Signatures of introgression across the allele frequency spectrum

Martin, Simon H.; Amos, William

doi:10.1101/2020.07.06.189043

Cited by 9 publications

(11 citation statements)

References 38 publications

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“…Genetic introgression among lineages were investigated by using ABBA‐BABA test implemented in Dsuite (Malinsky et al, 2021). We further used partitioned D frequency spectrum ( D FS ), in which D is split according to the frequencies of derived alleles, to verify particular gene flow event (Martin & Amos, 2020). We defined gene flow in species pair (i.e., P2 and P3 in ABBA‐BABA analysis) with two significant D values and verified by D FS as those with high level of gene flow, and categorized the others to the group with low level of gene flow.…”

Section: Methodsmentioning

confidence: 99%

Gene flow, linked selection, and divergent sorting of ancient polymorphism shape genomic divergence landscape in a group of edaphic specialists

Vasseur

et al. 2021

Molecular Ecology

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Interpreting the formation of genomic variation landscape, especially genomic regions with elevated differentiation (i.e. islands), is fundamental to a better understanding of the genomic consequences of adaptation and speciation. Edaphic islands provide excellent systems for understanding the interplay of gene flow and selection in driving population divergence and speciation. However, discerning the relative contribution of these factors that modify patterns of genomic variation remains difficult. We analysed 132 genomes from five recently divergent species in Primulina genus, with four species distributed in Karst limestone habitats and the fifth one growing in Danxia habitats. We demonstrated that both gene flow and linked selection have contributed to genome‐wide variation landscape, where genomic regions with elevated differentiation (i.e., islands) were largely derived by divergent sorting of ancient polymorphism. Specifically, we identified several lineage‐specific genomic islands that might have facilitated adaptation of P. suichuanensis to Danxia habitats. Our study is amongst the first cases disentangling evolutionary processes that shape genomic variation of plant specialists, and demonstrates the important role of ancient polymorphism in the formation of genomic islands that potentially mediate adaptation and speciation of endemic plants in special soil habitats.

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Section: Methodsmentioning

confidence: 99%

Gene flow, linked selection, and divergent sorting of ancient polymorphism shape genomic divergence landscape in a group of edaphic specialists

Vasseur

et al. 2021

Molecular Ecology

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“…populations within a species or among species [51], and reveal the genomic footprint of post speciation introgression [77]. The appeal of D statistics is its simplicity, but the timing and direction of introgression can not be inferred [78]. We downloaded the whole genome re-sequencing data of Siberian Musk Deer (M. moschiferus) from NCBI (Project ID: PRJNA574937), and used it as the outgroup.…”

Section: Gene Flow Analysismentioning

confidence: 99%

Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan

et al. 2022

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Background Many endangered species exist in small, genetically depauperate, or inbred populations, hence promoting genetic differentiation and reducing long-term population viability. Forest Musk Deer (Moschus berezovskii) has been subject to illegal hunting for hundreds of years due to the medical and commercial values of musk, resulting in a significant decline in population size. However, it is still unclear to what extent the genetic exchange and inbreeding levels are between geographically isolated populations. By using whole-genome data, we reconstructed the demographic history, evaluated genetic diversity, and characterized the population genetic structure of Forest Musk Deer from one wild population in Sichuan Province and two captive populations from two ex-situ centers in Shaanxi Province. Results SNP calling by GATK resulted in a total of 44,008,662 SNPs. Principal component analysis (PCA), phylogenetic tree (NJ tree), ancestral component analysis (ADMIXTURE) and the ABBA-BABA test separated Sichuan and Shaanxi Forest Musk Deer as two genetic clusters, but no obvious genetic differentiation was observed between the two captive populations. The average pairwise FST value between the populations in Sichuan and Shaanxi ranged from 0.05–0.07, suggesting a low to moderate genetic differentiation. The mean heterozygous SNPs rate was 0.14% (0.11%—0.15%) for Forest Musk Deer at the genomic scale, and varied significantly among three populations (Chi-square = 1.22, p < 0.05, Kruskal–Wallis Test), with the Sichuan population having the lowest (0.11%). The nucleotide diversity of three populations varied significantly (p < 0.05, Kruskal–Wallis Test), with the Sichuan population having the lowest genetic θπ (1.69 × 10–3). Conclusions Genetic diversity of Forest Musk Deer was moderate at the genomic scale compared with other endangered species. Genetic differentiation between populations in Sichuan and Shaanxi may not only result from historical biogeographical factors but also be associated with contemporary human disturbances. Our findings provide scientific aid for the conservation and management of Forest Musk Deer. They can extend the proposed measures at the genomic level to apply to other musk deer species worldwide.

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“…The solution for the comparative biology of introgression is to identify not only the proportion of introgression but also the timing. Several methods are making progress on this front (Edelman et al 2019;Martin and Amos 2021;Svedberg et al 2021), while some f-statistics approaches can identify likely introgression timing given a tree topology (Malinsky et al 2018). The future of the field thus may be better able to deal with some of the caveats we discuss next.…”

Section: Recent Versus Ancient Introgressionmentioning

confidence: 99%

A need for standardized reporting of introgression: Insights from studies across eukaryotes

et al. 2022

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With the rise of affordable next-generation sequencing technology, introgression-or the exchange of genetic materials between taxa-has become widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment of the frequency of introgression across eukaryotes in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by examining patterns of introgression across eukaryotes. We collated a single statistic, Patterson's D, which can be used as a test for introgression across 123 studies to further assess how taxonomic group, divergence time, and sequencing technology influence reports of introgression. Overall, introgression has mostly been measured in plants and vertebrates, with less attention given to the rest of the Eukaryotes. We find that the most frequently used metrics to detect introgression are difficult to compare across studies and even more so across biological systems due to differences in study effort, reporting standards, and methodology. Nonetheless, our analyses reveal several intriguing patterns, including the observation that differences in sequencing technologies may bias values of Patterson's D and that introgression may differ throughout the course of the speciation process. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities and highlight important areas of future research that can be better assessed once this unified approach is met.

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Signatures of introgression across the allele frequency spectrum

Cited by 9 publications

References 38 publications

Gene flow, linked selection, and divergent sorting of ancient polymorphism shape genomic divergence landscape in a group of edaphic specialists

Gene flow, linked selection, and divergent sorting of ancient polymorphism shape genomic divergence landscape in a group of edaphic specialists

Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan

A need for standardized reporting of introgression: Insights from studies across eukaryotes

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