Selection and gene flow shape genomic islands that control floral guides

Tavares, Hugo; Whibley, Annabel; Field, David L.; Bradley, Desmond; Couchman, Matthew; Copsey, Lucy; Elleouet, Joane S.; Burrus, Monique; Andalo, Christophe; Li, Miaomiao; Li, Qun; Xue, Yongbiao; Rebocho, Alexandra B.; Barton, Nicolas H.; Coen, Enrico

doi:10.1073/pnas.1801832115

Cited by 76 publications

(111 citation statements)

References 29 publications

Supporting

Mentioning

106

Contrasting

Order By: Relevance

“…One question that arises from this is whether selective sweeps (leading to [near-] fixation of SNPs in populations of pure species) or barriers to gene flow (selection in the hybrid zone in this case) cause divergence in this differentiated portion of genome (Tavares et al, 2018). One question that arises from this is whether selective sweeps (leading to [near-] fixation of SNPs in populations of pure species) or barriers to gene flow (selection in the hybrid zone in this case) cause divergence in this differentiated portion of genome (Tavares et al, 2018).…”

Section: Intrinsic and Extrinsic Causes In The Divergence Of Etneanmentioning

confidence: 99%

“…Senecio has experienced heterogeneous gene flow. One question that arises from this is whether selective sweeps (leading to [near-] fixation of SNPs in populations of pure species) or barriers to gene flow (selection in the hybrid zone in this case) cause divergence in this differentiated portion of genome (Tavares et al, 2018). Both of these would…”

Section: Intrinsic and Extrinsic Causes In The Divergence Of Etneanmentioning

confidence: 99%

See 1 more Smart Citation

Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna

et al. 2019

View full text Add to dashboard Cite

Defining what constitutes a species and understanding how new species form are central questions in evolutionary biology. The idea that speciation is driven by adaptation to distinct environmental conditions has a long history going back to Darwin's concept of new species formation by means of natural selection. Although natural selection is the main driver of evolutionary changes, its role in creating barriers to gene flow is not well understood. Adaptation to distinct environments (divergent selection) may lead to differentiation in loci responsible for adaptation or even fixation of different alleles in isolated populations. This can generate a mosaic with different genomic AbstractRecently diverged species present particularly informative systems for studying speciation and maintenance of genetic divergence in the face of gene flow. We investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations. We used a newly generated genome-wide single nucleotide polymorphism (SNP) dataset from 192 individuals collected over 18 localities along an elevational gradient to reconstruct the likely history of speciation, identify highly differentiated SNPs, and estimate the strength of divergent selection.We found that speciation in this system involved heterogeneous and bidirectional gene flow along the genome, and species experienced marked population size changes in the past. Furthermore, we identified highly-differentiated SNPs between the species, some of which are located in genes potentially involved in ecological differences between species (such as photosynthesis and UV response). We analysed the shape of these SNPs' allele frequency clines along the elevational gradient. These clines show significantly variable coincidence and concordance, indicative of the presence of multifarious selective forces. Selection against hybrids is estimated to be very strong (0.16-0.78) and one of the highest reported in literature. The combination of strong cumulative selection across the genome and previously identified intrinsic incompatibilities probably work together to maintain the genetic and phenotypic differentiation between these species -pointing to the importance of considering both intrinsic and extrinsic factors when studying divergence and speciation.

show abstract

Section: Intrinsic and Extrinsic Causes In The Divergence Of Etneanmentioning

confidence: 99%

Section: Intrinsic and Extrinsic Causes In The Divergence Of Etneanmentioning

confidence: 99%

Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna

et al. 2019

View full text Add to dashboard Cite

show abstract

“…This genomic concept is plausible on phenotypic considerations because even closely-related species differ by a multitude of traits. When such traits are carefully dissected, each has been found to be highly polygenic [4][5][6][7][8][9] , implying extensive genetic divergence. A particularly instructive case is the spermatogenic programs in Drosophila.…”

Section: Introductionmentioning

confidence: 99%

In the absence of reproductive isolation – Extensive gene flow after speciation

Wang¹,

Z²,

He³

et al. 2019

Preprint

View full text Add to dashboard Cite

In the biological species concept, much of the genomes cannot be exchanged between species 1,2 . In the modern genic view, species are distinct as long as genes that delineate the morphological, ecological and reproductive differences remain distinct 2 . The rest (or the bulk) of the genomes should be freely interchangeable. The core of the species concept therefore demands finding out the full potential of introgressions between species. In a survey of two closely related mangrove species (Rhizophora mucronata and R. stylosa) on the coasts of the western Pacific and Indian oceans, we found that the genomes are well delineated in allopatry, echoing their morphological and ecological divergence. The two species are sympatric/parapatric in the Daintree River area of northeastern Australia. In sympatry, their genomes harbor 7,700 and 3,100 introgression blocks, respectively, with each block averaging about 3-4 Kb. These fine-grained and strongly-penetrant introgressions suggest that each species must have evolved many differentially-adaptive (and, hence, non-introgressable) genes that contribute to speciation. We identify 30 such genes, seven of which are about flower development, within small genomic islets with a mean size of 1.4 Kb. In sympatry, the species-specific genomic islets account for only a small fraction (< 15%) of the genomes while the rest appears interchangeable.

show abstract

“…These confounding factors limit the potential of simple genome scan approaches, requiring careful interpretation of the main causes of excess F ST (e.g. Cruickshank & Hahn, , Tavares et al, ). Although advances have been made in F ST outlier detection, patterns of differentiation alone have limited power to inform us about the current interplay between selection and gene flow along the genome.…”

mentioning

confidence: 99%

“…Moreover, using the geographic context of populations provides a powerful way to distinguish genomic regions harbouring barrier loci. This allows us to overlay patterns of divergence across genomes with the location of loci resisting introgression, such as those displaying steep geographic clines in hybrid zones (Tavares et al, ).…”

mentioning

confidence: 99%

Breaking down barriers in morning glories

Field

Fraïssé

2019

Molecular Ecology

Self Cite

View full text Add to dashboard Cite

One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One problem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the study is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates.

show abstract

Selection and gene flow shape genomic islands that control floral guides

Cited by 76 publications

References 29 publications

Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna

Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna

In the absence of reproductive isolation – Extensive gene flow after speciation

Breaking down barriers in morning glories

Contact Info

Product

Resources

About