Podcasts about phylogenetics

Watch the real-life Zombie Fungus in action: https://www.youtube.com/watch?v=XuKjBIBBAL8Music by James Milor from PixabayInformation provided by:https://screenrant.com/girl-all-gifts-fungal-infection-hungries-explained/https://www.webmd.com/vitamins-and-supplements/cordycepsInterkingdom host jumping underground: Phylogenetic analysis of entomoparasitic fungi of the genus Cordyceps by Naruo Nikoh and Takema Fukatsu (2000). Molecular Biology and Evolution, 17(4), pg. 629-638. https://doi.org/10.1093/oxfordjournals.molbev.a026341 https://www.scientificamerican.com/blog/but-not-simpler/the-fungus-that-reduced-humanity-to-the-last-of-us/https://www.mskcc.org/cancer-care/integrative-medicine/herbs/cordycepsUnique bioactives from Zombie Fungus (Cordyceps) as promising multitargeted neuroprotective agents by Himadri Sharma, Niti Sharma, and Seong Soo A An (2023). Nutrients, 16(1). https://doi.org/10.3390/nu16010102https://www.healthline.com/nutrition/cordyceps-benefitshttps://en.m.wikipedia.org/wiki/Cordyceps

An ecosystem can be described as all the interactions that occur between organisms and their physical environment. The processes acting within an ecosystem operate on a wide range of spatial and temporal scales and include both biotic and abiotic factors. Ecosystem engineers are those species that have a significant impact on the availability of resources to other species and can be responsible for the creation, maintenance, modification or destruction of an ecosystem. The introduction, or even removal, of such a species can have profound effects on both physical and biological elements of an ecosystem. Whilst we can recognise the impact of ecosystem engineers in modern systems (e.g. the introduction of an invasive species), we don't fully understand what happens when an entirely new ecosystem engineering behaviour evolves. This has undoubtedly happened numerous times throughout geological time with the Great Oxygenation Event and the Cambrian Substrate Revolution being notable examples. Joining us for this episode is Dr Tom Smith, University of Oxford, who has been using a computational approach to try to model what happens when an ecosystem engineer is introduced into an environment. The open access study is available to read here.

In this episode of the I Can't Sleep Podcast, drift off as we explore the world of phylogenetics—because nothing says “bedtime relaxation” like evolutionary trees and species relationships.

Get ready! In this episode, we dive into how DNA, morphology, and life history are used to define organisms. We'll explore the history of naming organisms and discuss how those rules continue to evolve.

Dr. James O'Dwyer is an Assistant Professor in the Department of Plant Biology and the Carl R. Woese Institute for Genomic Biology at the University of Illinois, Urbana-Champaign. The research in James's lab uses computational and theoretical approaches to better understand the patterns we observe in the world. He is an ecologist and is particularly interested in biological complexity. The goal of his lab is to build models and make predictions that will provide us with novel and unexpected information about how nature works. In his free time, James enjoys hiking, traveling, and strategic board games like Settlers of Catan and Ticket to Ride. He was awarded a master's degree in Physics from the University of Durham, as well as a master's and PhD in Theoretical Physics from the University of Cambridge. James was awarded an Engineering and Physical Sciences Research Council Postdoctoral Fellowship conducting research at the University of Oregon and the University of Leeds in the United Kingdom, and he was also awarded an Omidyar Postdoctoral Fellowship at the Santa Fe Institute before accepting his current position. James is here with us today to tell us all about his journey through life and science.

Os ancestrais dos maiores animais do oceano já caminharam em terra. Separe trinta minutinhos do seu dia e descubra, com a Mila Massuda, sobre a origem evolutiva das baleias, golfinhos e botos. Apresentação: Mila Massuda (@milamassuda) Roteiro: Mila Massuda (@milamassuda) e Emilio Garcia (@emilioblablalogia) Revisão de Roteiro: Luisa Kahakura (@lukahakura) Técnica de Gravação: Caio de Santis (@caiodesantis) Editora: João Gabriel Caires (@kijaniiii) Mixagem e Masterização: Lívia Mello (@adiscolizard) Produção: Prof. Vítor Soares (@profvitorsoares), Matheus Herédia (@Matheus_Heredia) e BláBláLogia (@blablalogia) Gravado e editado nos estúdios TocaCast, do grupo Tocalivros (@tocalivros) REFERÊNCIAS GATESY, John; O'LEARY, Maureen A. Deciphering whale origins with molecules and fossils. Trends in Ecology & Evolution, v. 16, n. 10, p. 562-570, 2001. GEISLER, JONATHAN H. et al. Phylogenetic relationships of cetaceans to terrestrial artiodactyls. The evolution of artiodactyls, p. 19-31, 2007. O'LEARY, Maureen A.; UHEN, Mark D. The time of origin of whales and the role of behavioral changes in the terrestrial-aquatic transition. Paleobiology, v. 25, n. 4, p. 534-556, 1999. THEWISSEN, J. G. M. et al. From Land to Water: the Origin of Whales, Dolphins, and Porpoises. Evolution: Education and Outreach, v. 2, n. 2, p. 272–288, 16 abr. 2009.

The Middle Jurassic is incredibly important to our understanding of pterosaur evolution; however, the remarkable rarity and incompleteness of Middle Jurassic pterosaurs has long hampered scientific understanding of the lineage. Joining us this episode on the other side of the microphone is one of Palaeocast's own team members, Dr Liz Martin Silverstone, a Technical Specialist at the University of Bristol who has recently described Ceoptera evansae, a darwinopteran pterosaur from the Isle of Skye. Together, we explore the new specimen, how it fits in to the group, and the insights it can give us in to pterosaur evolution.

We continue our investgation into the plant known as Espadin in Oaxaca; This time following genetic trail. Dr. Jorge Nieto Sotelo from UNAM in Mexico City talks to us about Agave angustifolia and it's possible origins among other things. 

Synes du også resistens er vanskelig? Fatt mot og bli med oss i Pestpodden på en reise gjennom resistensen! I anledning Antibiotikauken 2023 har vi nemlig to spesialepisoder. I del èn får du en enkel intro til antimikrobiell resistens - mens i del to intervjuer vi en av verdens fremste eksperter og forskere på feltet; Adam Roberts. Gled deg!Referanser:1.Barlow M, Hall BG. Phylogenetic analysis shows that the OXA beta-lactamase genes have been on plasmids for millions of years. J Mol Evol. 2002;55(3):314-21.2.D'Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C, et al. Antibiotic resistance is ancient. Nature. 2011;477(7365):457-61.3. Holmes AH, Moore LS, Sundsfjord A, Steinbakk M, Regmi S, Karkey A, et al. Understanding the mechanisms and drivers of antimicrobial resistance. Lancet. 2016;387(10014):176-87.4.Woerther PL, Andremont A, Kantele A. Travel-acquired ESBL-producing Enterobacteriaceae: impact of colonization at individual and community level. J Travel Med. 2017;24(suppl_1):S29-s34.5.NORM/NORM-VET 2022. Usage of Antimicrobial Agents and Occurrence of Antimicrobial Resistance in Norway. Tromsø / Oslo 2023. ISSN:1502-2307 (print) / 1890-9965 (electronic). . 2022.7. https://atlas.ecdc.europa.eu/public/index.aspx?Dataset=27&HealthTopic=48.Antimicrobial Resistance C. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022;399(10325):629-55. Hosted on Acast. See acast.com/privacy for more information.

Article: https://www.drtimsaquatics.com/public-aquarium-and-aquaculture/nitrification-in-marine-aquaria/  Timestamps: 00:00 Start 3:30 Traditional view of Nitrification 5:28 What Bacteria Look like  8:29 Nitrification Classification 10:45 Winogradsky column 12:18 Microbiology 101  14:11 Culture Bias 17:41 Classic 2-Step Nitrification 26:15 Phylogenetics of Nitrifiers 34:29 Anammox 38:59 AOB-AOA Temperature Dependent 46:33 Comammox 51:19 Effect of Salinity

Jack and Michael sit down with Dr. Juliana Sterli who is a researcher with the National Scientific and Technical Research Council (CONICET) based out of the Museum of Paleontology Egidio Feruglio in Argentina. Dr. Sterli is an authority on fossil turtle morphology and evolution and has worked on multiple research projects aimed at investigating turtle phylogenetics at different scales. The conversation ranges from discussing what it is like to incorporate different types of data into phylogenetic analyses, the functional significance of specific features that made prehistoric turtles unique, chelonian neuroanatomy, the time of the Meiolaniid turtles, and much more.   Learn more about Dr. Sterli's research here: https://scholar.google.com/citations?user=U3JbknMAAAAJ&hl=en   Follow Dr. Sterli's work and adventures @yatachelys on Instagram/Twitter   Learn more about the Museum of Paleontology Egidio Feruglio here: https://mef.org.ar/home/   Learn more about the CheloniaCast Podcast here: theturtleroom.org/cheloniacast   All donations to the CheloniaCast Podcast Student Research Fund go towards supporting student led research projects focused on turtle and tortoise conservation and biology. Learn more here: https://theturtleroom.org/project/cheloniacast-podcast/   Host social media – Jason Wills - @chelonian.carter / Michael Skibsted - @michael.skibstedd / Jack Thompson - @jack_reptile_naturalist_302 / Wyatt Keil - @wyatts_wildlife_photography / Ken Wang - @americanmamushi

Evolutionary trees hold a dual meaning in the life of mathematician, Dr Julia Shore.During her PhD journey in phylogenetics, she used mathematical techniques to model intricate processes found in nature. But here's the twist - she did all of this while raising three children!In this episode, we explore the field of phylogenetics, where maths meets evolution. We explore Julia's work and  hear about her experiences of navigating the world of academic research while starting and raising a family.Show theme music: Kevin MacLeodHost: Olly Dove (@olly_dove)Co-Host: Georgia StewartProduction: Ryan SmithMedia & Promotion:Georgia Stewart (@ggstew25)

In this episode, David Dylus talks about Read2Tree, a tool that builds alignment matrices and phylogenetic trees from raw sequencing reads. By leveraging the database of orthologous genes called OMA, Read2Tree bypasses traditional, time-consuming steps such as genome assembly, annotation and all-versus-all sequence comparisons. Links: Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree (David Dylus, Adrian Altenhoff, Sina Majidian, Fritz J. Sedlazeck, Christophe Dessimoz) Background story Read2Tree on GitHub OMA browser The Guardian's podcast about Victoria Amelina and Volodymyr Vakulenko If you enjoyed this episode, please consider supporting the podcast on Patreon!

Nels and Vincent discuss new findings using phylogenetic approaches about how complex eukaryotic cells emerged from prokaryotic ancestors, which firmly place eukaryotes as a clade nested within the Asgard archaea. Hosts: Nels Elde and Vincent RacanielloS Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode •Join the MicrobeTV Discord server •Heimdallarchaeial ancestry of eukaryotes (Nature) Science Picks Nels – Juneteenth issue of Cell – collection of essays from black and brown scientists Vincent – Tara Oceans Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.03.547448v1?rss=1 Authors: Thiel, D., Yanez-Guerra, L. A., Kieswetter, A., Cole, A. G., Temmerman, L., Technau, U., Jekely, G. Abstract: Neuropeptides are ancient signaling molecules in animals but only few peptide receptors are known outside bilaterians. Cnidarians possess a large number of G protein-coupled receptors (GPCRs), the most common receptors of bilaterian neuropeptides, but most of these remain orphan with no known ligands. We searched for neuropeptides in the sea anemone Nematostella vectensis and created a library of 64 peptides derived from 33 precursors. In a large-scale pharmacological screen with these peptides and 161 N. vectensis GPCRs, we identified 31 receptors specifically activated by one of 14 peptides. Mapping GPCR and neuropeptide expression to single-cell sequencing data revealed how cnidarian tissues are extensively wired by multilayer peptidergic networks. Phylogenetic analysis identified no direct orthology to bilaterian peptidergic systems and supports the independent expansion of neuropeptide signaling in cnidarians from a few ancestral peptide-receptor pairs. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Episode 2250: Our random article of the day is Maximum parsimony (phylogenetics).

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.04.531117v1?rss=1 Authors: Milano, C. R., Ur, S. N., Gu, Y., Tromer, E. C., Zhang, J., Hochwagen, A., Corbett, K. D. Abstract: The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. In S. cerevisiae, the HORMAD protein Hop1 mediates enrichment of axis proteins at nucleosome-rich genomic islands through a central chromatin-binding region (CBR). Here, we use cryoelectron microscopy to show that the Hop1 CBR directly recognizes bent nucleosomal DNA through a composite interface in its PHD and winged helix-turn-helix domains. Targeted disruption of the Hop1 CBR-nucleosome interface causes loss of axis proteins from nucleosome-rich islands, reduces meiotic DNA double-strand breaks (DSBs), and leads to defects in chromosome synapsis. Synthetic effects with the disassemblase Pch2 suggest that nucleosome binding delays a conformational switch in Hop1 from a DSB-promoting, Pch2-inaccessible state to a DSB-inactive, Pch2-accessible state to regulate the extent of meiotic DSB formation. Phylogenetic analyses of meiotic HORMADs reveal an ancient origin of this domain, suggesting that these mechanisms are broadly conserved. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Article: Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass Journal: Nature Communications Year: 2022 Guest: Guangchao Sun Host: Arif Ashraf Abstract A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum (Paspalum vaginatum) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation. Cover art design and audio editing: Ragib Anjum --- Send in a voice message: https://podcasters.spotify.com/pod/show/no-time-to-read-podcast/message

Despite a warming planet, new research suggests that snakes in the UK may have more frosty mornings ahead. Then Sourish Kuttalam from Bangor University joins us to talk about a newly described viper from India. Become a Patreon: https://www.patreon.com/herphighlights Full reference list available here: http://www.herphighlights.podbean.com Main Paper References: Turner RK, Maclean IMD. 2022. Microclimate‐driven trends in spring‐emergence phenology in a temperate reptile (Vipera berus): Evidence for a potential “climate trap”? Ecology and Evolution 12. DOI: 10.1002/ece3.8623. Species of the Bi-Week: Kuttalam S, Santra V, Owens JB, Selvan M, Mukherjee N, Graham S, Togridou A, Bharti OK, Shi J, Shanker K, Malhotra A. 2022. Phylogenetic and morphological analysis of Gloydius himalayanus (Serpentes, Viperidae, Crotalinae), with the description of a new species. European Journal of Taxonomy 852. DOI: 10.5852/ejt.2022.852.2003. Other Links/Mentions: https://www.captiveandfieldherpetology.com/expeditions  Crinia georgiana, Quacking Frog call from frogid, By: Dale Roberts - https://www.frogid.net.au/frogs/crinia-georgiana  Editing and Music: Podcast edited by Emmy – https://www.fiverr.com/emmyk10  Intro/outro – Treehouse by Ed Nelson Species Bi-week theme – Michael Timothy Other Music – The Passion HiFi, https://www.thepassionhifi.com  

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.12.28.522111v1?rss=1 Authors: Dobbelaere, J., Su, T. Y., Erdi, B., Schleiffer, A., Dammermann, A. Abstract: Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. A defining feature of cilia is that they are evolutionarily ancient yet not universally conserved. In this study we have used the resulting presence and absence pattern in the genomes of diverse eukaryotes to identify a set of 386 human genes associated with cilium assembly or motility. Comprehensive tissue-specific RNAi in Drosophila and mutant analysis in C. elegans revealed signature ciliary defects for 70-80% of novel genes, a percentage similar to that for known genes within the cluster. Further characterization identified different phenotypic classes, including a set of genes related to the cartwheel component Bld10/Cep135 and two highly conserved regulators of cilium biogenesis. We believe this dataset to define the core set of genes required for cilium assembly and motility across eukaryotes, an invaluable resource for future studies of cilium biology and associated disorders. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.24.517872v1?rss=1 Authors: Mamun, M. A. A., Reza, M. A., Islam, M. S. Abstract: Lipid droplets (LDs) are storage organelles for neutral lipids. Our knowledge about fungal LD biogenesis is limited to budding yeast. Moreover, regulation of LD in multinucleated filamentous fungi with considerable metabolic activity is unknown. Here, 19 LD-associated proteins were identified in Aspergillus oryzae using colocalization screening of a previously established Enhanced green fluorescent protein (EGFP) fusion proteins library. Following a functional screening, 12 candidates have been identified as lipid droplet regulating (LDR) proteins, the loss of which resulted in aberrant LD biogenesis. LDR proteins bind to LD via the insertion of the putative amphipathic helices (AHs) which were investigated using AH-disruptive mutations and subsequent imaging. Further analysis revealed that LdrA with Opi1 domain is essential for cytoplasmic and nuclear LD biogenesis via a novel AH. Phylogenetic analysis demonstrated the pattern of their evolution, which was predominantly based-on gene duplication. Our study provides substantial molecular insights into LD biogenesis and creates a breakthrough in using reverse genetics for identifying LD-regulating proteins. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

On this ID the Future, philosopher of biology Paul Nelson further explores AlphaFold 2, a cutting edge computer program from Google's DeepMind designed to rapidly suss out important secrets in the realm of proteins, indispensable molecular biological workhorses that come in thousands of different shapes and sizes. Nelson enthuses about AlphaFold 2 but also explains why he is convinced that AlphaFold's creators have hit a series of immovable obstacles. The watchword here—orphans. Tune in to learn what these mischievous orphan proteins are about, and what they suggest for AlphaFold, evolution, and intelligent design. Source

1st isolation, molecular detection and phylogenetic analysis of FMDV A/AFRICA/G1, Sultanate of Oman by European Commission for the Control of FMD

Our recurring guest (who rarely recurs these days), Alex Danco, comes back for his sixth appearance on Infinite Loops! Important Links: Twitter: https://twitter.com/Alex_Danco Website: https://alexdanco.com/ Newsletter: https://danco.substack.com/ Show Notes: Our planned, but unplanned conversations Pink Floyd were philosophers From Heraclitus, to Lao Tzu, to Gita, to Deutsch Where does decision making come from? Projection 101 Can you versus can't you read people's mind Jim throwing big fancy words like “Phylogenetic inertia” Corn: The apex predator Self-serving nature of memetic theory The Mirror Philosophy What is a “creator”? Communication theory by Gregory Bateson The Founding Murderer Consequences of eating the fruit from the tree of knowledge "The most entertaining outcome is the most likely.” Hot media vs. Cool media The Wire, and dumb Stringer The state of accreditation Balancing mystery with transparency Knowing pop culture as a status symbol And MUCH more! Books Mentioned: The Science of Storytelling; by Will Storr The Status Game; by Will Storr Happy; by Derren Brown The Selfish Gene; by Richard Dawkins Steps to an Ecology of Mind; by Gregory Bateson War and Peace; by Leo Tolstoy

On Episode 94, Eric gives Josh a lesson on the evolution and genetics of humans over the last 2 million years. Please send your questions, comments, corrections and hate mail to RidingTheTorusPod@gmail.com You can find Eric's research notes for every episode here: https://drive.google.com/folderview?id=1syBwRsJ3b3YnOlUCXXFEEUpgF0NODLL2 Also! If you enjoy the Riding The Torus theme song, you can now download it for FREE from the Bueno Tornado bandcamp page. Here is the link: http://buenotornado.bandcamp.com/track/riding-the-torus-theme Hosts: Eric Beal - twitter.com/ericbealart Josh Campbell - twitter.com/josh_campbell

Conflicts in genetic phylogenetic trees and morphological phylogenetic trees pose a big problem for common ancestry.

Learn about how birds could help us predict natural disasters; fairy tales' old origins; and how breaks and sprains heal. Kivi Kuaka: how birds could be the key to an early warning system for natural disasters by Briana Brownell  Hakai Magazine. (2021). Can Birds Help Us Avoid Natural Disasters? | Hakai Magazine. Hakai Magazine; Hakai Magazine. https://www.hakaimagazine.com/news/can-birds-help-us-avoid-natural-disasters/  ‌The project - Kivi Kuaka. (2021, May 3). Kivi Kuaka. https://kivikuaka.fr/theproject/?lang=en  Your Favorite Fairy Tales Are Way Older Than You Think by Ashley Hamer  Folk tales are older than you think - Durham University. (2021). Dur.ac.uk. https://www.dur.ac.uk/news/research/?itemno=27041 ‌ Comparative phylogenetic analyses uncover the ancient roots of Indo-European folktales | Royal Society Open Science. (2016). Royal Society Open Science. https://royalsocietypublishing.org/doi/full/10.1098/rsos.150645 ‌ No fairy tale: Origins of some famous stories go back thousands of years. (2016, January 20). Science News. https://www.sciencenews.org/article/no-fairy-tale-origins-some-famous-stories-go-back-thousands-years  ‌Keats, J. (2017). The Origins of an Ancient Fairy Tale. Discover Magazine; Discover Magazine. https://www.discovermagazine.com/planet-earth/the-origins-of-an-ancient-fairy-tale  Fairy Tales: September 2021 podcast playlist | Podcast Brunch Club. (2021, August 31). Podcast Brunch Club. https://podcastbrunchclub.com/fairytales/  Why do breaks heal faster than sprains? by Cameron Duke  Clemence Lim. (2021, June 14). Better to break a bone than to tear a ligament or tendon? Ask your Physio. Core Concepts Physiotherapy; Core Concepts Pte Ltd. https://www.coreconcepts.com.sg/article/better-to-break-a-bone/  Healing Expectations for Different Tissue Types - Symmetry Physical Therapy. (2017, July 25). Symmetry Physical Therapy. https://symmetryptaustin.com/healing-expectations-for-different-tissue-types/  J Gordon Betts, Desaix, P., Johnson, E., Johnson, J. E., Korol, O., Kruse, D., Poe, B., Wise, J., Womble, M. D., Young, K. A., & College, O. (2013). Anatomy & physiology. Openstax College, Rice University. Ligament. (2020). Physiopedia. https://www.physio-pedia.com/Ligament  ligament | Definition, Function, Types, & Facts | Britannica. (2021). In Encyclopædia Britannica. https://www.britannica.com/science/ligament  Follow Curiosity Daily on your favorite podcast app to learn something new every day withCody Gough andAshley Hamer. Still curious? Get exclusive science shows, nature documentaries, and more real-life entertainment on discovery+! Go to https://discoveryplus.com/curiosity to start your 7-day free trial. discovery+ is currently only available for US subscribers. See omnystudio.com/listener for privacy information.

O convidado é paleontólogo, professor na Universidade Nova de Lisboa, onde ensina, entre outras, evolução, paleontologia de vertebrados e répteis e -- a sua principal área de investigação -- dinossauros, sobretudo do Jurássico de Portugal. É autor ou co-autor de mais 200 publicações nesta área e já há três décadas que  participa e organiza escavações de dinossauros em Portugal, sobretudo em colaboração com o Museu da Lourinhã, conhecido por sua importante colecção de dinossauros.  -> Apoie este projecto e faça parte da comunidade de mecenas do 45 Graus em: 45graus.parafuso.net/apoiar Octávio Mateus é conhecido do grande público sobretudo enquanto especialista em dinossauros. Porque essa é, de facto, a sua principal área de investigação, mas também porque o imaginário destes répteis que dominaram a Terra até há 66 milhões de anos é, por motivos vários, o que mais atrai a atenção das pessoas. Mas a área do convidado, a Paleontologia, é muito mais do que simplesmente dinossauros. É uma área da ciência que vai beber simultaneamente à Biologia e à Geologia para tentar explicar a História da vida na Terra nos últimos (pelo menos) 3.5 mil milhões de anos, e nas suas mais variadas formas. Esta foi, como vão perceber, uma conversa cheia (o Octávio é um excelente conversador), na qual abordámos imensos temas. Falámos sobre a História da vida na Terra, desde os primeiros organismos unicelulares até aos dinossauros, aos mamíferos e ao homo sapiens. Falámos do processo da evolução por selecção natural, e do modo como ele é muitas vezes contra-intuitivo (um tema que já tinha abordado nos dois episódios que gravei com o PGM). Falámos também de fósseis, que são a matéria-prima principal de um paleontólogo.  E, claro, falámos (muito) sobre dinossauros: quantos eram, o que sabemos sobre eles, o que não sabemos, e ainda...o que é que os pássaros nos podem dizer sobre eles. Porque a verdade é que os pássaros descendem directamente dos dinossauros. Aliás, formalmente, os pássaros são um tipo de dinossauro, pois descendem (são, aliás, os únicos descendentes) do grupo ao qual pertencia nada mais nada menos do que o famoso tiranossauro rex. _______________ Índice da conversa: (02:57) O que é a Paleontologia? (05:46) É possível ressuscitar espécies extintas? | Lobo-da-tasmânia (08:49) O que é um fóssil? | Fósseis de tecidos moles. | Quais as condições ideiais para a fossilização? | Como se faz a datação de um fóssil? | Qual é o fóssil mais antigo? (25:51) Macro-história da evolução da vida na Terra | 890-million-year-old sponge fossil may be the earliest animal yet found | Explosão do Câmbrico. | Corrida ao armamento evolutiva (49:19) Quando surgiram os dinossauros? | Conseguimos saber quantas espécies havia? | Os mamíferos | Evolução da biodiversidade na Terra ao longo do tempo. | Os vários eventos de extinção. | paleontologia.pt (55:02) As três grandes famílias de dinossauros. | Debate em torno de paper recente saído na Nature (57:43) Porque é que os dinossauros (e os pássaros) desenvolveram sacos de ar no interior do organismo? (1:01:57) O modo como o passado evolutivo de uma espécie restringe as adaptações que pode desenvolver. | O exemplo do nervo vago | O exemplo das hemorroidas.  (1:06:49) Como era possível os saurópodes serem tão grandes? Comparação com os cavalos. “Corrida ao armamento evolutiva” | Lei de Cope | Porque foram os maiores dinossauros aqueles que se extinguiram?  (1:14:55) As peculiaridades das espécies nas ilhas. Elefantes anões (extintos) (1:17:03) Aves vs (outros) dinossauros: os dinossauros tinham penas | Exaptações | Escamas.   (1:20:36) Porque é que a taxonomia de Lineu deixa de fazer sentido numa visão global da história da evolutiva da Terra (1:23:34) O que nos dizem as aves (e os répteis) sobre como eram os dinossauros? | Phylogenetic bracketing | Como no filme Jurassic Park foi feito o rugido do T-rex  (1:26:19) O que sabemos sobre como eram os dinossauros (fisionomia, comportamento, etc)? | Os dinossauros eram de sangue quente ou frio? Qual é a vantagem do sangue quente? Porque evoluiu? (1:32:24) A principal interrogação do convidado sobre os dinossauros. | Quanto tempo dura cada espécie? | Known unknowns vs unknown unknowns  (1:37:15) O que causou a extinção dos dinossauros (Cretaceous–Paleogene extinction event) |  (1:43:30) Há esperança de encontrar DNA de dinossauros? | Possível descoberta de DNA de t-rex | Record de DNA (completo) mais antigo (mamute) (1:46:24) Livro recomendado: A Ascensão e Queda dos Dinossauros, de Steve Brusatte _______________ Obrigado aos mecenas do podcast: Julie Piccini, Ana Raquel Guimarães Miguel van Uden, José LuÍs Malaquias, João Ribeiro, Francisco Hermenegildo, Nuno e Ana, Nuno Costa, Galaró family, Salvador Cunha, João Baltazar, Miguel Marques, Corto Lemos, Carlos Martins, Tiago Leite Luis, Maria Pimentel, Rui Amorim, RB, Pedro Frois Costa, Gabriel Sousa, Mário Lourenço, Arune Bhuralal, Isabel Oliveira, Ana Teresa Mota, Filipe Bento Caires, Luí­s Costa, Manuel Martins, Diogo Sampaio Viana, Francisco Fonseca, João Nelas, Tiago Queiroz, Ricardo Duarte, António Padilha, Rita Mateus, Daniel Correia, João Saro, Tomás Costa Rui Baldaia, Joana Margarida Alves Martins, Luis Marques, Hugo Correia, Duarte , Francisco Vasconcelos, Telmo , Jose Pedroso, MANNA Porto, José Proença, Carlos Manuel Lopes de Magalhães Lima, Maria Francisca Couto, joana Antunes, Nelson Poças, Francisco López Bermúdez, Carlos Silveira, Diogo Rombo, Bruno Lamas, Fábio Mota, Vítor Araújo, João Pereira, Francisco Valente, Nuno Balsas, Jorge Amorim, Rui Vilão, João Ferreira, Luís Elias, José Losa, Hélder Moreira, Diogo Fonseca, Frederico Apolónia, André Abrantes, Henrique Vieira, João Farinha, Paulo Fernandes, Nuno Lages, João Diamantino, Vasco SÁ Pinto, Rui Carrilho, Luis Quelhas Valente, Tiago Pires, Mafalda Pratas, Renato Vasconcelos, João Raimundo, Francisco Arantes, Francisco dos Santos, Mariana Barosa, Marta Baptista Coelho, João Castanheira, Pedro , rodrigo Brazão, Nuno Gonçalves, Pedro Rebelo, Tomás Félix, Vasco Lima, Joao Pinto, João Moreira, José Oliveira Pratas, João Diogo Silva, Marco Coelho, Joao Diogo, Francisco Aguiar , Tiago Costa da Rocha, João Crispim, Paulo dos Santos, Abílio Mateus, João Pinho , Andrea Grosso, Miguel Lamela, Margarida Gonçalves, Afonso Martins, João Barbosa, Luis Filipe, Renato Mendes, António Albuquerque, Francisco Santos, juu-san, Fernando Sousa, Pedro Correia, MacacoQuitado, Paulo Ferreira, Gabriela, Nuno Almeida, Francisco Manuel Reis, Daniel Almeida, Albino Ramos, Inês Patrão, Patrícia Esquível , Diogo Silva, Miguel Mendes, Luis Gomes, Ana Batista, Alberto Santos Silva, Cesar Correia, Susana Ladeiro, Gil Batista Marinho, Filipe Melo, Cheila Bhuralal, Bruno Machado, Miguel Palhas, isosamep, Robertt , Pedro F. Finisterra, Cristiano Tavares, Pedro Vieira, Jorge Soares, Maria Oliveira, Bruno Amorim Inácio, Nuno , Wedge, Pedro Brito, Manuel Botelho da Silva, Ricardo Leitão, Vítor Filipe, João Bastos, Natália Ribeiro, Bernardo Pimentel, Pedro Gaspar, Hugo Domingues _______________ Esta conversa foi editada por: Hugo Oliveira _______________ Bio: Nascido em 1975, é Professor Associado de Paleontologia na Universidade Nova de Lisboa (FCT). É licenciado em Biologia (Univ. de Évora) e Doutorado em Paleontologia pela Universidade Nova de Lisboa. O seu principal tema de interesse é a paleontologia de dinossauros (ossos, ovos e pegadas), sobretudo do Jurássico de Portugal, mas também aborda outros répteis (mosassauros, plesiossauros, crocodilos, tartarugas, etc.). É autor ou co-autor de mais 200 publicações (capítulos de livros, artigos científios e resumos de conferências). Desde 1991 que participa e organiza em escavações de dinossauros em Portugal, sobretudo em colaboração com o Museu da Lourinhã, conhecido por sua importante colecção de dinossauros. Em Angola descobriu o primeiro dinossauro desse país no âmbito do Projecto PaleoAngola. O seu interesse por dinossauros já o levou a realizar escavações a Estados Unidos, Brasil, Gronelândia, Laos, Tunísia, Moçambique, Mongólia, Marrocos e Angola. É Investigador Associado do AMNH - Museu Americano de História Natural (New York) e do Museu da Lourinhã.

In Episode 15 Bishop Richard Umbers is joined by Dean of St Pauls College Sydney, Dr Antone Martinho-Truswell and Dr Michael Elias from the CSIRO, to discuss the relationship between the theory of evolution and the Catholic faith. Dr Antone Martinho-Truswell is Dean of St Pauls College Sydney and Research Associate of the Department of Zoology at the University of Oxford, hiscontinuing research is focused primarily on learning and cognition in birds, primarily using mallard ducklings as a model. Dr Michael Elias has a PhD in Systematic Entomology and Phylogenetic, and currently works for the Australian National Insect Collection at Commonwealth Scientific and Industrial Research Organisation (CSIRO). 

Crocodiles are often referred to as “living fossils”, but if we compare modern and ancient species, does that label hold up? What different kind of morphologies (shapes) did past crocs have and how did they live? How quickly did this past diversity arise and why are we left with so few species today? What’s to stop them from diversifying again? In this episode, we speak to Dr Tom Stubbs, University of Bristol, about his recent work analysing changes in crocodylomorph disparity through time. We look at some of the weird and wonderful crocs of the past and work through his methods for calculating their rates of evolutionary innovation. Part 2 of 2

Crocodiles are often referred to as “living fossils”, but if we compare modern and ancient species, does that label hold up? What different kind of morphologies (shapes) did past crocs have and how did they live? How quickly did this past diversity arise and why are we left with so few species today? What’s to stop them from diversifying again? In this episode, we speak to Dr Tom Stubbs, University of Bristol, about his recent work analysing changes in crocodylomorph disparity through time. We look at some of the weird and wonderful crocs of the past and work through his methods for calculating their rates of evolutionary innovation. Part 1 of 2

https://www.youtube.com/watch?v=7ESK5SaP-bc (https://www.youtube.com/watch?v=7ESK5SaP-bc) Codewars: Achieve mastery through challenge (https://www.codewars.com/) CS50x 2021 (https://cs50.harvard.edu/x/2021/) Trie (https://en.wikipedia.org/wiki/Trie) https://www.youtube.com/watch?v=oaCinQIy8MI (https://www.youtube.com/watch?v=oaCinQIy8MI) The Newick tree format (https://evolution.genetics.washington.edu/phylip/newicktree.html) How to root a phylogenetic tree (http://cabbagesofdoom.blogspot.com/2012/06/how-to-root-phylogenetic-tree.html) Reconstruction:Proto-Indo-European/ǵenh₁- (https://en.wiktionary.org/wiki/Reconstruction:Proto-Indo-European/%C7%B5enh%E2%82%81-) *ǵenh - (https://prezi.com/xf8pybiccaru/?token=666acc95c244911a9dc4dca04b7ebb8ec8b97edc5ac96c605c6dd23f69caa971) Floppy disk (https://en.wikipedia.org/wiki/Floppy_disk) Magnetic tape (https://en.wikipedia.org/wiki/Magnetic_tape)

Politics & Life Sciences (PLS) Radio Dr Oliver Ratmann - Imperial College London-Faculty of Natural Sciences, Department of Mathematics, Lecturer in Statistics Oliver focuses on developing statistical methods to characterise the spread of infectious diseases, and to guide public health interventions. He has developed novel ways of harnessing viral sequence data in combination with time-resolved patient data to measure the population-level impact of interventions, most notably on mitigating the burden of HIV. MAJOR PROJECTS Novel molecular epidemiological methods for next generation sequencing data (part of Phylogenetics and Networks of Generalised HIV epidemics in Africa); Harnessing time-resolved patient records to contextualise and understand spread of HIV at the city level in Amsterdam, especially among men & women with a migration background (with HIV transmission elimination initiative Amsterdam); New tools to characterise spread of HIV in Seattle USA in near real time (part of NIH R01 with University of Washington); please see the Research page for details. Topic: Adults age 20 to 49 are biggest COVID-19 spreaders in US, study says (Guest gave quote in article) https://nypost.com/2021/02/03/adults-20-to-49-are-biggest-covid-19-spreaders-in-us-study/ Adults age 20 to 49 are the biggest spreaders of COVID-19 in the US, according to British researchers who say targeting this age group for vaccination could hasten school reopenings. A team at Imperial College London used cellphone data from more than 10 million people to calculate that 65 of 100 infections originated from those ages 20 to 49 in the US. They found that people in that age bracket accounted for about 72 percent of the cases after schools reopened in October. Less than 5 percent came from children, and less than 10 percent from teens. Adults ages 35 to 49 accounted for 41 percent of new cases through mid-August, compared to 35 percent for adults ages 20 to 34, according to the peer-reviewed study published in Science. “We find adults aged 20-49 are a main driver of the COVID-19 epidemic in the United State and are the only age groups contributing disproportionally to onward spread, relative to their population size,” Imperial College's Dr. Melodie Monod said.

My AP Biology Thoughts Welcome to My AP Biology Thoughts podcast, my name is Charles but you can call me Darwin and I am your host for today. This is podcast number 8 called Evolutionary Relationships. Today we will be discussing Phylogenetic trees and Cladograms. Segment 1: Introduction to Evolutionary RelationshipsPhylogenetic Tree-  A diagram that shows evolutionary relationships among species  Uses DNA sequences to find patterns in species There is a distinct difference between cladograms and phylogenetic trees. Cladograms are shaped like a “y” but with a lot more lines branching off. This diagram is based on hypothesis and does not use DNA sequencing. It's mainly based on homologous structures and noted similarities between animales. Each protruding line from the base represents a time where a structure split off, such as a heart having 4 chambers or having webbed feet.   Phylogenetic trees are mainly used to show time. It is shaped like a very geometric tree sideways. The trunk is the common ancestor for all of the species at the tip of the branches. Each junction represents a closer common ancestor. If a line stops short, that usually means the species went extinct. Cladograms- DNA sequencing is a process of finding common ancestors. Since All cells have DNA, which contain a series of different letters that describe that organism. If some of the sequences in DNA matches that of another species, that could mean they are related or share a common ancestor.  are different ways to find the common ancestor of a species, one way is to find homologous bones structures in creatures, which could relate species. However, the most definitive way to find common ancestors, is to look at similarities in DNA sequences.  Segment 2: Example of Phylogenetic Trees and CladogramsThere are tons of examples, and you can search up a diagram for any animal. Looking at a human Phylogenetic tree, we can see that humans are more closely related to chimpanzees than any other monkey. Also, Humans are more closely related to cats, than cows. In addition to looking at phylogenetic trees, you could look at similarities in DNA sequences. Cats are 85% similar to humans, while cows are about 80% similar. It doesn't seem like cats should be my brothers, however that remaining 15% has critical DNA letters that change various aspects of a creature. If we were to look at a cladogram, we would see the line for humans would be separate from cats, and the segment in between would represent a time where fur stops being useful or hind legs are being primarily used.  Segment 3: Digging Deeper and Making ConnectionsHow does this topic fit into the greater picture of evolution? Cladograms and Phylogenetic trees come hand in hand when determining common ancestors. These common ancestors are the key to seeing how the species was able to evolve and split off into different organisms. While cladograms help us determine specific structures and when organisms split off, they are not scientific. Meaning they're based off of hypothesis, or what we think it would look like. Phylogenetic trees are more scientific, meaning it helps show specifically who is the most recent common ancestor and who closely related organisms are to each other. It is quinicential in finding the common ancestor in order to see the steps a species took to evolve. We can also see the environmental pressures that a species endured and look at how it affected the present species. Thank you for listening to this episode of My AP Biology Thoughts. For more student-ran podcasts, make sure that you visit http://www.hvspn.com/ (www.hvspn.com). Thanks for listening! Music Credits:"Ice Flow" Kevin MacLeod (incompetech.com) Licensed under Creative Commons: By Attribution 4.0 License http://creativecommons.org/licenses/by/4.0/ Subscribe to our PodcastApple Podcasts Spotify Google Podcasts   Stitcher  ...

In this episode, we chat about phylogenetics with Xiang Ji. We start with a general introduction to the field and then go deeper into the likelihood-based methods (maximum likelihood and Bayesian inference). In particular, we talk about the different ways to calculate the likelihood gradient, including a linear-time exact gradient algorithm recently published by Xiang and his colleagues. Links: Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics (Xiang Ji, Zhenyu Zhang, Andrew Holbrook, Akihiko Nishimura, Guy Baele, Andrew Rambaut, Philippe Lemey, Marc A Suchard) BEAGLE: the package that implements the gradient algorithm BEAST: the program that implements the Hamiltonian Monte Carlo sampler and the molecular clock models

Lemurs are mammals of the order Primates, divided into 8 families and consisting of 15 genera and around 100 highly diverse species — 105 to be exact. They are native only to the island of Madagascar. Most lemurs are relatively small, have a pointed snout, large eyes, and a long tail. They are arboreal, living primarily in trees and nocturnal, preferring to be active at night, snacking on leaves and flowers, tree bark and sap. They are social animals, living in groups of a half dozen to up to 30 strong. The dominant female leads the group. Females have about one to size wee pups after mating with the sexiest, stinkiest males. Phylogenetic, genetic, and anatomical evidence all suggest that lemurs split from other primates on Africa around 62 million years ago and that the ancestral lemur lineage had dispersed to Madagascar by around 54 million years ago. Once on the island, the lemur lineage diversified.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.386979v1?rss=1 Authors: Bantis, L. E., Parente, D. J., Fenton, A. W., Swint-Kruse, L. Abstract: Amino acid variation at "rheostat" positions provides opportunity to modulate various aspects of protein function - such as binding affinity or allosteric coupling - across a wide range. Previously a subclass of "multiplex" rheostat positions was identified at which substitutions simultaneously modulated more than one functional parameter. Using the Miller laboratory's dataset of ~4000 variants of lactose repressor protein (LacI), we compared the structural properties of multiplex rheostat positions with (i) "single" rheostat positions that modulate only one functional parameter, (ii) "toggle" positions that follow textbook substitution rules, and (iii) "neutral" positions that tolerate any substitution without changing function. The combined rheostat classes comprised >40% of LacI positions, more than either toggle or neutral positions. Single rheostat positions were broadly distributed over the structure. Multiplex rheostat positions structurally overlapped with positions involved in allosteric regulation. When their phenotypic outcomes were interpreted within a thermodynamic framework, functional changes at multiplex positions were uncorrelated. This suggests that substitutions lead to complex changes in the underlying molecular biophysics. Bivariable and multivariable analyses of evolutionary signals within multiple sequence alignments could not differentiate single and multiplex rheostat positions. Phylogenetic analyses - such as ConSurf - could distinguish rheostats from toggle and neutral positions. Multivariable analyses could also identify a subset of neutral positions with high probability. Taken together, these results suggest that detailed understanding of the underlying molecular biophysics, likely including protein dynamics, will be required to discriminate single and multiplex rheostat positions from each other and to predict substitution outcomes at these sites. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.06.371120v1?rss=1 Authors: Matsuo, Y., Nose, A., Kohsaka, H. Abstract: Speed and trajectory of locomotion are characteristic traits of individual species. During evolution, locomotion kinematics is likely to have been tuned for survival in the habitats of each species. Although kinematics of locomotion is thought to be influenced by habitats, the quantitative relation between the kinematics and environmental factors has not been fully revealed. Here, we performed comparative analyses of larval locomotion in 11 Drosophila species. We found that larval locomotion kinematics are divergent among the species. The diversity is not correlated to the body length but is correlated instead to the minimum habitat temperature of the species. Phylogenetic analyses using Bayesian inference suggest that the evolutionary rate of the kinematics is diverse among phylogenetic trees. The results of this study imply that the kinematics of larval locomotion has diverged in the evolutionary history of the genus Drosophila and evolved under the effects of the minimum ambient temperature of habitats. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.29.361360v1?rss=1 Authors: Dang, T., Kishino, H. Abstract: A central focus of microbiome studies is the characterization of differences in the microbiome composition across groups of samples. A major challenge is the high dimensionality of microbiome datasets, which significantly reduces the power of current approaches for identifying true differences and increases the chance of false discoveries. We have developed a new framework to address these issues by combining (i) identifying a few significant features by a massively parallel forward variable selection procedure, (ii) mapping the selected species on a phylogenetic tree, and (iii) predicting functional profiles by functional gene enrichment analysis from metagenomic 16S rRNA data. We demonstrated the performance of the proposed approach by analyzing two published datasets from large-scale case-control studies: (i) 16S rRNA gene amplicon data for Clostridioides difficile infection (CDI) and (ii) shotgun metagenomics data for human colorectal cancer (CRC). The proposed approach improved the accuracy from 81% to 99.01% for CDI and from 75.14% to 90.17% for CRC. We identified a core set of 96 species that were significantly enriched in CDI and a core set of 75 species that were enriched in CRC. Moreover, although the quality of the data differed for the functional profiles predicted from the 16S rRNA dataset and functional metagenome profiling, our approach performed well for both databases and detected main functions that can be used to diagnose and study further the growth stage of diseases. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.28.358507v1?rss=1 Authors: Steinke, K., Mohie, O. S., Weber, T., Kovacs, A. T. Abstract: Microbes produce a plethora of secondary metabolites that although not essential for primary metabolism benefit them to survive in the environment, communicate, and influence differentiation. Biosynthetic gene clusters (BGCs) responsible for the production of these secondary metabolites are readily identifiable on the genome sequence of bacteria. Understanding the phylogeny and distribution of BGCs helps us to predict natural product synthesis ability of new isolates. Here, we examined the inter- and intraspecies patterns of absence/presence for all BGCs identified with antiSMASH 5.0 in 310 genomes from the B. subtilis group and assigned them to defined gene cluster families (GCFs). This allowed us to establish patterns in distribution for both known and unknown products. Further, we analyzed variations in the BGC structure of particular families encoding for natural products such as plipastatin, fengycin, iturin, mycosubtilin and bacillomycin. Our detailed analysis revealed multiple GCFs that are species or clade specific and few others that are scattered within or between species, which will guide exploration of the chemodiversity within the B. subtilis group. Uniquely, we discovered that partial deletion of BGCs and frameshift mutations in selected biosynthetic genes are conserved within phylogenetically related isolates, although isolated from around the globe. Our results highlight the importance of detailed analysis of BGCs and the remarkable phylogenetically conserved errodation of secondary metabolite biosynthetic potential in the B. subtilis group. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.21.348169v1?rss=1 Authors: Yu, G. Abstract: Ggtree supports mapping and visualizing associated external data on phylogeny with two general methods. The output of ggtree is a ggtree graphic object that can be rendered as a static image. Most importantly, the input tree and associated data that used in visualization can be extracted from the graphic object, making it an ideal data structure for publishing tree (image, tree and data in one single object) and thus enhance data reuse and analytic reproducibility. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.19.344986v1?rss=1 Authors: Morgenstern, B., Blanke, M. Abstract: Phylogenetic placement is the task of placing a query sequence of unknown taxonomic origin into a given phylogenetic tree of a set of reference sequences. Several approaches to phylogenetic placement have been proposed in recent years. The most accurate of them need a multiple alignment of the reference sequences as input. Most of them also need alignments of the query sequences to the multiple alignment of the reference sequences. A major field of application of phylogenetic placement is taxonomic read assignment in metagenomics. Herein, we propose App-SpaM, an efficient alignment-free algorithm for phylogenetic placement of short sequencing reads on a tree of a set of reference genomes. App-SpaM is based on the Filtered Spaced Word Matches approach that we previously developed. Unlike other methods, our approach neither requires a multiple alignment of the reference genomes, nor alignments of the queries to the reference sequences. Moreover, App-SpaM works not only on assembled reference genomes, but can also take reference taxa as input for which only unassembled read sequences are available. The quality of the results achieved with App-SpaM is comparable to the best available approaches to phylogenetic placement. However, since App-SpaM is not based on sequence alignment, it is between one and two orders of magnitude faster than those existing methods. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.09.334243v1?rss=1 Authors: Matsumoto, H., Mimori, T., Fukunaga, T. Abstract: Advances in experimental technologies such as DNA sequencing have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and immunogenomics. Thus, the importance of phylogenetic methods is increasingly being recognized, and the development of a novel phylogenetic approach can contribute to several areas of research. Recently, the use of hyperbolic geometry has attracted attention in artificial intelligence research. Hyperbolic space can better represent a hierarchical structure compared to Euclidean space, and can therefore be useful for describing and analyzing a phylogenetic tree. In this study, we developed a novel metric that considers the characteristics of a phylogenetic tree for representation in hyperbolic space. We compared the performance of the proposed hyperbolic embeddings, general hyperbolic embeddings, and Euclidean embeddings, and confirmed that our method could be used to more precisely reconstruct evolutionary distance. We also demonstrate that our approach is useful for predicting the nearest-neighbor node in a partial phylogenetic tree with missing nodes. This study highlights the utility of adopting a geometric approach for further advancing the applications of phylogenetic methods. The demo code is attached as a supplementary file in a compiled jupyter notebook. The code used for analyses is available on GitHub at https://github.com/hmatsu1226/HyPhyTree. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.09.333286v1?rss=1 Authors: Fukunaga, T., Iwasaki, W. Abstract: Reconstruction of gene-content evolutionary history is an essential approach for understanding how complex biological systems have been organized. However, the existing gene-content evolutionary models cannot formulate complex and heterogeneous gene gain/loss processes, which reflect diverse evolutionary events and greatly depend on gene families. In this study, we developed Mirage (MIxture model with a Realistic evolutionary rate model for Ancestral Genome Estimation), which allows different gene families to have flexible gene gain/loss rates, but reasonably limits the number of parameters to be estimated by the expectation-maximization algorithm. Simulation analysis showed that Mirage can accurately estimate complex and heterogeneous gene gain/loss rates and reconstruct gene-content evolutionary history. Application to empirical datasets demonstrated that our evolutionary model better fits genome data from various taxonomic groups than other models. Using Mirage, we revealed that gene families of metabolic function-related gene families displayed frequent gene gains and losses in all taxa investigated. The source code of Mirage is freely available at https://github.com/fukunagatsu/Mirage. 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/2020.10.05.326249v1?rss=1 Authors: Mas, A., Castano-Miquel, L., Carretero-Paulet, L., Colome, N., Canals, F., Lois, L. M. Abstract: Post-translational modification by Small Ubiquitin-related Modifier (SUMO) is an essential regulatory mechanism in eukaryotes. In the cell, SUMO conjugates are highly enriched in the nucleus and, consistently, SUMOylation machinery components are mainly nuclear. Nonetheless, cytosolic SUMO targets also exist and the mechanisms that facilitate SUMO conjugation in the cytosol are unknown. Here, we show that the nuclear localization of the Arabidopsis SUMO activating enzyme large subunit SAE2 is dependent on two nuclear localization signals, the canonical NLS1 and the non-canonical NLS2 identified and validated here. NLS2 is proteolytic processed from SAE2 during seed development, facilitating SAE2 enrichment in the cytosol. Results obtained using transgenic plants expressing different SAE2 proteoforms suggest that SAE2 cytosolic enrichment could constitute a rapid signal for growth arrest. Phylogenetic studies indicated that the Arabidopsis NLS1-NLS2 structural organization is conserved only in seed plants, providing a potential evolutionary role of cytosolic SUMOylation in seed appearance. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.25.310078v1?rss=1 Authors: Taiwo, I. A., Adeleye, N., Anwoju, F. O., Adeyinka, A., Uzoma, I. C., Bankole, T. T. Abstract: Background: Coronaviruses are a group of viruses that belong to the Family Coronaviridae, Genus Betacoronavirus. In December 2019, a new coronavirus disease (COVID-19) characterized by severe respiratory symptoms was discovered. The causative pathogen was a novel coronavirus known as 2019-nCoV and later as SARS-CoV-2. Within two months of its discovery, COVID-19 became a pandemic causing widespread morbidity and mortality. Methodology: Whole genome sequence data of SARS-CoV-2 isolated from Nigerian COVID-19 cases were retrieved by downloading from GISAID database. A total of 18 sequences that satisfied quality assurance (length > 29700 nts and number of unknown bases denoted as N < 5%) were used for the study. Multiple sequence alignment (MSA) was done in MAFFT (Version 7.471) while SNP calling was implemented in DnaSP (Version 6.12.03) respectively and then visualized in Jalview (Version 2.11.1.0). Phylogenetic analysis was with MEGA X software. Results: Nigerian SARS-CoV-2 had 99.9% genomic similarity with four large conserved genomic regions. A total of 66 SNPs were identified out of which 31 were informative. Nucleotide diversity assessment gave Pi = 0.00048 and average SNP frequency of 2.22 SNPs per 1000 nts. Non-coding genomic regions particularly 5 UTR and 3 UTR had a SNP density of 3.77 and 35.4 respectively. The region with the highest SNP density was ORF10 with a frequency of 8.55 SNPs/1000 nts). Majority (72.2%) of viruses in Nigeria are of L lineage with preponderance of D614G mutation which accounted for 11 (61.1%) out of the 18 viral sequences. Nigeria SARS-CoV-2 revealed 3 major clades namely Oyo, Ekiti and Osun on a maximum likelihood phylogenetic tree. Conclusion and Recommendation: Nigerian SARS-CoV-2 reveals high mutation rate together with preponderance of L lineage and D614G mutants. Implication of these mutations for SARS-CoV-2 virulence and the need for more aggressive testing and treatment of COVID-19 in Nigeria is discussed. Additionally, attempt to produce testing kits for COVID-19 in Nigeria should consider the conserved regions identified in this study. Strict adherence to COVID-19 preventive measure is recommended in view of Nigerian SARS-CoV-2 phylogenetic clustering pattern, which suggests intensive community transmission possibly rooted in communal culture characteristic of many ethnicities in Nigeria. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.23.310300v1?rss=1 Authors: Colavin, A., Atolia, E., Bitbol, A.-F., Huang, K. C. Abstract: Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's phylogenetic history and gives rise to concurrent variation between protein sequences that is not driven by selection for function. Here, we introduce a method for explicitly defining a phylogenetic dimension of coevolution signal, and demonstrate that coevolution can occur on multiple phylogenetic timescales within a single protein. Our method, Nested Coevolution (NC), can be applied as an extension to any coevolution metric. We use NC to demonstrate that poorly conserved residues can nonetheless have important roles in protein function. Moreover, NC improved structural-contact prediction over gold-standard coevolution-based methods, particularly in subsampled alignments with fewer sequences. NC also lowered the noise in detecting functional sectors of collectively coevolving residues. Sectors of coevolving residues identified after NC correction were more spatially compact and phylogenetically distinct from the rest of the protein, and strongly enriched for mutations that disrupt protein activity. Our conceptualization of the phylogenetic separation of coevolution represents an advance from previous pragmatic attempts to reduce phylogenetic artifacts in measurements of coevolution. Application of NC broadens the application of protein coevolution measurements, particularly to eukaryotic proteins with fewer naturally available sequences, and further elucidates relationships among protein evolution and genetic diseases. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.09.289108v1?rss=1 Authors: Spence, M. A., Mortimer, M., Buckle, A. M., Jackson, C. J. A. Abstract: Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer (HGT) due to their unexpectedly high homology. Here we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6000-sequence phylogeny that encompasses serpins from all kingdoms of life. We show that in addition to a central hub of highly conserved serpins, there has been extensive diversification of the superfamily into many novel functional clades. Our analysis indicates that the hub proteins are ancient and are similar because of convergent evolution, rather than the alternative hypothesis of HGT. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology. Copy rights belong to original authors. Visit the link for more info

Manon Ragonnet-Cronin joins The Lancet HIV Editor, Peter Hayward, to discuss the use of phylogenetic analysis to gain insight into HIV transmission in the UK, the potential role of non-disclosed MSM, and targeting of HIV interventions.