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57 results for “Barriers to gene flow”
Pervasive gene flow despite strong and varied reproductive barriers in swordtails
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Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene)
Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions <i>Silene dioica</i> (L.) Clairv. and <i>S. latifolia</i> Poiret. Demographic modeling indicated that the two species diverged with gene flow. The best-supported scenario with heterogeneity in both migration rate and effective population size suggested that a small proportion of the loci evolved without gene flow. Differentiation (F<sub>ST</sub>) and sequence divergence (d<sub>XY</sub>) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection. In between-species population pairs, isolation by distance was stronger for genomic regions with low between-species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated suggesting that linked selection due to shared recombination and gene density landscapes is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection shaped the genomic landscape of differentiation between the two <i>Silene </i>species, consistent with predictions for speciation in the face of gene flow.
Data from: Amazonian rivers are leaky barriers to gene flow in forest understory birds
<p>Ever since Alfred Russel Wallace's nineteenth-century observation that related terrestrial species are often separated on opposing riverbanks, major Amazonian rivers have been recognized as key drivers of speciation. However, rivers are dynamic entities whose widths and courses may vary through time. It thus remains unknown how effective rivers are at reducing gene flow and promoting speciation over long timescales. We fit demographic models to genomic sequence to reconstruct the history of gene flow in three pairs of avian taxa fully separated by different Amazonian rivers, and whose geographic ranges do not make contact in headwater regions. Models with gene flow were best fit, but still supported an initial period without any gene flow which ranged from 187,000 to over 959,000 years, suggesting that rivers are capable of initiating speciation through long stretches of allopatric divergence. Allopatry was followed by either bursts or prolonged episodes of gene flow that retarded genomic differentiation but did not homogenize populations. Our results support Amazonian rivers as key barriers that promoted speciation and the buildup of species richness, but they also suggest that river barriers are often leaky, with genomic divergence accumulating slowly due to episodes of substantial gene flow.</p>
Going against the flow: barriers to gene flow impact patterns of connectivity in cryptic coral reef gobies throughout the western Atlantic
<p class="CxSpFirst"><b>Aim</b>: Complex oceanographic features have historically caused difficulty in understanding gene flow in marine taxa. Here, we evaluate the impact of potential phylogeographic barriers to gene flow and assess demography and evolutionary history of a coral reef goby species complex. Specifically, we test how the Amazon River outflow and ocean currents impact gene flow.</p> <p class="CxSpMiddle"><b>Location</b>: Western Atlantic.</p> <p class="CxSpMiddle"><b>Taxon</b>: The bridled goby (<i>Coryphopterus glaucofraenum</i>) and sand-canyon goby (<i>C. venezuelae</i>) species complex.</p> <p class="CxSpMiddle"><b>Methods</b>: We used mitochondrial DNA and 2401 genomic SNPs to investigate evolutionary history and test hypotheses of how major barriers impact species-level differentiation. We used clustering algorithms and pairwise <i>F</i><sub>ST</sub> to assess population differentiation caused by minor barriers within and among regions. Finally, we tested alternate hypotheses of demographic history via coalescent simulations to determine the most plausible spread across the Western Atlantic.</p> <p class="CxSpMiddle"><b>Results</b>: We found two unique clades of <i>C. glaucofraenum</i> along the Brazilian coast and Atol das Rocas (AR) that are more closely related to <i>C. venzuelae</i>. Further genetic structure within the Caribbean and separately along the Brazilian coast led to at least two distinct populations in each location. Coalescent simulations indicated that an ancestral population of <i>C. venezuelae</i> split from <i>C. glaucofraenum</i> in the Caribbean, dispersed to Brazil, then spread to AR.</p> <p class="CxSpMiddle"><b>Main Conclusions</b>: Species-level genetic differentiation has resulted from the Amazon River outflow and isolation of AR. Population differentiation within the Caribbean matched previous studies indicating an east-west pattern of divergence. Brazilian population differentiation was impacted by the cold-water upwelling at Cabo Frio. Overall, this research highlights how barriers to gene flow impact speciation and genetic structure within western Atlantic gobies and provides insight into the role oceanographic features have in the speciation process of fishes.</p>
Data from: Demographically explicit scans for barriers to gene flow using gIMble
<p>Identifying regions of the genome that act as barriers to gene flow between recently diverged taxa has remained challenging given the many evolutionary forces that generate variation in genetic diversity and divergence along the genome, and the stochastic nature of this variation. Here we implement a composite likelihood approach for the quantification of barriers to gene flow. This analytic framework captures background selection and selection against locally maladaptive alleles (i.e. genomic barriers) in a model of isolation with migration (IM) as heterogeneity in effective population size (Ne) and effective migration rate (me), respectively. Variation in both effective demographic parameters is estimated in sliding windows via pre-computed likelihood grids. We have implemented genomewide IM blockwise likelihood estimation (gIMble) as a modular tool, which includes modules for pre-processing/filtering of genomic data and performing parametric bootstraps using coalescent simulations. To demonstrate the new approach, we analyse data from a well-studied sister species pair of tropical butterflies with a known history of post-divergence gene flow: Heliconius melpomene and H. cydno. Our analysis uncovers both large effect barrier loci (including well-known wing-pattern genes) and a genome-wide signal of polygenic barrier architecture.</p>
Data from: Demographically explicit scans for barriers to gene flow using gIMble
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Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene)
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Data from: Impact of a putative riverine barrier on genomic population structure and gene flow in the presence of sexual selection
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Data from: A genomic assessment of population structure and gene flow in an aquatic salamander identifies the roles of spatial scale, barriers, and river architecture
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Going against the flow: barriers to gene flow impact patterns of connectivity in cryptic coral reef gobies throughout the western Atlantic
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A spatial genomic approach identifies time lags and historic barriers to gene flow in a rapidly fragmenting Appalachian landscape
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Data from: Amazonian rivers are leaky barriers to gene flow in forest understory birds
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Data from: Immigrant inviability produces a strong barrier to gene flow between parapatric ecotypes of Senecio lautus
Speciation proceeds when gene exchange is prevented between populations. Determining the different barriers preventing gene flow can therefore give insights into the factors driving and maintaining species boundaries. These reproductive barriers may result from intrinsic genetic incompatibilities between populations, from extrinsic environmental differences between populations, or a combination of both mechanisms. We investigated the potential barriers to gene exchange between three adjacent ecotypes of an Australian wildflower to determine the strength of individual barriers and the degree of overall isolation between populations. We found almost complete isolation between the three populations mainly due to premating extrinsic barriers. Intrinsic genetic barriers were weak and variable amongst populations. There were asymmetries in some intrinsic barriers due to the origin of cytoplasm in hybrids, which combined with weak selection against hybrids has the potential to facilitate gene flow in the system, specifically from Dune and Headland ecotypes into the Island ecotype. Overall, these results suggest that reproductive isolation between these three populations is almost complete despite the absence of geographic barriers, and that the main drivers of this isolation are ecologically based, consistent with the mechanisms underlying ecological speciation.
Data from: Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean
Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.
Data from: Genome divergence and the genetic architecture of barriers to gene flow between Lycaeides idas and L. melissa
Genome divergence during speciation is a dynamic process that is affected by various factors, including the genetic architecture of barriers to gene flow. Herein we quantitatively describe aspects of the genetic architecture of two sets of traits, male genitalic morphology and oviposition preference, that putatively function as barriers to gene flow between the butterfly species Lycaeides idas and L. melissa. Our analyses are based on unmapped DNA sequence data and a recently developed Bayesian regression approach that includes variable selection and explicit parameters for the genetic architecture of traits. A modest number of nucleotide polymorphisms explained a small to large proportion of the variation in each trait, and average genetic variant effects were non-negligible. Several genetic regions were associated with variation in multiple traits or with trait variation within- and among-populations. In some instances genetic regions associated with trait variation also exhibited exceptional genetic differentiation between speices or exceptional introgression in hybrids. These results are consistent with the hypothesis that divergent selection on male genitalia has contributed to heterogeneous genetic differentiation, and that both sets of traits affect fitness in hybrids. Although these results are encouraging, we highlight several difficulties related to understanding the genetics of speciation.
Data from: Geographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest-savannah biome transition as a barrier to gene flow
The primary Afrotropical malaria mosquito vector Anopheles gambiae sensu stricto has a complex population structure. In western Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviours. To investigate patterns of macro-geographic population substructure, 25 An. gambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M-form being subdivided into distinct west, central and southern African genetic clusters. These clusters are coincident with the central African rainforest belt and northern and southern savannah biomes, which suggests restrictions to gene flow associated with the transition between these biomes. By contrast geographically patterned population substructure appears much weaker within the S-form.
Data from: Quantification of the zygotic barrier between interbreeding taxa using gene flow data
Hybridization and introgression via interspecific gene flow are common processes in the plant kingdom. The effectiveness of these processes is governed by the strengths of multiple zygotic barriers. These barriers have often been quantified in artificial settings using laborious and time-consuming hand-pollination experiments, but their quantification is nonexistent at the landscape level. In this study, we utilized gene flow data within a spatially explicit simulation to assess the strengths of zygotic barriers. Our model system consisted of Populusnigra and its hybrid, P.×canadensis, which interbreed under natural conditions. The study population was located in the floodplain of the Eder River in Central Germany. Pollen-mediated introgression rates from hybrid males into the seeds of individual female trees were used as the target pattern using an inverse modeling approach. Simulations that treated pollen from both taxa equally revealed a large discrepancy between the observed and modeled rates of introgression for both taxa. The discrepancy was reduced by introducing a zygotic barrier against the pollen from the hybrid males. The best model outcome indicated comparably strong zygotic barriers acting against pollen-mediated introgressive gene flow into the two parental taxa, P.nigra and P.×canadensis. The sensitivity of our model was tested by applying different dispersal functions. Four common probability density functions were used along with a pollen dispersal function that had previously been fitted to gene flow data from the same dataset. The best barrier value was almost independent of the dispersal functions used here. Moreover, it was within the range previously determined in hand-pollination-based investigations, validating our model. These data indicate that the inverse modeling approach is a powerful method for quantifying hidden processes, and we discuss its use as a valuable tool for generating new insights into plant mating systems that are relevant to evolutionary biology and risk analysis in conservation efforts
Data from: Hybridization and barriers to gene flow in an island bird radiation
While reinforcement may play a role in all major modes of speciation, relatively little is known about the timescale over which species hybridize without evolving complete reproductive isolation. Birds have high potential for hybridization, and islands provide simple settings for uncovering speciation and hybridization patterns. Here we develop a phylogenetic hypothesis for a phenotypically-diverse radiation of finch-like weaver-birds (Foudia) endemic to the western Indian Ocean islands. We find that unlike Darwin's finches, each island-endemic Foudia population is a monophyletic entity for which speciation can be considered complete. In explaining the only exceptions – mismatches between taxonomy, mitochondrial and nuclear data – phylogenetic and coalescent methods support introgressive hybridization rather than incomplete lineage sorting. Human introductions of known timing of one island-endemic species, to all surrounding archipelagos provide two fortuitous experiments; (1) population sampling at known times in recent evolutionary history, (2) bringing allopatric lineages of an island radiation into secondary contact. Our results put a minimum time bound on introgression (235 years), and support hybridization between species in natural close contact (parapatry), but not between those in natural allopatry brought into contact by human introduction. Time in allopatry, rather than in sympatry, appears key in the reproductive isolation of Foudia species.
Data from: Hybrid speciation in sparrows I: phenotypic intermediacy, genetic admixture and barriers to gene flow
Homoploid hybrid speciation is thought to require unusual circumstances to yield reproductive isolation from the parental species, and few examples are known from nature. Here we present genetic evidence for this mode of speciation in birds. Using Bayesian assignment analyses of 751 individuals genotyped for 14 unlinked, nuclear microsatellite loci, we show that the phenotypically intermediate Italian sparrow (Passer italiae) does not form a cluster of its own, but instead exhibits clear admixture (over its entire breeding range) between its putative parental species, the house sparrow (P. domesticus) and the Spanish sparrow (P. hispaniolensis). Further, the Italian sparrow possesses mitochondrial (mt) DNA haplotypes identical to both putative parental species (although mostly of house sparrow origin), indicating a recent hybrid origin. Today, the Italian sparrow has a largely allopatric distribution on the Italian peninsula and some Mediterranean islands separated from its suggested parental species by the Alps and the Mediterranean Sea, but occurs sympatrically with the Spanish sparrow on the Gargano peninsula in southeast Italy. No evidence of interbreeding was found in this sympatric population. However, the Italian sparrow hybridizes with the house sparrow in a sparsely populated contact zone in the Alps. Yet, the contact zone is characterized by steep clines in species-specific male plumage traits, suggesting that partial reproductive isolation may also have developed between these two taxa. Thus, geographic and reproductive barriers restrict gene flow into the nascent hybrid species. We propose that an origin of hybrid species where the hybrid lineage gets geographically isolated from the parental species, as seems to have happened here, might be more common in nature than previously assumed.
Data from: Contemporary human-altered landscapes and oceanic barriers limit bumble bee gene flow
Much of the world's terrestrial landscape is being altered by humans in the form of agriculture, urbanization, and pastoral systems, with major implications for biodiversity. Bumble bees are one of the most effective pollinators in both natural and cultivated landscapes, but are often the first to be extirpated in human-altered habitats. Yet, little is known about the role of natural and human-altered habitats in promoting or limiting bumble bee gene flow. In this study, I closely examine the genetic structure of the yellow-faced bumble bee, Bombus vosnesenskii, across the south-western US coast and find strong evidence that natural oceanic barriers, as well as contemporary human-altered habitats, limit bee gene flow. Heterozygosity and allelic richness were lower in island populations, while private allelic richness was higher in island populations compared to mainland populations. Genetic differentiation, measured for three indices across the 1000km study region, was significantly greater than the null expectation (FST =0.041, F'ST=0.044, Dest=0.155) and correlated with geographic distance. Furthermore, genetic differentiation patterns were most strongly correlated with contemporary (2011) not past (2006, 2001) resistance maps calibrated for high dispersal limitation over oceans, impervious habitat, and croplands. Despite the incorporation of dramatic elevation gradients, the analyses reveal that oceans and contemporary human land use, not mountains, are the primary dispersal barriers for B. vosnesenskii gene flow. These findings reinforce the importance of maintaining corridors of suitable habitat across the distribution range of native pollinators to promote their persistence and safeguard their ability to provide essential pollination services.
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