Presence Of Gene Flow Research Articles

Morphological Differentiation in the Damselfish Abudefduf saxatilis Along the Mexican Atlantic Coast is Associated with Environmental Factors and High Connectivity

Coastal regions represent environments with heterogenic ecological conditions and with potential barriers to dispersal, making them ideal systems to study the variation of morphology and genetics of the organisms inhabiting them. Using individuals of the damselfish Abudefduf saxatilis from the three main reef systems along the Mexican Atlantic coast, we examined genetic and environmental variation to evaluate their relative contribution to body and head shape, and body size. We determined if there was a relationship between morphological variation and environmental factors and whether morphological, mitochondrial DNA (mtDNA) and microsatellite variation were concordant. We found morphological differences among A. saxatilis individuals from the Tuxpan, Veracruz and Mexican Caribbean reef systems. Differences in body and head shape involved positions of pectoral fins and mouth. Individuals from Tuxpan and Veracruz were larger than those from the Mexican Caribbean. Furthermore, we found a significant correlation between shape (body and head) and environmental variables (chlorophyll-a, geostrophic velocity and temperature) as well as between body size and chlorophyll-a concentration. Both mtDNA and microsatellite markers detected high levels of genetic diversity and lack of population genetic differentiation among reefs, reef systems and between marine regions. We did not find a correlation between morphological and genetic differentiation. Our results suggest that the phenotypic differences of A. saxatilis along the Mexican Atlantic coast may be determined by environmental factors in the presence of gene flow.

A recombination suppressor contributes to ecological speciation in OSTRINIA moths.

Despite unparalleled access to species' genomes in our post-genomic age, we often lack adequate biological explanations for a major hallmark of the speciation process-genetic divergence. In the presence of gene flow, chromosomal rearrangements such as inversions are thought to promote divergence and facilitate speciation by suppressing recombination. Using a combination of genetic crosses, phenotyping of a trait underlying ecological isolation, and population genetic analysis of wild populations, we set out to determine whether evidence supports a role for recombination suppressors during speciation between the Z and E strains of European corn borer moth (Ostrinia nubilalis). Our results are consistent with the presence of an inversion that has contributed to accumulation of ecologically adaptive alleles and genetic differentiation across roughly 20% of the Ostrinia sex chromosome (~4 Mb). Patterns in Ostrinia suggest that chromosomal divergence may involve two separate phases-one driving its transient origin through local adaptation and one determining its stable persistence through differential introgression. As the evolutionary rate of rearrangements in lepidopteran genomes appears to be one of the fastest among eukaryotes, structural mutations may have had a disproportionate role during adaptive divergence and speciation in Ostrinia and in other moths and butterflies.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae).

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Genetic recombination variation in wild Robertsonian mice: on the role of chromosomal fusions and Prdm9 allelic background.

Despite the existence of formal models to explain how chromosomal rearrangements can be fixed in a population in the presence of gene flow, few empirical data are available regarding the mechanisms by which genome shuffling contributes to speciation, especially in mammals. In order to shed light on this intriguing evolutionary process, here we present a detailed empirical study that shows how Robertsonian (Rb) fusions alter the chromosomal distribution of recombination events during the formation of the germline in a Rb system of the western house mouse (Mus musculus domesticus). Our results indicate that both the total number of meiotic crossovers and the chromosomal distribution of recombination events are reduced in mice with Rb fusions and that this can be related to alterations in epigenetic signatures for heterochromatinization. Furthermore, we detected novel house mouse Prdm9 allelic variants in the Rb system. Remarkably, mean recombination rates were positively correlated with a decrease in the number of ZnF domains in the Prdm9 gene. The suggestion that recombination can be modulated by both chromosomal reorganizations and genetic determinants that control the formation of double-stranded breaks during meiosis opens new avenues for understanding the role of recombination in chromosomal speciation.

Divergent population structure and climate associations of a chromosomal inversion polymorphism across the Mimulus guttatus species complex.

Chromosomal rearrangement polymorphisms are common and increasingly found to be associated with adaptive ecological divergence and speciation. Rearrangements, such as inversions, reduce recombination in heterozygous individuals and thus can protect favourable allelic combinations at linked loci, facilitating their spread in the presence of gene flow. Recently, we identified a chromosomal inversion polymorphism that contributes to ecological adaptation and reproductive isolation between annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus. Here we evaluate the population genetic structure of this inverted region in comparison with the collinear regions of the genome across the M.guttatus species complex. We tested whether annual and perennial M.guttatus exhibit different patterns of divergence for loci in the inverted and noninverted regions of the genome. We then evaluated whether there are contrasting climate associations with these genomic regions through redundancy analysis. We found that the inversion exhibits broadly different patterns of divergence among annual and perennial M.guttatus and is associated with environmental variation across population accessions. This study is the first widespread population genetic survey of the diversity of the M.guttatus species complex. Our findings contribute to a greater understanding of morphological, ecological, and genetic evolutionary divergence across this highly diverse group of closely related ecotypes and species. Finally, understanding species relationships among M.guttatus sp. has hitherto been stymied by accumulated evidence of substantial gene flow among populations as well as designated species. Nevertheless, our results shed light on these relationships and provide insight into adaptation in life history traits within the complex.

Assessing the Maximum Contribution from Ancient Populations

Ancestral relationships between populations separated by time represent an often neglected dimension in population genetics, a field which historically has focused on analysis of spatially distributed samples from the same point in time. Models are usually straightforward when two time-separated populations are assumed to be completely isolated from all other populations. However, this is usually an unrealistically stringent assumption when there is gene flow with other populations. Here, we investigate continuity in the presence of gene flow from unknown populations. This setup allows a more nuanced treatment of questions regarding population continuity in terms of "level of contribution" from a particular ancient population to a more recent population. We propose a statistical framework which makes use of a biallelic marker sampled at two different points in time to assess population contribution, and present two different interpretations of the concept. We apply the approach to published data from a prehistoric human population in Scandinavia (Malmström H, Gilbert MTP, Thomas MG, Brandström M, Storå J, Molnar P, Andersen PK, Bendixen C, Holmlund G, Götherström A, et al. 2009. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol. 19:1758-1762) and Pleistocene woolly mammoth (Barnes I, Shapiro B, Lister A, Kuznetsova T, Sher A, Guthrie D, Thomas MG. 2007. Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Curr Biol. 17:1072-1075; Debruyne R, Chu G, King CE, Bos K, Kuch M, Schwarz C, Szpak P, Gröcke DR, Matheus P, Zazula G, et al. 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol. 18:1320-1326).

DIVERSIFICATION AND GENE FLOW IN NASCENT LINEAGES OF ISLAND AND MAINLAND NORTH AMERICAN TREE SQUIRRELS (TAMIASCIURUS)

Pleistocene climate cycles and glaciations had profound impacts on taxon diversification in the Boreal Forest Biome. Using population genetic analyses with multilocus data, we examined diversification, isolation, and hybridization in two sibling species of tree squirrels (Tamiasciurus douglasii and Tamiasciurus hudsonicus) with special attention to the geographically and genetically enigmatic population of T. hudsonicus on Vancouver Island, Canada. The two species differentiated only about 500,000 years ago, in the Late Pleistocene. The island population is phylogenetically nested within T. hudsonicus according to our nuclear analysis but within T. douglasii according to mitochondrial DNA. This conflict is more likely due to historical hybridization than to incomplete lineage sorting, and it appears that bidirectional gene flow occurred between the island population and both species on the mainland. This interpretation of our genetic analyses is consistent with our bioclimatic modeling, which demonstrates that both species were able to occupy this region throughout the Late Pleistocene. The divergence of the island population 40,000 years ago suggests that tree squirrels persisted in a refugium on Vancouver Island at the last glacial maximum, 20,000 years ago. Our observations demonstrate how Pleistocene climate change and habitat shifts have created incipient divergence in the presence of gene flow. Sequence data have been archived in GenBank—accession numbers: KF882736–KF885216.

Sensory trait variation in an echolocating bat suggests roles for both selection and plasticity

BackgroundAcross heterogeneous environments selection and gene flow interact to influence the rate and extent of adaptive trait evolution. This complex relationship is further influenced by the rarely considered role of phenotypic plasticity in the evolution of adaptive population variation. Plasticity can be adaptive if it promotes colonization and survival in novel environments and in doing so may increase the potential for future population differentiation via selection. Gene flow between selectively divergent environments may favour the evolution of phenotypic plasticity or conversely, plasticity itself may promote gene flow, leading to a pattern of trait differentiation in the presence of gene flow. Variation in sensory traits is particularly informative in testing the role of environment in trait and population differentiation. Here we test the hypothesis of ‘adaptive differentiation with minimal gene flow’ in resting echolocation frequencies (RF) of Cape horseshoe bats (Rhinolophus capensis) across a gradient of increasingly cluttered habitats.ResultsOur analysis reveals a geographically structured pattern of increasing RF from open to highly cluttered habitats in R. capensis; however genetic drift appears to be a minor player in the processes influencing this pattern. Although Bayesian analysis of population structure uncovered a number of spatially defined mitochondrial groups and coalescent methods revealed regional-scale gene flow, phylogenetic analysis of mitochondrial sequences did not correlate with RF differentiation. Instead, habitat discontinuities between biomes, and not genetic and geographic distances, best explained echolocation variation in this species. We argue that both selection for increased detection distance in relatively less cluttered habitats and adaptive phenotypic plasticity may have influenced the evolution of matched echolocation frequencies and habitats across different populations.ConclusionsOur study reveals significant sensory trait differentiation in the presence of historical gene flow and suggests roles for both selection and plasticity in the evolution of echolocation variation in R. capensis. These results highlight the importance of population level analyses to i) illuminate the subtle interplay between selection, plasticity and gene flow in the evolution of adaptive traits and ii) demonstrate that evolutionary processes may act simultaneously and that their relative influence may vary across different environments.

A review on studies of speciation in the presence of gene flow: evolution of reproductive isolation

A review on studies of speciation in the presence of gene flow: evolution of reproductive isolation

경주국립공원 내 야생 작약(Paeonia lactiflora Pall.) 집단의 유전다양성 분석

ABSTRACT: Paeonia lactiflora is a valuable natural resource for horticulture and traditional Chinese medicine. To pro-pose conservation strategy and future utility of the wild Paeonia lactiflora populations recently found around the Gyeo-ngju National Park, genetic diversity analysis using microsatellite markers were performed. Three populations in and nearthe Gyeongju N.P. and one population from Jilin, China were analyzed for five microsatellite markers, producing 61 alle-les with mean observed heterozygosity(H o ) of 0.452. F ST value (0.11642) suggested moderate level of genetic differen-tiation among the populations, and hierarchical AMOVA suggested most of the genetic variation resides within/amongthe individuals rather than among-population. While AMOVA with F ST suggested lack of genetic differentiation betweenthe regional (Korean vs. Chinese) populations, AMOVA with R ST , which incorporates the allele sizes, suggested consid-erable differentiation between them, but without significant statistical support. STRUCTURE analysis also suggestedsegregation of regional populations with presence of gene flow among the three Gyeongju N.P. populations. Consideringsmall population size and scarcity of mature individuals, further protection and long-term monitoring are needed.

Speciation of two desert poplar species triggered by Pleistocene climatic oscillations.

Despite the evidence that the Pleistocene climatic fluctuations have seriously affected the distribution of intraspecific diversity, less is known on its impact on interspecific divergence. In this study, we aimed to test the hypothesis that the divergence of two desert poplar species Populus euphratica Oliv. and P. pruinosa Schrenk. occurred during the Pleistocene. We sequenced 11 nuclear loci in 60 individuals from the two species to estimate the divergence time between them and to test whether gene flow occurred after species separation. Divergence time between the two species was estimated to be 0.66-1.37 million years ago (Ma), a time at which glaciation was at its maximum in China and deserts developed widely in central Asia. Isolation-with-Migration model also indicated that the two species had diverged in the presence of gene flow. We also detected evidence of selection at GO in P. euphratica and to a lesser extent at PhyB2. Together, these results underscore the importance of Pleistocene climate oscillations in triggering plant speciation as a result of habitats divergence.

Trends of karyotypical evolution in the pearl cichlid, Geophagus brasiliensis, from southern Brazil

Chromosomal rearrangements such as inversions can facilitate speciation even in the presence of gene flow. The present study aims to analyze the karyotypic variation in six populations of Geophagus brasiliensis from southern Brazil. All specimens showed 2n=48 chromosomes, but three karyotypes were found to have one, two or three pairs of submetacentric chromosomes. Although G. brasiliensis did not exhibit variation in the diploid number, it presented a wide interpopulational variation mainly regarding the karyotype formula and specific chromosomal markers. Differences in the location of the major and minor rDNA loci were observed among the populations. Moreover, different patterns were observed in the distribution of the constitutive heterochromatin, presenting intra- and interpopulational variation. This supports the hypothesis that this taxon represents a complex species or that cryptic species are included in this group, indicating a possibleprocess of sympatric speciation. By potentially restricting gene flow between heterokaryotypes, the segregating chromosome rearrangements we describe for G. brasiliensis may play a role in diversification in this species complex.

Ecological speciation in anemone‐associated snapping shrimps (Alpheus armatus species complex)

Divergent natural selection driven by competition for limited resources can promote speciation, even in the presence of gene flow. Reproductive isolation is more likely to result from divergent selection when the partitioned resource is closely linked to mating. Obligate symbiosis and host fidelity (mating on or near the host) can provide this link, creating ideal conditions for speciation in the absence of physical barriers to dispersal. Symbiotic organisms often experience competition for hosts, and host fidelity ensures that divergent selection for a specific host or host habitat can lead to speciation and strengthen pre-existing reproductive barriers. Here, we present evidence that diversification of a sympatric species complex occurred despite the potential for gene flow and that partitioning of host resources (both by species and by host habitat) has contributed to this diversification. Four species of snapping shrimps (Alpheus armatus, A.immaculatus, A.polystictus and A.roquensis) are distributed mainly sympatrically in the Caribbean, while the fifth species (A.rudolphi) is restricted to Brazil. All five species are obligate commensals of sea anemones with a high degree of fidelity and ecological specificity for host species and habitat. We analysed sequence data from 10 nuclear genes and the mitochondrial COI gene in 11-16 individuals from each of the Caribbean taxa and from the only available specimen of the Brazilian taxon. Phylogenetic analyses support morphology-based species assignments and a well-supported Caribbean clade. The Brazilian A.rudolphi is recovered as an outgroup to the Caribbean taxa. Isolation-migration coalescent analysis provides evidence for historical gene flow among sympatric sister species. Our data suggest that both selection for a novel host and selection for host microhabitat may have promoted diversification of this complex despite gene flow.

Interspecific differentiation and gene flow between two desert poplars inferred from six vacuolar Na+/H+exchanger loci

Populus euphratica Olivier and P. pruinosa Schrenk are known for their tolerance to highly saline and arid habitats, and overlapping distribution. We examined interspecific differentiation and gene flow between these two species at six loci that encode vacuolar Na+/H+ exchanger genes. Interspecific divergence varied greatly between sampled loci and could collectively delimit the two species well. Simulations based on the isolation–migration model suggested gene flow primarily from P. euphratica into P. pruinosa. This asymmetrical gene flow may be related to the adaptive survival of the introgressed individuals. Our findings suggest that these species may have diverged in the presence of gene flow and that local adaptation may have played an important role in maintaining the distinct species lineages by restricting gene flow between them. Our results together indicate that interspecific divergence and gene flow differ greatly between members of the same gene family, possibly due to differential subfunctionalization and/or neofunctionalization during ongoing speciation of these two poplar species.

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).

Genetic, phenotypic and ecological divergence with gene flow at the Isthmus of Tehuantepec: the case of the azure‐crowned hummingbird (Amazilia cyanocephala)

AbstractAimWe test whether populations of the Mesoamerican azure‐crowned hummingbird, Amazilia cyanocephala (Trochilidae), located east and west of the Isthmus of Tehuantepec are genetically, morphologically and environmentally differentiated and examine the relative role of drift and selection in driving diversification.LocationMexico.MethodsWe sequenced the mitochondrial ATPase‐6 and ATPase‐8 genes and the control region of 130 individuals collected throughout the range of the species in Mexico. Population genetic methods and coalescent tests were used to reconstruct the phylogeography of the species. Morphological and niche variation between genetic groups of A. cyanocephala were assessed.ResultsThe data revealed two genetic groups separated by the Isthmus of Tehuantepec in the late Pleistocene (49,300–75,800 years ago), with the split occurring in the presence of gene flow. Deviations from demographic equilibrium were detected for the two genetic groups, indicating more recent population expansions. Amazilia cyanocephala individuals from populations on either side of the Isthmus of Tehuantepec differed in morphology and were distributed in unique environmental space. A coalescent‐based test indicated that selection is driving the observed morphological differentiation.Main conclusionsOur findings implicate the Isthmus of Tehuantepec as a permeable barrier driving recent diversification of A. cyanocephala in the presence of gene flow. The two A. cyanocephala mitochondrial DNA (mtDNA) groups corresponding with morphological and environmental niche differences, in concert with the results of a coalescent‐based test, suggest that selection has been strong enough to counteract the effects of gene flow.

Gene Flow between Nigerian Sheep Breeds as Revealed by Microsatellite DNA Markers

The presence and level of gene flow between the four major Nigerian sheep breeds (West African Dwarf (WAD), Yankasa, Balami and Uda) was assessed using microsatellite DNA markers. DNA was extracted from 50μl of whole blood using the ZymoBeadTM Genomic DNA Kit The DNA was amplified by PCR in a MyCyclerTM Thermal Cycler (Biorad, Hercules, CA) using 15 microsatellite markers selected. DNA fragment analysis of microsatellite markers was carried out using the Applied BioSystems 3730xl DNA Analyzer (Applied Biosystems, Carlsbad, CA, USA). The level of gene flow or population structure was assessed by STRUCTURE software and barplots generated by DISTRUCT. At K=2, two clusters was constituted from breeds descending from Balami and Yankasa, both of which are from Northern region in Nigeria. At K=3 and K=4, one more cluster emerged and further analyses did not reveal any additional strong high level substructure, so separating the entire the entire datasets into 3 major clusters was chosen as the final configuration. There are however, several cases of admixtures in the genome of some of the individuals that constitute the cluster. Yankasa and Balami breed had more cases of admixtures followed by Uda while the WAD was the least breed with cases of admixtures. The values of genetic differentiation ranged between 0.11 and 0.19 with the highest mean value of 0.14. These results reveal the presence of gene flow among the Nigerian sheep breeds.

Historical demographic dynamics underlying local adaptation in the presence of gene flow

The range of a species is the result of the relative contribution of spatial tracking of environmental requirements and adaptation to ecological conditions outside the ancestral niche. The appearance of novel habitats caused by climatic oscillation can promote range expansion and accompanying demographic growth. The demographic dynamics of populations leave a signal in \\ patterns. We modeled three competing scenarios pertaining to the circumstance of a range expansion by the Karoo Scrub-Robin into newly available habitat resulting from the increasing aridification of southern Africa. Genetic variation was contrasted with the theoretical expectations of a spatial range expansion, and compared with data of a putative adaptive trait. We infer that this bird likely colonized the arid zone, as a consequence of adaptive evolution in a small peripheral population, followed by an expansion with recurrent exchange of migrants with the ancestral populations.

Detecting the footprints of divergent selection in oaks with linked markers

Genome scans are increasingly used to study ecological speciation, providing a useful genome-wide perspective on divergent selection in the presence of gene flow. Here, we compare current approaches to detect footprints of divergent selection in closely related species. We analyzed 192 individuals from two interfertile European temperate oak species using 30 nuclear microsatellites from eight linkage groups. These markers present little intraspecific differentiation and can be used in combination to assign individual genotypes to species. We first show that different outlier detection tests give somewhat different results, possibly due to model constraints. Second, using linkage information for these markers, we further characterize the signature of divergent selection in the presence of gene flow. In particular, we show that recombination estimates for regions with outlier markers are lower than those for a control region, in line with a prediction from ecological speciation theory. Most importantly, we show that analyses at the haplotype level can distinguish between truly divergent (bi-directional) selection and positive selection in one of the two species, offering a new and improved method for characterizing the speciation process.

Breeding without Breeding

We developed a deterministic model to optimize DNA fingerprinting effort in the presence of gene flow during the application of Breeding without Breeding. The method considers trait’s heritability, level of gene flow, selection differential, and the proportion of progeny test subjected to fingerprinting (truncation). All the model’s variables individually or in concert proved important; however, the trait’s heritability magnitude played the most important role in minimizing the selection of contaminated individuals and it could be used as a surrogate to traits with low heritability.