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 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 Low genetic divergence and variation in coastal dune populations of the widespread terrestrial orchid Epipactis helleborine

2020 ◽  
Vol 193 (3) ◽  
pp. 419-430 ◽  
Author(s):  
Hans Jacquemyn ◽  
Hanne De Kort ◽  
An Vanden Broeck ◽  
Rein Brys
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Divergence ◽  
Coastal Dune ◽  
Terrestrial Orchid ◽  
Colonization Event ◽  
History Of ◽  
Epipactis Helleborine ◽  
Seed Introduction

Abstract Reconstructing the early history of species divergence and quantifying the level of standing genetic variation in diverging populations are central to our understanding of ecotype formation and ultimately speciation. In this study, we used single nucleotide polymorphisms to reconstruct the evolutionary history of species divergence in coastal dune populations of the widespread terrestrial orchid Epipactis helleborine and to investigate the level of standing genetic variation in 29 coastal dune populations in a fragmented dune landscape along the Belgian and French coast. Additionally, we used seed introduction experiments to assess the potential for gene flow into existing populations after long-distance seed dispersal and the ability to colonize vacant sites. Our results showed that coastal dune populations diverged only recently from inland populations, went through a significant bottleneck and were most probably the result of a single colonization event. Current levels of population genetic diversity are low and not related to population size or spatial isolation. The sampled dune populations also showed little genetic differentiation, and no apparent spatial genetic structure was observed. Seed introduction experiments showed that seeds of coastal dune populations germinated easily in both occupied and unoccupied sites in dune habitat, indicating that the availability of suitable mycorrhizal fungi is not limiting the distribution of coastal dune populations and that gene flow through seeds has probably contributed to the observed low levels of genetic differentiation. Overall, these results are consistent with a process of genetic divergence after a single, recent colonization event, followed by extensive gene flow among populations.

scholarly journals Uplift and erosion of genomic islands with standing genetic variation

2016 ◽  
Author(s):  
Tyler D. Hether
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Biological Diversity ◽  
Empirical Studies ◽  
Theoretical Models ◽  
Divergent Selection ◽  
Genomic Islands ◽  
Island Formation ◽  
Standing Variation ◽  
Uplift And Erosion

AbstractDetails of the processes that generate biological diversity have long been of interest to evolutionary biologists. A common theme in nature is diversification via divergent selection with gene flow. Empirical studies on this topic find variable genetic differentiation throughout the genome, that genetic differentiation is non-randomly distributed, and that loci of adaptive significance are often found clustered together within “genomic islands of divergence”. Theoretical models based on new mutations show how these genomic islands can arise and grow as a result of a complex interaction of various evolutionary and genic processes. In the current study, I ask if such genomic islands can alternatively arise from divergent selection from standing genetic variation and I tested this using a simple two locus model of selection. There are numerous ways in which standing genetic variation can be partitioned (e.g., between alleles, between loci, and between populations) and I tested which of these scenarios can give rise to an island pattern compared to no genomic differentiation or complete genomic differentiation. I found that divergent selection, even without reciprocal gene exchange between populations, following a bout of admixture can relatively quickly produce an island pattern. Moreover, I found two pathways in which islands can form from divergence from standing variation: 1) through the build up of islands and 2) through the breakdown of larger, genome-wide differentiation. Lastly, similar to new mutation theory, I found that the frequency of recombination is an important determinant of island formation from standing genetic variation such that mating behavior of a species (e.g., facultative or obligate sexual) can impact the likelihood of island formation.

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 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 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.

scholarly journals Developmental rate: A unifying mechanism for sympatric divergence in postglacial fishes?

2012 ◽  
Vol 58 (1) ◽  
pp. 21-34 ◽  
Author(s):  
Megan V. Mcphee ◽  
David L. G. Noakes ◽  
Fred W. Allendorf
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Genetic Recombination ◽  
Rapid Evolution ◽  
Developmental Rate ◽  
Ecological Speciation ◽  
Divergent Selection ◽  
Fish Populations ◽  
Trophic Polymorphism ◽  
Individual Traits

Abstract Morphologically divergent ecotypes arise in fish populations on postglacial time scales, and resource polymorphisms are often invoked to explain their origin. However, genetic recombination can constrain the ability of divergent selection to produce reproductive isolation in sympatry. Recombination breaks up favorable combinations of traits (“adaptive suites”) if individual traits are affected by different loci. Recombination also breaks up any association between traits under divergent selection and traits contributing to reproductive isolation. Thus, ecological speciation in the absence of preexisting barriers to gene flow is more likely when pleiotropy minimizes the number of loci involved. Here, we revisit research conducted by Carl Hubbs in the early 1900s on the effects of developmental rate on morphological traits in fishes. Hubbs’ work provides a mechanism to explain how sympatric divergence by trophic polymorphism can occur despite the challenges of recombination. We consider the implications of Hubbs’ observations for ecological speciation with gene flow in fishes, as well as rapid evolution in captive fish populations.

scholarly journals Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes

2012 ◽  
Vol 367 (1587) ◽  
pp. 395-408 ◽  
Author(s):  
Paul A. Hohenlohe ◽  
Susan Bassham ◽  
Mark Currey ◽  
William A. Cresko
Keyword(s):  
Linkage Disequilibrium ◽  
Gene Flow ◽  
Fresh Water ◽  
Threespine Stickleback ◽  
Divergent Selection ◽  
Genomic Islands ◽  
Next Generation Sequencing Data ◽  
Rate Variation ◽  
Long Distance ◽  
Genomic Architecture

Population genomic studies are beginning to provide a more comprehensive view of dynamic genome-scale processes in evolution. Patterns of genomic architecture, such as genomic islands of increased divergence, may be important for adaptive population differentiation and speciation. We used next-generation sequencing data to examine the patterns of local and long-distance linkage disequilibrium (LD) across oceanic and freshwater populations of threespine stickleback, a useful model for studies of evolution and speciation. We looked for associations between LD and signatures of divergent selection, and assessed the role of recombination rate variation in generating LD patterns. As predicted under the traditional biogeographic model of unidirectional gene flow from ancestral oceanic to derived freshwater stickleback populations, we found extensive local and long-distance LD in fresh water. Surprisingly, oceanic populations showed similar patterns of elevated LD, notably between large genomic regions previously implicated in adaptation to fresh water. These results support an alternative biogeographic model for the stickleback radiation, one of a metapopulation with appreciable bi-directional gene flow combined with strong divergent selection between oceanic and freshwater populations. As predicted by theory, these processes can maintain LD within and among genomic islands of divergence. These findings suggest that the genomic architecture in oceanic stickleback populations may provide a mechanism for the rapid re-assembly and evolution of multi-locus genotypes in newly colonized freshwater habitats, and may help explain genetic mapping of parallel phenotypic variation to similar loci across independent freshwater populations.

AsaGEI2d: a new variant of a genomic island identified in a group of Aeromonas salmonicida subsp. salmonicida isolated from France, which bears the pAsa7 plasmid

2021 ◽  
Author(s):  
Antony T Vincent ◽  
Laurent Intertaglia ◽  
Victor Loyer ◽  
Valérie E Paquet ◽  
Émilie Adouane ◽  
...  
Keyword(s):  
Genomic Island ◽  
Insertion Site ◽  
Aeromonas Salmonicida ◽  
Genomic Islands ◽  
The Other ◽  
Fish Pathogen ◽  
Integrase Gene ◽  
New Variant ◽  
Cat Gene ◽  
Unique Genes

Abstract Genomic islands (Aeromonas salmonicida genomic islands, AsaGEIs) are found worldwide in many isolates of Aeromonas salmonicida subsp. salmonicida, a fish pathogen. To date, five variants of AsaGEI (1a, 1b, 2a, 2b and 2c) have been described. Here, we investigate a sixth AsaGEI, which was identified in France between 2016 and 2019 in 20 A. salmonicida subsp. salmonicida isolates recovered from sick salmon all at the same location. This new AsaGEI shares the same insertion site in the chromosome as the other AsaGEI2s as they all have a homologous integrase gene. This new AsaGEI was thus named AsaGEI2d, and has 5 unique genes compared to the other AsaGEIs. The isolates carrying AsaGEI2d also bear the plasmid pAsa7, which was initially found in an isolate from Switzerland. This plasmid provides resistance to chloramphenicol thanks to a cat gene. This study reveals more about the diversity of the AsaGEIs.

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