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/10.1101/2023.09.14.557739https://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 increase mutational robustness and genetic diversity, but not speed of phenotypic evolution due to inactivation of one copy (but this is for increases in original trait, green fluorescence? I thought this should be most evident in new trait, blue fluorescence...). https://doi.org/10.1101/2023.09.25.559237 https://twitter.com/YSchaerli/status/1706261954619191798
Transient eco-evolutionary dynamics early in a phage epidemic have strong and lasting impact on the long-term evolution of bacterial defences. Theory and experiments show what influences the balance between selected vs. acquired resistance evolution in a phage-bacteria system. High host growth favors selection of resistant mutants, high pathogen transmission favors acquired CRISPR immunity. https://doi.org/10.1371/journal.pbio.3002122https://twitter.com/PLOSBiology/status/1703692715743916085
Engineering:
Using the E. coli Alleleome in Strain Design. Genetic variation derived from adaptive laboratory evolution of E. coli to specific conditions and standing variation in wild strains represent largely non-overlapping evolutionary spaces that be combined in directed evolution and strain design. https://doi.org/10.1101/2023.09.17.558058
The role of learning in the evolution of status signalling: a modeling approach. Simulations of agents engaging in pairwise fights and status signaling show that honest and dishonest-signaling individuals can coexist if costs of signaling are not proportional to quality and individuals can learn from experience. https://doi.org/10.1101/2023.09.19.558427https://twitter.com/cdanielcadena/status/1705213834653249547
Differential evolution of cooperative traits in aggregative multicellular bacterium Myxococcus xanthus driven by varied population bottleneck sizes. Bottlenecks affect different cooperative traits in different ways in the social bacterium Myxococcus xanthus, selecting for some and against others. https://doi.org/10.1101/2023.09.20.558552 https://twitter.com/iamsamayp/status/1706100974816006606
Human
origin ascertained for SARS-CoV-2 Omicron-like spike sequences detected
in wastewater: a targeted surveillance study of a cryptic lineage in an
urban sewershed. The famous detective saga tracking down that
one poor soul in Wisconsin pooping out cryptic lineages like there's no
tomorrow, updated preprint. https://doi.org/10.1101/2022.10.28.22281553
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...
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...
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 ...
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