A highly contiguous reference genome for the Alpine ibex (Capra ibex)

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

Published: June 27, 2024

Abstract Anthropogenic hybridization, the unintentional hybridization with a non-native or domestic species in human-dominated environments, is major concern for conservation and challenge management decisions. Genetically depleted are expected to be particularly vulnerable introgression since can restore introduce new adaptive genetic variation alleviate effects of inbreeding through hybrid vigour. However, defining precise sets deleterious beneficial mutations resulting from anthropogenic complex limited by quality genomic resources. The Alpine ibex ( Capra ), native Alps, faced near-extinction two centuries ago, but programs have successfully restored its populations. known hybridize goat hircus ) occasionally leading swarm formation. Past has been observed at immune-related genes was suggested had an effect. also carry mutation load reintroduction bottlenecks, which could alleviated admixture. Here, we produced chromosome-level reference genome based on Oxford Nanopore sequencing coupled high-throughput chromosome conformation capture. highly contiguous assembly 2.66 Gbp reveals 30 chromosomes augmented 98.8% complete RNAseq-assisted gene model prediction. presents overall high degree synteny compared goat, number structural variants spanning 38 Mb insertion deletions, as well 49 inversions. We identified near not within histocompatibility (MHC), immune-relevant complex, where previous studies found signals introgression. between likely facilitates recombination haplotypes is, therefore, accordance observation swarms. To determine impact recent admixture, resequenced eight individuals sampled swarms Northern Italy. Swarm carried 18-80% representing up 3rd generation hybrids, including one F1 hybrid. will facilitate quantifying maladaptive introduced goats guide efforts.

Language: Английский

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Inference of Locus-Specific Population Mixtures From Linked Genome-Wide Allele Frequencies

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(7)

Published: July 1, 2024

Abstract Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation mixture proportions along genome expected organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics population splits mixtures. However, current assume a single rate for entire do not explicitly account linkage. Here, we introduce TreeSwirl, novel method inferring branch lengths locus-specific using genome-wide allele frequency data, assuming that admixture graph known has inferred. TreeSwirl builds upon TreeMix uses Gaussian processes estimate presence gene flow diverged populations. contrast TreeMix, our model infers employing hidden Markov accounts Through simulated demonstrate can accurately handle complex demographic scenarios. It also outperforms related D- f-statistics terms accuracy sensitivity detect introgressed loci.

Language: Английский

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Genetic evidence of a hybrid swarm between Alpine ibex (Capra ibex) and domestic goat (C. hircus)

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(8)

Published: July 28, 2024

Abstract Improving the understanding of causes and effects anthropogenic hybridization is fundamental to ensure species conservation, particularly in case between wild their domestic relatives. Knowledge missing for many also because a lack appropriate tools hybrid identification. Here, coupling genotype phenotype analysis, we carried out an extensive investigation ongoing Alpine ibex Capra , mountain ungulate conservation concern from genetic perspective. By genotyping 63 diagnostic 465 neutral SNPs, 20 suspected hybrids 126 without suspicious phenotype, representing 8 populations across major part distribution, found evidence goat. We identified different levels including backcrosses into both Our results suggest reproductive barriers two good survival success hybrids. Hybridization was locally intense, like swarm, but not spread rest distribution. Most were discovered locations north‐west Italy, while random sampling individuals areas did provide recent hybridization. method, based on amplicon sequencing SNPs specifically developed this purpose, allowed us identify up fourth fifth generations suitable samples quality, although with varying certainty regarding exact number passed since Based paired analysis guidelines first identification field procedure reliable

Language: Английский

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Characterisation of the historic demographic decline of the British European polecat population

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

Published: Nov. 3, 2024

Abstract The European polecat ( Mustela putorius ) has a widespread distribution across many countries of mainland Europe, but is documented to be declining within these ranges. In Britain, direct persecution led severe decline the population during 19 th century. Unlike populations, it now recovering much its former range. genomic and conservation implications such demographic decline, followed by current recovery, have still characterised in Britain. Here we carry out population-level whole-genome analyses 65 polecats from Britain (Wales, England) mainland. Welsh show unique genetic structure compared English populations. We also reconstructed history quantify magnitude bottleneck. Our confirmed drastic polecat’s effective size, with bottleneck around 40 generations ago (1854-1872). investigated whether signatures reflected this event found that had significantly less diversity than ones, not polecats. Runs homozygosity load present genomes indicated recent historic inbreeding. increase British could due admixture events, serves as distinct population, which crucial for overall

Language: Английский

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