This Week In Evolution

Nels and Vincent consider evolution of antibody immunity to SARS-CoV-2, and update the situation on novel virus variants of concern with potentially altered fitness and reactivity with antibodies. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Evolution of SARS-CoV-2 antibodies (Nature) mRNA vaccine-elicited antibodies to variants (bioRxiv) Scott Hensley thread (Twitter) Analysis of B.1.17 lineage (virological) Trevor Bedford thread (Twitter) Andrew Rambaut on variant naming (Twitter) Letters read on TWiEVO 64 Time stamps by Jolene. Thanks! Science Picks Nels – Biden Administration PCAST and The Hill We Climb Vincent – Four inaugural quotations – Lincoln, Roosevelt, Kennedy, Biden Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent wrap up 2020 with a discussion of novel variants of SARS-CoV-2 that have emerged in the United Kingdom and South Africa, how to interpret the rapidly emerging genome sequence data and what to look for in the coming weeks as these variants spread across the globe. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Preliminary genomic characterization of UK variant (virological) Clinical outcomes of infection with Orf8 variants (Lancet) Global Report Investigating Novel Coronavirus Haplotypes (GRINCH) South African SARS-CoV-2 lineage (medRxiv) Time stamps by Jolene. Thanks! Science Picks Nels – Katalin Karikos’ career and mRNA vaccines Vincent – Reverse Engineering of mRNA vaccine Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Daniel joins Nels and Vincent to discuss his new book on army ants, the wickedest insects ever to roam the planet, and his research on them and clonal raider ants. Hosts: Nels Elde and Vincent Racaniello Guest: Daniel Kronauer Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode This Week in Ants (TWiEVO 13) Raiders of the Lost Orco (TWiEVO 18) Army Ants by Daniel Kronauer Time stamps by Jolene. Thanks! Science Picks Daniel – Desert Navigator by Rüdiger Wehner and Insects of Suriname by Maria Sibylla Merian Nels – NPR Scicommers Vincent – The Vintage Beauty Of Soviet Control Rooms Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent discuss an opinion piece on 12 evolutionary insights into how the COVID-19 pandemic is shaping human nature, and prolonged SARS-CoV-2 reproduction in an immunosuppressed patient. Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Microbe.TV on instagram Pandemic exposes human nature (PNAS) Carl Bergstrom calls BS (Twitter) Prolonged SARS-CoV-2 reproduction in patient (J Inf Dis) Letters read on TWiEVO 61 Time stamps by Jolene. Thanks! Science Picks Nels – Scott Edwards bikes across US; support diversity in evolution Vincent – 30 computers sculpture project Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

On the fifth anniversary of TWiEVO, Nels and Vincent invite 12 evolutionary biologists to describe exciting future directions for the field and their laboratory in the next five years. Hosts: Nels Elde and Vincent Racaniello Guests: Lillian Fritz Laylin, Talia Karasov, Andrew Kern, Sarah Tishkoff, Dmitri Petrov, Nancy Chen, Amanda Larracuente, John McCutcheon, Ambika Kamath, Chip Aquadro, Rebekah Rogers, Yaniv Braindvain, and Harmit Malik Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Science Picks Nels - Science Mill Virtual Tour and Benefit Vincent - Das Coronavirus summaries Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv  

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