This Week In Evolution

Nels and Vincent answer listener questions and discuss a newly discovered virus of amoeba with a nearly complete ORFan genome: none of the proteins encoded in the viral genome look like any other proteins. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Yaravirus (PNAS) Letters read on TWiEVO 59 Time stamps by Jolene. Thanks! Science Picks Nels - Blog by Ambika Kamath Vincent - TWiVerse Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Simon and Heather join TWiEVO to discuss their analysis of the evolutionary history of ACE2 usage by coronaviruses in the Sarbecovirus genus. Hosts: Nels Elde and Vincent Racaniello Guests: Simon Anthony and Heather Wells Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Evolutionary history of sarbecovirus ACE2 binding (bioRxiv) Bombali virus in bats (Nat Micro) Herpesviruses in Puerto Rican bats (bioRxiv) Adenovirus and herpesvirus in great apes (PLoS One) Time stamps by Jolene. Thanks! Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Jessie, Allie and Tyler join Nels and Vincent to describe their work on deep mutational scanning of the SARS-CoV-2 receptor binding domain. Hosts: Nels Elde and Vincent Racaniello Guests: Jesse Bloom, Allie Greaney, and Tyler Starr Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Bloom Laboratory Deep mutational scanning of SARS-CoV-2 RBD (bioRxiv) Time stamps by Jolene. Thanks! Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent continue their discussion of SARS-CoV-2 evolution, including understanding recurrent mutations in the viral genome, and the potential for re-emergence of the virus from an animal reservoir. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO SARS-CoV-2 genomic diversity (Inf, Genet, Evol) Re-emergence of SARS-CoV-2 (bioRxiv) Tackling SARS-CoV-2 rumors (virological.org) Letters read on TWiEVO 56 Image credit Time stamps by Jolene. Thanks! Science Picks Nels - The Cell in Evolution Vincent - Visual Science Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent continue their discussion of SARS-CoV-2 evolution, with a report that the coronavirus proofreading enzyme stimulates RNA recombination, and debunking the conclusion that a change in the viral spike glycoprotein is associated with increased human to human transmission. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO CoV proofreading enzyme stimulates recombination (bioRxiv) CoV spike mutation pipeline (bioRxiv) Issues with CoV sequencing data (virological.org) Bill Hanage on selection vs bottleneck (threader.app) Image credit Time stamps by Jolene. Thanks! Science Picks Nels - In Memoriam: Gordon Lark Vincent - John Oliver Discussion of Antibody Tests Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent continue their discussion of SARS-CoV-2 from an evolutionary viewpoint, including function of the furin cleavage site, whether Vervet cells are an informative system, another bat isolate, and a nomenclature to assist genomic epidemiology. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO SARS-CoV-2 in Vero cells (bioRxiv) More related SARSr virus from bat (bioRxiv) Patient isolates in Vero cells (medRxiv) Nomenclature for genomic epidemiology (bioRxiv) Time stamps by Jolene. Thanks! Science Picks Nels - EvoEco seminars Vincent - Coronavirus book for children Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent continue their discussion of SARS-CoV-2 from an evolutionary viewpoint, focusing on what the genome sequences tell us about the virus. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Clement Chow with COVID-19 (Salt Lake Trib) Scientists exposed to coronavirus (Nature) CoV by Britt Glaunsinger (YouTube) Genetic epidemiology of novel coronavirus (nextstrain.org) Time stamps by Jolene. Thanks! Science Picks Nels - Science Mill Explorer Zone Vincent - COVID-19 treatment and therapy tracker Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent examine SARS-CoV-2 from an evolutionary viewpoint, examining what the spike glycoprotein sequence informs us about the origin of the virus. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Distinct CoV name needed (Lancet) Proximal origin of SARS-COV-2 (virological) CoV spillovers not rare (Goats and Soda) SARS-CoV-2 phylodynamics analysis (virological) Bat CoV surveillance in China (PLoS Path) Image credit Time stamps by Jolene. Thanks! Science Picks Nels - Alejandro Sanchez TED Talk Vincent - WHO SARS-CoV-2 Sitrep Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent dive deep into evolution and consider how new proteins emerged billions of years ago, when there were no other proteins to serve as starting material. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Primordial emergence of a nucleic acid binding protein (bioRxiv) Tawfik laboratory Image credit Letters read on TWiEVO 51 Time stamps by Jolene. Thanks! Science Picks Nels - Universal principled review Vincent - Hostile Planet by National Geographic Listener Pick Courtney - Nightwish Endless Forms Most Beautiful and Shudder Before The Beautiful Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent discuss signatures of sex chromosome evolution revealed by assembly of a young vertebrate Y chromosome from 3-spined stickleback fish. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Assembly of a young vertebrate Y chromosome (bioRxiv) Image credit Letters read on TWiEVO 50 Time stamps by Jolene. Thanks! Science Picks Nels - Genome from a 5,700-Year-Old Wad of Chewed Gum Vincent - NJ Sea-Level Rise Reports Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Rich joins Nels and Vincent for a debriefing on the 4th Ringberg Symposium on Giant Virus Biology in Tegernsee, Germany. Hosts: Nels Elde and Vincent Racaniello Guest: Rich Condit Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Endless giant virus forms most beautiful (TWiV 575) 4th Ringberg Giant Virus Meeting Program (pdf) Photographs by Matthias Fischer Time stamps by Jolene. Thanks! Science Picks Rich - Flightradar24 Nels - Deutsches Museum Munich Vincent - Diversify Microbiology Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent reveal a new choanoflagellate that forms multicellular cup shaped colonies that respond to light to alternate between feeding and swimming behavior. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Microbial accomplices in multicellularity (TWiEVO 11) Light regulated collective contractility (Science) Image credit Letters read on TWiEVO 48 Time stamps by Jolene. Thanks! Science Picks Nels - How to write a great science paper by Cormac McCarthy Vincent - Natural Selection Store Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent trace the origins of Saccharomyces cerevisiae strains used to make beer, and find that ales and lagers are made with yeasts that were derived from those used to make European grape wine and Asian rice wine. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Origins of beer yeasts (PLoS Biol) Chateau Jiahu beer Time stamps by Jolene. Thanks! Science Picks Nels - Population fluctuations in 10 biggest cities Vincent - 1.7 million year old rhino tooth (original Nature paper) Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent analyze the genomes of canine transmissible tumors to provide insight into the worldwide spread of the disease from its origin in a single dog 4000-8500 years ago, and its diversity, mutation, and evolution. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Evolution and mutation of canine transmissible cancer (Science) Clam cancers (TWiEVO 17) Sixth modality of infectious disease (PLoS Path) Time stamps by Jolene. Thanks! Science Picks Nels - Vasa Museum in Stockholm Vincent - Nobel Museum in Stockholm Listener Pick Irene - @EndlessFormsand #PlantScienceFascinatesMe #plantsday Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

At ASM Microbe in San Francisco, Nels and Vincent meet up with Talia Karasov who reveals that in contrast to agriculture, wild plants are colonized by multiple lineages of pathogenic bacteria. Hosts: Nels Elde and Vincent Racaniello Guest: Talia Karasov Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Talia Karasov in the Bergelson lab Arabidopsis thaliana and Pseudomonas (Cell Host Micr) Time stamps by Jolene. Thanks! Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

At ASM Microbe in San Francisco, Nels and Vincent meet up with Paul Turner to talk about evolutionary considerations in using bacteriophages to treat infections with antibiotic-resistant bacteria. Hosts: Nels Elde and Vincent Racaniello Guest: Paul Taylor Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Turner Lab at Yale Phage therapy: A renewed approach (Cell Host Microbe) Phage treatment of aortic graft (Evol Med Pub Health) Time stamps by Jolene. Thanks! Science Picks Nels- Science Glass Vincent- Phage therapy for disseminated Mycobacterial infection Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Dustin Rubinstein joins Nels and Vincent to discuss coevolution of genome architecture and social behavior, and studying social transitions in sponge-dwelling snapping shrimp. Hosts: Nels Elde and Vincent Racaniello Guest: Dustin Rubinstein Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Co-evolution of genome architecture and social behavior (Trend Ecol Evol) Social transitions in snapping shrimp (Curr Op Insect Sci) Time stamps by Jolene. Thanks! Science Picks Dustin- Genesis: The Deep Origin of Societies 1 by E.O. Wilson, and The Human Swarm by Mark O. Moffett Nels- For Love of Insects by Thomas Eisner Vincent- Quacks blamed for Pakistan HIV-1 outbreak Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent review the contribution of multiple Denisovan lineages to the modern Papuan genome. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Denisovan ancestries in Papuans (Cell) Prof Murray Cox Image credit Letters read on TWiEVO 42 Time stamps by Jolene. Thanks! Science Picks Nels- Sydney Brenner - What Genomes Can Tell Us About the PastVincent- Scientific Communication in a Post-Truth Society Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent explore the evolution of new protein-coding genes de novo from nocoding DNA sequences, using the antifreeze protein of northern codfish as a model. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Evolution of antifreeze protein gene in codfish (PNAS) Codfish diversity (Cheng lab) Frankentomatoes (Huff Post) Image credit Time stamps by Jolene. Thanks! Science Picks Nels- Science at Sundance reviews Vincent- The Rise and Fall of Scientific Authority Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent move back to reproductive isolation - this time, pre-zygotic, in the charismatic orchid bee where the males make chemically distinct perfumes to attract mates of the same species. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Olfactory receptor gene underlies reproductive isolation (biorXiv) Image credit Time stamps by Jolene. Thanks! Science Picks Nels- Nature Zen: Orchid Bees Are Shiny Vincent- What You Believe About Science Denial May Be All Wrong Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv