Facilitated introgression from domestic goat into Alpine ibex at immune loci

Molecular Ecology, Год журнала: 2024, Номер 33(14)

Опубликована: Июнь 7, 2024

Abstract Hybridization can result in the transfer of adaptive genetic material from one species to another, known as introgression. Bottlenecked (and hence genetically depleted) are expected be particularly receptive introgression, since introgression introduce new or previously lost variation. The Alpine ibex ( Capra ), which recently recovered near extinction, is hybridize with domestic goat aegagrus hircus and signals found at major histocompatibility complex were suggested potentially adaptive. Here, we combine two ancient whole genomes 29 modern 31 representing six related investigate genome‐wide patterns confirm potential relevance immune loci. We identified low rates admixture through various F statistics screening for putative introgressed tracts. Further results based on demographic modelling consistent have occurred during last 300 years, coinciding bottleneck, that each generation, 1–2 out 100 had a parent. putatively haplotypes enriched immune‐related genes, where value alternative alleles may give individuals otherwise depleted diversity selective advantage. While interbreeding prevalent issue conservation, this specific case, it resulted Our findings highlight interplay between hybridization, evolution, risks benefits associated anthropogenic influences wild species.

Язык: Английский

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Reproductive isolation in a three‐way contact zone

Molecular Ecology, Год журнала: 2024, Номер 33(5)

Опубликована: Янв. 18, 2024

Abstract Contact zones between divergent forms within a species provide insight into the role of gene flow in adaptation and speciation. Previous work has focused on contact involving only two forms, but nature, many more than populations may overlap simultaneously experience flow. Patterns introgression wild are, therefore, likely much complicated is often assumed. We begin to address this gap current knowledge by investigating patterns divergence across complex natural zone. use phenotypic genomic data confirm existence three‐way zone among freshwater resident, saltwater resident migratory three‐spined stickleback ( Gasterosteus aculeatus ) island North Uist, Scottish Western Isles. find evidence for hybridization, mostly forms. Despite analyses reveal pairwise islands all that are maintained Genomic cline also selection and/or hybrid incompatibilities regions. Divergent regions occur multiple chromosomes involve known adaptive loci several chromosomal inversions. identify distinct immune expression profiles no transgressive hybrids. Our results suggest reproductive isolation zone, despite some reduced recombination inversions play an important maintaining isolation.

Язык: Английский

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Performance evaluation of adaptive introgression classification methods

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 14, 2024

Abstract Introgression, the incorporation of foreign variants through hybridization and repeated backcross, is increasingly being studied for its potential evolutionary consequences, one which adaptive introgression (AI). In recent years, several statistical methods have been proposed detection loci that undergone introgression. Most these tested developed to infer presence Neanderthal or Denisovan AI in humans. Currently, behaviour when faced with genomic datasets from scenarios other than human lineage remains unknown. This study therefore focuses on testing performance using test data sets simulated under various inspired by history human, wall lizard ( Podarcis ) bear Ursus lineages. These lineages were chosen represent different combinations divergence migration times. We impact parameters, as well rate, population size, selection coefficient recombination hotspots, three (VolcanoFinder, Genomatnn MaLAdapt) a standalone summary statistic (Q95( w , y )). Furthermore, hitchhiking effect an adaptively introgressed mutation can strong flanking regions, discrimination between windows classes i.e. AI/non-AI). For this reason, types non-AI are taken into account our analyses: independently neutral windows, adjacent window AI, coming second chromosome unlinked AI. Our results highlight importance taking training order correctly identify Finally, tests show based Q95 seem be most efficient exploratory

Язык: Английский

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Widespread adaptive introgression of MHC genes across vertebrate hybrid zones

Molecular Biology and Evolution, Год журнала: 2024, Номер 41(10)

Опубликована: Сен. 26, 2024

Abstract Interspecific introgression is a potentially important source of novel variation adaptive significance. Although multiple cases are well documented, broader generalizations about its targets and mechanisms lacking. Multiallelic balancing selection, particularly when acting through rare allele advantage, an evolutionary mechanism expected to favor introgression. This because introgressed alleles likely confer immediate selective facilitating their establishment in the recipient species even face strong genomic barriers Vertebrate major histocompatibility complex genes well-established long-term multiallelic so widespread expected. Here, we evaluate this hypothesis using data from 29 hybrid zones formed by fish, amphibians, squamates, turtles, birds, mammals at advanced stages speciation. The key prediction more extensive compared genome-wide was tested with three complementary statistical approaches. We found evidence for genes, providing link between process underlying mechanism. Our work identifies as general which can acquire novel, possibly regain previously lost, that may enhance defense against pathogens increase potential.

Язык: Английский

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Facilitated introgression from domestic goat into Alpine ibex at immune loci

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 23, 2023

Abstract Introgression is expected to be adaptive at loci under balancing selection, for instance relevant the immune response, but these generally also contain ancient polymorphisms. Ancient genomics a promising tool detect recent introgression and disentangle it from Alpine ibex ( Capra ), wild goat species native European Alps, faced near-extinction two centuries ago, has recovered thanks successful restoration programs. Previously, signals of domestic aegagrus hircus ) into genome were found major histocompatibility complex. This was suggested potentially since introduced new diversity gene locus important immunity. But no genome-wide analyses have been performed confirm potential relevance loci. Here we take advantage whole genomes combined with 29 modern 31 representing six related investigate patterns introgression. Our complementary analysis putatively introgressed haplotypes demographic modelling suggests 2.3% ancestry among ibex. The estimated happened during last 300 years coinciding time when had very small population size. Further an enrichment immune-related genes, where value alternative alleles may give individuals otherwise depleted genetic selective advantage.

Язык: Английский

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Plastic and genomic change of a newly established lizard population following a founder event

Molecular Ecology, Год журнала: 2023, Номер 33(10)

Опубликована: Дек. 22, 2023

Understanding how phenotypic divergence arises among natural populations remains one of the major goals in evolutionary biology. As part competitive exclusion experiment conducted 1971, 10 individuals Italian wall lizard (Podarcis siculus (Rafinesque-Schmaltz, 1810)) were transplanted from Pod Kopište Island to nearby island Mrčaru (Adriatic Sea). Merely 35 years after introduction, newly established population on had shifted their diet predominantly insectivorous towards omnivorous and changed significantly a range morphological, behavioural, physiological ecological characteristics. Here, we combine genomic quantitative genetic approaches determine relative roles adaptation plasticity driving this rapid shift. Our results show genome-wide differentiation between ancestral population, with weak erosion Island. Adaptive processes following founder event are indicated by highly differentiated loci associating ecologically relevant traits, and/or having putatively adaptive role across multiple populations. Diverged traits related head size shape or bite force showed moderate heritability crossing experiment, but between-population differences these did not persist common garden environment. confirm existence sufficient additive variance for evolve under selection while also demonstrating that genotype environment interactions main drivers at early stage.

Язык: Английский

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MHC class II supertypes affect survival and lifetime reproductive success in a migratory songbird

Authorea (Authorea), Год журнала: 2024, Номер unknown

Опубликована: Авг. 28, 2024

The major histocompatibility complex (MHC) plays a critical role in the immune response against pathogens. Its high polymorphism is thought to be mainly consequence of host-pathogen co-evolution, but elucidating mechanism(s) driving MHC evolution remains challenging for natural populations. We investigated diversity class II genes wild population pied flycatchers Ficedula hypoleuca, and tested its associations with two key components individual fitness: lifetime reproductive success survival. Among 180 breeding adults our study population, we found 182 unique exon 2 alleles. alleles showed strong signal positive selection grouped into 9 functional supertypes based on physicochemical properties at inferred antigen-binding sites. Three were > 98% sampled individuals, indicating that they are nearly fixed population. no rare as all present >70% individuals. related different associated lower offspring production over time, while third was positively Overall, substantial allelic relationship between specific fitness accordance notion balancing maintains possibly fluctuating underlying mechanism. absence suggests not driven by rare-allele advantage.

Язык: Английский

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MHC Class II Supertypes Affect Survival and Lifetime Reproductive Success in a Migratory Songbird

Molecular Ecology, Год журнала: 2024, Номер 33(22)

Опубликована: Окт. 24, 2024

The major histocompatibility complex (MHC) plays a critical role in the immune response against pathogens. Its high polymorphism is thought to be mainly consequence of host-pathogen co-evolution, but elucidating mechanism(s) driving MHC evolution remains challenging for natural populations. We investigated diversity class II genes wild population pied flycatchers Ficedula hypoleuca and tested its associations with two key components individual fitness: lifetime reproductive success survival. Among 180 breeding adults our study population, we found 182 unique exon 2 alleles. alleles showed strong signal positive selection grouped into nine functional supertypes based on physicochemical properties at inferred antigen-binding sites. Three were > 98% sampled individuals, indicating that they are nearly fixed population. no rare as all present 70% individuals. related different associated lower offspring production over time, while third was positively Overall, substantial allelic relationship between specific fitness accordance notion balancing maintains possibly fluctuating underlying mechanism. absence suggests not driven by rare-allele advantage.

Язык: Английский

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