Widespread introgression across a phylogeny of 155 Drosophila genomes

Current Biology, Journal Year: 2021, Volume and Issue: 32(1), P. 111 - 123.e5

Published: Nov. 16, 2021

Language: Английский

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Genetic load: genomic estimates and applications in non-model animals

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 23(8), P. 492 - 503

Published: Feb. 8, 2022

Language: Английский

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The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(1), P. e1011110 - e1011110

Published: Jan. 18, 2024

In the presence of recombination, evolutionary relationships between a set sampled genomes cannot be described by single genealogical tree. Instead, are related complex, interwoven collection genealogies formalized in structure called an ancestral recombination graph (ARG). An ARG extensively encodes ancestry genome(s) and thus is replete with valuable information for addressing diverse questions biology. Despite its potential utility, technological methodological limitations, along lack approachable literature, have severely restricted awareness application ARGs evolution research. Excitingly, recent progress reconstruction simulation made ARG-based approaches feasible many systems. this review, we provide accessible introduction exploration ARGs, survey breakthroughs, describe to further existing goals open avenues inquiry that were previously inaccessible genomics. Through discussion, aim more widely disseminate promise genomics encourage broader development adoption inference.

Language: Английский

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Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(2)

Published: Jan. 10, 2022

Hybridization and resulting introgression are important processes shaping the tree of life appear to be far more common than previously thought. However, how genome evolution was shaped by various genetic evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data 227 individuals from multiple widespread Populus species characterize their contemporary patterns quantify genomic signatures past introgression. We observe a high frequency confirm that ambiguous in fact F1 hybrids. Seven were identified, which experienced different demographic histories resulted strikingly varied efficacy selection burdens deleterious mutations. Frequent has been found pervasive feature throughout speciation these species. The retained introgressed regions, generally, tend contain reduced load located regions recombination. also find pairs with substantial differences effective population size, inferred have undergone selective sweeps at greater expected frequencies lower suggesting likely higher potential provide beneficial variation for small populations. Our results, therefore, illustrate demography recombination interplayed both positive negative determining hybridization.

Language: Английский

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The temporal and genomic scale of selection following hybridization

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(12)

Published: March 15, 2024

Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks understanding evolutionary dynamics within hybrid populations that underlie these have been lacking. Due to clock-like effect recombination hybrids breaking up parental haplotypes, drift and produce predictable ancestry variation at varying spatial genomic scales through time. Here, we develop methods based on Discrete Wavelet Transform study scale local its association with rates show capture temporal genome-wide after hybridization. We apply published datasets from swordtail fish ( Xiphophorus ) baboons Papio inferred Neanderthal modern humans. Across systems, upward 20% broadest can be attributed systematic against introgressed alleles, consistent strong acting early-generation hybrids. Signatures fine suggest over longer time scales; however, our ability confidently infer is likely limited by inherent biases current estimating contiguous segments similarity. approaches will become widely applicable as data systems increasingly available help shed light generalities consequences interspecific

Language: Английский

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Pervasive gene flow despite strong and varied reproductive barriers in swordtails

Nature Ecology & Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: March 26, 2025

Abstract The evolution of reproductive barriers leads to the formation new species. However, recent research has demonstrated that hybridization been pervasive across tree life even in presence strong barriers. Using swordtail fishes (genus Xiphophorus ), an emerging model system, we document overlapping mechanisms act as gene flow between birchmanni and cortezi by combining genomic sequencing from natural hybrid populations, experimental laboratory crosses, behavioural assays, sperm measures developmental studies. We show assortative mating plays a role maintaining subpopulations with distinct ancestry within populations. F 2 hybrids identify several regions strongly impact viability. Strikingly, two these underlie genetic incompatibilities X. its sister species malinche . Our results demonstrate ancient played origin this shared incompatibility. Moreover, mismatch at incompatible remarkably similar consequences for phenotypes survival × hybrids. findings varied shape exchange naturally hybridizing highlight complex evolutionary outcomes hybridization.

Language: Английский

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Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species

Ichthyology & Herpetology, Journal Year: 2021, Volume and Issue: 109(3)

Published: Sept. 28, 2021

Species delimitation is a first step for realizing the extent of biodiversity and relevant all downstream applications in biology. The production large genome-scale datasets non-model organisms combined with development methodological tools have allowed researchers to examine fine-scale processes speciation such as timing origin, degree migration, population-size changes, selection, drift, recombination. Studies using reptiles amphibians have, part, paved way use methods exploring delimitation. While these methodologies improved our understanding diversification, are far from agreeing upon set criteria delimit species. In cases where genetic lineages discovered that unique geographic areas, usually agree two entities exist. Disagreement about taxonomic status often centers on reproductive isolation between taxa probability remaining distinct. However, frequently inferred without examining gene flow, nature hybrid zones, or determining amount type introgression. Here, we review some vexing problems delimiting amphibians, which include by distance, flow differential allelic introgression, zone dynamics, genomic islands divergence. We also respond recent literature criticizing model-based species North American snakes context advancements address how scientists can move forward studies speciation.

Language: Английский

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Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation

Genome Research, Journal Year: 2022, Volume and Issue: 32(9), P. 1669 - 1684

Published: Aug. 10, 2022

Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report high-quality genome assemblies a male Pamir argali ( O . ammon polii , 2 n = 56), female Tibetan sheep aries 54), hybrid sheep, high-throughput sequencing 425 ovine animals, including sheep. We detected genomic synteny Chromosome two acrocentric chromosomes argali. revealed consistent satellite repeats around chromosome breakpoints, which could have resulted fusion. observed many more with karyotype 54 than 55, be explained by selfish centromeres, possible decreased rate normal/balanced sperm, increased incidence early pregnancy loss aneuploid ewes or rams. identified genes variants associated important morphological production traits (e.g., body weight, cannon circumference, hip height, tail length) that show significant variations. strong selective signature at mutation (c.334C > A, p.G112W) TBXT confirmed its association length among populations wide geographic origins. produced an intercross population 110 F offspring varied number vertebrae validated causal whole-genome analysis. verified function using CRISPR-Cas9 editing. Our results provide insights into chromosomal speciation evolution foundation for breeding other animals.

Language: Английский

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Introgression

Current Biology, Journal Year: 2022, Volume and Issue: 32(16), P. R865 - R868

Published: Aug. 1, 2022

Language: Английский

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Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations

iScience, Journal Year: 2022, Volume and Issue: 25(7), P. 104672 - 104672

Published: June 26, 2022

The phenotypic diversity of African cattle reflects adaptation to a wide range agroecological conditions, human-mediated selection preferences, and complex patterns admixture between the humpless Bos taurus (taurine) humped indicus (zebu) subspecies, which diverged 150-500 thousand years ago. Despite extensive admixture, all possess taurine mitochondrial haplotypes, even populations with significant zebu biparental male uniparental nuclear ancestry. This has been interpreted as result dispersal ultimately stemming from bulls imported South Asia during last three millennia. Here, we assess whether ancestry at mitochondrially targeted genes in admixed is impacted by mitonuclear functional interactions. Using high-density SNP data, find evidence for coevolution across hybrid increase genes. Our results, therefore, support hypothesis incompatibility genome genome.

Language: Английский

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