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112 results for “divergence with gene flow”
Genomic and phenotypic divergence‐with‐gene‐flow across an ecological and elevational gradient in a neotropical bird
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Data from: Genetic divergence and one-way gene flow influence contemporary evolution and ecology of a partially migratory fish
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Data from: Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea)
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Faster‐haplodiploid evolution under divergence‐with‐gene‐flow: Simulations and empirical data from pine‐feeding hymenopterans
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Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow
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Phylogenomic analysis reveals dispersal-driven speciation and divergence with gene flow in Lesser Sunda Flying Lizards (Genus Draco)
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Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination
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Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella
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Data and Code for: Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia
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Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds
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Estimation of species divergence times in presence of cross-species gene flow
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Ecological divergence and the history of gene flow in the Nearctic milksnakes (Lampropeltis triangulum complex)
<p>Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers to gene flow. These studies may conclude absence of population structure, lineage structure that indicates unique species have been discovered, or suggest more research is needed prior to delimitation. Comparative risks of delimiting species incorrectly or failing to delimit species are usually not weighed and a more detailed return to these problems with more data often does not occur. With genomic data and better modeling capabilities we can more clearly delimit species by understanding causes of speciation with respect to biogeography and migration between lineages, the location of hybrid zones in relationship to the ecology of parental lineages, and differential introgression of genes between taxa. Here we examine the origins of three Nearctic milksnakes (<i>Lampropeltis elapsoides, L. triangulum, </i>and <i>L. gentilis</i>) using genomic-scale data to better understand the diversification of these taxa previously delimited based on a smaller genetic dataset. Methods that reject pure isolation by distance in favor of environmentally driven reduction in gene flow clearly indicate that all three lineages should continue to be recognized as unique species. These results underscore conspicuous environmental changes that occur between the sister-taxa forming due to changes in habitat from the Great Plains (GP) to the forested regions of the Eastern Nearctic (ENA). This area has been recognized for turnover of reptile and amphibian species but with few phylogeographic studies examining environmental-genetic structure in this region. We show that the two species meeting at the GP/ENA, <i>L. triangulum </i>and <i>L. gentilis</i>, likely formed in the mid-Pleistocene and have maintained partial reproductive isolation over much of this time, exchanging fewer than one migrant/generation, and formed a hybrid zone with differential introgression of loci. We also show that when <i>L. triangulum</i> and <i>L. gentilis</i> are each in contact with the much older <i>L. elapsoides</i>, some limited gene flow has occurred. We conclude that phylogenetic reticulation in this genus, and likely for many other taxa, is common across throughout time. Furthermore, the application of the biological species concept to the whole genome will give rise to grave misunderstandings of the complexities of how species form and remain unique even in the face of gene flow.</p>
Effect of the Central American Isthmus on gene flow and divergence of the American crocodile Crocodylus acutus
<p>The final formation of the Central American Isthmus (CAI) about 3.5 Ma altered global ocean circulation, connected North and South America terrestrial biotas and established the Caribbean Sea. The nature of this event creates a natural scenario to test vicariance, divergence, and speciation by allopatry. Studies have shown the effect of the CAI on marine and terrestrial species, but none have examined a large-bodied amphibious taxon. We used RAD sequencing on populations of the American crocodile <em>Crocodylus acutus</em>, to study the genomic variation of <em>C. acutus</em> on both sides of the CAI, infer its demographic history and measure the effect of the opening of the Panama Canal. Our results showed three genomic clusters: 1) Caribbean and the Panama Canal, 2) Pacific coast, and 3) Coiba island. The estimated divergence times between the Caribbean and Pacific populations are about 20 ka, which is two orders of magnitude younger than the formation of the CAI, but coincides with the Last Glacial Maximum. We hypothesize the glacial/interglacial cycles facilitated gene flow between the Caribbean and Pacific crocodile populations after the formation of the CAI, masking any genomic divergence the CAI may have caused. There is no evidence of gene flow associated with the opening of the Panama Canal.</p>
Data from: Genome-wide patterns of divergence and gene flow across a butterfly radiation
The Heliconius butterflies are a diverse recent radiation comprising multiple levels of divergence with on-going gene flow between species. The recently sequenced genome of Heliconius melpomene allowed us to investigate the genomic evolution of this group using dense RAD marker sequencing. Phylogenetic analysis of 54 individuals robustly supported reciprocal monophyly of H. melpomene and H. cydno and refuted previous phylogenetic hypotheses that H. melpomene may be paraphylectic with respect to H. cydno. H. timareta also formed a monophyletic clade closely related but distinct from H. cydno with H. heurippa falling within this clade. We find evidence for pervasive gene flow between sympatric populations of the sister clades H. melpomene and H. cydno/timareta, particularly between H. cydno and H. melpomene from Central America and between H. timareta and H. melpomene from the eastern slopes of the Andes. Between races, divergence is primarily explained by isolation-by-distance; and there is little, if any, genetic population structure between parapatric races, suggesting that hybrid zones between races are not zones of secondary contact. Our results support previous findings that colour pattern loci are shared between populations and species with similar colour pattern elements. Further this pattern is almost unique to these genomic regions with only a very small number of other loci showing significant similarity between populations and species with similar colour patterns.
Data from: Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow
The demographic and phylogeographic histories of species provide insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of species histories with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird (Xenops minutus). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited in areas between these barriers. In addition, we inferred positive population growth for most populations and detected evidence of historical gene flow between populations that are now physically isolated. Although we were able to reconstruct the history of Xenops minutus with unprecedented resolution, we had difficulty conclusively relating this history to the landscape events implicated in many Neotropical diversification hypotheses. We suggest that even if many traditional diversification hypotheses remain untestable, investigations using genomic datasets will provide greater resolution of species histories in the Neotropics and elsewhere.
Data from: Ecological disturbance influences adaptive divergence despite high gene flow in golden perch (Macquaria ambigua): implications for management and resilience to climate change
Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia using a genome-wide SNP dataset. The MDB spans across arid to wet and temperate to sub-tropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow, and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management.
Data from: How populations differentiate despite gene flow: sexual and natural selection drive phenotypic divergence within a land fish, the Pacific leaping blenny
Background: Divergence between populations in reproductively important features is often vital for speciation. Many studies attempt to identify the cause of population differentiation in phenotype through the study of a specific selection pressure. Holistic studies that consider the interaction of several contrasting forms of selection are more rare. Most studies also fail to consider the history of connectivity among populations and the potential for genetic drift or gene flow to facilitate or limit phenotypic divergence. We examined the interacting effects of natural selection, sexual selection and the history of connectivity on phenotypic differentiation among five populations of the Pacific leaping blenny (Alticus arnoldorum), a land fish endemic to the island of Guam. Results: We found key differences among populations in two male ornaments—the size of a prominent head crest and conspicuousness of a coloured dorsal fin—that reflected a trade-off between the intensity of sexual selection (male biased sex ratios) and natural selection (exposure to predators). This differentiation in ornamentation has occurred despite evidence suggesting extensive gene flow among populations, which implies that the change in ornament expression has been recent (and potentially plastic). Conclusions: Our study provides an early snapshot of divergence in reproductively important features that, regardless of whether it reflects genetic or plastic changes in phenotype, could ultimately form a reproductive barrier among populations.
Data from: Estimating the impact of divergent mating phenology between residents and migrants on the potential for gene flow
Gene flow between populations can allow the spread of beneficial alleles and genetic diversity between populations, with importance to conservation, invasion biology, and agriculture. Levels of gene flow between populations vary not only with distance, but also with divergence in reproductive phenology. Since phenology is often locally adapted, arriving migrants may be reproductively out of synch with residents, which can depress realized gene flow. In flowering plants, the potential impact of phenological divergence on hybridization between populations can be predicted from overlap in flowering schedules—the daily count of flowers capable of pollen exchange—between a resident and migrant population. The accuracy of this prospective hybridization estimate, based on parental phenotypes, rests upon the assumptions of unbiased pollen transfer between resident and migrant active flowers. We tested the impact of phenological divergence on resident–migrant mating frequencies in experiments that mimicked a single large gene flow event. We first prospectively estimated mating frequencies two lines of Brassica rapaselected or early and late flowering. We then estimated realized mating frequencies retrospectively through progeny testing. The two estimates strongly agreed in a greenhouse experiment, where procedures ensured saturating, unbiased pollination. Under natural pollination in the field, the rate of resident–migrant mating, was lower than estimated by phenological divergence alone, although prospective and retrospective estimates were correlated. In both experiments, differences between residents and migrants in flowering schedule shape led to asymmetric hybridization. Results suggest that a prospective estimate of hybridization based on mating schedules can be a useful, although imperfect, tool for evaluating potential gene flow. They also illustrate the impact of mating phenology on the magnitude and symmetry of reproductive isolation.
Data from: Local selection modifies phenotypic divergence among Rana temporaria populations in the presence of gene flow
In ectotherms, variation in life-history traits among populations is common and suggests local adaptation. However, geographic variation itself is not a proof for local adaptation, since genetic drift and gene flow may also shape patterns of quantitative variation. We studied local and regional variation in means and phenotypic plasticity of larval life history traits in the common frog Rana temporaria using six populations from central Sweden, breeding in either open canopy or partially closed canopy ponds. To separate local adaptation from genetic drift we compared differentiation in quantitative genetic traits (QST) obtained from a common garden experiment with differentiation in presumably neutral microsatellite markers (FST). We found that R. temporaria populations differ in means and plasticities of life-history traits in different temperatures at local, and in Fst at regional scale. Comparisons of differentiation in quantitative traits and in molecular markers suggested that natural selection was responsible for the divergence in growth and development rates as well as in temperature-induced plasticity, indicating local adaptation. However, at low temperature the role of genetic drift could not be separated from selection. Phenotypes were correlated with forest canopy closure but not with geographical or genetic distance. These results indicate that local adaptation can evolve in the presence of ongoing gene flow among populations, and that natural selection is strong in this system.
Data from: Genetic divergence with ongoing gene flow is maintained by the use of different hosts in phytophagous ladybird beetles genus Henosepilachna
Adaptation to different environments can promote population divergence via natural selection even in the presence of gene flow–a phenomenon that typically occurs during ecological speciation. To elucidate how natural selection promotes and maintains population divergence during speciation, we investigated the population genetic structure, degree of gene flow and heterogeneous genomic divergence in three closely related Japanese phytophagous ladybird beetles: Henosepilachna pustulosa, H. niponica and H. yasutomii. These species act as a generalist, a wild thistle (Cirsium spp.) specialist and a blue cohosh (Caulophyllum robustum) specialist, respectively, and their ranges differ accordingly. The two specialist species widely co-occur but are reproductively isolated solely due to their high specialisation to a particular host plant. Genome-wide amplified fragment-length polymorphism (AFLP) markers and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences demonstrated obvious genome-wide divergence associated with both geographic distance and ecological divergence. However, a hybridisation assessment for both AFLP loci and the mitochondrial sequences revealed a certain degree of unidirectional gene flow between the two sympatric specialist species. Principal coordinates analysis (PCoA) based on all of the variable AFLP loci demonstrated that there are genetic similarities between populations from adjacent localities irrespective of the species (i.e. host range). However, a further comparative genome scan identified a few fractions of loci representing approximately 1% of all loci as different-host associated outliers. These results suggest that these three species had a complex origin, which could be obscured by current gene flow, and that ecological divergence can be maintained with only a small fraction of the genome is related to different host use even when there is a certain degree of gene flow between sympatric species pairs.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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