Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila

eLife, Journal Year: 2021, Volume and Issue: 10

Published: June 22, 2021

To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures seasonal occurring in parallel among Drosophila melanogaster populations. Specifically, estimated allele frequencies genome-wide from flies sampled early and late the growing season 20 widely dispersed We frequency shifts across North America Europe, demonstrating that is a general phenomenon temperate fly Seasonally fluctuating polymorphisms are enriched large chromosomal inversions, find broad concordance between spatial change. The direction change at seasonally variable can be predicted by weather conditions weeks prior sampling, linking environment genomic response selection. Our results suggest an important evolutionary force affecting patterns genetic variation .

Language: Английский

---

Chromosomal inversion polymorphisms shape the genomic landscape of deer mice

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(12), P. 1965 - 1979

Published: Oct. 17, 2022

Abstract Chromosomal inversions are an important form of structural variation that can affect recombination, chromosome structure and fitness. However, because be challenging to detect, the prevalence hence significance segregating within species remains largely unknown, especially in natural populations mammals. Here, by combining population-genomic long-read sequencing analyses a single, widespread deer mouse ( Peromyscus maniculatus ), we identified 21 polymorphic large (1.5–43.8 Mb) cause near-complete suppression recombination when heterozygous (0–0.03 cM Mb −1 ). We found inversion breakpoints frequently occur centromeric telomeric regions often flanked long inverted repeats (0.5–50 kb), suggesting they probably arose via ectopic recombination. By genotyping across species’ range, do not harbour deleterious mutational loads, many likely maintained as polymorphisms divergent selection. Comparisons forest prairie ecotypes mice revealed 13 contribute differentiation between populations, which five exhibit significant associations with traits implicated local adaptation. Taken together, these results show have impact on genome genetic diversity facilitate adaptation range this species.

Language: Английский

---

How chromosomal inversions reorient the evolutionary process

Journal of Evolutionary Biology, Journal Year: 2023, Volume and Issue: 36(12), P. 1761 - 1782

Published: Nov. 9, 2023

Abstract Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce effective rate recombination in heterozygous state. They play major role adaptation, as well other evolutionary processes such speciation. Although inversions have been studied since 1920s, they remain difficult to investigate because reduced conferred by them strengthens effects drift hitchhiking, which turn can obscure signatures selection. Nonetheless, numerous found be under Given recent advances population genetic theory empirical study, here we review how different mechanisms selection affect evolution inversions. A key difference between mutations, single nucleotide variants, is fitness an inversion may affected larger number frequently interacting processes. This considerably complicates analysis causes underlying We discuss extent these disentangled, approach. often roles adaptation speciation, but direct their obscured characteristic makes so unique (reduced arrangements). In this review, examine impact evolution, weaving together both theoretical studies. emphasize most patterns overdetermined (i.e. caused multiple processes), highlight new technologies provide path forward towards disentangling mechanisms.

Language: Английский

---

Feature selection for classification with Spearman’s rank correlation coefficient-based self-information in divergence-based fuzzy rough sets

Expert Systems with Applications, Journal Year: 2024, Volume and Issue: 249, P. 123633 - 123633

Published: March 11, 2024

Language: Английский

---

Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(4), P. 791 - 805

Published: Feb. 20, 2024

Abstract Variation in the size and number of axial segments underlies much diversity animal body plans. Here we investigate evolutionary, genetic developmental mechanisms driving tail-length differences between forest prairie ecotypes deer mice ( Peromyscus maniculatus ). We first show that long-tailed perform better an arboreal locomotion assay, consistent with tails being important for balance during climbing. then identify six genomic regions contribute to tail length, three which associate caudal vertebra length other number. For all loci, allele increases indicative cumulative effect natural selection. Two associated variation contain Hox gene clusters. Of those, find allele-specific decrease Hoxd13 expression embryonic bud mice, its role elongation. Additionally, embryos have more presomitic mesoderm than this correlates increase neuromesodermal progenitors, are modulated by Hox13 paralogues. Together, these results suggest a development adaptive morphology on microevolutionary timescale.

Language: Английский

---

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(7), P. 1408 - 1426

Published: April 5, 2024

ABSTRACT Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on phenotypic traits and local adaptation to abiotic biotic stress. In this study, we employed woolly grape ( Vitis retordii ), species native the tropical subtropical regions East Asia with both coastal inland habitats, as valuable model for examining SVs adaptation. We assembled haplotype‐resolved chromosomal reference genome grape, conducted population genetic analyses based whole‐genome sequencing (WGS) data from populations. The demographic revealed recent bottlenecks in all populations asymmetric gene flow population. total, 1,035 genes associated adaptive regulation salt stress, radiation, environmental were detected underlying selection by SNPs population, which 37.29% 65.26% SNPs, respectively. Candidate such FSD2 , RGA1 AAP8 tolerance found be highly differentiated selected during process habitats SV regions. Our study highlights importance adaptation; candidate related stress climatic environments important genomic resources future breeding programs grapevine its rootstocks.

Language: Английский

---

Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(2), P. 339 - 351

Published: Jan. 9, 2024

Language: Английский

---

Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long‐snouted seahorse

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(24)

Published: Jan. 27, 2024

Abstract Chromosomal inversions can play an important role in divergence and reproductive isolation by building maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion arise, are maintained over long term, ultimately, whether contribute to speciation. The long‐snouted seahorse ( Hippocampus guttulatus ) is genetically subdivided into geographic lineages marine‐lagoon ecotypes, with shared structural variation underlying lineage ecotype divergence. Here, we aim characterize variants reconstruct their history suspected formation. We generated a near chromosome‐level genome assembly described genome‐wide patterns diversity through analysis 112 whole‐genome sequences from Atlantic, Mediterranean, Black Sea populations. By also analysing linked‐read sequencing data, found evidence for two chromosomal were several megabases length showed contrasting allele frequency ecotypes across species range. reveal these represent ancient intraspecific polymorphisms, likely being divergent selection other pseudo‐overdominance. A possible selective coupling was further supported absence specific haplotype putative functional interaction reproduction. Lastly, detected gene flux eroding inverted alleles at varying levels inversions, impact on dynamics contribution

Language: Английский

---

Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

Published: Jan. 31, 2025

Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block can have effects on fitness. To study the role large in massive evolutionary radiation Lake Malawi cichlids, we used long-read technologies to identify four and two tandem span half each respective chromosome, which encompass over 10% genome. Each inversion is fixed one states within seven major ecogroups, suggesting they played separation lake lineages specific habitats. One exception benthic sub-radiation, where both inverted non-inverted continue segregate group. The histories three six suggest transferred from pelagic Diplotaxodon group ancestors at time sub-radiation was seeded. remaining found subset species living deep waters. We show some these as XY sex-determination systems but also likely limited total species. Our work suggests been under sexual natural selection cichlids will be understanding how this adaptive evolved.

Language: Английский

---

Inversions and parallel evolution

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1856)

Published: June 13, 2022

Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local and evolution is major goal evolutionary genomics. It now known that by preventing break-up favourable combinations alleles across multiple loci, genetic architectures reduce recombination, like chromosomal inversions, can make an important contribution adaptation. However, little about whether inversions also contribute disproportionately Our aim here highlight this knowledge gap, showcase existing studies, illustrate with without using simple models. We predict generating stronger effective selection, speed up adaptive process or enable where it would be impossible otherwise, but highly dependent on spatial setting. further empirical work needed, in particular cover broader taxonomic range understand relative importance compared regions inversions. This article part theme issue ‘Genomic architecture supergenes: causes consequences’.

Language: Английский

---