This Week In Evolution

Nels and Vincent discuss the observation that cells on a boundary of a solid tumor have higher growth rates compared to those in the center and how to model this difference using genome sequencing data. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode •Join the MicrobeTV Discord server •Evolutionary models of solid tumor growth (Nat Ecol Evol) Science Picks Nels – TWiV 1000 Vincent – The dream of wiping out polio might need a rethink Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent review a study of the dogs of Chernobyl which reveals that genetically distinct populations with different amounts of western breed contributions to their genomes, the first step in assessing the effects of exposure to long-term ionizing radiation. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode •Join the MicrobeTV Discord server •The dogs of Chernobyl (Science Adv) •What the dogs of Chernobyl can teach us (Stat) •Letters read on TWiEVO 88 Science Picks Nels – Hellbent documentary and Insufficient evidence for natural selection associated with the Black Death Vincent – BioRender Listener Pick Walter – Oded Rechavi and interview Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nathan joins Nels and Vincent to discuss his approach to understanding how species adopt novel traits to overcome challenges, and its application to identifying coding and noncoding sequence changes that underlie mammalian hairlessness. Hosts: Nels Elde and Vincent Racaniello Guest: Nathan Clark Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode •Join the MicrobeTV Discord server •Gene loss in marine mammals (TWiEVO 34) •Gene change underlying mammalian hair loss (eLife) •Letters read on TWiEVO 87 Science Picks Nels – Local news coverage of Amanda, Maria, and Nathan’s paper Vincent – Discovering Retroviruses by Anna Marie Skalka Nathan – Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent discuss how evolution of changes in stop codon assignment might occur, and a novel mechanism for altering the meaning of translation stop codons discovered in a trypanosomatid with the apropos name, Blastocrithidia nonstop. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode •Join the MicrobeTV Discord server •Novel stop codon reassignment mechanisms (Nature) Science Picks Nels – Protein Synthesis: An epic on the cellular level  Vincent – Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes discussed on TWiM 277 Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent discuss the use of genome sequence data for over 4,000 domestic, semi-feral, and wild canids to understand the genetic drivers of canine behavior. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Genetic drivers of canine diversification (Cell) Time stamps by Jolene. Thanks! Science Picks Nels – Ghosts of Science Past Still Haunt Us by C. Brandon Ogbunu Vincent – The Biggest Ideas in the Universe by Sean Carroll Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent review the use of ancient DNA to identify loci that may have been under selection during the Black Death by studying populations before, during, and after the pandemic. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Evolution of immune genes associated with Black Death (Nature) ERAP2 and respiratory disease (medRxiv) Time stamps by Jolene. Thanks! Science Picks Nels – Interview with Paul Turner in Current Biology and Map of the World if you are a fish Vincent – Smallpox and its eradication Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Florian Maderspacher from Current Biology joins Nels and Vincent to discuss a special issue of the journal on birds. Hosts: Nels Elde and Vincent Racaniello Guest: Florian Maderspacher Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Current Biology Birds Special Issue Scott Edwards bikes across the US (Audubon) Support Diversity Issues in Evolution (Go Fund Me) Time stamps by Jolene. Thanks! Science Picks Florian – Favorite birds of authors/contributors in Birds issue Nels –Loss of avian intromittent organs as a sperm competition strategy: a race to be last Vincent – Malaria at the Bronx Zoo (TWiP 110) Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent consider evidence that a single amino acid change in the TKTL1 gene might have led to greater neurogenesis in the frontal cortex of modern humans compared with Neanderthals. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Human TKTL1 implies greater neurogenesis (Science) Everyone’s a little bit Neanderthal (TWiEVO 8) Tragic gene flow from Neanderthals (TWiV 676) Time stamps by Jolene. Thanks! Science Picks Nels – Unusual display of elements Vincent – Sykdomspulsen and summary Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent discuss how duplication of a gene encoding a transcription factor led to evolution of a novel cell type in the slime mold Dictyostelium. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Gene duplication leads to novel cell type (Current Biol) Evolution of multicellularity (TWiEVO 11) Letters read on TWiEVO 81 Time stamps by Jolene. Thanks! Science Picks Nels – Dall-E artificial intelligence meets art Vincent – John Bonner’s slime mold movies Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Louise Moncla joins Nels and Vincent to review her use of genomics to understand emergence, evolution, and transmission of respiratory viruses including influenza virus H5N1, mumps virus, and SARS-CoV-2. Hosts: Nels Elde and Vincent Racaniello Guest: Louise Moncla Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Within-host diversity of influenza virus H5N1 (PLoS Path) Mumps virus outbreak in Washington (eLive) SARS-CoV-2 tight transmission bottlenecks (PLoS Path) Time stamps by Jolene. Thanks! Science Picks Nels – JWST Images Vincent – 3rd International Symposium on Infectious Diseases of Bats and Program Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent discuss an analysis of the drivers of evolution of SARS-CoV-2 during chronic infections, indicating that a tradeoff exists between antibody evasion and fitness. Hosts: Nels Elde and Vincent Racaniello Click arrow to play Download TWiEVO 79  (103 MB .mp3, 86 min) Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode SARS-CoV-2 evolution during chronic infection (Nat Med) Letters read on TWiEVO 79 Time stamps by Jolene. Thanks! Science Picks Nels – NASA scientists say images from the Webb telescope nearly brought them to tears Vincent – FDA: Don’t rush a move to change the Covid-19 vaccine composition Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent provide an update on cases of monkeypox, and summarize a biochemical view of three changes in the SARS-CoV-2 spike protein that may balance positive and negative selection. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode ECDC monkeypox risk assessment (pdf) Monkeypox virus genomes (Nextstrain) Discussion of monkeypox virus genome sequencing (virological.org) Balancing positive and negative selection in spike protein (Biochem) Time stamps by Jolene. Thanks! Science Picks Nels – Science on the Side podcast by Morgan Nelson and Ty Chiaro  Vincent – Richard Ernst Lecture 2022 Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Alex joins Nels and Vincent to discuss his work which demonstrates that somatic mutation rates scale with lifespan in mammals. Hosts: Nels Elde and Vincent Racaniello Guest: Alex Cagan Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Somatic mutation and age (Nature) Zombie gene in elephants (TWiEVO 26) Time stamps by Jolene. Thanks! Science Picks Alex – Paper.app Nels – Fifty years since Lewontin’s apportionment of human diversity Vincent – An Exceptional Village Listener Pick Martha – Plagues Upon the Earth by Kyle Harper Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent describe how a single amino acid change can allow E. coli to replace the essential gut symbiont of the stinkbug Plautia stali. Hosts: Nels Elde and Vincent Racaniello Click arrow to play Download TWiEVO 75  (103 MB .mp3, 86 min) Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Making E. coli an insect mutualist (bioRxiv) Letters read on TWiEVo 76 Time stamps by Jolene. Thanks! Science Picks Nels – Inequality in science and the case for a new agenda Vincent – Foundations of Virology by Fred Murphy Listener Pick Sam – Saturday Morning Breakfast – Evolutionist Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent review isolation of SARS-CoV-2-like viruses from bats in Laos that can replicate in human cells. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode SARS-CoV-2 like viruses in bats in Laos (Nature) Vampire vax (TWiV 809) Time stamps by Jolene. Thanks! Science Picks Nels – Erich Jarvis on scientists and public engagement Vincent – Polio type 1 in Africa Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Joe Graves joins Nels and Vincent to discuss his career in evolutionary biology and his recent book that answers questions about race and racism. Hosts: Nels Elde and Vincent Racaniello Guest: Joe Graves Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode On Racism, Not Race (Amazon) African Americans in evolutionary science (Behav Ecol Sociobiol) Biological variation and the normal (Am J Hum Biol) Time stamps by Jolene. Thanks! Science Picks Nels – Where is Webb? Vincent – Black Microbiologists Association Joe – Biology versus bias Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent review three aspects of SARS-CoV-2: phylogenetics of Omicron, a two-step fitness selection for variants, and putative RNA insertions from host genomes. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Two-step fitness selection for SARS-CoV-2 variants (Cell Rep) Host origins of SARS-CoV-2 genome insertions (Virological) Time stamps by Jolene. Thanks! Science Picks Nels – Plant virus satellite accelerates wing formation in insect Vincent – A plant virus that switched to vertebrates Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent discuss evolutionary evidence for an epidemic of coronavirus infection over 20,000 years ago in East Asia, and reconstruction of the membrane differences between bacteria and Archaea reveals unexpected differences in permeability. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Ancient coronavirus epidemic in East Asia (Curr Biol) Gene-culture coevolution and human evolutionary transition (Proc Roy Soc B) Membrane permeability at the lipid divide (bioRxiv) Time stamps by Jolene. Thanks! Science Picks Nels – Slowed canonical progress in large fields of science Vincent – Virology Live Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent explain a method to calculate the mutation rate of SARS-CoV-2, and the role of a single amino acid change in spike in enhancing fitness of the delta variant and enabling it to out-compete the alpha variant. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode SARS-CoV-2 mutation rate (Genome Biology Evolution) Delta spike change enhances fitness (bioRxiv) Time stamps by Jolene. Thanks! Science Picks Nels – Leading Edge Symposium Vincent – Epidemiological and evolutionary dynamics of SARS-CoV-2 Listener Pick Thomas – The gene’s-eye view of evolution by J. Arvid Ågren Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Carl Zimmer joins Nels to talk about science writing, science communication, viruses, and his new book, On Life’s Edge. Host: Nels Elde Guest: Carl Zimmer Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode On Life’s Edge by Carl Zimmer Time stamps by Jolene. Thanks! Science Picks Nels – Remembrance of Dick Lewontin Carl – From telomere to telomere: the transcriptional and epigenetic state of human repeat elements Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv