Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(7), P. e3000391 - e3000391

Published: July 24, 2019

Speciation genomic studies aim to interpret patterns of genome-wide variation in light the processes that give rise new species. However, interpreting "landscape" speciation is difficult, because many evolutionary can impact levels variation. Facilitated by first chromosome-level assembly for group, we use whole-genome sequencing and simulations shed on have shaped landscape during a radiation monkeyflowers. After inferring phylogenetic relationships among 9 taxa this radiation, show highly similar diversity (π) differentiation (FST) landscapes emerged across group. Variation these was strongly predicted local density functional elements recombination rate, suggesting been widespread natural selection. Using varying divergence times between pairs taxa, correlations FST genome features arose almost immediately after population split become stronger over time. Simulations evolution suggest background selection (BGS; i.e., against deleterious mutations) alone too subtle generate observed patterns, but scenarios involve positive genetic incompatibilities are plausible alternative explanations. Finally, tests introgression reveal evidence heterogeneous gene flow radiation. Combined with previous adaptation system, conclude correlation informs us about contributing rapid

Language: Английский

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Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow

Evolution Letters, Journal Year: 2018, Volume and Issue: 2(4), P. 297 - 309

Published: Aug. 1, 2018

Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying with flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on regions of high differentiation. However, not all architectures potentially are expected to show extreme Here, we develop an approach that combines hybrid zone analysis (i.e., focuses spatial patterns allele frequency change) system-specific simulations identify loci inconsistent neutral evolution. We apply this genome-wide SNP set from ideally suited study organism, intertidal snail

Language: Английский

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Evaluating genomic signatures of “the large X‐effect” during complex speciation

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(19), P. 3822 - 3830

Published: June 25, 2018

The ubiquity of the "two rules speciation"-Haldane's rule and large X-effect-implies a general, special role for sex chromosomes in evolution intrinsic postzygotic reproductive isolation. recent proliferation genome-scale analyses has revealed two further general observations: (a) complex speciation involving some form gene flow is not uncommon, (b) male- female-heterogametic taxa tend to show elevated differentiation relative autosomes. Together, these observations are consistent with histories which population genetic at autosomal loci reduced by while natural selection against hybrid incompatibilities renders relatively refractory flow. Here, I summarize multilocus genomic evidence greater on X (or Z) vs. autosomes consider possible causes. review common circumstances no and/or interspecific that nevertheless expected elevate then theory why X-effects exist and, more generally, mediating local adaptation. observed levels chromosome differentiation, many cases, appear simple explanations requiring neither nor Discerning signatures during will therefore require go beyond chromosome-scale summaries explicitly test differential introgression, integrate experimental data.

Language: Английский

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Multiple chromosomal rearrangements in a hybrid zone betweenLittorina saxatilisecotypes

Molecular Ecology, Journal Year: 2018, Volume and Issue: 28(6), P. 1375 - 1393

Published: Dec. 8, 2018

Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation speciation. However, biases discovery reporting of inversions make it difficult to assess their prevalence biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats detect rearrangements de novo. We report 17 polymorphic single locality the coastal marine snail, Littorina saxatilis. Patterns diversity field recombination controlled crosses provide strong evidence at least majority these inversions. Most show clinal changes frequency habitats, suggestive divergent selection, but only one appears be fixed different arrangements two habitats. Consistent with widespread balancing selection polymorphisms, argue combination heterosis can explain observed patterns should considered other systems spanning environmental gradients.

Language: Английский

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From molecules to populations: appreciating and estimating recombination rate variation

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 21(8), P. 476 - 492

Published: May 29, 2020

Language: Английский

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Pleistocene glacial cycles drive isolation, gene flow and speciation in the high‐elevation Andes

New Phytologist, Journal Year: 2018, Volume and Issue: 219(2), P. 779 - 793

Published: June 4, 2018

Summary Mountain ranges are amongst the most species‐rich habitats, with many large and rapid evolutionary radiations. The tempo mode of diversification in these systems key unanswered questions biology. Here we study Andean Lupinus radiation to understand processes driving very montane systems. We use genomic transcriptomic data multiple species populations, apply phylogenomic demographic analyses test whether proceeded without interspecific gene flow – as expected if orogeny geographic isolation were main drivers or was accompanied by flow, which case other probably involved. uncover several episodes between species, including recent events likely have been prompted changes habitat connectivity during Pleistocene glacial cycles. Furthermore, find that heterogeneously distributed across genome. argue exceptionally fast partly a result Late cycles, associated cycles expansion contraction secondary contact species. heterogeneous genome suggests role for selection ecological speciation this system.

Language: Английский

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Avian Diversity: Speciation, Macroevolution, and Ecological Function

Annual Review of Ecology Evolution and Systematics, Journal Year: 2020, Volume and Issue: 51(1), P. 533 - 560

Published: Aug. 28, 2020

The origin, distribution, and function of biological diversity are fundamental themes ecology evolutionary biology. Research on birds has played a major role in the history development these ideas, yet progress was for many decades limited by focus patterns current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from recent wave integrative studies combining comprehensive phylogenetic, environmental, functional trait data at unprecedented scales. We review empirical advances describe how they reshaping our understanding global bird processes which it arises, with implications avian biogeography ecology. Further expansion integration sets may help resolve longstanding debates about origins biodiversity offer framework predicting response ecosystems environmental change.

Language: Английский

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A comparison of genomic islands of differentiation across three young avian species pairs

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(23), P. 4839 - 4855

Published: Sept. 6, 2018

Abstract Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions high relative differentiation (i.e., “islands differentiation” in F ST ), but there is much debate regarding the causes this pattern. We briefly review prominent models islands and compare patterns three closely related pairs New World warblers with goal evaluating support for four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black‐throated green Audubon's/myrtle warblers) consists forms that were likely separated western eastern North American refugia during cycles Pleistocene glaciations have now come into contact Canada, where each a narrow hybrid zone. show strong differences their heterogeneity , suggesting differing selective forces and/or responses to similar among pairs. Across most genome, levels within‐group nucleotide diversity ( π Within ) are almost as large between‐group distance Between within pair, recent common ancestry gene flow. In two pairs, pattern peaks having low suggests sweeps spread geographically differentiated groups, followed by local differentiation. This “sweep‐before‐differentiation” model consistent signatures flow yellow‐rumped warbler complex. These findings add our growing understanding speciation complex process can involve phases adaptive introgression partially populations.

Language: Английский

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Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex

Proceedings of the National Academy of Sciences, Journal Year: 2017, Volume and Issue: 115(2)

Published: Dec. 26, 2017

Significance One of the outstanding questions in understanding how new species form is reproductive isolation arises. In particular, relative roles gene flow and natural selection creating two separate remains open for debate. Here we show within four continuously speciating lineages a poplar that local genomic differentiation populations not associated with either rate recent or time divergence. By contrast, found these islands divergence most likely came about by selective processes—sorting ancient genetic polymorphisms incidental hitchhiking linked variations. These findings substantially enhance our changes speciation.

Language: Английский

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Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast

Science Advances, Journal Year: 2019, Volume and Issue: 5(12)

Published: Dec. 5, 2019

The study of parallel ecological divergence provides important clues to the operation natural selection. Parallel often occurs in heterogeneous environments with different kinds environmental gradients locations, but genomic basis underlying this process is unknown. We investigated genomics rapid adaptation marine snail Littorina saxatilis response two independent axes (crab-predation versus wave-action and low-shore high-shore). Using pooled whole-genome resequencing, we show that sharing regions high differentiation between generally low increases at smaller spatial scales. identify shared for each axis most these overlap candidate chromosomal inversions. Several inversion are divergent polymorphic across many localities. argue inversions could store variation fuels environments, possibly as balanced polymorphism by adaptive gene flow.

Language: Английский

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