Lmst

Our new #preprint changes the way we look at an “extinction vortex” in which a small population loses fitness, causing it to become even smaller https://www.biorxiv.org/content/10.1101/2024.10.25.620329v1.
#MutationalMeltdown #EffectivePopulationSize #EvolutionaryRescue #PopulationGenetics #EvolGenPaper @wmawass @jdmatheson @uliseshmc 1/7

Our latest paper https://elifesciences.org/articles/87335
directly measures the #EffectivePopulationSize that matters to #NearlyNeutralTheory / #DriftBarrier theory, as the degree to which #CodonBias differs from expectations from GC content. Surprisingly, stronger #NaturalSelection -> higher #IntrinsicStructuralDisorder proteins
#MolecularEvolution #PopulationGenetics #EvolgenPaper 1/

Our latest #preprint https://ecoevorxiv.org/repository/view/6959/ explains why fitness can be defined in so many ways, and which version(s) you should use when. Fitness quantifies what #NaturalSelection favors. @gdoulcier #EvolGenPaper #Evolution 1/

Such a cool system. A fun project to work on. First DMI in maize I believe. And cool meiotic drive, sRNA, and teosinte introgression. #EvolgenPaper https://www.biorxiv.org/content/10.1101/2023.07.12.548689v1

Our preprint describes how #EffectivePopulationSize affects #AminoAcid usage. https://www.biorxiv.org/content/10.1101/2023.02.01.526552v2. Within highly exchangeable pairs of amino acids, high Ne species are able to prefer #arginine over #lysine, and #valine over #isoleucine. This matches #thermophile preferences, as expected from theories of marginal protein stability at mutation-selection-drift balance. 1/6
@hanonmcshea #NearlyNeutralTheory #MolecularEvolution #EvolgenPaper

Delighted to share our new Science #EvolgenPaper! https://www.science.org/doi/10.1126/science.abn3107

We introduce #TOGA, a #ComparativeGenomics method that combines the detection of orthologous genes with gene annotation. In plain words, TOGA can take advantage of a well-annotated #genome and transfer its annotations to a genome of a different species (e.g., from the human genome to that of a squirrel). 1/2

This figure highlights how TOGA can integrate annotation and orthology inference based on intronic and intergenic alignments (among other things).

Using a high-quality genome as reference, TOGA can generate gene annotations, can identify orthologs/duplicated/lost genes, can produce codon alignments, as well as assembly quality benchmarks for genomes of query species.

Neat new #EvolgenPaper by @gvbarroso.

The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation:

https://peercommunityjournal.org/articles/10.24072/pcjournal.267/

Excited to sit down with this one!

Our extensively revised preprint now goes beyond clarifying Haldane’s arguments about the #CostOfSelection / #SubstitutionalLoad / #SelectiveDeaths, it also significantly extends them, and applies the resulting model to data https://www.biorxiv.org/content/10.1101/2021.11.01.466728v2
@jdmatheson @moi #EvolgenPaper #PopulationGenetics #NaturalSelection #FitnessComponents #GeneticLoad 1/10

Analyses of the first 'type D' killer whale genomes to be sequenced published online today in the Journal of Heredity. Over 65% of the autosomes are in long ROH making them among the most inbred mammals sequenced to date. https://doi.org/10.1093/jhered/esac070 #EvolgenPaper

Out today in PNAS: "The paradox of adaptive trait clines with nonclinal patterns in the underlying genes" https://www.pnas.org/doi/full/10.1073/pnas.2220313120 This study shows that under complex multivariate adaptation, trait clines can evolve despite nonmonotonic allele frequency patterns across environmental gradients. These patterns are not discovered by genotype–environment association methods, which are widely used to discover adaptation. #EvolutionPaper #EcoEvo #SLiM #Genetics #Genomics #EvolgenPaper #PopGen

A complex multivariate case with range expansion and multiple refugia. (A) The six selective landscapes from Bioclim in western Canada; background colors correspond to the optimum trait value on each landscape and point colors correspond to the evolved trait value at that location. (B) Allele frequency patterns at the derived allele of QTNs for each landscape. (C) Evolved population structure on the landscape with individuals colored according to assignment to ancestral clusters. Intermediate colors represent admixture. (D) Accuracy of the redundancy analysis (RDA) predicted standardized trait value from Eq. 1 compared among i) the base model, ii) the base model plus the addition of three nuisance Bioclim variables, a pRDA with structure either corrected by iii) geography or iv) principal components, and v) a polygenic score based on genotype–environment associate (GEA) outliers calculated with latent factor mixed models. For the polygenic score, the number of GEA outliers and the false discovery rate (FDR) are shown within the bar for each environment.

Our latest #preprint develops a new metric of #CodonAdaptation (not just #CodonBias) to measure the kind of #EffectivePopulationSize that matters to #NearlyNeutralTheory, and uses it to discover that #NaturalSelection prefers high #IntrinsicStructuralDisorder https://www.biorxiv.org/content/10.1101/2023.03.02.530449v1 1/6
#MolecularEvolution #PopulationGenetics #EvolgenPaper

New preprint by
Carl Veller and myself on the interpretation of population and family-based genome-wide association studies in the presence of confounding

https://www.biorxiv.org/content/10.1101/2023.02.26.530052v1

#GWAS interpretation is tricky, for three broad reasons: indirect effects of relatives, genetic confounding, and environmental confounding—where genetic confounding (long-distance LD) arises due to population structure, assortative mating, and selection. #EvolgenPaper

Recently we also evaluated how well a widely-used method called "gradient forests" performs for the estimation of "genomic vulnerability". In this paper we highlight some strengths and weaknesses of the approach. Notably, genetic drift can cause small populations to have large "offset" values, highlighting issues with current interpretations and estimations. #EvolutionPaper #Evolution #EvolGenPaper https://onlinelibrary.wiley.com/doi/10.1111/eva.13354

Results of neutral simulations, where no selective pressure is imposed by the underlying environmental clines. (a) The relationship between GF cumulative importance and environment across increasing, decreasing, and equal deme sizes across the environmental gradient. GF Offset increased comparatively more when deme sizes were small. (b). A strong negative linear Pearson's correlation between the GF Offset and deme size in 10 replicates, regardless of the direction of the population gradient.

In our recent "Inversion Invasions" paper we studied the conditions under which inversions invade genomes and become involved in adaptation. We found that inversions were more likely to be involved in adaptation when the genetic basis of the adaptive trait was highly polygenic. #EvolgenPaper #EvolutionPaper #PopulationGenetics @royalsociety https://royalsocietypublishing.org/doi/10.1098/rstb.2021.0200 We developed this plot to visualize how inversions capture and gain genetic variation through time.

We developed this plot to visualize how inversions capture and gain adaptive genetic variation through time. Figure 4. A summary of the origin dynamics of inversions. (a) The number of adaptive inversions belonging to each of three possible categories of capture and/or gain. (b–d) An example simulation (highly polygenic architecture, strong selection, m = 0.25) highlighting the dynamics of capture and gain. The mean inversion effect size on the phenotype is plotted through time for (b) all adaptive inversions, (c) all nonadaptive inversions and (d) inversions from the paired no-selection control simulation. Each track line is an inversion with the seven adaptive inversions labelled as i–vii (see main text for more details on the origin dynamics of each of these inversions). Colours represent which deme the inverted arrangement is at a higher frequency in (deme 1 in blue and deme 2 in red with phenotypic optimums at +1 or −1, respectively) with coloured stars on the x-axis marking the generation the corresponding inversion arose. Bubble size is the FST value for the inversion at each time step. (e) Manhattan plot corresponding to the same example simulation with labels i–vii above each inversion colour coded to match labels in (b) with the generation of origin for each inversion listed above the inversion labels.

Our latest #preprint https://www.biorxiv.org/content/10.1101/2022.01.11.475913v2 @jdmatheson calls for significant change to the theory of #BackgroundSelection, a phenomenon by which some genomic segments of some individuals don’t count toward an #EffectivePopulationSize because they contain too many deleterious mutations. 1/5

#MolecularEvolution #PopulationGenetics #MutationLoad #EvolgenPaper

Cool #preprint of #EvolutionaryBiology by Bohutínská et al: "Repeated adaptation to whole genome duplication in outcrossing Arabidopsis is mediated by mosaic adaptive haplotypes" #EvolgenPaper
https://www.biorxiv.org/content/10.1101/2023.01.11.523565v1

Figure 1 from the preprint: Hypotheses about sources of adaptive alleles in a diploid-polyploid system. Top panel, allele trees in diploids vs polyploids. Bottom panel, single allelic vs. mosaic allelic sources of haplotypes.

These were later updated to be #EvolgenPaper #EvolutionPaper [and remember the internal caps] to avoid the underscores.

#EvolgenPaper Synchronous effective population size changes and genetic stability of forest trees through glacial cycles https://www.biorxiv.org/content/10.1101/2023.01.05.522822v1

Updated perspective piece on why human genetics should move away from using "genetic ancestry" groups as a sample description.

https://arxiv.org/abs/2207.11595

#EvolgenPaper #EvolutionPaper

recirculating to start using hashtags

OK sounds like #EvolgenPaper is good hashtag for adding to toots and threads on Evolutionary and Population Genetics papers

We could use #EvolutionPaper for papers more generally associated with Evolutionary Biology.

Please RT this and consider using these for tooting about papers, your own of those of others. That way we'll be able to keep track of them all more.

#EvolgenPaper

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