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517 results for “Genomic adaptation”

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dryad40/100

Data from: Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protist Tetrahymena thermophila

1. Populations that expand their range can undergo rapid evolutionary adaptation of life-history traits, dispersal behaviour, and adaptation to the local environment. Such adaptation may be aided or hindered by sexual reproduction, depending on the context. 2. However, few empirical and experimental studies have investigated the genetic basis of adaptive evolution during range expansions. Even less attention has been given to the question how sexual reproduction may modulate such adaptive evolution during range expansions. 3. We here studied genomic adaptation during experimental range expansions of the protist Tetrahymena thermophilain landscapes with a uniform environment or a pH-gradient. Specifically, we investigated two aspects of genomic adaptation during range expansion. Firstly, we investigated adaptive genetic change in terms of the underlying numbers of allele frequency changes from standing genetic variation and de novo variants. We focused on how sexual reproduction may alter this adaptive genetic change. Secondly, we identified genes subject to selection caused by the expanding range itself, and directional selection due to the presence or absence of the pH-gradient. We focused this analysis on alleles with large frequency changes that occurred in parallel in more than one population to identify the most likely candidate targets of selection. 4. We found that sexual reproduction altered adaptive genetic change both in terms of de novo variants and standing genetic variation. However, sexual reproduction affected allele frequency changes in standing genetic variation only in the absence of long-distance gene flow. Adaptation to the range expansion affected genes involved in cell divisions and DNA repair, whereas adaptation to the pH-gradient additionally affected genes involved in ion balance, and oxidoreductase reactions. These genetic changes may result from selection on growth and adaptation to low pH. 5. In the absence of gene flow, sexual reproduction may have aided genetic adaptation. Gene flow may have swamped expanding populations with maladapted alleles, thus reducing the extent of evolutionary adaptation during range expansion. Sexual reproduction also altered the genetic basis of adaptation in our evolving populations via de novo variants, possibly by purging deleterious mutations or by revealing fitness benefits of rare genetic variants.

opencc-zeroOct 2021View details →

zenodo40/100

Analyses for: Genome-wide parallelism underlies contemporary adaptation in urban lizards

R scripts and data files for all analyses and visualizations in "Genome-wide parallelism underlies contemporary adaptation in urban lizards" (Winchell et al., 2023, PNAS) R scripts as R-markdown code files in 3 parts are executable with files in datafiles compressed folder. R markdown files also exported as PDF's in 3 parts with code output.

opencc-by-4.0Dec 2022View details →

dryad40/100

Supplementary data for: Genomics of secondarily temperate adaptation in the only non-Antarctic icefish

White-blooded Antarctic icefishes are an example of extreme biological specialization both to the chronic cold of the Southern Ocean and to life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Despite these constraints, a single icefish species, the pike icefish Champsocephalus esox, is presently found in temperate South American waters. To study the genetic mechanisms underlying temperate adaptation in this species, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of Antarctic icefishes. However, we observe evidence of chromosomal rearrangements, some of which coincide with regions of elevated genetic divergence in pike icefish populations. Our results show several key biological pathways under selection, including genes related to the mitochondria, iron transport, and light sensing, highlighting candidates behind temperate adaptation in this species. The C. esox genome also shows antifreeze glycoprotein pseudogenization, likely due to relaxed selection following ancestral escape from Antarctica. While the organization of the canonical antifreeze glycoprotein locus is conserved in both C. esox and C. gunnari, both species show a translocation of antifreeze genes, previously unobserved in notothenioids. Our results present the first genomic characterization of a secondarily temperate notothenioid to date and serve as a basis for understanding the group's adaptive potential against a rapidly changing Antarctic environment.

opencc-zeroFeb 2023View details →

dryad40/100

Local adaptation and the evolution of genome architecture in threespine stickleback

Theory predicts that local adaptation should favour the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine vs. freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harbouring multiple quantitative trait loci (QTL) for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these "genomic islands" is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly of the closely-related tubesnout (Aulorhyncus flavidus) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and Lineage-Specific Genes (LSGs) were enriched around genomic islands, and that all three chromosomes harbouring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9x and 2.9x more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci.

opencc-zeroSep 2023View details →

dryad40/100

Genomic features for adaptation and evolutionary dynamics of four Asian domestic carps

The four major Asian domestic carps, namely grass carp, black carp, bighead carp, and silver carp, belonging to Cypriniformes, and are among the most important aquaculture species and sources of animal protein in China. they have similar habitats, closely phylogenetic relationships, and large body sizes. However, they differ in their diet preferences, behavior, and physical traits. Here, to better understand their evolution, we generated the chromosome-level genomes of the four domestic carps. We uploaded the assembled genomes of four carps, the gene annotation files in gff format of four carps, the protein sequences files of four carps, and the analysis code or pipeline used in the article, and the readme file. This study shed light on the genomic bases driving species divergence and adaptation, providing valuable insights for future research in this field.

opencc-zeroOct 2023View details →

dryad40/100