-and-bust cycles driven by nutrient fluxes, microbial interactions, plant-driven microbial interactions, and signaling interactions. Finding the source of these boom-and-bust cycles can help people to manage the microbiome communities and produce plant-beneficial communities for agricultural purposes. Rhizosphere soil is soil closely associated with the root and is distinct from rhizoplane soil that directly touches the root. The endophytic rhizosphere are those microbes that get inside the root. Many scientists view these communities as a continuum rather than sharply delineated. Plants provide necessary carbon for the largely heterotrophic soil microbiota, and these microorganisms help the plants in several ways too: Microbes mediate plant growth by production of plant growth hormones. Microbes provide nutrients through mechanisms like nitrogen fixation or phosphorus solubilization. Microbes protect the plant from stress or drought conditions. Through a University of Minnesota plant pathology program, potatos were passaged in a field for over 2 decades to study potato diseases. Over time, researchers found fewer diseases in test crops, which led the plot to be abandoned in the late 1970s. In the 1980s, Dr. Neil Anderson planted potatoes to see if they would develop disease, but neither Verticillium wilt nor potato scab developed among the plants. Soil from the field (and on the potatoes) contained Streptomyces isolates that showed antimicrobial activity against bacteria, fungi, nematodes, and oomycetes. This discovery led Neil, new University of Minnesota professor Linda, and their collaborators to study the antimicrobial activity of natural Streptomyces isolates from around the world. Inoculation quickly adds specific microbial lineages to soil microbiome communities. Alternatively, land can be managed by providing nutrients to encourage the growth of specific species, like Streptomyces, within a given plot, but this takes longer to develop. How are soil microbiomes inoculated? Microbes can be: Added to the seed coating before planting. Placed in the furrow when the seed is planted. Distributed into the irrigation system. Links for this Episode: Linda Kinkel website at University of Minnesota Essarioui A. et al. Inhibitory and Nutrient Use Phenotypes Among Coexisting Fusarium and Streptomyces Populations Suggest Local Coevolutionary Interactions in Soil. Environmental Microbiology. 2020. Schlatter D.C. et al. Inhibitory Interaction Networks Among Coevolved Streptomyces Populations from Prairie Soils. PLoS One. 2019. Schlatter D.C. et al. Resource Use of Soilborne Streptomyces Varies with Location, Phylogeny, and Nitrogen Amendment. Microbial Ecology. 2013. Small Things Considered blog: Are Oomycetes Fungi or What? International Year of Plant Health HOM Tidbit: Austin-Bourke P.M. Emergence of Potato Blight, 1843-1846. Nature. 1965.
All about classification and "the tree of motha f***in life!" --- Send in a voice message: https://anchor.fm/bioforbastards/message
Join us to talk all about the powers and compelling potentials of endophytic fungi and other microbes with Dr. James White. We discuss the evolutionary roles of endophytes, the ubiquity of these symbiotes, and their implications in the scientific community. .James White obtained a Masters degree in Mycology and Plant Pathology from Auburn University, Alabama, and the Ph.D. in Mycology and Botany from the University of Texas.Dr. White is a Professor of Plant Biology, and specializes in symbiosis research particularly with endophytic microbes. He is the author of more than 200 articles, and author and editor of reference books on the biology, taxonomy, and phylogeny of fungal endophytes. He and the students in his lab are exploring diversity of endophytic microbes and the various impacts that they have on host plants. Show Notes: https://drive.google.com/drive/folders/1JzhunMnD3v8OwErsQ2kjyKE3p2AADe_M?usp=sharing
Hello bug lovers! Today is a unique episode, where Mike and Jonathan talk about their history playing Pokemon games and what that has to do with entomology. Come learn all about virtual monsters that resemble arthropods and pick out a favorite one! Also, maybe ponder if Pokemon presents an opportunity for entomology educators to connect with their audiences in different ways!Mike's favorite bug-type Pokemon is the wonderful ButterfreeJonathan's favorite is the terrifying PinsirShow NotesAmerican Entomologist Article on Pokemon and Entomologyhttps://academic.oup.com/ae/article/64/3/159/5098346Entomology Today interview on last articlehttps://entomologytoday.org/2018/10/22/how-pokemon-opens-door-entomology-education/The Entomological Diversity of Pokemonhttps://jgeekstudies.org/2018/10/12/entomological-diversity-of-pokemon/The Phylogeny of Pokemon https://www.improbable.com/airchives/paperair/volume18/v18i4/Phylogeny-Pokemon.pdfQuestions? Comments? Follow the show on Twitter @Arthro_PodshowFollow the hosts on Twitter @bugmanjon, @JodyBugsmeUNL, and @MSkvarla36Get the show through Apple Podcasts!Subscribe to our feed on Feedburner! We're also on Stitcher!This episode is freely available on archive.org and is licensed under Creative Commons: By Attribution 3.0. http://creativecommons.org/licenses/by/3.0/
A short one about all the categories we put life into. For detailed notes (PowerPoints) visit www.BiologyForBastards.com --- Send in a voice message: https://anchor.fm/bioforbastards/message
Learn a bunch of fun and unfortunate fact about how we as humans develop in the womb.
Interview with Aron Ra. We talk about phylogeny and electric cars.Investing Skeptically: Asset Allocation Part 1, Cancer Insurance.Bonus audio:- Catholic Church & R. Kelly from Saturday Night Live- Suck it Jesus from Kathy Griffin- Great Dictator from Charlie ChaplinEnd Music:Not Dead Yet - Ralph Covert & The Bad Examples
The gang discusses a few papers that look at the evolutionary history, biogeography, and life habit of Mesozoic turtles. Specifically, they look at a paper about a stem turtle with interesting information about the evolutionary history of turtle morphology, a paper on a special fossil of a marine turtle with exceptionally preserved eggs, and a paper that investigates the biogeographic history of turtles. Basically, its a whole lotta turtles! Meanwhile, James resurrects some old arguments, Curt revisits cherished film scenes, and Amanda has a new obsession. Up-Goer Five (James Edition): The group look at two papers that are looking at animals with four legs and hard parts on the outside that they can hide in. These things are found on land with legs and in the water with water legs that they use for being not on land. This is a very long set of words, so we will call them hard boys. The first paper is looking at a hard boy that was full of little round things that would become babies. This is the second hard boy to be found with almost babies and can tell us whether hard boys had lots of babies or not a lot of babies. Hard boys that are in the water usually have a lot of babies that are not expected to live very long; this long dead hard boy actually had not many babies, so although it lived in the water it expected its babies to live. The second paper is looking at where hard boys lived in the past and how they got to be where they are today. The paper shows that hard boys started in one place that was very big and that they stayed on it as it broke up over time. As it broke up they also moved between the bits, so the hard boys were able to move between the bits even though they are usually slow. They keep doing this until the bits get too far from each other to let the hard boys move across. References: Li, Chun, et al. "A Triassic stem turtle with an edentulous beak." Nature560.7719 (2018): 476. Ferreira, Gabriel S., et al. "Phylogeny, biogeography and diversification patterns of side-necked turtles (Testudines: Pleurodira)." Royal Society open science 5.3 (2018): 171773. Cadena, Edwin‐Alberto, et al. "A gravid fossil turtle from the Early Cretaceous reveals a different egg development strategy to that of extant marine turtles." Palaeontology (2018).
This episode contains rants about the anomaly of working-class republican-ism, molecular phylogenetics, a new population of Funeral Sage, and a relict population of Alaska Cypress
Cette fois, Amplitudes se fait pirater par l'équipe de Tartine de Contrebasse au complet, pour une émission qui met l'escroquerie en abyme et adopte sa plus belle posture de l'imposture. Du free jazz et de l'ambient pastoral, des bandes magnétiques et de la drum'n'bass, ou encore de l'expé-tribalo-radicaloritualiste quadraphonique et du dark ambient industriel qui n'en est pas vraiment, Incoherent Phylogeny 2 porte son nom haut et fort pour deux heures de grand n'importe quoi autopromotionnel que les tartineurs sont fiers de vous présenter en direct après deux ans de préparation. Tracklist : Tomonari Nozaki - Through Death to Eternity O Morto - Dadès Arikon - Gitter Pillar Matter - T001 Anatole Petit + James Welburn + Frank Szardenings - TeOnAnAcAtLXXL Bank of Forever - She Will Give Us What We Need Jasmine Guffond - The Devil Is in the Default Ryan Andersen - Parasitic Apnea (Dronny Darko Remix) Charbel Haber - Polyester Wet Dreams Stromboli - Glider Monolog - Curfew Zenjungle + Siavash Amini - Influx Damian Valles - Wraiths Razgraad - Ditch Digger Jr. Ain't Never Scared James Murray - Two Times Two AES Dana - The Gradual District
Cette fois, Amplitudes se fait pirater par l'équipe de Tartine de Contrebasse au complet, pour une émission qui met l'escroquerie en abyme et adopte sa plus belle posture de l'imposture. Du free jazz et de l'ambient pastoral, des bandes magnétiques et de la drum'n'bass, ou encore de l'expé-tribalo-radicaloritualiste quadraphonique et du dark ambient industriel qui n'en est pas vraiment, Incoherent Phylogeny 2 porte son nom haut et fort pour deux heures de grand n'importe quoi auto-promotionnel que les tartineurs sont fiers de vous présenter en direct après deux ans de préparation. Tracklist : Tomonari Nozaki - Through Death to Eternity O Morto - Dadès Arikon - Gitter Pillar Matter - T001 Anatole Petit + James Welburn + Frank Szardenings - TeOnAnAcAtLXXL Bank of Forever - She Will Give Us What We Need Jasmine Guffond - The Devil Is in the Default Ryan Andersen - Parasitic Apnea (Dronny Darko Remix) Charbel Haber - Polyester Wet Dreams Stromboli - Glider Monolog - Curfew Zenjungle + Siavash Amini - Influx Damian Valles - Wraiths Razgraad - Ditch Digger Jr. Ain't Never Scared James Murray - Two Times Two AES Dana - The Gradual District Photo : Ehoarn Bidault
Cette fois, Amplitudes se fait pirater par l'équipe de Tartine de Contrebasse au complet, pour une émission qui met l'escroquerie en abyme et adopte sa plus belle posture de l'imposture. Du free jazz et de l'ambient pastoral, des bandes magnétiques et de la drum'n'bass, ou encore de l'expé-tribalo-radicaloritualiste quadraphonique et du dark ambient industriel qui n'en est pas vraiment, Incoherent Phylogeny 2 porte son nom haut et fort pour deux heures de grand n'importe quoi auto-promotionnel que les tartineurs sont fiers de vous présenter en direct après deux ans de préparation. Tracklist : Tomonari Nozaki - Through Death to Eternity O Morto - Dadès Arikon - Gitter Pillar Matter - T001 Anatole Petit + James Welburn + Frank Szardenings - TeOnAnAcAtLXXL Bank of Forever - She Will Give Us What We Need Jasmine Guffond - The Devil Is in the Default Ryan Andersen - Parasitic Apnea (Dronny Darko Remix) Charbel Haber - Polyester Wet Dreams Stromboli - Glider Monolog - Curfew Zenjungle + Siavash Amini - Influx Damian Valles - Wraiths Razgraad - Ditch Digger Jr. Ain't Never Scared James Murray - Two Times Two AES Dana - The Gradual District Photo : Ehoarn Bidault
You probably don't believe in Bigfoot, but if you do, you probably have difficulty proving the existence of the noble Sasquatch to so-called scientists! Ever wonder why? Whatever you believe, scienceman Alex Duckles and his trusty producer Ben Schultz will confirm your beliefs as they discuss the strange realm of cryptozoology, a world once inhabited by such creepy cryptids as mythical gorillas, giraffe dragons, and grizzly-polar bear hybrid! Additionally, Alex's Brain Bubble is burst by pond monster YouTube videos. Science in the News is sorrowful as we mourn the lost of Koko, while reflecting on her legacy. Things We Like: Theodore Roosevelt (Theodore Rex by Edmund Morris); Green Lantern mythos (videos by Comics Explained); Luke Cage Season 2 (on Netflix); homeopathy? Big Naturalish shout-outs to George Eberhart, the Encyclopedia of Mysterious Creatures, the Patterson-Gimlin film, Carl Sagan, phylogeny, gigantopithecus, ichyosaurs, and the unseen thylacine. Check out the article that inspired this episode on Medium! --Recorded in the Washington, D.C. metro area
Marketing Study Lab Helping You Pass Marketing Qualifications
We have a transatlantic feel to this episode as it features a conversation with Dr. Carl Marci, the Chief Neuroscientist at Nielsen Consumer Neuroscience who I met in the freezing city of Boston, Massachusetts, I’m pretty sure it has thawed a little by now. You’ll know how cold it was if you’ve seen my recent video that was posted, filmed just outside City Hall, where you can see the statue of one of the greatest basketball players of all time Bill Russell, now I filmed this on purpose, as what you can’t see is that this statue is surrounded by plinths depicting what Bill champions. On each was a different statement – teamwork, craftsmanship, imagination, commitment, words to inspire and motivate and this reminded me of why I started this podcast in the first place. I am passionate about what I do and the profession of Marketing, so if I can inspire one of you commit to developing your skills, dream bigger than you currently are, work harder to perfect your craft or build a culture around you that allows people to thrive then this would be more that I could ever have imagined would be possible for me to achieve with this podcast, and this is what I aim to do in the valuable time that you have allowed me access, so thank you. Back to Dr. Carl Marci (taking a deep breath here as his accolades extensive) – A BA in psychology, an MA in psychology and philosophy, before becoming a Doctor at Harvard Medical School. But that wasn't enough as he went on to train in biometrics and the neuroscience of emotion and now is a provider of consumer based neuroscience using biometrics, and other technologies for measuring non-conscious processes related to media and marketing and how they effect consumer behavior and decision making. Happy Marketing Everyone! Peter www.marketingstudylab.co.uk www.linkedin.com/company/marketing-study-lab/ www.facebook.com/marketingstudylab/ https://twitter.com/mktstudylab (@mktstudylab) Music Featured on this Podcast: Sleepy in the Garden Lobo Loco www.musikbrause.de Creative Commons License LinksNielsen: http://www.nielsen.com/uk/en.html Nielsen Neuroscience: http://www.nielsen.com/us/en/solutions/capabilities/consumer-neuroscience.html Williams-Sonoma Bread Maker Price Case Study:http://myemail.constantcontact.com/Williams-Sonoma-Pricing-Tactic-Grows-Sales-for-Bread-Machine.html?soid=1102052405533&aid=JioWyC1Fesc CIM Mentoring Program: https://www.cim.co.uk/more/mentoring/ Books:Crossing the Chasm: Marketing and Selling Technology Products to Mainstream Customers: https://amzn.to/2jhp2e8 App:New York Times: http://www.nytimes.com/services/mobile/index.html Theory:Ontogeny recapitulates Phylogeny: https://en.wikipedia.org/wiki/Recapitulation_theory Idol:Bill Bradley: http://www.billbradley.com
This episode, we’re taking the time to talk about a subject that comes up just about every episode: the classification and relationships of living organisms. Taxonomy, Phylogeny, and the Tree of Life! In the news: giant ground sloth diets, how whales got huge, the crunching jaws of T. rex, and the evolution of soldier bees! Time markers: Intro & Announcements: 00:00:00 News: 00:05:30 Main discussion: 00:28:00 Check out our blog for bonus info and pictures: http://commondescentpodcast.wordpress.com/ Follow and Support us on: Patreon: https://www.patreon.com/commondescentpodcast Twitter: https://twitter.com/CommonDescentPC Facebook: https://www.facebook.com/commondescentpodcast/ iTunes: https://itunes.apple.com/us/podcast/the-common-descent-podcast/id1207586509?mt=2 Stitcher: http://www.stitcher.com/podcast/common-descent/the-common-descent-podcast The Podcast music is “On the Origin of Species” by Protodome. More music like this at http://ocremix.org.
Prof. Jean-Pierre FLANDROIS, Bioinformatics, Phylogeny and Evolutionary Genomics Group, Université Claude Bernard Lyon 1.
Prof. Jean-Pierre FLANDROIS, Bioinformatics, Phylogeny and Evolutionary Genomics Group, Université Claude Bernard Lyon 1.
A recent paper about carnivorous bats, and a puzzle about a cube you break in the desert. music: www.bensound.com
Sturgeons are known worldwide for their caviar but these ancient fishes are critically endangered and at risk of extinction. Casey Dillman discusses the threats to these fishes as well their phylogeny.
What kind of fish has retractable eyes? Zeehan Jaafar from the Division of Fishes discusses the evolution, life history characters and terrestriality of mudskippers.
Eight months ago Open Metalcast went on hiatus. The short of it was because my father-in-law was needing more elder care and we needed to shore up resources for his care. Unfortunately he passed away last year. This show is dedicated to him, even though he likely never heard it or knew it existed. We miss you, Dad. So I have eight months to catch up on of sharing Creative Commons Metal Music with you. Let's get started with music from Phylogeny, The Afterthought Ecstasty, Sonus Mortis, Wildernessking, Negative Voice, Akaitsuki, two tracks from EWÏG FROST, and Lèpoka. It's good to be back, though I wish it were under better circumstances. Show notes after the break * (00:12) Seizure of the Tremoctopus by Phylogeny from Phylogeny (BY-SA) * (04:55) Paradoxal Subjugation by First Fragment from The Afterthought Ecstasy (BY-NC) * (10:04) The Crypt Of The Death Prophet by Sonus Mortis from War Prophecy (BY-NC-ND) * (16:32) With Arms Like Wands by Wildernessking from Mystical Future (BY-NC-ND) * (24:47) Limitation by Negative Voice from Limitation [single release] (BY-NC) * (30:09) Ryujin by Akaitsuki from Akaitsuki (BY-SA) * (34:00) A1-The Railroad to Hell by EWÏG FROST from The Railroad to Hell EP (BY-NC-ND) * (36:32) A2- Black Rollin' Thunder Clouds by EWÏG FROST from The Railroad to Hell EP (BY-NC-ND) * (41:26) Beerserkers by Lèpoka from Beerserkers [2016 album] (BY-NC-ND) Please support the bands in this show! Buy a T-Shirt, head to the shows, or give them a hug. Whatever you can do to help these bands keep making music, please do it! Also check out the other great podcasts at Metal Injection, as well as news, videos, interviews, reviews and more. If you have any suggestions for Creative Commons licensed metal, send me a link at craig@openmetalcast.com.
Eight months ago Open Metalcast went on hiatus. The short of it was because my father-in-law was needing more elder care and we needed to shore up resources for his care. Unfortunately he passed away last year. This show is dedicated to him, even though he likely never heard it or knew it existed. We miss you, Dad. So I have eight months to catch up on of sharing Creative Commons Metal Music with you. Let's get started with music from Phylogeny, The Afterthought Ecstasty, Sonus Mortis, Wildernessking, Negative Voice, Akaitsuki, two tracks from EWÏG FROST, and Lèpoka. It's good to be back, though I wish it were under better circumstances. (00:12) Seizure of the Tremoctopus by Phylogeny from Phylogeny (BY-SA) (04:55) Paradoxal Subjugation by First Fragment from The Afterthought Ecstasy (BY-NC) (10:04) The Crypt Of The Death Prophet by Sonus Mortis from War Prophecy (BY-NC-ND) (16:32) With Arms Like Wands by Wildernessking from Mystical Future (BY-NC-ND) (24:47) Limitation by Negative Voice from Limitation [single release] (BY-NC) (30:09) Ryujin by Akaitsuki from Akaitsuki (BY-SA) (34:00) A1-The Railroad to Hell by EWÏG FROST from The Railroad to Hell EP (BY-NC-ND) (36:32) A2- Black Rollin' Thunder Clouds by EWÏG FROST from The Railroad to Hell EP (BY-NC-ND) (41:26) Beerserkers by Lèpoka from Beerserkers [2016 album] (BY-NC-ND) Please support the bands in this show! Buy a T-Shirt, head to the shows, or give them a hug. Whatever you can do to help these bands keep making music, please do it! Also check out the other great podcasts at Metal Injection, as well as news, videos, interviews, reviews and more. If you have any suggestions for Creative Commons licensed metal, send me a link at craig@openmetalcast.com. Open Metalcast #124 (MP3) Open Metalcast #124 (OGG)
00:00:00 - Way way back in the 1980's some scientists found a... thing. No this isn't the start of an excellent John Carpenter movie, it's something that happened in real life! Only this year did someone get around to describing the thing, and it turns out they couldn't. Does this new animal deserve a new phylum all to itself? Listen and decide for yourself! 00:22:54 - Ethanol is a great way to preserve specimens when done properly. It's also a great way to socialize, but again, only when used properly. Here are three examples of its proper use. Charlie kicks back a Phosphorescent Pale from the sentimental Island Hoppin' Brewery, near where he got hitched. Patrick enjoys a Devils Tale collaboration from Devil's Backbone Brewing Company and Coronado Brewing Company. He's come so far from his early days as a hops detractor. Ryan claims the greatest beer in the history of the show, a bold claim but can he pull it off? You be the judge, for he sups a Camarasaurus Cream Ale from Fossil Brewing Company! 00:30:31 - Speaking of ruling the drinks segment, who really rules the earth? And, assuming humans are dominant now, who takes over when we're gone? A think piece from LiveScience prompts a free-wheeling discussion that ends in an obvious answer (hint: AI). In other news, new species of hominids keep popping up basically all the time. That's cool . Unless any of this isn't even real, and then who really cares, right? 01:20:15 - PaleoPOWs are a lot like AI, once turned on it's difficult to get them to stop. Patrick presents a new recurring donation from Steven C. Thanks Steven! Charlie also has a donation to pair with a story and a few questions from the UNGA. The story is touching, and the questions are hard. Namely, what ultimately controls the tree line? It's not at all simple, but the guys take a stab at it. Finally, Ryan has an easier question about how solar panels work from Mike S. And a quick message to all parents of 4th graders: This school year you all get into any US National Park unit for FREE! Check out the details here: Every Kid In A Park. Thanks for listening and be sure to check out the Brachiolope Media Network for more great science podcasts! Music for this week's show: Family Tree - TV on the Radio Ambulance - TV on the Radio Golden Age - TV on the Radio
Fakultät für Biologie - Digitale Hochschulschriften der LMU - Teil 05/06
Fri, 14 Aug 2015 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/18684/ https://edoc.ub.uni-muenchen.de/18684/1/Maba_Dao_Lamega.pdf Maba, Dao Lamèga
Brontosaurus was an extinct name for an extinct animal, but a new study brings the “Thunder Lizard” title roaring back to life! But how does a name get dropped, and how does it get brought back again? Follow us into the winding world of paleontology taxonomy, the study of names. In the 1870s two giant hip […] The post News Bite: Brontosaurus revived! appeared first on Past Time Paleo.
Fakultät für Biologie - Digitale Hochschulschriften der LMU - Teil 05/06
This dissertation addresses an issue of key importance to the field of systematics, namely how to foster taxonomic work and the dissemination of knowledge about species by taking full advantage of electronic data and bioinformatic tools. I tested and applied modern systematic tools to produce an electronic monograph of a family of flowering plants, Caricaceae. In addition to a taxonomic revision, a molecular phylogeny of the family that includes representatives of all biological species clarifies the evolutionary relationships. Based on the plastid and nuclear DNA data, I inferred historical processes that may have shaped the evolution of the Caricaceae and explain their current geographic distribution.
TranscriptSpeaker 1: Spectrum's. Next. Speaker 2: N. N. N. N. Speaker 3: [inaudible].Speaker 1: Welcome to spectrum the science and technology show on k a l x, [00:00:30] Berkeley, a biweekly 30 minute program, bringing you interviews, featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 4: Good afternoon. I'm Rick Karnofsky. Brad swift and I are the hosts of today's show. Today we're talking with doctors, Tonya Wilkie and Chris Rink of the Department of Energy Joint Genome Institute in Walnut Creek. They recently published an article entitled insights into the Phylogeny and coding potential [00:01:00] of microbial dark matter in which they have to characterized through relationships between 201 different genomes and identified some unique genomic features. Tonya and Chris, welcome to spectrum. Speaker 5: Thanks for having us. Thank you. Speaker 4: So Tanya, what is microbial dark matter? Speaker 5: We like to take life as we know it and put it in an evolutionary tree in a tree of life. And what this assists us is to figure out the evolutionary histories of organisms and the relationships between [00:01:30] related groups of organisms. So what does this mean? It's to say we take microbial diversity as we know it on this planet and we place it in this tree of life. What you will find is that there will be some major branches in this tree, about 30 of them, and we call these major branches Fila that are made up of organisms that you can cultivate. So we can grow them on plates in the laboratory, we can grow them in Allen Meyer, flask and liquid media. We can study that for CLG. We can figure out what substrates they metabolize, [00:02:00] we can figure out how they behave under different conditions. Speaker 5: Many of them we can even genetically modify. So we really know a lot about these organisms and we can really figure out, you know, how do they function, what are the genetic underpinnings that make them function the way they do in the laboratory and also in the environment where they come from. So now coming back to this tree of life, if you keep looking at this tree of life, uh, we will find at least another 30 off these major branches that we refer to as [00:02:30] Canada. Dot. Sila and these branches have no cultivators, representatives, so all the organisms that make up these branches, we have not yet been able to cultivate in the laboratory. We call these kind of dot, Fila or microbial dark matter. And the term dark matter. All biological dark matter has been coined by the Steve Craig Laboratory at Stanford University when they published the first genomes after a candidate, phylum TM seven. We know that dark matter is in most if not all [00:03:00] ecosystems. So we find it in most ecosystems, but to get at their complete genetic makeup. That's the key challenge. Speaker 4: Yeah. And if you, if you want to push it through the extreme, there are studies out there estimating the number of bacteria species they are and how many we can cultivate. And the result is all there. The estimation of the studies we can cultivate about, you know, one or 2% of all the microbial species out there. So basically nine to 9% is still out there and we haven't even looked at it. So this really, this major on culture microbes and majority is [00:03:30] still waiting out there to be explored. So that sort of carries on the analogy to cosmological dark matter in which there's much more of it than what we actually see and understand. Right. Speaker 5: So how common and how prevalent are, are these dark matter organisms? Yeah, that's a really good question. So in some environments they are what we would consider the rabbi biosphere. So they are actually at fairly low abundance, but our methods are sensitive enough to still pick them up. [00:04:00] In other environments. We had some sediment samples where some of these candidate file, our, actually what we would consider quite abandoned, it's a few percent, let's say 2% of opiate candidate phylum that to us, even 2% is quite abandoned. Again, you have to consider the whole community. And if one member is a 2%, that's, that's a pretty dominant community members. So I'd arise from environment, environment Speaker 4: and Chris, where were samples collected from? So altogether we sampled nine sampling sites all over the globe [00:04:30] and we tried to be as inclusive as possible. So we had marine samples, freshwater samples, sediment samples, um, some samples from habitats with very high temperatures and also a sample from a bioreactor. And there were a few samples among them that for which we had really great hopes. And among them were um, samples from the hot vans from the bottom of Pacific Ocean. The samples we got were from the East Pacific virus sampling side, and that's about 2,500 meters below the store phase. And [00:05:00] the sample there, you really need a submersible that's a small submarine and you can launch from a research vessel. In our case, those samples were taken by Elvin from the woods hole oceanographic institution and now you have a lot of full Canik activity and also the seawater seeps into the earth crust goes pretty deep and gets heated up. Speaker 4: And when it comes back out as a hydrothermal event, it has up to [inaudible] hundred 50 to 400 degrees Celsius. And it is enriched in chemicals such as a sulfur or iron. [00:05:30] It makes us immediately with the surrounding seawater, which is only about a two degrees Celsius. So it's a very, it's a very challenging environment because you have this gradient from two degrees to like 400 degrees within a few centimeters and you have those chemicals that uh, the organisms, the micro organisms could use blast. There is no sunlight. So we thought that's a very interesting habitat to look for. Microbial, dark matter. There were several samples. That's a to us. One of them is the Homestake [00:06:00] mine in South Dakota and that's an old gold mine that is not used anymore since 2002 but are there still scientific experiments going on there? It's a very deep mine, about 8,000 feet deep and we could all sample from about 300 feet. Speaker 4: And we were surprised about this Ikea diversity we found in those samples. There were a few Akia that were not close to any, I don't know another key out there for some of them. We even had to propose new archaeal Fila. Stepping back a bit, Chris, [00:06:30] can you tell us more about Ikea and perhaps the three domains of life? The three domains were really established by Culver's with his landmark paper in 1977 and what he proposed was a new group of Derek here. So then he had all together three domains. You had the bacteria and archaea and the eukaryotes, the eukaryote state. There are different one big differences to have the nucleus, right? They have to DNA in the nucleus and it also includes all the higher taxa. But then you have also their key and the bacteria. [00:07:00] And those are two groups that only single cell organisms, but they are very distant related to each other, the cell envelope, all. And also the cell duplication machinery of the archaea is closer to the eukaryotes than it is to the bacteria. Speaker 5: Yeah, and it's interesting, I mean Ikea, I guess we haven't sequenced some that much yet, but Ikea are very important too, but people are not aware of them. They know about bacteria, but Ikea and maybe because there aren't any RKO pathogen [00:07:30] and we'd like to think about bacteria with regards to human health, it's very important. That's why most of what we sequence are actually pathogens, human pathogens. So we sequence, I don't know how many strains of your senior pastors and other pathogenic bacteria, but archaea are equally important, at least in the environment. But because we rarely find them associated with humans, we don't really think about archaea much. Our people aren't really aware of Ikea. Speaker 4: Talk about their importance, Speaker 5: the importance [00:08:00] in the environment. So Ikea are, for example, found in extreme environments. We find them in Hydro Soma environments. We find them in hot springs. Uh, we, they have, they have biotechnological importance and not a lot of, quite useful in enzymes that are being used in biotechnology are derived from Ikea in part because we find them in these extreme environments and hot environments and they have the machinery to deal with this temperature. So they have enzymes that function [00:08:30] properly at high temperature and extreme conditions, really extreme on the commerce extreme or fields. And that makes them very attractive bio technologically because some of these enzymes that we would like to use should be still more tolerant or should have these features that are sort of more extreme. Um, so we can explain it them for a biotech technological applications. [inaudible] Speaker 6: [inaudible] [00:09:00] you are listening to spectrum on k l x Berkeley. I'm Rick [inaudible] and I'm talking with Kanya vulgate and Chris, her and Kate about using single cell genomics. You're expand our knowledge that the tree of life, Speaker 5: [00:09:30] so again, we called up a range of different collaborators and they were all willing to go back to these interesting sites, even to the hydrothermal vent and get us fresh sample. No one turned us down. So we, we, we screened them again to make sure they are really of the nature that we would like to have them and the ones that were suitable. We then fed into our single cell workflow. Can you talk briefly about that screening? There were two screens in waft. One screen was narrowing down the samples themselves and we received a lot more sample, I would say at least [00:10:00] three times as many sample as we ended up using. And we pre-screened these on a sort of barcode sequencing level. And so we down selected them to about a third. And then within this third we sorted about 9,000 single cells and within these 9,000 single cells, only a subset of them went through successful single cell, whole genome amplification. And out of that set then we were only, we were able to identify another subset. And [00:10:30] in the end we selected 200 for sequencing 201 Speaker 4: and how does single cell sequencing work? Speaker 5: So to give you a high level overview, you take a single cell directly from the environment, you isolate it, and there's different methodologies to do that. And then you break it open, you expose the genetic material within the cell, the genome, and then you amplify the genome. And some single cells will only have one copy of that genome. And we have a methodology, it's a whole genome amplification process that's called multiple displacement amplification [00:11:00] or MDA. And that allows us to make from one copy of the genome, millions and billions of copies. One copy of the genome corresponds to a few family or grams of DNA. We can do much with it. So we have to multiply, we have to make these millions and billions of copies of the genome to have sufficient DNA for next generation sequencing. Speaker 4: Are there other extreme environments that you guys didn't take advantage of in this study that might be promising? Definitely. Um, so we, [00:11:30] we created the list already off environments that would be interesting to us based on, you know, on the results from the last start in the experience we have with environmental conditions and the is microbes we've got out of it. So we're definitely planning to have a followup study where we explore all those, um, habitats that we couldn't include in this, uh, study. Speaker 5: So some examples of the Red Sea and some fjords in Norway and their various that were after Speaker 4: the, that the Black Sea is a very interesting environment too. It's, it's completely anoxic, high levels of sulfide [00:12:00] and it's, it's really, it's huge. So that's a very interesting place to sample too. And how historically have we come to this tree in the old days? And I mean the, the, the pre sequencing area, um, the main criteria that scientists use to categorize organisms whilst the phenotype. That's the, the morphology, the biochemical properties, the development. And that was used to put, uh, organisms into categories. And then with the dawn of the sequencing area, and that was [00:12:30] mainly, um, pushed by the Sanger sequencing, the development of the Sanger sequencing in the 70s. We finally had another and we could use and that was the DNA sequence of organisms. And that was used to classify and categorize organisms. Does a phenotyping still play a role in modern phylogeny? It still does play a role in modern philosophy in the, especially for eukaryotes. Speaker 4: Well you have a very significant phenotype. So what you do there is you can compare a phenotyping information with the [00:13:00] genomic information and on top of that even, uh, information from all the ontology and you try to combine all the information you have doing for, let's say, for the evolutionary relationships among those organisms in modern times, the phylogeny of bacteria, Nokia, it's mainly based on molecular data. Part of our results were used to infer phylogenetic relationships into the started. The evolutionary history of those microbes. We'll be, well do you have for the first time is we now have chine [00:13:30] ohms for a lot of those branches of the tree where before we only had some barcodes so we knew they were there, but we had no information about the genomic content and they'll seem to be hafted for the first time. We can actually look at the evolutionary history of those microbes and there were two, two main findings in our paper. Speaker 4: One was that for a few groups, the f the placement that taxonomic placement in the tree of life was kind of debated in the past. We could help to clarify that. For example, one group is they clock chemo needs [00:14:00] and it was previously published. It could be part of the farm of the spiral kids, but we could Cully show with our analysis that they are their own major branch entry of laughter or their own file them and a a second result. That's, I think it's very important that that's because they didn't share a lot of jeans with others. Bifurcates is that, that's, that's right. So if you placed him in a tree of life, you can see that the don't cluster close parakeets, they'll come out on the other side by out by themselves, not much resembling if the spark is there. And the second result was [00:14:30] that, uh, we found several of those main branches of the tree of life, those Fila the class of together consistently in our analysis. Speaker 4: And so we could group them together and assign super filer to them. One example is a sweet book, Zero Fila Debra Opa 11 or the one and Chino too, and also almost clustered together. So we proposed a super final name. Potesky and Potesky means I'm bear or simple. And we choose that because they have a reduced and streamlined genome. That's another common feature. [00:15:00] I'm Andrea and I, I have to say that, you know, looking into evolutionary relationships, it is, it is a moving target because as Tanya mentioned, especially for microbes and bacteria and like here, there's still so many, um, candidates that are out there for which we have no genomic information. So we definitely need way more sequences, um, to get a better idea of the evolutionary relationships of all the books. Your Nokia out there Speaker 6: [00:15:30] spectrum is a public affairs show about science on k a l x Berkeley. Our guests today are Tanya. Okay. And Chris Rink k you single cell genomics to find the relationships between hundreds of dark matter of microbes. Speaker 4: And can you speak to the current throughput? I would have thought that gathering up organisms in such extreme environments was really the time limiting factor. [00:16:00] But I suppose if you have this archive, other steps might end up taking a while. I will say the most time consuming step is really to to sort those single cells and then to lyse the single cells and amplify the genome and then of course to screen them for the, for genomes of interest for microbial like metagenomes [inaudible] that was a big part of the study. So actually getting the genomic information out of the single cells and if that can be even more streamlined than uh, and push to a higher or even more stupid level, I think [00:16:30] that will speed up the recovery of, of novel microbial dogmatic genomes quite a bit. Speaker 5: Well, we have a pretty sophisticated pipeline now at the JGI where we can do this at a fairly high throughput, but as Chris said, it still takes time and every sample is different. Every sample behaves different depending on what the properties of the samples are. You may have to be treated in a certain way to make it most successful for this application and other staff in the whole process that takes a long time is the key. The quality control [00:17:00] of the data. So the data is not as pretty as a sequencing data from an isolet genome where you get a perfect genome back and the sequence data that you get back is fairly, even the coverage covered all around the genome. Single cell data is messy. The amplification process introduces these artifacts and issues. It can introduce some error because you're making copies of a genome. Speaker 5: So errors can happen. You can also introduce what we call comeric rearrangement. That means that pieces of DNA [00:17:30] go together that shouldn't go together. Again, that happens during the amplification process. It's just the nature of the process. And on top of that, parts of the genome amplify nicely and other parts not so nice. So the overall sort of what we call sequence coverage is very uneven. So the data is difficult to deal with. We have specific assembly pipelines that we do. We do a sort of a digital normalization of the data before we even deal with the data, so it's not as nice. And then on top of that you can have contamination. So the whole process is very [00:18:00] prone to contamination. Imagine you only have one copy of a single cell, five Phantogram, one circle of DNA and any little piece of DNA that you have in that prep that sometimes as we know comes with the reagents. Speaker 5: Because reagents are not designed to deal with such low template molecules. They will call amplify, they will out-compete or compete with your template. So what you end up with in your sequence is your target and other stuff that was in was in the reagents or again, in your prep. We have very rigorous [00:18:30] process of cleaning everything. We you read a lot of things we sterilize, so we need to get rid of any DNA to not, um, to, to have a good quality genome in the end. And so that said, we have developed tools and pipelines at our institute now that specifically help us detect contamination. Sometimes it's not easy to detect it and then remove it. We want to make sure that the single cell genomes that we released at as single cell genome ABC are really ABC and not a plus x and [00:19:00] B plus k because accidentally something came along and contaminated the prep. And especially with candidate Fila, it's, it's fairly difficult to detect tech contamination because what would help us would be if we would have referenced genomes, we're actually generating this reference genome so we don't have a good reference to say, yeah, this is actually, that's our target organism and the rest is public contamination, so it's very tricky. Speaker 4: Are there other examples for [00:19:30] single cell sequencing being used on this many organisms Speaker 5: on this many organisms? No, not that I'm aware of. I know there's an effort underway and the h and p, the human microbiome project where they also identified there, they nicely call it the most wanted list, so they have the target organisms that are quite abundant in different microbiomes within the human body associated with the human body and they've been very successfully able to cultivate. A lot of them bring a lot of them in culture [00:20:00] and it may be easier for the h and p because we can mimic the conditions within the body a little bit better and more controlled. We know our body temperature and we know sort of what the middle year is in the different parts of our body. So it's a little bit easier to bring these organisms and culture than going to the hydrothermal vent and try and recreate these conditions which are extremely difficult to recreate. So that said, um, there are some that they are now targeting with single cell sequencing. So that's another large effort [00:20:30] that I know of that's specifically using single cell genomics to get at some of these reference genomes. Speaker 4: Can you get more out of this then? Sort of phylogenetic links? We found a few unique genomic features and one on one dimension is we found a recode. It's stopped caught on in, in two of those, a bacteria from the hot vans I mentioned earlier. And to give you a little bit of background, so, um, it's, we know the genetic information of each sale is and coded in its DNA, but in order to [00:21:00] make use of this genomic information, this genetic information has to be translated into proteins. And then proteins that could be enzymes that are employed in the metabolism to keep the cell going. And a dispensation is pretty universal between the three domains of life. The way it works, we have three basis in your DNA and three basis are called the core done. And each call is translated in the one amino acid. Speaker 4: So this way you'll build a chain of amino acids and then this chain is for a folder [00:21:30] and then you have your ready made protein. This call them triplet. This three basis also work for start and stop. So there are certain colons that tell the cell, okay, that's where you start a protein. And another called in to tell us the cell. So that's, that's where you enter prod and you're done with it. There are some slight variations, but in general does a universally called, is perceived between all three domains of life. And what we found was very interesting in two of those bacteria from the hot vans. Ah, those two caecilian bacteria, we found the [00:22:00] recording. So one of the accord on did not called for a stop code on anymore, but in the quarter's for an amino acid in that case, glycine. And that has never been seen before. Were you surprised by these results? Speaker 5: To us, they were surprising because they were unique and they were different. On the other hand, I have to say I'm not that surprised because we haven't, like Russ said, we haven't looked at heart yet and considering that we can only cultivate a few percent of all the microbial diversity that exists on this planet as far as, [00:22:30] as far as we know it, it's not that surprising that you find these novel functions and there's these unique features and novel genetic codes because it's really, it's a highly under-explored area. Speaker 4: It is very rewarding. But if you look in the future, um, how much is still out of the sequence? Of course we're interested in that. So we looked at all the files show diversity that's known, that's out there based on this, um, biomarkers that Tony mentioned earlier and we just compared it to the genomes that we have sequenced so far. And we really want [00:23:00] to know, so if you want to cover let's say about 50% of all the fall diversity that's out there, how many achievements do we still have to sequence and the number of the estimate was we need to sequence at least 16,004 more genomes Speaker 5: and this is a moving target. So this is as we know, diversity of today it and every day we sample my environments, we sequence them deeper and everyday our diversity estimates increase. So what we've done with these 201 it's the tip of the iceberg but it's a start. Speaker 4: [00:23:30] Well Tanya and Chris, thanks for joining us. Thanks for having us. Thanks for having us. Yeah. Speaker 6: [inaudible] that's what shows are archived on iTunes to you. We've queued a simple link for you. The link is tiny, url.com/calex Speaker 7: spectrum Speaker 8: irregular feature of spectrum is a calendar [00:24:00] of some of the science and technology related events happening in the bay area over the next two weeks. Here's Brad swift and Renee Rao here today. Majority tomorrow. Expanding technological inclusion, technological inclusion is not an issue for some of us. It is an issue for all of us. Mitchell Kapore, co-chair of [inaudible] center for social impact and a partner at Kapore capital. We'll moderate a panel discussion among the following [00:24:30] presenters, Jennifer r Guayle, executive director of Latino to Kimberly Bryant, founder of Black Girls Code Connie Mack Keebler, a venture capitalist with the collaborative fund. Vivek Wadhwa academic researcher, writer and entrepreneur here today. Majority tomorrow is free and open to everyone on a first come first seated basis. This is happening on the UC Berkeley campus in Soutar de Di Hall [inaudible] [00:25:00] Auditorium Monday October 7th at 4:00 PM Speaker 7: the second installment of the six part public lecture series, not on the test. The pleasure and uses of mathematics will be held this October 9th Dr. Keith Devlin will deliver a lecture on underlying mathematics in video games. Dr Devlin will show how casual video games that provide representation of mathematics enabled children and adults to learn basic mathematics by playing in the same way people [00:25:30] learn music by learning to play the piano. Professor Devlin is a mathematician at Stanford, a Co founder and president of Inner Tube Games and the math guy of NPR. The lecture will be held on October 9th at 7:00 PM in the Berkeley City College Auditorium located at 2050 Center street in Berkeley. The event is free and open to the public. Speaker 8: The Leonardo arts science evening rendezvous or laser is a lecture series with rotating barrier venues. October 9th there will be a laser [00:26:00] at UC Berkeley. Presenters include Zan Gill, a former NASA scientists, Jennifer Parker of UC Santa Cruz, Cheryl Leonard, a composer, Wayne Vitali, founding member of gamelons Sakara [inaudible]. This is Wednesday, October 9th from 6:30 PM to 9:00 PM on the UC Berkeley campus in barrels hall room 100 Speaker 7: how can we prevent information technology [00:26:30] from destroying the middle class? Jaron Lanier, is it computer scientists, Kim Poser, visual artist and author. October 14th linear will present his ideas on the impact of information technology on his two most recent books are title. You are not a gadget and who owns the future. The seminar will be held in Sue Taja, Dai Hall, but not auditorium on the UC Berkeley campus. Monday, October 14th from 11:00 AM to noon [00:27:00] and that with some science news headlines. Here's the Renee, the intergovernmental panel on climate change released part of its assessment report. Five last Friday. The more than 200 lead authors on their report included Lawrence Berkeley National Labs, Michael Warner and William Collins who had a chapters on longterm climate change productions and climate models. The report reinforces previous conclusions that over the next century, the continents will warm [00:27:30] with more hot extremes and fewer cold extremes. Precipitation patterns around the world will also continue changing. One-Arm Collins noted that climate models since the last report in 2007 have improved significantly as both data collection and mechanistic knowledge have grown using these models. Scientists made several projections of different scenarios for the best, worst and middling cases of continued greenhouse emissions. Speaker 7: [00:28:00] Two recent accomplishments by commercial space programs are notable. Orbital Sciences launched their sickness spacecraft on September 18th a top the company's rocket and Tara's from wallops island, Virginia. On September 28th the Cygnus dock did the international space station for the first time, a space x rocket carrying and Canadian satellite has launched from the California coast in a demonstration flight of a new Falcon rocket. The next generation. Rocket boasts [00:28:30] upgraded engines designed to improve performance and carry heavier payloads. The rocket is carrying a satellite dead kiss IOP, a project of the Canadian Space Agency and other partners. Once in orbit it will track space weather. Speaker 2: Mm mm mm. Mm Huh. Speaker 7: The music [00:29:00] heard during the show was written and produced by Alex Simon. Yeah. Speaker 3: Thank you for listening to spectrum. If you have comments about the show, please send them to us via email. Address is [inaudible] dot [inaudible] dot com Speaker 9: [inaudible]. See acast.com/privacy for privacy and opt-out information.
TranscriptSpeaker 1: Spectrum's. Next. Speaker 2: N. N. N. N. Speaker 3: [inaudible].Speaker 1: Welcome to spectrum the science and technology show on k a l x, [00:00:30] Berkeley, a biweekly 30 minute program, bringing you interviews, featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 4: Good afternoon. I'm Rick Karnofsky. Brad swift and I are the hosts of today's show. Today we're talking with doctors, Tonya Wilkie and Chris Rink of the Department of Energy Joint Genome Institute in Walnut Creek. They recently published an article entitled insights into the Phylogeny and coding potential [00:01:00] of microbial dark matter in which they have to characterized through relationships between 201 different genomes and identified some unique genomic features. Tonya and Chris, welcome to spectrum. Speaker 5: Thanks for having us. Thank you. Speaker 4: So Tanya, what is microbial dark matter? Speaker 5: We like to take life as we know it and put it in an evolutionary tree in a tree of life. And what this assists us is to figure out the evolutionary histories of organisms and the relationships between [00:01:30] related groups of organisms. So what does this mean? It's to say we take microbial diversity as we know it on this planet and we place it in this tree of life. What you will find is that there will be some major branches in this tree, about 30 of them, and we call these major branches Fila that are made up of organisms that you can cultivate. So we can grow them on plates in the laboratory, we can grow them in Allen Meyer, flask and liquid media. We can study that for CLG. We can figure out what substrates they metabolize, [00:02:00] we can figure out how they behave under different conditions. Speaker 5: Many of them we can even genetically modify. So we really know a lot about these organisms and we can really figure out, you know, how do they function, what are the genetic underpinnings that make them function the way they do in the laboratory and also in the environment where they come from. So now coming back to this tree of life, if you keep looking at this tree of life, uh, we will find at least another 30 off these major branches that we refer to as [00:02:30] Canada. Dot. Sila and these branches have no cultivators, representatives, so all the organisms that make up these branches, we have not yet been able to cultivate in the laboratory. We call these kind of dot, Fila or microbial dark matter. And the term dark matter. All biological dark matter has been coined by the Steve Craig Laboratory at Stanford University when they published the first genomes after a candidate, phylum TM seven. We know that dark matter is in most if not all [00:03:00] ecosystems. So we find it in most ecosystems, but to get at their complete genetic makeup. That's the key challenge. Speaker 4: Yeah. And if you, if you want to push it through the extreme, there are studies out there estimating the number of bacteria species they are and how many we can cultivate. And the result is all there. The estimation of the studies we can cultivate about, you know, one or 2% of all the microbial species out there. So basically nine to 9% is still out there and we haven't even looked at it. So this really, this major on culture microbes and majority is [00:03:30] still waiting out there to be explored. So that sort of carries on the analogy to cosmological dark matter in which there's much more of it than what we actually see and understand. Right. Speaker 5: So how common and how prevalent are, are these dark matter organisms? Yeah, that's a really good question. So in some environments they are what we would consider the rabbi biosphere. So they are actually at fairly low abundance, but our methods are sensitive enough to still pick them up. [00:04:00] In other environments. We had some sediment samples where some of these candidate file, our, actually what we would consider quite abandoned, it's a few percent, let's say 2% of opiate candidate phylum that to us, even 2% is quite abandoned. Again, you have to consider the whole community. And if one member is a 2%, that's, that's a pretty dominant community members. So I'd arise from environment, environment Speaker 4: and Chris, where were samples collected from? So altogether we sampled nine sampling sites all over the globe [00:04:30] and we tried to be as inclusive as possible. So we had marine samples, freshwater samples, sediment samples, um, some samples from habitats with very high temperatures and also a sample from a bioreactor. And there were a few samples among them that for which we had really great hopes. And among them were um, samples from the hot vans from the bottom of Pacific Ocean. The samples we got were from the East Pacific virus sampling side, and that's about 2,500 meters below the store phase. And [00:05:00] the sample there, you really need a submersible that's a small submarine and you can launch from a research vessel. In our case, those samples were taken by Elvin from the woods hole oceanographic institution and now you have a lot of full Canik activity and also the seawater seeps into the earth crust goes pretty deep and gets heated up. Speaker 4: And when it comes back out as a hydrothermal event, it has up to [inaudible] hundred 50 to 400 degrees Celsius. And it is enriched in chemicals such as a sulfur or iron. [00:05:30] It makes us immediately with the surrounding seawater, which is only about a two degrees Celsius. So it's a very, it's a very challenging environment because you have this gradient from two degrees to like 400 degrees within a few centimeters and you have those chemicals that uh, the organisms, the micro organisms could use blast. There is no sunlight. So we thought that's a very interesting habitat to look for. Microbial, dark matter. There were several samples. That's a to us. One of them is the Homestake [00:06:00] mine in South Dakota and that's an old gold mine that is not used anymore since 2002 but are there still scientific experiments going on there? It's a very deep mine, about 8,000 feet deep and we could all sample from about 300 feet. Speaker 4: And we were surprised about this Ikea diversity we found in those samples. There were a few Akia that were not close to any, I don't know another key out there for some of them. We even had to propose new archaeal Fila. Stepping back a bit, Chris, [00:06:30] can you tell us more about Ikea and perhaps the three domains of life? The three domains were really established by Culver's with his landmark paper in 1977 and what he proposed was a new group of Derek here. So then he had all together three domains. You had the bacteria and archaea and the eukaryotes, the eukaryote state. There are different one big differences to have the nucleus, right? They have to DNA in the nucleus and it also includes all the higher taxa. But then you have also their key and the bacteria. [00:07:00] And those are two groups that only single cell organisms, but they are very distant related to each other, the cell envelope, all. And also the cell duplication machinery of the archaea is closer to the eukaryotes than it is to the bacteria. Speaker 5: Yeah, and it's interesting, I mean Ikea, I guess we haven't sequenced some that much yet, but Ikea are very important too, but people are not aware of them. They know about bacteria, but Ikea and maybe because there aren't any RKO pathogen [00:07:30] and we'd like to think about bacteria with regards to human health, it's very important. That's why most of what we sequence are actually pathogens, human pathogens. So we sequence, I don't know how many strains of your senior pastors and other pathogenic bacteria, but archaea are equally important, at least in the environment. But because we rarely find them associated with humans, we don't really think about archaea much. Our people aren't really aware of Ikea. Speaker 4: Talk about their importance, Speaker 5: the importance [00:08:00] in the environment. So Ikea are, for example, found in extreme environments. We find them in Hydro Soma environments. We find them in hot springs. Uh, we, they have, they have biotechnological importance and not a lot of, quite useful in enzymes that are being used in biotechnology are derived from Ikea in part because we find them in these extreme environments and hot environments and they have the machinery to deal with this temperature. So they have enzymes that function [00:08:30] properly at high temperature and extreme conditions, really extreme on the commerce extreme or fields. And that makes them very attractive bio technologically because some of these enzymes that we would like to use should be still more tolerant or should have these features that are sort of more extreme. Um, so we can explain it them for a biotech technological applications. [inaudible] Speaker 6: [inaudible] [00:09:00] you are listening to spectrum on k l x Berkeley. I'm Rick [inaudible] and I'm talking with Kanya vulgate and Chris, her and Kate about using single cell genomics. You're expand our knowledge that the tree of life, Speaker 5: [00:09:30] so again, we called up a range of different collaborators and they were all willing to go back to these interesting sites, even to the hydrothermal vent and get us fresh sample. No one turned us down. So we, we, we screened them again to make sure they are really of the nature that we would like to have them and the ones that were suitable. We then fed into our single cell workflow. Can you talk briefly about that screening? There were two screens in waft. One screen was narrowing down the samples themselves and we received a lot more sample, I would say at least [00:10:00] three times as many sample as we ended up using. And we pre-screened these on a sort of barcode sequencing level. And so we down selected them to about a third. And then within this third we sorted about 9,000 single cells and within these 9,000 single cells, only a subset of them went through successful single cell, whole genome amplification. And out of that set then we were only, we were able to identify another subset. And [00:10:30] in the end we selected 200 for sequencing 201 Speaker 4: and how does single cell sequencing work? Speaker 5: So to give you a high level overview, you take a single cell directly from the environment, you isolate it, and there's different methodologies to do that. And then you break it open, you expose the genetic material within the cell, the genome, and then you amplify the genome. And some single cells will only have one copy of that genome. And we have a methodology, it's a whole genome amplification process that's called multiple displacement amplification [00:11:00] or MDA. And that allows us to make from one copy of the genome, millions and billions of copies. One copy of the genome corresponds to a few family or grams of DNA. We can do much with it. So we have to multiply, we have to make these millions and billions of copies of the genome to have sufficient DNA for next generation sequencing. Speaker 4: Are there other extreme environments that you guys didn't take advantage of in this study that might be promising? Definitely. Um, so we, [00:11:30] we created the list already off environments that would be interesting to us based on, you know, on the results from the last start in the experience we have with environmental conditions and the is microbes we've got out of it. So we're definitely planning to have a followup study where we explore all those, um, habitats that we couldn't include in this, uh, study. Speaker 5: So some examples of the Red Sea and some fjords in Norway and their various that were after Speaker 4: the, that the Black Sea is a very interesting environment too. It's, it's completely anoxic, high levels of sulfide [00:12:00] and it's, it's really, it's huge. So that's a very interesting place to sample too. And how historically have we come to this tree in the old days? And I mean the, the, the pre sequencing area, um, the main criteria that scientists use to categorize organisms whilst the phenotype. That's the, the morphology, the biochemical properties, the development. And that was used to put, uh, organisms into categories. And then with the dawn of the sequencing area, and that was [00:12:30] mainly, um, pushed by the Sanger sequencing, the development of the Sanger sequencing in the 70s. We finally had another and we could use and that was the DNA sequence of organisms. And that was used to classify and categorize organisms. Does a phenotyping still play a role in modern phylogeny? It still does play a role in modern philosophy in the, especially for eukaryotes. Speaker 4: Well you have a very significant phenotype. So what you do there is you can compare a phenotyping information with the [00:13:00] genomic information and on top of that even, uh, information from all the ontology and you try to combine all the information you have doing for, let's say, for the evolutionary relationships among those organisms in modern times, the phylogeny of bacteria, Nokia, it's mainly based on molecular data. Part of our results were used to infer phylogenetic relationships into the started. The evolutionary history of those microbes. We'll be, well do you have for the first time is we now have chine [00:13:30] ohms for a lot of those branches of the tree where before we only had some barcodes so we knew they were there, but we had no information about the genomic content and they'll seem to be hafted for the first time. We can actually look at the evolutionary history of those microbes and there were two, two main findings in our paper. Speaker 4: One was that for a few groups, the f the placement that taxonomic placement in the tree of life was kind of debated in the past. We could help to clarify that. For example, one group is they clock chemo needs [00:14:00] and it was previously published. It could be part of the farm of the spiral kids, but we could Cully show with our analysis that they are their own major branch entry of laughter or their own file them and a a second result. That's, I think it's very important that that's because they didn't share a lot of jeans with others. Bifurcates is that, that's, that's right. So if you placed him in a tree of life, you can see that the don't cluster close parakeets, they'll come out on the other side by out by themselves, not much resembling if the spark is there. And the second result was [00:14:30] that, uh, we found several of those main branches of the tree of life, those Fila the class of together consistently in our analysis. Speaker 4: And so we could group them together and assign super filer to them. One example is a sweet book, Zero Fila Debra Opa 11 or the one and Chino too, and also almost clustered together. So we proposed a super final name. Potesky and Potesky means I'm bear or simple. And we choose that because they have a reduced and streamlined genome. That's another common feature. [00:15:00] I'm Andrea and I, I have to say that, you know, looking into evolutionary relationships, it is, it is a moving target because as Tanya mentioned, especially for microbes and bacteria and like here, there's still so many, um, candidates that are out there for which we have no genomic information. So we definitely need way more sequences, um, to get a better idea of the evolutionary relationships of all the books. Your Nokia out there Speaker 6: [00:15:30] spectrum is a public affairs show about science on k a l x Berkeley. Our guests today are Tanya. Okay. And Chris Rink k you single cell genomics to find the relationships between hundreds of dark matter of microbes. Speaker 4: And can you speak to the current throughput? I would have thought that gathering up organisms in such extreme environments was really the time limiting factor. [00:16:00] But I suppose if you have this archive, other steps might end up taking a while. I will say the most time consuming step is really to to sort those single cells and then to lyse the single cells and amplify the genome and then of course to screen them for the, for genomes of interest for microbial like metagenomes [inaudible] that was a big part of the study. So actually getting the genomic information out of the single cells and if that can be even more streamlined than uh, and push to a higher or even more stupid level, I think [00:16:30] that will speed up the recovery of, of novel microbial dogmatic genomes quite a bit. Speaker 5: Well, we have a pretty sophisticated pipeline now at the JGI where we can do this at a fairly high throughput, but as Chris said, it still takes time and every sample is different. Every sample behaves different depending on what the properties of the samples are. You may have to be treated in a certain way to make it most successful for this application and other staff in the whole process that takes a long time is the key. The quality control [00:17:00] of the data. So the data is not as pretty as a sequencing data from an isolet genome where you get a perfect genome back and the sequence data that you get back is fairly, even the coverage covered all around the genome. Single cell data is messy. The amplification process introduces these artifacts and issues. It can introduce some error because you're making copies of a genome. Speaker 5: So errors can happen. You can also introduce what we call comeric rearrangement. That means that pieces of DNA [00:17:30] go together that shouldn't go together. Again, that happens during the amplification process. It's just the nature of the process. And on top of that, parts of the genome amplify nicely and other parts not so nice. So the overall sort of what we call sequence coverage is very uneven. So the data is difficult to deal with. We have specific assembly pipelines that we do. We do a sort of a digital normalization of the data before we even deal with the data, so it's not as nice. And then on top of that you can have contamination. So the whole process is very [00:18:00] prone to contamination. Imagine you only have one copy of a single cell, five Phantogram, one circle of DNA and any little piece of DNA that you have in that prep that sometimes as we know comes with the reagents. Speaker 5: Because reagents are not designed to deal with such low template molecules. They will call amplify, they will out-compete or compete with your template. So what you end up with in your sequence is your target and other stuff that was in was in the reagents or again, in your prep. We have very rigorous [00:18:30] process of cleaning everything. We you read a lot of things we sterilize, so we need to get rid of any DNA to not, um, to, to have a good quality genome in the end. And so that said, we have developed tools and pipelines at our institute now that specifically help us detect contamination. Sometimes it's not easy to detect it and then remove it. We want to make sure that the single cell genomes that we released at as single cell genome ABC are really ABC and not a plus x and [00:19:00] B plus k because accidentally something came along and contaminated the prep. And especially with candidate Fila, it's, it's fairly difficult to detect tech contamination because what would help us would be if we would have referenced genomes, we're actually generating this reference genome so we don't have a good reference to say, yeah, this is actually, that's our target organism and the rest is public contamination, so it's very tricky. Speaker 4: Are there other examples for [00:19:30] single cell sequencing being used on this many organisms Speaker 5: on this many organisms? No, not that I'm aware of. I know there's an effort underway and the h and p, the human microbiome project where they also identified there, they nicely call it the most wanted list, so they have the target organisms that are quite abundant in different microbiomes within the human body associated with the human body and they've been very successfully able to cultivate. A lot of them bring a lot of them in culture [00:20:00] and it may be easier for the h and p because we can mimic the conditions within the body a little bit better and more controlled. We know our body temperature and we know sort of what the middle year is in the different parts of our body. So it's a little bit easier to bring these organisms and culture than going to the hydrothermal vent and try and recreate these conditions which are extremely difficult to recreate. So that said, um, there are some that they are now targeting with single cell sequencing. So that's another large effort [00:20:30] that I know of that's specifically using single cell genomics to get at some of these reference genomes. Speaker 4: Can you get more out of this then? Sort of phylogenetic links? We found a few unique genomic features and one on one dimension is we found a recode. It's stopped caught on in, in two of those, a bacteria from the hot vans I mentioned earlier. And to give you a little bit of background, so, um, it's, we know the genetic information of each sale is and coded in its DNA, but in order to [00:21:00] make use of this genomic information, this genetic information has to be translated into proteins. And then proteins that could be enzymes that are employed in the metabolism to keep the cell going. And a dispensation is pretty universal between the three domains of life. The way it works, we have three basis in your DNA and three basis are called the core done. And each call is translated in the one amino acid. Speaker 4: So this way you'll build a chain of amino acids and then this chain is for a folder [00:21:30] and then you have your ready made protein. This call them triplet. This three basis also work for start and stop. So there are certain colons that tell the cell, okay, that's where you start a protein. And another called in to tell us the cell. So that's, that's where you enter prod and you're done with it. There are some slight variations, but in general does a universally called, is perceived between all three domains of life. And what we found was very interesting in two of those bacteria from the hot vans. Ah, those two caecilian bacteria, we found the [00:22:00] recording. So one of the accord on did not called for a stop code on anymore, but in the quarter's for an amino acid in that case, glycine. And that has never been seen before. Were you surprised by these results? Speaker 5: To us, they were surprising because they were unique and they were different. On the other hand, I have to say I'm not that surprised because we haven't, like Russ said, we haven't looked at heart yet and considering that we can only cultivate a few percent of all the microbial diversity that exists on this planet as far as, [00:22:30] as far as we know it, it's not that surprising that you find these novel functions and there's these unique features and novel genetic codes because it's really, it's a highly under-explored area. Speaker 4: It is very rewarding. But if you look in the future, um, how much is still out of the sequence? Of course we're interested in that. So we looked at all the files show diversity that's known, that's out there based on this, um, biomarkers that Tony mentioned earlier and we just compared it to the genomes that we have sequenced so far. And we really want [00:23:00] to know, so if you want to cover let's say about 50% of all the fall diversity that's out there, how many achievements do we still have to sequence and the number of the estimate was we need to sequence at least 16,004 more genomes Speaker 5: and this is a moving target. So this is as we know, diversity of today it and every day we sample my environments, we sequence them deeper and everyday our diversity estimates increase. So what we've done with these 201 it's the tip of the iceberg but it's a start. Speaker 4: [00:23:30] Well Tanya and Chris, thanks for joining us. Thanks for having us. Thanks for having us. Yeah. Speaker 6: [inaudible] that's what shows are archived on iTunes to you. We've queued a simple link for you. The link is tiny, url.com/calex Speaker 7: spectrum Speaker 8: irregular feature of spectrum is a calendar [00:24:00] of some of the science and technology related events happening in the bay area over the next two weeks. Here's Brad swift and Renee Rao here today. Majority tomorrow. Expanding technological inclusion, technological inclusion is not an issue for some of us. It is an issue for all of us. Mitchell Kapore, co-chair of [inaudible] center for social impact and a partner at Kapore capital. We'll moderate a panel discussion among the following [00:24:30] presenters, Jennifer r Guayle, executive director of Latino to Kimberly Bryant, founder of Black Girls Code Connie Mack Keebler, a venture capitalist with the collaborative fund. Vivek Wadhwa academic researcher, writer and entrepreneur here today. Majority tomorrow is free and open to everyone on a first come first seated basis. This is happening on the UC Berkeley campus in Soutar de Di Hall [inaudible] [00:25:00] Auditorium Monday October 7th at 4:00 PM Speaker 7: the second installment of the six part public lecture series, not on the test. The pleasure and uses of mathematics will be held this October 9th Dr. Keith Devlin will deliver a lecture on underlying mathematics in video games. Dr Devlin will show how casual video games that provide representation of mathematics enabled children and adults to learn basic mathematics by playing in the same way people [00:25:30] learn music by learning to play the piano. Professor Devlin is a mathematician at Stanford, a Co founder and president of Inner Tube Games and the math guy of NPR. The lecture will be held on October 9th at 7:00 PM in the Berkeley City College Auditorium located at 2050 Center street in Berkeley. The event is free and open to the public. Speaker 8: The Leonardo arts science evening rendezvous or laser is a lecture series with rotating barrier venues. October 9th there will be a laser [00:26:00] at UC Berkeley. Presenters include Zan Gill, a former NASA scientists, Jennifer Parker of UC Santa Cruz, Cheryl Leonard, a composer, Wayne Vitali, founding member of gamelons Sakara [inaudible]. This is Wednesday, October 9th from 6:30 PM to 9:00 PM on the UC Berkeley campus in barrels hall room 100 Speaker 7: how can we prevent information technology [00:26:30] from destroying the middle class? Jaron Lanier, is it computer scientists, Kim Poser, visual artist and author. October 14th linear will present his ideas on the impact of information technology on his two most recent books are title. You are not a gadget and who owns the future. The seminar will be held in Sue Taja, Dai Hall, but not auditorium on the UC Berkeley campus. Monday, October 14th from 11:00 AM to noon [00:27:00] and that with some science news headlines. Here's the Renee, the intergovernmental panel on climate change released part of its assessment report. Five last Friday. The more than 200 lead authors on their report included Lawrence Berkeley National Labs, Michael Warner and William Collins who had a chapters on longterm climate change productions and climate models. The report reinforces previous conclusions that over the next century, the continents will warm [00:27:30] with more hot extremes and fewer cold extremes. Precipitation patterns around the world will also continue changing. One-Arm Collins noted that climate models since the last report in 2007 have improved significantly as both data collection and mechanistic knowledge have grown using these models. Scientists made several projections of different scenarios for the best, worst and middling cases of continued greenhouse emissions. Speaker 7: [00:28:00] Two recent accomplishments by commercial space programs are notable. Orbital Sciences launched their sickness spacecraft on September 18th a top the company's rocket and Tara's from wallops island, Virginia. On September 28th the Cygnus dock did the international space station for the first time, a space x rocket carrying and Canadian satellite has launched from the California coast in a demonstration flight of a new Falcon rocket. The next generation. Rocket boasts [00:28:30] upgraded engines designed to improve performance and carry heavier payloads. The rocket is carrying a satellite dead kiss IOP, a project of the Canadian Space Agency and other partners. Once in orbit it will track space weather. Speaker 2: Mm mm mm. Mm Huh. Speaker 7: The music [00:29:00] heard during the show was written and produced by Alex Simon. Yeah. Speaker 3: Thank you for listening to spectrum. If you have comments about the show, please send them to us via email. Address is [inaudible] dot [inaudible] dot com Speaker 9: [inaudible]. Hosted on Acast. See acast.com/privacy for more information.
Fakultät für Biologie - Digitale Hochschulschriften der LMU - Teil 05/06
Thu, 6 Jun 2013 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/16459/ https://edoc.ub.uni-muenchen.de/16459/1/Soehner_Sylvia.pdf Söhner, Sylvia ddc:570, ddc:500
The 16th to the 18th December 2012 saw University College Dublin host The Palaeontological Association (PalAss) 56th annual general meeting. Palaeocast were present at the conference for quite a few reasons: firstly, it's always good to try and keep on top of the latest research in the field and conferences are the places to be for hearing a lot of ideas, covering a diverse array of topics, in a short period of time; secondly, we wanted to promote ourselves to the delegate in the hope of securing further interviews for the coming year; and thirdly, we wanted to drum up support for our 'Palaeo101' initiative which should finally be taking off this year.
Darwinian Synthesis; Unity of Type and Conditions of Existence; Instinct and Behavior; Ants - Swarm Behavior; Bees - Complex Nonteleological Construction; Geological Succession; Embryology; Ontogeny; Phylogeny
Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for them has led to a variety of naming styles, multiple synonyms and misleading homographs that obscure variant relationships and complicate database searches. We propose here a unified nomenclature for variants of all five classes of histones that uses consistent but flexible naming conventions to produce names that are informative and readily searchable. The nomenclature builds on historical usage and incorporates phylogenetic relationships, which are strong predictors of structure and function. A key feature is the consistent use of punctuation to represent phylogenetic divergence, making explicit the relationships among variant subtypes that have previously been implicit or unclear. We recommend that by default new histone variants be named with organism-specific paralog-number suffixes that lack phylogenetic implication, while letter suffixes be reserved for structurally distinct clades of variants. For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure.
Stadler, T (ETH Zürich) Thursday 23 June 2011, 12:10-12:30
Gusfield, DM (University of California, Davis) Monday 20 June 2011, 10:00-11:00
Fakultät für Biologie - Digitale Hochschulschriften der LMU - Teil 04/06
Fri, 6 May 2011 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/14076/ https://edoc.ub.uni-muenchen.de/14076/1/Krueger_Manuela.pdf Krüger, Manuela ddc:570, ddc:500, Fakultät für Biol
Ontogeny? Phylogeny? Recapitulates? What the what? This is another pairing that’s been rattling around in my brain forever, and a few years ago I was pleased to learn that Ken Schles is also a fan. Enough time passed for him to forget … Continue reading →
The Tree of Life must be discovered through rigorous analysis. Genetic information is crucial because appearances can be deceiving, and species that look similar can prove to be genetically very dissimilar and not share recent common ancestors. Two criteria, used to determine what the "correct" Tree is, are simplicity and whether the tree maximizes the probability of observing what we actually see.
Fakultät für Biologie - Digitale Hochschulschriften der LMU - Teil 03/06
The Thelephorales (Basidiomycota, Fungi) form a monophyletic group with approximately 177 accepted species. The Thelephorales are cosmopolitan and encompass mainly ectomycorrhizal species. Unlike many fungal lineages, evolutionary trends within and between members of Thelephorales still remain incompletely assessed. Additionally, most phylogenetic investigations on fungi have failed to include representative samples from tropical Africa. In the present study started four years ago, we have assessed and documented some of the diversity of tropical African Thelephorales. It represents a part of a future broader but continuous project aiming for a complete monograph, and highlighting the anatomical and molecular relevance of tropical species in the evolutionary interpretation of Thelephorales in general. The study was started in the northern Guinean seasonal forests, located from central to north Benin (West Africa). Northern Guinean seasonal forests are characterised by a low specific plant richness, but predominated by a few ectomycorrhizal trees of the Caesalpiniaceae (Isoberlinia doka Craib & Stapf Isoberlinia tomenteosa (Harms) Craib & Stapf, Burkea africana Hook., and Afzelia africana Smith), Dipterocarpaceae (Monothes kerstingii Gilg.) and Euphorbiaceae (Uapaca guineensis Müll. Arg.). Four collecting trips were undertaken during the rainy seasons of 2003, 2004, 2005 and 2006. Specimens of Thelephorales and soil cores were randomly sampled under native ectomycorrhizal trees. The collecting trips yielded over 800 specimens of Thelephorales and 60 EcM samples in total. Taxonomic investigations and species concepts of the specimens were assessed using a combination of both molecular and anatomo-morphological approaches. All examined specimens were sorted into 19 morphologically different species. In this dissertation four new species are described and illustrated. A full description is provided for each species, together with reliable line drawings and, where possible, with SEM micrographs. Anatomic studies have confirmed and emphasised the commonality of irregularly shaped thin hyphae on the rhizomorph surfaces of many African species. Novel anatomical features hitherto unknown within Thelephorales, and rarely recorded for Hymenomycetes in general, are recorded. Detailed anatomical comparison with type species has enabled us to depict fundamental arguments about the discrimination of thelephoroid genera. We report fundamental differences in spore ornamentation between African and temperate tomentelloid species. Using molecular PCR methods, we confirmed the high divergence rate of the ITS regions of thelephoroid fungi. Within morphologically close specimens, the ITS rDNA sequence deviation generally ranges between 0.0 to 2.68%. However, genetic distance between some specimens (e.g.Tomentella furcata Yorou & Agerer and T. cf. furcata nom. prov.) illustrates how morphologically convergent specimens may be greatly divergent with regard to their ITS rDNA. Phylogenetically, tropical African species of Thelephorales are either basal or terminal within various clades of investigated temperate, boreal and tropical species. Generally, they highly deviate from temperate and boreal closest species by 4.3 to 12.9% with regard to the ITS rDNA sequences. Northern Guinean seasonal forests harbour a great diversity of Thelephorales that are, however, hard to detect due to the down-facing growth of fruit bodies of most resupinate Thelephorales, and the annual burning of required substrates. Only one species, Tomentella africana Yorou & Agerer, is widespread and commonly recorded. Many other species occur scarcely on fragmented substrates. Though the Thelephorales are cosmopolitan, we failed to record species that are reported to have a worldwide distribution. Notably, representatives of the resupinate thelephoroid genera Pseudotomentella Svrček and Tomentellopsis Hjortstam were missing, as well as species of the mainly temperately distributed family Bankeraceae. In this study, we provide evidence of the ectomycorrhizal formation between Thelephorales and native tropical African forest trees. Anatomical and molecular characterisation of ectomycorrhizae formed between Thelephorales and native West African forest trees (namely Afzelia africana and Uapaca guineensis) are provided for the first time. The present studies are based on original material collected in some Ceasalpinioid /Euphorbiaceae-dominated vegetation types found from central to north Benin. The Zambesian Centre of Endemism, located in South-East Africa, also harbours a variety of different ectomycorrhizal trees including Brachstegia spp, Julbernadia spp, and Isoberlinia spp. Stands dominated by monospecific ectomycorrhizal forest trees are also present in the rain forests of South Cameroon. The variety of ectomycorrhizal tree species present in tropical Africa implies a greater species richness of Thelephorales than that currently reported from Benin. The present thesis represents a keystone study and provides baseline data for a continuing monograph of Thelephorales in tropical Africa. Intensive monographic and taxonomical investigations will undoubtedly reveal many interesting, and probably plesiomorphic, anatomical features from tropical Thelephorales. In this context, detailed anatomical investigations integrated with DNA sequence analyses and phylogenetic inferences are promising tools for discriminating thelephoroid species in general, and tropical ones in particular. Taxonomic novelties in this study: Tomentella capitata Yorou & Agerer Tomentella brunneocystidia Yorou & Agerer Tomentella furcata Yorou & Agerer Tomentella africana Yorou & Agerer
Mossel, E (California) Friday 21 December 2007, 11:50-12:10 PLGw03 - Future Directions in Phylogenetic Methods and Models
Lacey, M (Tulane) Monday 17 December 2007, 15:30-15:50 PLGw03 - Future Directions in Phylogenetic Methods and Models
Naylor, G (Florida State) Monday 17 December 2007, 16:10-16:30 PLGw03 - Future Directions in Phylogenetic Methods and Models
Fakultät für Biologie - Digitale Hochschulschriften der LMU - Teil 02/06
This study focuses on one brown-colored representative of the green sulfur bacteria, Chlorobium sp. BS-1, that survives by means of anoxygenic photosynthesis even at very low light intensities. This unusual representative of the green sulfur bacteria lives in the chemocline of the Black Sea, which is located at 80 to 120 m depth, offering only 0.0005 % (winter) to 0.002 % (summer) of surface irradiance (0.00075 to 0.0022 µmol Quanta m-2 s-1). The Black Sea represents the world’s biggest anoxic water body, and it is permanently stratified. An overview of the habitat Black Sea and the research on phyotosynthetic bacteria in the Black Sea chemocline gives the article Anoxygenic phototrophic bacteria in the Black Sea chemocline (pages 53 ff.) In the second article, Physiology and phylogeny of green sulfur bacteria forming a monospecific phototrophic assemblage at 100 m depth in the Black Sea (pages 75 ff.), it is shown that Chl. sp. BS-1 represents a novel phylotype in the marine cluster of green sulfur bacteria and is the only detectable phylotype of green sulfur bacteria in the Black Sea chemocline. It was shown that Chl. sp. BS-1 is the first organism known to date which fixes 14CO2 under laboratory conditions even at light intensities as low as 0.015 µmol Quanta m-2 s-1 which is much lower than the light intensity in any typical habitat of green sulfur bacteria. Therefore it is the best adapted species to extremely low light intensities documented. The major adaptive mechanism to extremely low light intensities might be a significant change in the secondary homologs of the main photosynthetic pigment, bacteriochlorophyll e (BChl e). The dominance of farnesyl esters and the presence of four unusual geranyl ester homologs of BChl e were revealed by HPLC analysis in cells shifted from 3 to 0.1 µmol Quanta m-2 s-1. Together with in situ light measurements and in situ BChl e concentrations, the growth experiments allowed for the calculation of doubling times and significance of the photosynthetic activity for the carbon and sulfur cycle in the Black Sea chemocline. With doubling times of a minimum of 3.1 years (for summer light intensity) and the contribution of only 0.002 - 0.01 % to total sulfide oxidation in the chemocline Chl. sp. BS-1 represents the slowest growing population of green sulfur bacteria known to date and does not contribute significantly to the carbon or sulfur cycle. The article Subfossil DNA sequences of green sulfur bacteria as indicators for past water column anoxia in the Black Sea (page 119 ff.) gives insight into the history of the strain Chl. sp. BS-1 and the green sulfur bacteria in the Black Sea during the last few thousand years. The Black Sea today is considered as closest contemporary analogue to past sulfidic oceans and its biogeography over several thousand years is well documented in its stratified sedimentary record. Since the 16S rRNA gene sequence of Chl. sp. BS-1 might be a useful indicator for past photic zone anoxia, the presence of its fingerprints in past periods of the Black Sea was investigated. 16S rRNA gene sequences of green sulfur bacteria from samples of Black Sea sediments up to 7 m below seafloor were amplified and sequenced. Nine green sulfur bacterial 16S rRNA gene sequences were identified. Surprisingly, not only green sulfur bacterial fingerprints were found but also closely related species clustering at the basis of the green sulfur bacterial subtree, together with not yet cultured species detected all over the world. The new cluster was called “deep-branching green sulfur bacteria” though it was not possible to enrich live organisms with medium for photosynthetic green sulfur bacteria. The chemocline strain Chl. sp. BS-1, found in Units III, II and I (>9000 years b.p. until today), and two other sequences, found in sediments of Unit IIb (between 8200 yr. b.p. and 5000 yr.b.p) only, were the only two sequences clustering with the marine green sulfur bacteria. The other green sulfur bacterial sequences clustered with freshwater or low-salt adapted species, indicating an allochthonous introduction of these sequences to the Black Sea sediments. A long-distance transport of green sulfur bacteria even through oxygenated water is possible since the group has protective mechanisms agains oxygen intoxication. In the article An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent (pages 105 ff.) a strain is presented which was enriched from beneath a deep sea hydrothermal vent, Chlorobium bathyomarinum GSB1. It was shown to resist more than 16 days of oxygenated medium. Since this strain was isolated only from the vicinity of a vent and was shown to depend on photosynthesis, it might survive photosynthetically by exclusively using geothermal radiation. It might be the first green sulfur bacterium which is adapted to light intensities even lower than in the Black Sea chemocline. A lot of newly obtained sequences during this study evoked the necessity of a phylogenetic analysis. The article Biodiversity and Phylogeny of the family Chlorobiaceae based on comparison of multiple genetic regions (pages 145 ff.) discusses the phylogenetic system of the green sulfur bacteria, which is to date not satisfactory with respect to resolution of the group. A new system is presented which is based on green sulfur bacterial sequences of isolated strains and environmental sequences from the NCBI database (www.ncbi.nlm.nih.gov). The 16S rRNA gene phylogenetic tree revealed the need for a revised phylogenetic system of green sulfur bacteria and showed a close correlation of ecology, i.e. the habitat of the respective species, and phylogeny. Consequently, functional genes might reflect the adaptation to different habitats better than 16S rRNA gene sequences. Three different markers were used for an alternative phylogenetic analysis: ITS (16S-23S rRNA intergenic spacer region), bchG, and sigma factor A, respectively. Only sigma factor A showed a significantly higher resolution of the phylogenetic system of green sulfur bacteria and should be considered as more powerful tool than the16S rRNA gene to classify green sulfur bacteria.
Li, H (Wellcome Trust Sanger) Monday 03 September 2007, 12:10-12:30 PLGw01 - Current Challenges and Problems in Phylogenetics
Kucera, M (Tubingen) Wednesday 05 September 2007, 09:00-10:00 PLGw01 - Current Challenges and Problems in Phylogenetics
Presented by Lachlan Whatmore, News by Ian Woolf, Phylogeny by Lachlan Whatmore, The difference between the X and Y chromosomes by Marc West, Produced by Matt Clarke.
Fakultät für Biologie - Digitale Hochschulschriften der LMU - Teil 02/06
Zusammenfassung In der vorliegenden Arbeit wurde die Phylogenie der kurzzungigen Bienengattung Andrena, sowie die der langzungigen Bienentribus Anthophorini unter besonderer Berücksichtigung der Gattung Habropoda untersucht. Mit ca. 1500 gültig beschriebenen Arten weltweit stellt die holarktische Bienengattung Andrena (Sandbienen) die größte Bienengattung überhaupt dar. Die Phylogenie dieser Gattung ist bislang nur unzureichend erforscht worden. So beschränkten sich frühere Untersuchungen nur auf einige wenige Untergattungen oder bestimmte regionale Vertreter von Andrena, aber berücksichtigten niemals die gesamte Gattung und all ihre verschiedenen Untergattungen. Im Rahmen dieser Untersuchung, welche 84 Vertreter der 99 gegenwärtig bekannten Andrena-Untergattungen einschließt, wurde eine kladistische Analyse, basierend auf 162 morphologischen Merkmalen durchgeführt. Eine mögliche Merkmalsentwicklung im Hinblick auf die verwendete Polarität wurde diskutiert. Insgesamt wurden 107 Taxa kodiert, von denen fünf je einen Verterter aller anderen Gattungen der Unterfamilie Andreninae representierten. Aufgrund der ebenfalls ungeklärten Verwandschaftsverhältnisse innerhalb der Andreninae wurde ein hypothetischer Vorfahre als Außengruppe verwendet. Eine heuristische Analyse ohne Merkmalsgewichtung ergab insgesamt sechs maximal sparsame Kladogramme (MPTs) mit einer Länge von 1875 Schritten. Das strikte Konsensus-Kladogramm dieser sechs Bäume ließ sieben Großgruppen innerhalb der Gattung Andrena erkennen. Die Monophylie von Andrena wurde durch fünf, nicht-homoplastische Synapomorphien begründet. Cubiandrena stellte sich als nicht zu Andrena gehörig heraus und wird als eigene Gattung betrachtet. Eine zweite Analyse unter Verwendung iterativer Mermalsgewichtung (a posteriori Gewichtung) resultierte in einem einzigen Kladogramm. Dieses stimmte in einigen Teilen mit den Ergebnissen der ungewichteten Analyse überein, zeigte aber auch deutliche Unterschiede zu diesen. In beiden Analysen wurden 14 Gruppen festgestellt, die die gleichen Taxa zusammenfassten, elf davon wiesen eine identische Baumtopologie auf. In beiden Analysen erwies sich Andrena als die am stärksten abgeleitete Gattung innerhalb der Andreninae, während Euherbstia den ursprünglichsten Vertreter darstellte. Die holarktisch verbreiteten Untergattungen Larandrena, Micrandrena und Ptilandrena erwiesen sich sowohl in der ungewichteten als auch in der gewichteten Anlyse als polyphyletische Taxa. Amerika wird als Ursprungsort der Andreninae angesehen, während die Gattung Andrena, wahrscheinlich altweltlichen Ursprungs (Mittelmeergebiet oder Zentralasien) ist, da die meisten ursprünglichen Untergattungen eine ausschließlich paläarktische Verbreitung aufweisen. Während sich die holarktische Verbreitung von Andrena wahrscheinlich auf Ausbreitungsvorgänge am Ende der Kreidezeit und im frühen Tertiär zurückführen läßt, scheint die Entstehung rein nearktischer und paläarktischer Untergattungen auf Vikarianzereignissen, verursacht durch die beginnende Ausdehnung des Atlantiks und die damit einhergehende Trennung der nordamerikanischen und europäischen Landmassen seit dem mittleren Eozän, zu beruhen. Die vorliegende Studie beinhaltet außerdem eine molekulare Analyse eines 758 basenpaarlangen DNA Abschnittes der mitochondrialen Cytochrom Oxidase I für 27 zentraleuropäische Andrena-Arten. Die untersuchten Arten repräsentieren 21 verschiedene Untergattungen, sowie sieben Vertereter der Untergattung Micrandrena. Als Außengruppe wurde Panurgus verwendet. Die Parsimonie-Analyse der ungewichteten COI-Daten ergab ein einzelnes MPT mit einer Länge von 1724 Schritten, in welchem fünf Großgruppen unterschieden wurden. Die Untergattung Micrandrena, welche einen Schwerpunkt der Analyse bildete, erwies sich als eindeutig polyphyletisch. Folgende Taxa der Gattung Andrena wurden als neu für die Wissenschaft beschrieben: Calcarandrena subgen. n., Hamandrena subgen. n., Platygalandrena subgen. n.; A. (Carandrena) planti sp. n., A. (Euandrena) yangi sp. n., A. (Habromelissa) nantouensis sp. n., A. (Larandrena) susanneae sp. n., A. (Leucandrena) cheni sp. n., A. (Micrandrena) taiwanensis Dubitzky 2002, A. (Pallandrena) christineae sp. n., A. (Pallandrena) scheuchli sp. n., A. (Simandrena) heinzi sp. n. and A. lehmanni Schönitzer & Dubitzky 2002. Die folgenden zwei Taxa wurden in den Status einer Art erhoben: A. eburnea Warncke, 1975 stat. n. and A. impasta Warncke, 1975 stat. n. Die folgende Untergattung wurde zur Gattung erhoben: Cubiandrena Warncke, 1968 stat. n. Im zweiten Teil dieser Arbeit wurde die Phylogenie der Anthophorini untersucht. Die Anthophorini stellen eine der größten Triben von mittelgroßen bis großen, nestbauenden Bienen der Unterfamilie Apinae dar, und umfassen etwa 710 Arten aus sieben Gattungen. Die kladistische Analyse der Anthophorini basierte auf 51 morphologischen Merkmalen und umfasste 26 Innengruppen-Taxa, welche alle bekannten Gattungen und die wichtigsten Untergattungen der Tribus repräsentierten. Als Außengruppe wurde Centris verwendet. Die Analyse resultierte in zwei MPTs mit einer Länge von 132 Schritten. Die folgende Baumtopologie auf Gattungsebene konnte festgestellt werden: ((Habrophorula, Elaphropoda) (Habropoda (Deltoptila (Pachymelus (Amegilla, Anthophora))))). Eine zweite, von manchen Autoren vertretene Tribus, die Habropodini, konnte nicht bestätigt werden, da diese ein paraphyletisches Taxon bildet. Die Monophylie der Anthophorini sowie all ihrer Gattungen wurde bestätigt. Basierend auf den Ergebnissen der kladistischen Analyse und den biogeographischen Daten der Anthophorini wurde eine mögliche Hypothese zur Evolution der Anthophorini entwickelt. Demnach entwickelten sich alle Anthophorini-Gattungen, abgesehen von Anthophora und Amegilla, die frühestens im Oligozän entstanden sein dürften, wahrscheinlich bereits in der späten Kreidezeit. Der nordliche Teil Südostasiens (Indien bis Südost China) kann als wahrscheinlichster Ursprungsort und als Radiationszentrum der Anthophorini angesehen werden, da in dieser Region die meisten Gattungen sowie die ursprünglichsten Vertreter dieser Tribus vorkommen. Amerika wurde wahrscheinlich dreimal unabhängig von Vertretern der Anthophorini besiedelt: Von Habropoda (Obere Kreide bis Tertiär), von einem Deltoptila-ähnlichen Vorfahren (Obere Kreide bis Tertiär) und von Anthophora (Tertiär bis Quartär). Die rezente Verbreitung von Deltoptila und Pachymelus impliziert, daß die Evolution dieser Gattungen höchstwahrscheinlich auf Vikarianzereignisse zurückzuführen ist, während die Verbreitung aller anderen Gattungen auf einfachen verbreitungsdynamischen Prozessen wie Ausbreitung (Habropoda, Anthophora, Amegilla) oder Isolation (Elaphropoda, Habrophorula) aufgrund ökologischer oder abiotischer (klimatischer) Faktoren beruhen dürfte. Darüber hinaus wurde die Phylogenie der Gattung Habropoda, welche weltweit etwa 60 Arten umfasst, näher untersucht. Eine durchgeführte kladistische Analyse 25 paläarktischer und orientalischer Habropoda-Arten, welche alle wichtigen altweltlichen Gruppen dieser Gattung repräsentieren, basierte auf 41 morphologischen Merkmalen und ergab 3 MPTs mit einer Länge von 96 Schritten. Basierend auf dem Konsensus-Baum ergab sich folgende Baumtopologie auf Untergattungsebene: (Fulvohabropoda ((Oculhabropoda, Phyllohabropoda) (Zonhabropoda, Habropoda s. str.))). Wahrscheinlich entwickelten sich die Hauptlinien von Habropoda bereits in der Oberen Kreide im nördlichen Teil Südostasiens. Die beginnende Auffaltung des Himalayas im Eozän hat dann möglicherweise eine Trennung der Gattung in eine paläarktische (Habropoda s. str., Zonhabropoda) und eine orientalische (alle anderen Untergattungen sowie isoliert stehende Arten) Entwicklungslinie bewirkt und wahrscheinlich eine verstärkte Radiation innerhalb der Untergattung Fulvohabropoda ausgelöst. Das Vorkommen von Zonhabropoda in Ostasien scheint sekundär zu sein und ist höchstwahrscheinlich auf jüngere Ausbreitungsprozesse entlang der asiatischen Steppen nordlich des Himalayas zurückzuführen. Während der Isolation entstandene klimatische Anpassungen verhinderten möglicherweise die Ausbreitung von Zonhabropoda in Richtung Südostasien. Im Rahmen einer Revision der taiwanesischen Habropoda-Arten und ihrer parasitoiden Kuckucksbienen aus der Gattung Tetralonioidella wurde außerdem die Koevolution zwischen den Vertretern dieser beiden Bienengattungen anhand ihrer jahreszeitlichen und höhenabhängigen Verbreitungsmuster untersucht. Die folgenden Taxa aus den Gattungen Habropoda und Tetralonioidella wurden als neu für die Wissenschaft beschrieben: Fulvohabropoda subgen. n., Oculhabropoda subgen. n., Phyllohabropoda subgen. n., Zonhabropoda subgen. n.; Habropoda (Phyllohabropoda) christineae sp. n., Habropoda (Phyllohabropoda) sinensis taiwana ssp. n. and Tetralonioidella heinzi sp. n.. Tetralonioidella himalayana formosana stat. n. wurde in den Rang einer Unterart gestuft und für Habropoda tainanicola tainanicola Strand, 1913 wurde ein Lectotypus designiert.
Fakultät für Biologie - Digitale Hochschulschriften der LMU - Teil 01/06
The attelabid genus Euops SCHOENHERR is demonstrated to constitute a monophyletic group based on the following synapomorphies: 1) mycetangia of the female for storage of fungus spores consisting of three different reservoirs and associated setose structures, 2) a patch of modified setae of the female venter, usually associated with exocrinous glands, 3) enlarged eyes. Systematics, evolutionary history and biology of Curculionoidea and Attelabidae are summarized. The "Papuan region" is treated herein as comprising the provinces of Maluku and Irian Jaya of Indonesia, Papua New Guinea, and the Solomon Islands. A summary of the natural history of this region is given. Approximately two years were spent in the field to supplement the sparse material available from museum collections for this study. Selected, monophyletic species groups of Euops are treated in a monographic way: the spinosus-group (ten species described as new), the pygmaeus-group (one species redescribed, 13 species described as new), the quadrifasciculatus-group (four species redescribed, six species described as new), the simulans-group (three species redescribed, 19 species described as new), and the subgenus Neosynaptops (two species redescribed, seven species described as new). These monographs are attached to the present summary as appendices. New standards are proposed for taxonomic descriptions of Euops species: the transfer apparatus of the male genitalia proved to be of critical importance for the diagnosis of species. Other characters of male and female genitalia, of the mouthparts, the metanotum, and the proventriculus are useful in phylogenetic reconstruction and in the diagnosis of species groups. These and other characters are described for the first time. Methods for their appropriate preparation and examination by SEM and light microscopy are proposed. The literature published on Euops is reviewed and a bibliography is given. At the commencement of this study (1998), 134 species and 10 subspecies of Euops were recognized as valid worldwide. A synopsis of Papuan Euops is given. Before the commencement of this study 24 valid species of Papuan Euops, based on inadequate descriptions, were known to science. These are redescribed to meet the new standards. Where necessary, lectotypes are designated. One species (E. picipes VOSS) is placed into synonymy. One subspecific name (Euops femoralis f. ruficornis Voss) is elevated to species level. 52 species are added by formal descriptions. At present (2002), 76 described species are reported for the Papuan region, constituting 40 % of the world fauna (189 described species). Another 108 undescribed species from the Papuan region are listed. These could not be described herein but they will be so in later publications. Thus, at present 184 Euops species are known from the Papuan region constituting 58 % of the world fauna (320 ascertained species). Cladistic analyses are performed for each of the monographed species groups. An overall analysis is done using selected species. Five other genera of Attelabidae were included as outgroup representatives. The monophyly of the recognized species groups of Euops was confirmed except for the simulans-group which is difficult to define at its base. A clade comprising Apoderus, Lamprolabus and Euscelophilus is supported mainly by derived characters of the prementum, plesiomorphic in Attelabus and in Euops. It is predicted that the rank of the "Apoderinae" will have to be downgraded after a phylogenetic analysis of the Attelabidae. The worldwide distribution of Euops is a paleotropical one. This could reflect an ancient Gondwanic pattern or a more recent one through rapid dispersal. Evidence for and against each hypothesis is discussed. Within the Papuan region most species groups of Euops are strictly confined to the area of the Sahul shelf. Off-shore islands, such as Maluku or the Solomons, have a depauperate fauna. The areas of endemism observed are usually not compatible with geological terrains. Rapid dispersal overland is postulated. The Philippines and Sulawesi adjoining to the West have a speciose but uniform fauna, belonging exclusively to the subgenus Suniops. The fauna of Maluku consists of equal parts of Suniops species arrived from the west and of other species of Papuan Euops groups from the east. There is little overlap between the Papuan fauna of Euops and a moderately rich Australian one. The origins of the highly secluded Papuan fauna of Euops remain obscure. Although Euops occupies an altitudinal range from sea level to 3535 m, there is a maximum of diversity between 700 m and 800 m altitude. Diversity remains at a high level to an altitude of 1600 m or further, with an increase in the endemism of species. This pattern is different from groups such as birds and ants, whose diversity decreases evenly along an altitudinal gradient. It is suggested that this fact should be considered in priority assessments for conservation measures. A table of the association with host plants is given. Species of the pygmaeus-group are reported to feed exclusively on the fresh leaf flush of Nothofagus. Species of its presumed adelphotaxon, the quadrifasciculatus-group, are recorded from Myrtaceae. Such a pattern is unusual among phytophagous insects and different scenarios for a host switch are discussed. Preliminary data on the association with fungi are provided. Fungi isolated from the mycetangia of different Euops species exhibit different mycological characters (e.g. coloration) and presumably belong to different species. They all belong to the genus Penicillium. It was found that spores obtained from the mycetangia can be stored for extended periods in sterilized water. Future studies should make use of this fact to export fungus samples and to cultivate them under more favourable laboratory conditions than usually available in tropical countries. A trend curve of the discovery of Euops species in the Papuan region is discussed. It reveals that the saturation phase is not yet reached. It is estimated that the area studied harbours at least 300 species of Euops, making it the most diverse region for this genus in the world.
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