scholarly journals Gene flow, divergent selection and resistance to introgression in two species of morning glories ( Ipomoea )

2019 ◽  
Vol 28 (7) ◽  
pp. 1709-1729 ◽  
Author(s):  
Joanna L. Rifkin ◽  
Allan S. Castillo ◽  
Irene T. Liao ◽  
Mark D. Rausher
Keyword(s):  
Gene Flow ◽  
Divergent Selection ◽  
Morning Glories

scholarly journals Ecological Divergence and the Origins of Intrinsic Postmating Isolation with Gene Flow

2011 ◽  
Vol 2011 ◽  
pp. 1-15 ◽  
Author(s):  
Aneil F. Agrawal ◽  
Jeffrey L. Feder ◽  
Patrik Nosil
Keyword(s):  
Linkage Disequilibrium ◽  
Gene Flow ◽  
Natural Selection ◽  
Theoretical Models ◽  
Ecological Speciation ◽  
Divergent Selection ◽  
Postmating Isolation ◽  
Divergent Natural Selection ◽  
Mathematical Exploration ◽  
Neutral Gene

The evolution of intrinsic postmating isolation has received much attention, both historically and in recent studies of speciation genes. Intrinsic isolation often stems from between-locus genetic incompatibilities, where alleles that function well within species are incompatible with one another when brought together in the genome of a hybrid. It can be difficult for such incompatibilities to originate when populations diverge with gene flow, because deleterious genotypic combinations will be created and then purged by selection. However, it has been argued that if genes underlying incompatibilities are themselves subject to divergent selection, then they might overcome gene flow to diverge between populations, resulting in the origin of incompatibilities. Nonetheless, there has been little explicit mathematical exploration of such scenarios for the origin of intrinsic incompatibilities during ecological speciation with gene flow. Here we explore theoretical models for the origin of intrinsic isolation where genes subject to divergent natural selection also affect intrinsic isolation, either directly or via linkage disequilibrium with other loci. Such genes indeed overcome gene flow, diverge between populations, and thus result in the evolution of intrinsic isolation. We also examine barriers to neutral gene flow. Surprisingly, we find that intrinsic isolation sometimes weakens this barrier, by impeding differentiation via ecologically based divergent selection.

scholarly journals Sharing of chloroplast haplotypes among red oak species suggests interspecific gene flow between neighboring populations

Botany ◽  
2015 ◽  
Vol 93 (10) ◽  
pp. 691-700 ◽  
Author(s):  
Ruhua Zhang ◽  
Andrew L. Hipp ◽  
Oliver Gailing
Keyword(s):  
Gene Flow ◽  
Chloroplast Dna ◽  
Genetic Markers ◽  
Dna Markers ◽  
Divergent Selection ◽  
Red Oak ◽  
Interspecific Gene Flow ◽  
Red Oaks ◽  
Chloroplast Dna Markers ◽  
Chloroplast Haplotypes

The North American red oak species Quercus rubra L., Quercus ellipsoidalis E. J. Hill, Quercus velutina Lam., and Quercus coccinea Münchh. are morphologically similar and showed very low interspecific differentiation at most nuclear genetic markers in our earlier analyses (<10%). However, a few genetic markers showed interspecific differentiation values (up to 84%) above neutral expectations, a pattern of genomic divergence consistent with models of ecological speciation in the face of gene flow and strong divergent selection. Accordingly, these interfertile species are predicted to maintain differential adaptations to drought, while neutral regions of the genome appear to be homogenized by interspecific gene flow. According to this model of maintenance of species integrity by divergent selection with gene flow, we expect a sharing of chloroplast haplotypes between interspecific population pairs. We analyzed maternally inherited chloroplast DNA markers for the first time in interspecific populations of the red oaks (section Lobatae) to provide additional evidence for contemporary gene flow between Q. rubra and Q. ellipsoidalis and between Q. velutina and Q. ellipsoidalis. Very low interspecific differentiation (GST = 0.023), but pronounced genetic differentiation among populations from different regions (GST = 0.277) across species, and sharing of regional chloroplast haplotypes between species in sympatric and neighboring populations provided strong evidence for contemporary interspecific gene flow. The pattern of divergence at chloroplast DNA markers in red oaks suggests interspecific gene flow that resulted in a sharing of chloroplast types while the ecological and morphological distinctness of species was maintained.

scholarly journals Divergent selection and primary gene flow shape incipient speciation of a riparian tree on Hawaii Island

2019 ◽  
Author(s):  
Jae Young Choi ◽  
Michael Purugganan ◽  
Elizabeth A. Stacy
Keyword(s):  
Gene Flow ◽  
Divergent Selection ◽  
Genomic Islands ◽  
Disruptive Selection ◽  
Metrosideros Polymorpha ◽  
Incipient Speciation ◽  
Island Endemic ◽  
Hawaii Island ◽  
Riparian Tree ◽  
Primary Gene

AbstractA long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within HawaiianMetrosideros, a hyper-variable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin ofMetrosideros polymorphavar.newellii(newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wideM. polymorphavar.glaberrima(glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii’s origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 million years. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e.secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e.primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.Author summaryA long-standing question in evolution is whether or not new species can arise in the presence of gene flow, which is expected to inhibit the formation of reproductive isolating barriers. We investigated the genomics underlying the origin of a Hawaii Island-endemic riparian tree and purported case of incipient sympatric speciation due to disruptive selection across a sharp forest-riparian ecotone. We find extensive evidence of ongoing gene flow between the riparian tree and its closest relative along with local genomic regions resistant to admixture that likely formed through selection on genes for ecological adaptation and/or reproductive isolation. These results strongly suggest that where disruptive selection is strong, incipient speciation with gene flow is possible even in long-lived, highly dispersible trees.

scholarly journals Theoretical Expression for the Evolution of Genomic Island of Speciation: From Its Birth to Preservation

2019 ◽  
Author(s):  
T. Sakamoto ◽  
H. Innan
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Divergence ◽  
Genomic Island ◽  
Evolutionary Process ◽  
Ecological Speciation ◽  
Divergent Selection ◽  
Genomic Islands ◽  
Theoretical Expression ◽  
Locally Adaptive

AbstractEcological speciation could be driven by divergent selection that works to maintain phenotypes that are adaptive to each niche. In its early stages, genetic divergence (or FST) can be maintained around the target sites of divergent selection, while in other regions, genetic variation can be mixed by gene flow or migration. Such regions of elevated genetic divergence are called genomic islands of speciation. In this work, we theoretically consider the evolutionary process of a genomic island of speciation, from its birth to stable preservation. Under a simple two-population model, we use a diffusion approach to obtain analytical expressions for the probability of initial establishment of a locally adaptive allele, the reduction of genetic variation due to the spread of the adaptive allele, and the process to the development of a sharp peak of divergence. Our result would be useful to understand how genomes evolve through ecological speciation with gene flow.

scholarly journals Population-genomic inference of the strength and timing of selection against gene flow

2017 ◽  
Vol 114 (27) ◽  
pp. 7061-7066 ◽  
Author(s):  
Simon Aeschbacher ◽  
Jessica P. Selby ◽  
John H. Willis ◽  
Graham Coop
Keyword(s):  
Gene Flow ◽  
Recombination Rate ◽  
Divergent Selection ◽  
Adaptive Divergence ◽  
Serpentine Soils ◽  
Evolutionary Mechanisms ◽  
Local Conditions ◽  
Local Environments ◽  
Genome Wide ◽  
A Genome

The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations. Our theory shows that the selection density (i.e., the selection coefficient per base pair) is a key parameter underlying this relationship. We then develop a procedure for parameter estimation that accounts for the confounding effect of background selection. Applying this method to two datasets from Mimulus guttatus, we infer a strong signal of adaptive divergence in the face of gene flow between populations growing on and off phytotoxic serpentine soils. However, the genome-wide intensity of this selection is not exceptional compared with what M. guttatus populations may typically experience when adapting to local conditions. We also find that selection against genome-wide introgression from the selfing sister species M. nasutus has acted to maintain a barrier between these two species over at least the last 250 ky. Our study provides a theoretical framework for linking genome-wide patterns of divergence and recombination with the underlying evolutionary mechanisms that drive this differentiation.

scholarly journals Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island

2019 ◽  
Vol 37 (3) ◽  
pp. 695-710 ◽  
Author(s):  
Jae Young Choi ◽  
Michael Purugganan ◽  
Elizabeth A Stacy
Keyword(s):  
Gene Flow ◽  
Evolutionary Biology ◽  
Woody Species ◽  
Divergent Selection ◽  
Genomic Islands ◽  
Disruptive Selection ◽  
Metrosideros Polymorpha ◽  
Hawaii Island ◽  
Riparian Tree ◽  
Primary Gene

Abstract A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hypervariable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii’s origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3–1.2 My. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e., secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e., primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.

scholarly journals Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow

2015 ◽  
Vol 16 (3) ◽  
pp. 203-212 ◽  
Author(s):  
M. J. Rivas ◽  
S. Dominguez-Garcia ◽  
A. Carvajal-Rodriguez
Keyword(s):  
Gene Flow ◽  
Divergent Selection ◽  
Genomic Signature

scholarly journals Speciation and gene flow across an elevational gradient in New Guinea kingfishers

2019 ◽  
Author(s):  
Ethan Linck ◽  
Benjamin G. Freeman ◽  
John P. Dumbacher
Keyword(s):  
Gene Flow ◽  
Nuclear Dna ◽  
New Guinea ◽  
Ecological Speciation ◽  
High Elevation ◽  
Divergent Selection ◽  
Secondary Contact ◽  
Gene Trees ◽  
Tropical Mountains

AbstractClosely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks, and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high elevation and low elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modeling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that while in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.

scholarly journals Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range

2021 ◽  
Author(s):  
Dragos Postolache ◽  
Sylvie ODDOU-MURATORIO ◽  
Elia Vajana ◽  
Francesca Bagnoli ◽  
Erwann Guichoux ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Fagus Sylvatica ◽  
European Beech ◽  
Divergent Selection ◽  
Forest Trees ◽  
Temperature And Precipitation ◽  
Precipitation Regimes ◽  
Fagus Sylvatica L

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139 candidate genes involved either in phenology or in stress responses. We inferred neutral genetic structure and processes (drift and gene flow) and performed differentiation outlier analyses and gene-environment association (GEA) analyses to detect signatures of divergent selection. Beech range-wide genetic structure was consistent with the species previously identified postglacial expansion scenario and recolonization routes. Populations showed high diversity and low differentiation along the major expansion routes. A total of 52 loci were found to be putatively under selection and 15 of them turned up in multiple GEA analyses. Temperature and precipitation related variables were equally represented in significant genotype-climate associations. Signatures of divergent selection were detected in the same proportion for stress response and phenology-related genes. The range-wide adaptive genetic structure of beech appears highly integrated, suggesting a balanced contribution of phenology and stress-related genes to local adaptation, and of temperature and precipitation regimes to genetic clines. Our results imply a best-case scenario for the maintenance of high genetic diversity during range shifts in beech (and putatively other forest trees) with a combination of gene flow maintaining within-population neutral diversity and selection maintaining between-population adaptive differentiation.

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