Speciation as a sieve for ancestral polymorphism

Guerrero, Rafael F.; Hahn, Matthew W.

doi:10.1111/mec.14290

Cited by 98 publications

(70 citation statements)

References 49 publications

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“…An alternative explanation for high ‐F ST + d XY islands has been proposed recently (Guerrero & Hahn ). Guerrero and Hahn showed that these regions can be the result of balanced polymorphisms in the ancestral population that have been “sieved” by the speciation process when different alleles are fixed in each descendent population.…”

Section: Resultsmentioning

confidence: 90%

Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea

et al. 2019

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Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long‐lived tree species, combining it with double digest restriction site–associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, four of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.

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Section: Resultsmentioning

confidence: 90%

Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea

et al. 2019

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“…Shared variation among species may reflect unsorted polymorphisms from structured ancestral populations rather than hybridization. Introgression events can also be hard to distinguish from ongoing balancing selection of ancestral polymorphism that is sieved between species (Guerrero and Hahn ).…”

Section: Discussionmentioning

confidence: 99%

“…; Malinsky et al. ; McGirr and Martin ), although other processes besides differential gene flow across the genome can produce similar heterogeneous patterns (Noor and Bennett ; Nachman and Payseur ; Cutter and Payseur ; Cruickshank and Hahn ; Guerrero and Hahn ; Ravinet et al. ).…”

Section: Introductionmentioning

confidence: 99%

Don't throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation

2018

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Genomic data has revealed complex histories of colonization and repeated gene flow previously unrecognized in some of the most celebrated examples of sympatric speciation and radiation. However, much of the evidence for secondary gene flow into these radiations comes from summary statistics calculated from sparse genomic sampling without knowledge of which specific genomic regions introgressed. This tells us little about how gene flow potentially influenced sympatric diversification. Here, we investigated whole genomes of Barombi Mbo crater lake cichlids for fine‐scale patterns of introgression with neighboring riverine cichlid populations. We found evidence of secondary gene flow into the radiation scattered across <0.24% of the genome; however, from our analyses, it is not clear if the functional diversity in these regions contributed to the ecological, sexual, and morphological diversity found in the lake. Unlike similar studies, we found no obvious candidate genes for adaptive introgression and we cannot rule out that secondary gene flow was predominantly neutral with respect to the diversification process. We also found evidence for differential assortment of ancestral polymorphisms found in riverine populations between sympatric sister species, suggesting the presence of an ancestral hybrid swarm. Although the history of gene flow and colonization is more complicated than previously assumed, the lack of compelling evidence for secondary gene flow's role in species diversification suggests that we should not yet rule out one of the most celebrated examples of sympatric speciation in nature without a more thorough investigation of the timing and functional role of each introgressed region.

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“…Particularly in the absence of gene flow, selection due to, for instance, local ecological adaptation can result in reduced within‐population diversity and indirectly inflate F ST (Cruickshank & Hahn, 2014). In comparison to purifying and positive selection, long‐term balancing selection favours the maintenance of advantageous polymorphisms for many generations, which instead result in genomic regions with elevated genetic diversity and reduced F ST (Charlesworth, 2006; Guerrero & Hahn, 2017). As deleterious mutations are assumed to be much more common compared to beneficial mutations, background selection has been argued to play a major role in the evolution of diversity (Burri, 2017; Lohmueller et al, 2011; Phung et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Evidence for widespread selection in shaping the genomic landscape during speciation of Populus

Wang

Street

Park³

et al. 2020

Molecular Ecology

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Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome‐wide patterns of within‐ and between‐ species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole‐genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long‐term balancing selection have also been crucial components in shaping patterns of genome‐wide variation during the speciation process.

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Speciation as a sieve for ancestral polymorphism

Cited by 98 publications

References 49 publications

Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea

Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea

Don't throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation

Evidence for widespread selection in shaping the genomic landscape during speciation of Populus

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