Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.)

Souissi, Amira; Bonhomme, François; Manchado, Manuel; Bahri-Sfar, Lilia; Gagnaire, Pierre‐Alexandre

doi:10.1038/s41437-018-0079-9

Cited by 37 publications

(40 citation statements)

References 68 publications

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“…For example, a recent study of ibis hybridization using diagnostic markers found no significant negative β SNPs, in spite of the ibis hybrid zone probably only being 60 or so years old (Oswald et al 2019). In contrast, a study of recent sole (Solea aegyptiaca x S. senegalensis) hybridization found 52% of all loci exhibited an extreme β value, with 26% of all loci exhibiting a negative β estimate (Souissi et al 2018). For an example of research on an older hybrid zone, blacktailed deer and mule deer have been hybridizing for approximately 8000 years, and when genomic clines were estimated using 95 SNPs, four were found to have extreme β estimates (two positive and two negative; Haines et al 2019).…”

Section: Discussionmentioning

confidence: 94%

Locus-specific introgression in young hybrid swarms: drift dominates selection

McFarlane

Senn

Smith

et al. 2020

Preprint

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Closely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These anthropogenic hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44997 SNPs to identify loci introgressing at excessive rates when compared to the genome wide expectation in an anthropogenic hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centers that were significantly different from the genome wide expectation, and 17.6% had excessive rates of introgression. Based on simulations, we believe that many of these markers have diverged from average due to drift, rather than because of selection. Future work could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are indeed responding to selection in anthropogenic hybrid zones.

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Section: Discussionmentioning

confidence: 94%

Locus-specific introgression in young hybrid swarms: drift dominates selection

McFarlane

Senn

Smith

et al. 2020

Preprint

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“…We estimated the Weir and Cockerham (1984) pairwise FST between sampling sites and tested for significant genetic differences with 1 000 permutations over loci using the R package StAMPP (Pembleton et al, 2013). Finally, we used the approach applied in Souissi et al (2018) to evaluate geographical patterns of allelic clines along the transition zone at every locus without pruning the datasets for physical LD. Specifically, we used the R package HZAR (Derryberry et al, 2014) to calculate the center and the slope of the allelic cline for each SNP.…”

Section: Population Structurementioning

confidence: 99%

Beyond parallel evolution: when several species colonize the same environmental gradient

Moan

Gaggiotti

Henriques

et al. 2019

Preprint

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Genomic signatures associated with population divergence, speciation and the evolutionary mechanisms responsible for these are key research topics in evolutionary biology.Evolutionary radiations and parallel evolution have offered opportunities to study the role of the environment by providing replicates of ecologically driven speciation. Here, we apply an extension of the parallel evolution framework to study replicates of ecological speciation where multiple species went through a process of population divergence during the colonization of a common environmental gradient. We used the conditions offered by the North Sea -Baltic Sea environmental transition zone and found clear evidence of population structure linked to the Baltic Sea salinity gradient in four flatfish species. We found highly heterogeneous signatures of population divergence within and between species, and no evidence of parallel genomic architecture across species associated with the divergence.Analyses of demographic history suggest that Baltic Sea lineages are older than the age of the Baltic Sea itself. In most cases, divergence appears to involve reticulated demography through secondary contact, and our analyses revealed that genomic patterns of divergence were likely the result of a combination of effects from past isolation and subsequent adaptation to a new environment. In one case, we identified two large structural variants associated with the environmental gradient, where populations were inferred to have diverged in the presence of gene flow. Our results highlight the heterogeneous genomic effects associated with complex interplays of evolutionary forces, and stress the importance of genomic background for studies of parallel evolution. 2006), but so far the comparative framework has not been extended with the use of higher genome coverage.Here, we used a comparative population genomic approach to study the evolutionary processes involved during the colonization of the Baltic Sea. We studied population structure of four closely related (but genetically isolated) flatfish species: turbot (Scophthalmus maximus), common dab (Limanda limanda), European plaice (Pleuronectes platessa) andEuropean flounder (Platichthys flesus). These species were considered replicates of population divergence and were analysed independently. Our analyses showed heterogeneous genetic patterns of North Sea (NS) -Baltic Sea (BS) differentiation across species, both for magnitudes and genomic patterns of differentiation. Most of the genetic differences found were strongly associated with the environmental gradient of the NBTZ.However, the majority of the genomic regions underlying the NS-BS divergence were not shared between species. The timing of divergence between NS-BS populations was inferred to be five to ten times older than the age of the Baltic Sea. In three species, population divergence was inferred to involve past isolation followed by a secondary contact phase, and our analyses revealed that highly diverged genomic regions were likely the result of ...

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“…Behavioral divergence is considered to be a major factor driving the evolution of reproductive barriers (Mayr, 1963;Turissini, McGirr, Patel, David, & Matute, 2017;West-Eberhard, 1983). However, recent studies of speciation using next-generation sequencing indicate substantial gene flow between closely related taxa despite strong intrinsic and/or extrinsic costs to hybridization (e.g., Cooper, Sedghifar, Nash, Comeault, & Matute, 2018;Rafati et al, 2018;Souissi, Bonhomme, Manchado, Bahri-Sfar, & Gagnaire, 2018). Such findings emphasize the importance of understanding the behavioral mechanisms underlying assortative mating in determining the permeability of species boundaries upon secondary contact (Kopp et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Vocal divergence is concordant with genomic evidence for strong reproductive isolation in grasshopper mice (Onychomys)

Campbell

Arévalo

Martin

et al. 2019

Ecology and Evolution

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Behavioral barriers to gene flow often evolve faster than intrinsic incompatibilities and can eliminate the opportunity for hybridization between interfertile species. While acoustic signal divergence is a common driver of premating isolation in birds and insects, its contribution to speciation in mammals is less studied. Here we characterize the incidence of, and potential barriers to, hybridization among three closely related species of grasshopper mice (genus Onychomys). All three species use long‐distance acoustic signals to attract and localize mates; Onychomys arenicola and Onychomys torridus are acoustically similar and morphologically cryptic whereas Onychomys leucogaster is larger and acoustically distinct. We used genotyping‐by‐sequencing (GBS) to test for evidence of introgression in 227 mice from allopatric and sympatric localities in the western United States and northern Mexico. We conducted laboratory mating trials for all species pairs to assess reproductive compatibility, and recorded vocalizations from O. arenicola and O. torridus in sympatry and allopatry to test for evidence of acoustic character displacement. Hybridization was rare in nature and, contrary to prior evidence for O. torridus/O. arenicola hybrids, only involved O. leucogaster and O. arenicola. In contrast, laboratory crosses between O. torridus and O. arenicola produced litters whereas O. leucogaster and O. arenicola crosses did not. Call fundamental frequency in O. torridus and O. arenicola was indistinguishable in allopatry but significantly differentiated in sympatry, a pattern consistent with reproductive character displacement. These results suggest that assortative mating based on a long‐distance signal is an important isolating mechanism between O. torridus and O. arenicola and highlight the importance of behavioral barriers in determining the permeability of species boundaries.

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Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.)

Cited by 37 publications

References 68 publications

Locus-specific introgression in young hybrid swarms: drift dominates selection

Locus-specific introgression in young hybrid swarms: drift dominates selection

Beyond parallel evolution: when several species colonize the same environmental gradient

Vocal divergence is concordant with genomic evidence for strong reproductive isolation in grasshopper mice (Onychomys)

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