Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

Journal of Evolutionary Biology, Journal Year: 2017, Volume and Issue: 30(8), P. 1450 - 1477

Published: Aug. 1, 2017

Speciation, the evolution of reproductive isolation among populations, is continuous, complex, and involves multiple, interacting barriers. Until it complete, effects this process vary along genome can lead to a heterogeneous genomic landscape with peaks troughs differentiation divergence. When gene flow occurs during speciation, barriers restricting locally in patterns heterogeneity. However, heterogeneity also be produced or modified by variation factors such as background selection selective sweeps, recombination mutation rate variation, density. Extracting flow, divergent from modifying presents major challenge speciation genomics. We argue one principal aims field identify barrier loci involved limiting flow. first summarize expected signatures at loci, regions linked them across entire genome. then discuss that complicate interpretation observed landscape. Finally, we end road map for future research: proposal how account these progress towards understanding nature loci. Despite difficulties interpreting empirical data, availability promising technical analytical methods will shed further light on important roles have shaping speciation.

Language: Английский

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Recombination rate variation shapes barriers to introgression across butterfly genomes

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(2), P. e2006288 - e2006288

Published: Feb. 7, 2019

Hybridisation and introgression can dramatically alter the relationships among groups of species, leading to phylogenetic discordance across genome between populations. Introgression also erode species differences over time, but selection against at certain loci acts maintain postmating barriers. Theory predicts that barriers made up many throughout should lead a broad correlation recombination rate, which determines extent on deleterious foreign alleles will affect neutral physically linked loci. Here, we describe variation in genealogical three Heliconius butterflies: H. melpomene (mel), cydno (cyd), timareta (tim), using whole genomes 92 individuals, ask whether this be explained by heterogeneous introgression. We find vary predictably chromosomal scale. By quantifying rate admixture proportions, then show rates are predicted rate. This implies highly polygenic, with acting introgressed most genome. In addition, long chromosomes, have lower rates, produce stronger average than short chromosomes. Finally, consistent difference two pairs either side Andes, suggests architecture Our findings illustrate how combined effects hybridisation, recombination, natural selection, multitudes periods, sculpt species.

Language: Английский

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Adaptive introgression: a plant perspective

Biology Letters, Journal Year: 2018, Volume and Issue: 14(3), P. 20170688 - 20170688

Published: March 1, 2018

Introgression is emerging as an important source of novel genetic variation, alongside standing variation and mutation. It adaptive when such introgressed alleles are maintained by natural selection. Recently, there has been explosion in the number studies on introgression. In this review, we take a plant perspective centred four lines evidence: (i) introgression, (ii) selection, (iii) phenotype (iv) fitness. While advances genomics have contributed to our understanding introgression porous species boundaries (task 1), detection signatures selection 2), investigation critically requires links phenotypic fitness (tasks 3 4). We also discuss conservation implications face climate change. Adaptive particularly rapidly changing environments, mutation alone may only offer limited potential for adaptation. conclude that clarifying magnitude effects with improved statistical techniques, coupled evidence, great management efforts.

Language: Английский

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Hybridization in Plants: Old Ideas, New Techniques

PLANT PHYSIOLOGY, Journal Year: 2016, Volume and Issue: 173(1), P. 65 - 78

Published: Nov. 28, 2016

Hybridization has played an important role in the evolution of many lineages. With growing availability genomic tools and advancements analyses, it is becoming increasingly clear that gene flow between divergent taxa can generate new phenotypic diversity, allow for adaptation to novel environments, contribute speciation. have immediate consequences through expression hybrid vigor. On longer evolutionary time scales, hybridization lead local adaption introgression alleles transgressive segregation and, some cases, result formation species. Studying both abundance deep historical roots plant biology. Many hypotheses concerning how why contributes biological diversity currently being investigated were first proposed tens even hundreds years ago. In this Update, we discuss genetic are revolutionizing our ability document occurrence investigate outcomes plants.

Language: Английский

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Inferring Phylogenetic Networks Using PhyloNet

Systematic Biology, Journal Year: 2018, Volume and Issue: 67(4), P. 735 - 740

Published: March 3, 2018

PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, main functionalities consisted measures comparing network topologies single heuristic reconciling gene trees with species tree. Since then, has grown significantly. The now includes wide array methods inferring networks from data sets unlinked loci while accounting both reticulation (e.g., hybridization) incomplete lineage sorting. In particular, allows maximum parsimony, likelihood, Bayesian inference tree estimates. Furthermore, directly sequence (sequence alignments or biallelic markers) is implemented. Maximum parsimony based on an extension "minimizing deep coalescences" criterion to networks, whereas likelihood are multispecies coalescent. All allow multiple individuals per species. As computing computationally hard, evaluation using pseudolikelihood measure. summarizes results various analyzes generates extended Newick format that readily viewable by existing visualization software.

Language: Английский

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Understanding explosive diversification through cichlid fish genomics

Nature Reviews Genetics, Journal Year: 2018, Volume and Issue: 19(11), P. 705 - 717

Published: Aug. 15, 2018

Language: Английский

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Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

Nature Genetics, Journal Year: 2016, Volume and Issue: 48(9), P. 1077 - 1082

Published: July 18, 2016

Magnus Nordborg and colleagues report a genomic analysis of all 27 known species in the genus Arabidopsis. They find evidence for complex speciation history that is not accurately reflected by traditional bifurcating tree identify widespread shared polymorphisms between species. The notion as reproductively isolated units related through implies gene trees should generally agree with sister taxa share unless they diverged recently be equally closely to outgroups. It now possible evaluate this model systematically. We sequenced multiple individuals from described representing entire Arabidopsis genus. Cluster identified seven groups, corresponding capture structure However, at level trees, only separation thaliana remaining was universally supported, and, overall, amount polymorphism demonstrated reproductive isolation considerably more recent than estimated divergence times. uncovered cases past flow contradict tree. Finally, we showed pattern differs ontologies, suggesting role selection.

Language: Английский

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Interpreting the genomic landscape of introgression

Current Opinion in Genetics & Development, Journal Year: 2017, Volume and Issue: 47, P. 69 - 74

Published: Sept. 18, 2017

Introgression, the transfer of genetic material between species through hybridisation, occurs in many taxa and has important consequences. Genomic studies allow us to characterise landscape introgression across genome, shedding light on both its adaptive benefits incompatibilities that help maintain barriers. Studies taking a genome-wide view suggest may be common, but introgressed variation is selected against throughout much genome. Confounding factors can complicate interpretations from these data, computational simulations have proved vital illustrate expected patterns under different scenarios. Future developments will move beyond correlative evidence explicit models account for how selection drift influence variation.

Language: Английский

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The role of gene flow in rapid and repeated evolution of cave‐related traits in Mexican tetra, Astyanax mexicanus

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(22), P. 4397 - 4416

Published: Sept. 25, 2018

Abstract Understanding the molecular basis of repeatedly evolved phenotypes can yield key insights into evolutionary process. Quantifying gene flow between populations is especially important in interpreting mechanisms repeated phenotypic evolution, and genomic analyses have revealed that admixture occurs more frequently diverging lineages than previously thought. In this study, we resequenced 47 whole genomes Mexican tetra from three cave populations, two surface outgroup samples. We confirmed are polyphyletic Astyanax mexicanus present our data set. The likely diverged much recently previous mitochondrial estimates 5–7 mya. Divergence their phylogenetically closest population occurred ~161 191 k generations ago. favoured demographic model for most pairs accounts divergence with secondary contact heterogeneous across genome, rigorously identified among all sampled. Therefore, evolution cave‐related traits rapidly thought, trogolomorphic maintained despite populations. recency these estimated events suggests selection may drive cave‐derived traits, as opposed to disuse drift. Finally, show a phenotype QTL enriched regions low caves, suggesting be transferred caves via flow. Our study shows must considered studies independent, trait evolution.

Language: Английский

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Analysis of Population Genomic Data from Hybrid Zones

Annual Review of Ecology Evolution and Systematics, Journal Year: 2017, Volume and Issue: 48(1), P. 207 - 229

Published: Aug. 16, 2017

Hybrid zones provide a powerful opportunity to analyze ecological and evolutionary interactions between divergent lineages. As such, research on hybrid has played prominent role in the fields of biology systematics. Herein, we clarify what are, is (and not) known about them, how different types genomic data contribute our understanding zones. We then review two key topics, namely, analyses have revealed basis dynamics speciation directly affect processes. In latter case, emphasize importance contingency context outcomes hybridization. Throughout, highlight limitations unknowns, suggest approaches most likely advance processes general.

Language: Английский

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