The genetic architecture of polygenic local adaptation and its role in shaping barriers to gene flow

Genetics, Journal Year: 2024, Volume and Issue: 228(3)

Published: Aug. 22, 2024

Abstract We consider how the genetic architecture underlying locally adaptive traits determines strength of a barrier to gene flow in mainland-island model. Assuming general life cycle, we derive an expression for effective migration rate when local adaptation is due variation at many loci under directional selection on island, allowing arbitrary fitness and dominance effects across loci. show can be combined with classical single-locus diffusion theory accurately predict multilocus differentiation between mainland island migration–selection–drift equilibrium determine beyond which collapses, while accounting drift weak linkage. Using our efficient numerical tools, then present detailed study barriers flow, showing that total sufficiently strong, more recessive generates stronger flow. heterogeneous architectures affect characterizing migration–selection balance different distributions effects. find generally yields genome-wide have important effect observable divergence not too large. Lastly, limits approach as become tightly linked, predictions remain accurate over large biologically relevant domain.

Language: Английский

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Genomic Introgression Between Critically Endangered and Stable Species of Darwin's Tree Finches on the Galapagos Islands

Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(1)

Published: Jan. 1, 2025

Natural hybridisation among rare or endangered species and stable congenerics is increasingly topical for the conservation of species-level diversity under anthropogenic impacts. Evidence beneficial genes being introgressed into selected in hybrids raises concurrent questions about its evolutionary significance. In Darwin's tree finches on island Floreana (Galapagos Islands, Ecuador), Critically Endangered medium finch (Camarhynchus pauper) undergoes introgression with small parvulus), regularly backcross C. parvulus. Earlier studies 2005-2013 documented an increase frequency Camarhynchus using field-based microsatellite data. With single nucleotide polymorphism (SNP) data from same sampled 2005 2013 (n = 95), we examine genome-wide divergence across parental hybrid birds evidence selection hybrids. We found that just 18% previously assigned based microsatellites could be to SNPs. Over half (63%) were reassigned parvulus, though showed concordance prior assignments. Of 4869 private alleles birds, 348 at a high (≥ 0.30) exceeded their origin 89%-96% time. For detected both years (N 536) between 11%-76% underwent 13%-61% decrease 2013, which was sensitive sampling effort. identified 28 candidates via local PCA outlier tests. Alleles annotated associated inflammation, immunity, brain function development. provide critically may aid retention adaptive genetic threatened extinction.

Language: Английский

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Evolution of Hybrid Inviability Associated With Chromosome Fusions

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 3, 2025

ABSTRACT Chromosomal rearrangements, such as inversions, have received considerable attention in the speciation literature due to their hampering effects on recombination. Less is known about how other chromosome fissions and fusions, can affect evolution of reproductive isolation. Here, we use crosses between populations wood white butterfly ( Leptidea sinapis ) with different karyotypes identify genomic regions associated hybrid inviability. We map inviability candidate loci by contrasting allele frequencies F 2 hybrids that survived until adult stage individuals same cohort succumbed incompatibilities. Hybrid high genetic differentiation parental populations, reduced recombination rates, are enriched near fusions. By analysing sequencing coverage, exclude aneuploidies a direct link Instead, our results point an indirect relationship possibly related fused chromosomes. Thus, postzygotic isolation chromosomal providing crucial empirical evidence for idea number differences taxa contribute speciation.

Language: Английский

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The recombination landscape of introgression in yeast

PLoS Genetics, Journal Year: 2025, Volume and Issue: 21(2), P. e1011585 - e1011585

Published: Feb. 12, 2025

Meiotic recombination is an evolutionary force that acts by breaking up genomic linkage, increasing the efficacy of selection. Recombination initiated with a double-strand break which resolved via crossover, involves reciprocal exchange genetic material between homologous chromosomes, or non-crossover, results in small tracts non-reciprocal material. Crossover and non-crossover rates vary species, populations, individuals, across genome. In recent years, rate has been associated distribution ancestry derived from past interspecific hybridization (introgression) variety species. We explore this interaction introgression sequencing spores detecting crossovers non-crossovers two crosses yeast Saccharomyces uvarum . One cross strains each contain their sister S. eubayanus , while other no present. find landscape significantly different crosses, some these differences can be explained presence one cross. Crossovers are reduced heterozygous compared to syntenic regions without introgression. This translates allele shuffling within introgressed regions, overall reduction on most chromosomes Our suggest influence landscape, contributes initial purging generations following event.

Language: Английский

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The Distribution and Dispersal of Large Haploblocks in a Superspecies

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: March 17, 2025

ABSTRACT Haploblocks are regions of the genome that coalesce to an ancestor as a single unit. Differentiated haplotypes in these can result from accumulation mutational differences low‐recombination chromosomal regions, especially when selective sweeps occur within geographically structured populations. We introduce method identify large well‐differentiated haploblock (LHBRs), based on variance standardised heterozygosity (ViSHet) nucleotide polymorphism (SNP) genotypes among individuals, calculated across genomic region (500 SNPs our case). apply this greenish warbler ( Phylloscopus trochiloides ) ring species, using newly assembled reference and at more than 1 million 257 individuals. Most chromosomes carry distinctive LHBR, containing 4–6 distinct associated with geography, enabling detection hybridisation events transition zones between differentiated LHBRs have exceptionally low within‐haplotype variation moderately between‐haplotype distance, suggesting their establishment through recurrent varying geographic scales. Meiotic drive is potentially powerful mechanism producing such sweeps, likely often represent centromeric where recombination restricted. Links populations enable introgression favoured we one showing highly discordant distribution compared most genome, being present two distantly separated similar latitudes both east central Asia. Our results set stage for detailed studies haploblocks, including location, gene content contribution reproductive isolation.

Language: Английский

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Archaic introgression and the distribution of shared variation under stabilizing selection

PLoS Genetics, Journal Year: 2025, Volume and Issue: 21(3), P. e1011623 - e1011623

Published: March 31, 2025

Many phenotypic traits are under stabilizing selection, which maintains a population’s mean value near some optimum. The dynamics of and trait architectures selection have been extensively studied for single populations at steady state. However, natural seldom state often structured in way. Admixture introgression events may be common, including over human evolutionary history. Because results against the minor allele trait-affecting locus, alleles from parental ancestry will selected after admixture. We show that site-frequency spectrum can used to model genetic architecture such traits, allowing study complex multi-population settings. use simple deterministic two-locus predict reduction introgressed around trait-contributing loci. From this individual-based simulations, we introgressed-ancestry is depleted When between two diverged occurs both directions, as has inferred humans Neanderthals, locations regions with tend shared across populations. argue optima explain recent observations human-introgressed Neanderthal genome overlap Neanderthal-ancestry deserts humans.

Language: Английский

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Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(12)

Published: Nov. 21, 2023

Abstract Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important force. Using whole-genome sequencing data from 22 species guenons (tribe Cercopithecini), one world's largest primate radiations, we show that rampant gene flow characterizes their history identify ancient across deeply divergent lineages differ ecology, morphology, karyotypes. Some events resulted mitochondrial introgression between distant lineages, likely facilitated by cointrogression coadapted nuclear variants. Although genomic landscapes were largely lineage specific, found genes with immune functions overrepresented introgressing regions, line adaptive introgression, whereas involved pigmentation morphology may contribute to reproductive isolation. In reports other systems might facilitate diversification, find some most species-rich guenon clades are admixed origin. This study provides insights into prevalence, role, outcomes ancestral a large mammalian radiation.

Language: Английский

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Polygenic response of sex chromosomes to sexual antagonism

Evolution, Journal Year: 2023, Volume and Issue: 78(3), P. 539 - 554

Published: Dec. 28, 2023

Abstract Sexual antagonism occurs when males and females differ in their phenotypic fitness optima but are constrained evolution to these because of shared genome. The sex chromosomes, which have distinct evolutionary “interests” relative the autosomes, theorized play an important role sexually antagonistic conflict. However, responses chromosomes autosomes usually been considered independently, that is, via contrasting response a gene located on either X chromosome or autosome. Here, we study coevolutionary selection acting polygenic phenotype. We model phenotype initially under stabilizing around single optimum, followed by sudden divergence male female optima. find that, absence dosage compensation, promotes toward inducing male-biased autosomes. Dosage compensation obscures female-biased interests X, causing it contribute equally change. further demonstrate fluctuations adaptive landscape can generate prolonged intragenomic conflict accentuate differential this

Language: Английский

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Stabilizing selection generates selection against introgressed DNA

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 20, 2024

Abstract DNA introgressed from one population into another is often deleterious to the recipient if two populations have diverged genetically another. Previous explanations of this phenomenon posited negative interactions between donor-population alleles and population’s genome or environment, higher genetic load in donor population. Here, we show that stabilizing selection on quantitative traits—even around same optimal trait values when are demographically identical—generates against minor-parent ancestry a formed via unequal admixture populations. We calculate rate at which purged under mechanism, both early generations after long term, verify these calculations with whole-genome simulations. Because its ubiquity, offers general mechanism for effect ancestry.

Language: Английский

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Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 11, 2023

In vertebrates, there are two known mechanisms by which meiotic recombination is directed to the genome: in humans, mice, and other mammals, occurs almost exclusively where protein PRDM9 binds, while species lacking an intact

Language: Английский

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