Evoluncheons

Hello interwebz!   Back for #Evoluncheons after a week of travel and drowning in a sea of papers. This took all day again -_-    Actually organizing by #evolution themes from now on, hopefully easier to digest: Fundamentals: Strong environmental memory revealed by experimental evolution in static and fluctuating environments . Switching barcoded yeast mutants between carbon sources leads to results that are different from what we would expect based on their fitness in each carbon source without switching. Mutants with greater differences in fitness between static environments show the greatest deviations from expectation. https://doi.org/10.1101/2023.09.14.557739 https://twitter.com/clabreu/status/1706324819631862158   A direct experimental test of Ohno's hypothesis . Susumu Ohno proposed gene duplications should facilitate evolution of proteins with novel functions. FACS-powered experimental evolution of fluorescent protein libraries confirms duplications incr...

How         zit        errbady Been absolutely slammed in the lab before I travel next week, so we're late and not going in depth today. But wow some absolute bangers out there the last couple weeks. Lots of zoonosis and wildlife epidemiology, theme of this issue. Sorry cancer folks, this one's almost all infection biology. Engineering is evolution: a perspective on the biological design process. Philosophical musings fromlike-minded synthetic biologists thinking about evolution. Directed evolution is rational engineering. https://osf.io/urq9w Host functional traits as the nexus for multilevel infection patterns. Short perspective of how host biology and ecology across scales shapes disease ecology. https://www.sciencedirect.com/science/article/abs/pii/S0169534723002227 Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold. You share an antiviral defense mechanism with the gunk growing on yo...

Back from travel and I had time to spot lots of interesting science to dump here, maybe too many this week. A lot of bacterial and phage microbial ecology this week, a dash of cancer, antibiotics, and covid. Lots of game theory! I like that the focus is changing week to week. We have:   Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein Another week, another Lauring Lab paper. They assay 84% of all substitutions in the AH1N1 flu polymerase catalytic subunit, since it’s commonly involved in host adaptations when jumping species barriers. They compare their experimental data of the fitness effects of individual mutations to observational data from flu genomic surveillance. A lot of interesting lessons here, but I’ll note real mutational landscapes are a lot more constrained than the experimental data shows, in good part determined by mutation accessibility. https://doi.org/10.1101/2023.08.27.554986 ...

  Not a lot of papers since I’m traveling—but also science twitter is dying?! I need to find new ways of spotting cool papers. Apologies for the heavy infection biology focus on these :/ Transmission bottleneck size estimation from de novo viral genetic variation . I saw this work presented at a conference in May, the Koelle lab is fantastic at this stuff. The authors develop a new, more careful approach to estimating how many viral particles are responsible for establishing a successful new infection (the transmission bottleneck size). The approach uses a branching process model of within-host viral growth to generate probability distributions used to infer maximum-likelihood estimates for bottleneck size and mutation rate per infection cycle given within-host growth metrics fit to empirical data from pathogen genomic sequencing. They confirm the bottlenecks for SARS-CoV-2 and influenza virus A are both close to 1. https://www.biorxiv.org/content/10.1101/2023.08.14.553219v1 ...

There are lots of papers this week, buckle up Predicting evolutionary outcomes through the probability of accessing sequence variants . Thanks Sarah for sharing this one! This is such a simple but important idea. Essentially, evolution follows not only the contours of the fitness landscape but also the “genotype-accessibility landscape”, which is shaped by stuff like codon bias and biochemical mechanisms of mutation changing the likelihoods of some mutations. They look at some examples of this in fu. https://www.science.org/doi/full/10.1126/sciadv.ade2903   Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2 . These folks do some population genetics archaeology to try to put together what was happening with the genomes of SARS-CoV-1 and SARS-CoV-2 around the time they jumped into humans. They find most things are under purifying selection (which is generally the case with viruses as they “live on the (evolut...

Some papers and resources from the past couple of weeks! Big backlog here, something for everyone here: Genetic effects on molecular network states explain complex traits . Molecular Systems Biology papers are usually fun (imo). Here, the authors show how mutations result in system-level homeostatic adjustments that can actually be described in terms of PKA and TOR signaling. It’s an interesting exploration into how exactly genotype manifests into phenotype. https://www.embopress.org/doi/full/10.15252/msb.202211493 https://twitter.com/AndreasBeyer012/status/1683417817666732035   Evolutionary histories of breast cancer and related clones . A tour de force where the authors apply phylogenomics to reconstruct the evolution of breast cancer cell lineages over the lifetime (!) of human patients. What surprised and interested me (a non-cancer biologist) the most was that although all cancer cells descended from a common ancestor with cer...

    Here are my picks of papers for the week:   Emergent coexistence in multispecies microbial communities . Álvaro Sánchez does some pretty neat, elegant work showing that if you break down a stable synthetic microbial community by studying all pairwise interactions of its members, almost every single time you’ll get one member of the pair outcompeting and excluding the other. The point of doing this is to show that ecological complexity isn’t a consequence of coexistence, but rather that coexistence is a consequence of ecological complexity. Not the first time I see this idea explored, but it’s a cool one. https://www.science.org/doi/10.1126/science.adg0727 , or open access here: https://europepmc.org/article/MED/37471535   Sequential mutations in exponentially growing populations. This theoretical paper seems to have some useful approaches to estimate the number of mutants in an exponentially growing population using branching processe...

  If you’re here for the weekly paper picks, I’ve got some cool ones this week too :D   Antigenic strain diversity predicts different biogeographic patterns of invasion and maintenance of anti-malarial drug resistance. This paper tackles one of the major questions my epidemiology research was originally concerned with: why malaria parasites evolve resistance to drugs more easily in low-transmission settings. I’d say I was scooped, but I kind of drifted into other questions after half answering it in my first evolution paper, so good on these folks for addressing the matter carefully. The main innovation here that I hadn’t considered in earlier work is showing that immunity plays an important role by providing an evolutionary pressure that pushes population genetic change along in high transmission, high genetic diversity settings, even when the pressures of immunity and drug selection are on different loci. If anyone’s interested, I’ll probably journal c...

  There are some real bangers I’m having a look at this week, oh boy:   Evolution of a minimal cell. They took the Venter Institute’s minimal mycoplasma cell and tracked its evolution in vitro. Such a simple and cool idea, can’t believe it hadn’t been done before. Came out today, haven’t had a good look yet. https://www.nature.com/articles/s41586-023-06288-x   Evolutionary shortcuts via multi-nucleotide substitutions and their impact on natural selection analyses . tldr; if you assume that substitution mutations can only happen one SNP at a time, you highly underestimate positive selection, so here are better ways of analyzing genomes. https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msad150/7217158   Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities . Weirdo virus-ish transposon-ish DNA elements are a major mechanism of horizontal gene transfer in nematodes, and even m...