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794 results for “Gene flow”
Fig. 3 in Limited gene flow among Cydia pomonella (Lepidoptera: Tortricidae) populations in two isolated regions in China: Implications for utilization of the SIT
Fig. 3. Dendrogram generated by NJ analysis representing the genetic distance among populations of Cydia pomonella. The topology was tested by bootstrap analysis with 1,000 replicates. The scale bar represents 2.0% genetic distance. The sampling locations include JinTa (JJT), YinDa (JYD), XiDong (JXD) and ZongZai (JZZ) of Jiuquan Region, and Luo Tuocheng (ZLT), NiJiaying (ZNJ), MinYong (ZMY) and XiaoMan (ZXM) of Zhangye Region.
Fig. 1 in Limited gene flow among Cydia pomonella (Lepidoptera: Tortricidae) populations in two isolated regions in China: Implications for utilization of the SIT
Fig. 1. Sampling regions and locations of Cydia pomonella in Hexi Corridor of China. (I) map of China, the Hexi Corridor is indicated in the dash box; (II) enlarged map of Hexi Corridor, the 2 sampling regions are indicated as (A) Jiuquan region and (B) Zhangye region; (III) enlarged map of the sampling regions and sampling locations. The sampling locations includes JinTa (JJT), YinDa (JYD), XiDong (JXD), and ZongZai (JZZ) of the Jiuquan Region, and Luo Tuocheng (ZLT), NiJiaying (ZNJ), MinYong (ZMY) and XiaoMan (ZXM) of the Zhangye Region.
Fig. 2 in Limited gene flow among Cydia pomonella (Lepidoptera: Tortricidae) populations in two isolated regions in China: Implications for utilization of the SIT
Fig. 2. Bayesian clustering analysis by use of STRUCTURE, which indicates the presence of 2 clusters. Proportion of membership coefficient for 8 Cydia pomonella populations falling into the 2 clusters is depicted by 2 different shades of gray, respectively. The sampling locations include JinTa (JJT), YinDa (JYD), XiDong (JXD) and ZongZai (JZZ) of Jiuquan Region, and Luo Tuocheng (ZLT), NiJiaying (ZNJ), MinYong (ZMY) and XiaoMan (ZXM) of Zhangye Region.
Fig. 4 in Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile.
Fig. 4. Results of the Geneland analysis. A: Bar plot of posterior probability density according to the number of clusters; B: posterior probability maps for the delimited clusters.
Fig. 3 in Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile.
Fig. 3. Pairwise FST between localities of Telmatobius pefauri obtained using mitochondrial (A) and microsatellite (B) data. The colour scale corresponding to the values of FST is shown to the right of each matrix. Significant (Bonferroni corrected) comparisons showing p <0.05, p <0.01 and p <0.001 are denoted by *, ** and ***, respectively.
Fig. 2 in Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile.
Fig. 2. Median-joining network based on the fragment of the analysed control region. Table 1. Indices of mitochondrial diversity, nuclear diversity, and inbreeding coefficients (FIS) by locality
Fig. 1 in Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile.
Fig. 1. Study area, distribution of Telmatobius pefauri. Localities, 1: Socoroma (Socoroma River); 2: Murmuntani; 3: Copaquilla; 4: Chapiquiña; 5: Belén; 6: Lupica; 7: Saxamar. Localities 2 and 3 belong to the Seco River drainage; localities 4–7 belong to the Tignamar River drainage. Basin limits are indicated with dashed lines. The inset map shows the study area (highlighted by a red box) in relation to South America. SAAD = South American Arid Diagonal.
Fig. 5 in Drainage Network Morphology Influences Population Structure and Gene Flow of the Andean Water Frog (Anura: Telmatobiidae) of the Atacama Desert, Northern Chile.
Fig. 5. Scatter plot for the first two principal components obtained in the Principal Components Analysis using SSR data.
Figure 1 in Gene Flow Patterns of the Aedes aegypti (Diptera: Culicidae) Mosquito in Colombia: a Continental Comparison Suggests Multiple Invasion Routes and Gene Exchange
Figure 1 Geographic location of the A. aegypti populations included in this study and gene-flow models evaluated. In both graphics, circles indicate the populations and arrows represent the gene flow between populations. A) Scale at American continent level (N = 2,996 specimens from six locations: Mexico – North America (M-NA), Venezuela (VZ), Peru (PE), Brazilian Amazon (BrAm), southeastern Brazil (SEBr), and Colombia (CO). B) Scale at South America level (N = 1,083 specimens from six locations: Venezuela, Peru, Brazilian Amazon (5 locations; Brazilian Amazon (BrAM), Manaus (MAO), Belém (BL). Boa Vista (BV), Rio Branco (RB), Porto Velho (PV)), Southeastern Brazil (SEBr) and Colombia (2 locations; Sucre (S), Quindio (Q)).
Figure 4. Phylogeny constructed through Bayesian inference estimated from the 35H in Gene Flow Patterns of the Aedes aegypti (Diptera: Culicidae) Mosquito in Colombia: a Continental Comparison Suggests Multiple Invasion Routes and Gene Exchange
Figure 4. Phylogeny constructed through Bayesian inference estimated from the 35H found of the ND4 gene for the A. aegypti populations in the American continent. The blue horizontal bars above the branches reflect the 95% CI for the branch supports. The color bars (blue, green, and red) on the tree terminals indicate which haplotypes are exclusive for a specific population. The dotted lines on the right side of the tree and numbers I or II indicate to what clade each of the terminals belong. H1-Col (Colombia (Sucre and Quindio), Venezuela, Peru, M-NA, Brasil (MA-O, RBPV, SEBr, BE-L)), H4 (Venezuela, M-NA, Brasil (MA-O, RBPV, BEL)), H3 (Venezuela, M-NA, Brazil (RBPV, SEBr, BE-L)), H2-Col (Colombia (Sucre), Venezuela, Peru, M-NA, Brazil (RBPV, SEBr, BE-L)), H13 (M-NA, Brazil (SEBr)), H8 (Venezuela, Brazil (SEBr)).
Figure 3 in Gene Flow Patterns of the Aedes aegypti (Diptera: Culicidae) Mosquito in Colombia: a Continental Comparison Suggests Multiple Invasion Routes and Gene Exchange
Figure 3. Representation of the gene-flow model with greater subsequent probability in the scenarios of the Americas and South America.A. Scale at American continent level (N = 2,996 specimens from six locations: Mexico–North America, Venezuela, Peru, Brazilian Amazon, southeastern Brazil, and Colombia. Within the continent context, the Stepping Stone 1 model shows through the green vectors the way the gene flow occurs among the different populations evaluated. B. Scale at South America level; the Full-migration model indicates migration among all the populations, hence, plotting of the potential migration routes through passive land transport (Pan-American highway) and riverine paths (principal rivers).
Balancing selection at a wing pattern locus is associated with major shifts in genome-wide patterns of diversity and gene flow
<p>Selection shapes genetic diversity around target mutations, yet little is known about how selection on specific loci affects the genetic trajectories of populations, including their genome-wide patterns of diversity and demographic responses. Here we study the patterns of genetic variation and geographic structure in a neotropical butterfly, <em>Heliconius numata</em>, and its closely related allies in the so-called melpomene-silvaniform clade. <em>H. numata</em> is known to have evolved an inversion supergene which controls variation in wing patterns involved in mimicry associations with distinct groups of co-mimics. Butterflies show disassortative mate preferences and heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) among extant polymorphic and monomorphic populations of <em>H. numata</em>, 2) between <em>H. numata</em> and its close relatives, and 3) between ancestral lineages. We show that <em>H. numata</em> populations which carry the inversions as a balanced polymorphism show markedly distinct patterns of diversity compared to all other taxa. They show the highest genetic diversity and effective population size estimates in the entire clade, as well as a low level of geographic structure and isolation by distance across the entire Amazon basin. By contrast, monomorphic populations of <em>H. numata</em> as well as its sister species and their ancestral lineages all show lower effective population sizes and genetic diversity, and higher levels of geographical structure across the continent. One hypothesis is that the large effective population size of polymorphic populations could be caused by the shift to a regime of balancing selection due to the genetic load and disassortative preferences associated with inversions. Testing this hypothesis with forward simulations supported the observation of increased diversity in populations with the supergene. Our results are consistent with the hypothesis that the formation of a supergene triggered a change in gene flow, causing a general increase in genetic diversity and the homogenisation of genomes at the continental scale.</p>
Lack of pollinators selects for increased selfing, restricted gene flow and resource allocation in the rare Mediterranean sage Salvia brachyodon
<p>Salvia brachyodon (Lamiaceae): raw data on flower morphometry, nectar concentration and volume and seed weight according various pollination treatments.</p>
Data for: Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow
<p>Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome-wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplain forest, and riverine islands exhibiting progressively lower levels of structure. Although morphological traits used as proxies for individual-level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species from more dynamic riverine habitats. Our results suggest that the habitat in which a species occurs drives the degree of population genetic structuring via its impact on long-term fluctuations in levels of gene flow, with species in highly dynamic habitats having particularly elevated gene flow. These differences in genetic variation across taxa specialized in distinct habitats may lead to disparate responses to environmental change or habitat-specific diversification dynamics over evolutionary time scales.</p>
Sexual recombination and temporal gene flow maintain host resistance and genetic diversity
<p>Infectious disease can threaten host populations. Hosts can rapidly evolve resistance during epidemics, with this evolution often modulated by fitness trade-offs (e.g., between resistance and fecundity). However, many organisms switch between asexual and sexual reproduction, and this shift in reproductive strategy can also alter how resistance in host populations persists through time. Recombination can shuffle alleles selected for during an asexual phase, uncoupling the combinations of alleles that facilitated resistance to parasites and altering the distribution of resistance phenotypes in populations. Furthermore, in host species that produce diapausing propagules (e.g., seeds, spores, or resting eggs) after sex, accumulation of propagules into and gene flow out of a germ bank introduce allele combinations from past populations. Thus, recombination and gene flow might shift populations away from the trait distribution reached after selection by parasites. To understand how recombination and gene flow alter host population resistance, we tracked the genotypic diversity and resistance distributions of two wild populations of cyclical parthenogens. In one population, resistance and genetic diversity increased after recombination whereas, in the other, recombination did not shift already high resistance and genetic diversity. In both lakes, resistance remained high after temporal gene flow. This observation surprised us: due to costs to resistance imposed by a fecundity-resistance trade-off, we expected that high population resistance would be a transient state that would be eroded through time by recombination and gene flow. Instead, low resistance was the transient state, while recombination and gene flow re-established or maintained high resistance to this virulent parasite. We propose this outcome may have been driven by the joint influence of fitness trade-offs, genetic slippage after recombination, and temporal gene flow via the egg bank.</p>
Supplementary material for: PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow
<p>We consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This model generalizes two traditional versions of the network coalescent: with independent or common inheritance. At each reticulation, multiple lineages of a given locus are inherited from parental populations chosen at random, either independently across lineages, or with positive correlation according to a Dirichlet process. This process may account for locus-specific probabilities of inheritance, for example.</p> <p>We implemented the simulation of gene trees under these network coalescent models in the Julia package PhyloCoalSimulations, which depends on PhyloNetworks and its powerful network manipulation tools. Input species phylogenies can be read in extended Newick format, either in numbers of generations or in coalescent units. Simulated gene trees can be written in Newick format, and in a way that preserves information about their embedding within the species network. This embedding can be used for downstream purposes, such as to simulate species-specific processes like rate variation across species, or for other scenarios as illustrated in this note. This package should be useful for simulation studies and simulation-based inference methods. The software is available open source with documentation and a tutorial at <a href="https://github.com/cecileane/PhyloCoalSimulations.jl">https://github.com/cecileane/PhyloCoalSimulations.jl</a>.</p>
Semipermeable species boundaries create opportunities for gene flow and adaptive potential
<p><span>Hybridisation and gene flow can have both deleterious and adaptive consequences for natural populations and species. To better understand the extent of hybridisation in nature and the balance between its beneficial and deleterious outcomes in a changing environment, information on naturally hybridising non-model organisms is needed. This requires the characterisation of the structure and extent of natural hybrid zones. Here we study natural populations of five keystone mound-building wood ant species in the <em>Formica</em> <em>rufa</em> group across Finland. No genomic studies across the species group exist, and the extent of hybridisation and genomic differentiation in sympatry is unknown. Combining genome-wide and morphological data, we demonstrate more extensive hybridisation than was previously detected between all five species in Finland. Specifically, we reveal a mosaic hybrid zone between <em>F. aquilonia, F. rufa </em>and<em> F. polyctena</em>, comprising further generation hybrid populations. Despite this, we find that <em>Formica rufa, F. aquilonia, F. lugubris, </em>and<em> F. pratensis</em> form distinct gene pools in Finland. We also find that hybrids occupy warmer microhabitats than the non-admixed populations of cold-adapted F. aquilonia, and suggest that warm winters and springs, in particular, may benefit hybrids over <em>F. aquilonia</em>, the most abundant <em>F. rufa</em> group species in Finland. In summary, our results indicate that extensive hybridisation may create adaptive potential that could promote wood ant persistence in a changing climate. Additionally, they highlight the potentially significant ecological and evolutionary consequences of extensive mosaic hybrid zones, within which independent hybrid populations face an array of ecological and intrinsic selection pressures.</span></p>
Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks
<p>In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HyDe to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program bpp to reanalyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HyDe, and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data.</p>
Data and scripts for the colour analysis from: Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish
<p>Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on <em>Amphiprion clarkii </em>(Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of <em>A. clarkii</em> has been under debate. We used whole-genome resequencing data of 67 <em>A. clarkii</em> specimens spread across the Indian and Pacific Oceans to characterise the species' population structure, demographic history, and colour polymorphism. We found that <em>A. clarkii</em> spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasises how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm.</p>
Supplementary material for: PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow
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