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794 results for “Gene flow”
Coevolving plasmids drive gene flow and genome plasticity in host-associated intracellular bacteria
<p>Comparative genomics and modeling of plasmids of the obligate host-associated intracellular phylum chlamydiae. </p>
Microsatellite genotype data and leaf morphological data of the publication "Bidirectional gene flow between Fagus sylvatica L. and F. orientalis Lipsky despite strong genetic divergence"
<p>These data sets were used for analyses in the publication "Bidirectional gene flow between <em>Fagus sylvatica</em> L. and<em> F. orientalis</em> Lipsky despite strong genetic divergence" accepted in Forest Ecology and Management <a href="https://www.sciencedirect.com/journal/forest-ecology-and-management/vol/537/suppl/C">Volume 537</a>, 1 June 2023, 120947, <a href="https://doi.org/10.1016/j.foreco.2023.120947">https://doi.org/10.1016/j.foreco.2023.120947</a></p> <p>For details about the data, please read the corresponding ReadMe files.</p>
Divergence, gene flow and the origin of leapfrog geographic distributions: the history of color pattern variation in Phyllobates poison-dart frogs
<p>The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. Phyllobates poison frogs. We found evidence for high levels of gene flow between neighboring populations but not over long distances, indicating that gene flow between populations exhibiting the central phenotype may have a homogenizing effect that maintains their similarity, and that introgression between "leapfroging" taxa has not played a prominent role as a driver of phenotypic diversity in <i>Phyllobates</i>. Although phylogenetic analyses suggest that the leapfrog distribution was formed through independent evolution of the peripheral (i.e. leapfrogging) populations, the elevated levels of gene flow between geographically close populations poise alternative scenarios, such as the history of phenotypic change becoming decoupled from genome-averaged patterns of divergence, which we cannot rule out. These results highlight the importance of incorporating gene flow between populations into the study of geographic variation in phenotypes, both as a driver of phenotypic diversity and as a confounding factor of phylogeographic inferences.</p>
Mapped read data and files and scripts from: Vicariance followed by secondary gene flow in a young gazelle species complex
<p>Grant's gazelles have recently been proposed to be a species complex comprising three highly divergent mtDNA lineages (<em>Nanger granti</em>, <em>N. notata</em> and <em>N. petersii</em>). The three lineages have non-overlapping distributions in East Africa, but without any obvious geographical divisions, making them an interesting model for studying the early stage evolutionary dynamics of allopatric speciation in detail. Here we use genomic data obtained by restriction site-associated (RAD) sequencing of 106 gazelle individuals to shed light on the evolutionary processes underlying Grant's gazelle divergence, to characterize their genetic structure and to assess the presence of gene flow between the main lineages in the species complex. We date the species divergence to 134,000 years ago, which is recent in evolutionary terms. We find population subdivision within <em>N. granti</em>, which coincides with the previously suggested two subspecies, <em>N.g. granti</em> and <em>N.g. robertsii</em>. Moreover, these two lineages seem to have hybridized in Masai Mara. Perhaps more surprisingly given their extreme genetic differentiation, <em>N. granti</em> and <em>N. petersii</em> also show signs of prolonged admixture in Mkomazi, which we identified as a hybrid population most likely founded by allopatric lineages coming into secondary contact. Despite the admixed composition of this population, elevated X-chromosomal differentiation suggests that selection may be shaping the outcome of hybridization in this population. Our results therefore provide detailed insights into the processes of allopatric speciation and secondary contact in a recently radiated species complex.</p>
Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.
Data from: Independently evolved and gene flow‐accelerated pesticide resistance in two‐spotted spider mites
<p>Pest species are often able to develop resistance to pesticides used to control them, depending on how rapidly resistance can emerge within a population or spread from another resistant population. We examined the evolution of bifenazate resistance in China in the two‐spotted spider mite (TSSM) <em>Tetranychus</em> <em>uticae</em> Koch (Acari: Tetranychidae), one of the most resistant arthropods, by using bioassays, detection of mutations in the target <em>cytb</em> gene, and population genetic structure analysis using microsatellite markers. Bioassays showed variable levels of resistance to bifenazate. The <em>cytb</em> mutation G126S, which confers medium resistance in TSSM to bifenazate, had previously been detected prior to the application of bifenazate and was now widespread, suggesting likely resistance evolution from standing genetic variation. G126S was detected in geographically distant populations across different genetic clusters, pointing to the independent origin of this mutation in different TSSM populations. A novel A269V mutation linked to a low‐level resistance was detected in two southern populations. Widespread resistance associated with a high frequency of the G126S allele was found in four populations from the Beijing area which were not genetically differentiated. In this case, a high level of gene flows likely accelerated the development of resistance within this local region, as well as into an outlying region distant from Beijing. These findings, therefore, suggest patterns consistent with both local evolution of pesticide resistance as well as an impact of migration, helping to inform resistance management strategies in TSSM.</p>
Interspecific introgression and widespread intraspecific gene flow in a clade of tropical and subtropical seabirds
<p>The mechanisms that restrict gene flow between populations and facilitate population differentiation and speciation vary across the tree of life. In systems where physical barriers to gene flow are dynamic over time and space, such as many marine species, genetic introgression may be a major factor in the speciation process. In sympatric species of seabirds, hybridization has been frequently observed but few studies have investigated patterns of introgression. We used whole-genome sequence data to test for interspecific introgression between five pairs of tropical and subtropical seabird species and to test for gene flow within species across major land mass barriers and ocean basins. We found evidence for introgression between: blue-footed (<em>Sula</em> <em>nebouxii</em>) and Peruvian boobies (<em>S. variegata</em>); masked (<em>S. dactylatra</em>) and Nazca boobies (<em>S. granti</em>); and blue-footed and Nazca boobies. We found no evidence of introgression between blue-footed and brown boobies (<em>S. leucogaster</em>), or masked and brown boobies, despite observed hybridization between these species. We also found evidence for gene flow across several major land masses in three pantropical species: red-footed (<em>S. sula</em>), brown, and masked boobies. Finally, we report mixed evidence for ancient introgression between brown boobies and the ancestor of blue-footed, Peruvian, masked, and Nazca boobies. Our work indicates (1) that interspecific introgression has shaped contemporary booby diversity in the eastern Pacific, and (2) that contemporary physical barriers to gene flow between booby colonies are not absolute. Our findings contribute novel insights to the growing body of evidence that introgression is a widespread evolutionary process.</p>
FIGURE 2 in Speciation with gene flow in marine systems
FIGURE 2 Cladogram of the hypotheses of Animalia (after Dunn et al., 2014) and Chromista (after CavalierSmith, 2018) phylogenies. Animalia and Chromista clades in which marine species have been described, are marked blue, with clades in which potential cases of ecological speciation with gene flow Downloaded from Brill.com 12/12/2023 03:01:49PM have been identified in orangevia. Open LettersAccess refer.toThis examples is an of openspecies accessshown articlein fig. 1. distributed under the terms of the prevailing CC-BY license at the time of publication. http://creativecommons.org/licenses/by-nc/4.0
FIGURE 1 in Speciation with gene flow in marine systems
FIGURE 1 Examples of some species which potentially arose through ecological speciation with gene flow. The octocoral Eunicea flexuosa (a; photo by Y.W. Lau), the Caribbean hamlet Hypoplectrus unicolor (b; photo by O. Puebla), the intertidal gastropod Littorina saxatilis (c; photo by P. Larsson), the nudibranch Phestilla minor (d; photo by A. Fritts-Penniman), the Japanese greenling Hexagrammos otakii (e; photo by Z. Kanamoto), the corallivorous gastropod Coralliophila violacea (f; photo by S.E. Simmonds), the Downloaded from Brill.com 12/12/2023 03:01:49PM seahorse Hippocampus erectus (via g; Open photo by Access E.. RoseThis), the is an snapping open access shrimparticle Alpheus armatus distributed(h;under photothe terms by A. Anker), the undescribed, coral-associated of gobytheGobiodon prevailingsp. B (CC-BY i; photo licenseby P. at L. the Mundaytime),of and the publication. Caribbean sponge Chondrilla caribensis (j; photo by N.J. de Voogdhttp):. //creativecommons.org/licenses/by-nc/4.0
FIGURE 3 in Speciation with gene flow in marine systems
FIGURE 3 Genetic mechanisms of single traits driving divergence. Disruptive selection acting on a mating cue (e.g., colour pattern or body size) targeted by a preference locus elsewhere in the genome ('classic magic trait', after Servedio et al., 2011) results into assortative mating (a). In case of habitat or host differentiation and mating on the host species, disruptive selection may directly lead to assortative mating (b), without the need for a preference locus ('automatic magic trait'). Figures after Servedio et al. (2011). Downloaded from Brill.com 12/12/2023 03:01:49PM via Open Access. This is an open access article distributed under the terms of the prevailing CC-BY license at the time of publication. http://creativecommons.org/licenses/by-nc/4.0
Tracing evolutionary trajectories in the presence of gene flow in South American temperate lizards (Squamata: Liolaemus kingii group)
<p>Evolutionary processes behind lineage divergence often involve multidimensional differentiation. However, in the context of recent divergences, the signals exhibited by each dimension may not converge. In such scenarios, incomplete lineage sorting, gene flow, and scarce phenotypic differentiation are pervasive. Here, we integrated genomic (RAD loci of 90 individuals), phenotypic (linear and geometric traits of 823 and 411 individuals, respectively), spatial, and climatic data to reconstruct the evolutionary history of a speciation continuum of liolaemid lizards (<em>Liolaemus kingii</em> group). Specifically, we (i) inferred the population structure of the group and contrasted it with the phenotypic variability; (ii) assessed the role of post-divergence gene flow in shaping phylogeographic and phenotypic patterns; and (iii) explored eco-geographic drivers of diversification across time and space. We inferred eight genomic clusters exhibiting leaky genetic borders coincident with geographic transitions. We also found evidence of post-divergence gene flow resulting in transgressive phenotypic evolution in one species. Predicted ancestral niches unveiled suitable areas in southern and eastern Patagonia during glacial and interglacial periods. Our study underscores integrating different data and model-based approaches to determine the underlying causes of diversification, a challenge faced in the study of recently diverged groups. We also highlight <em>Liolaemus</em> as a model system for phylogeographic and broader evolutionary studies.</p>
Data from: Do genetic loci that cause reproductive isolation in the lab inhibit gene flow in nature?
<p>The genetic dissection of reproductive barriers between diverging lineages provides enticing clues into the origin of species. One strategy uses linkage analysis in experimental crosses to identify genomic locations involved in phenotypes that mediate reproductive isolation. A second framework searches for genomic regions that show reduced rates of exchange across natural hybrid zones. It is often assumed that these approaches will point to the same loci, but this assumption is rarely tested. In this perspective, we discuss the factors that determine whether loci connected to postzygotic reproductive barriers in the laboratory are inferred to reduce gene flow in nature. We synthesize data on the genetics of postzygotic isolation in house mice, one of the most intensively studied systems in speciation genetics. In a rare empirical comparison, we measure the correspondence of loci tied to postzygotic barriers via genetic mapping in the laboratory and loci at which gene flow is inhibited across a natural hybrid zone. We find no evidence that the two sets of loci overlap beyond what is expected by chance. In light of these results, we recommend avenues for empirical and theoretical research to resolve the potential incongruence between the two predominant strategies for understanding the genetics of speciation.</p>
Data from: Restriction site-associated DNA sequencing reveals local adaptation despite high levels of gene flow in Sardinella lemuru (Bleeker, 1853) along the northern coast of Mindanao, Philippines
<p>Stock identification and delineation are important in the management and conservation of marine resources. These were highlighted as priority research areas for Bali sardinella (<em>Sardinella lemuru</em>) which is among the most commercially important fishery resources in the Philippines. Previous studies have already assessed the stocks of <em>S. lemuru</em> between Northern Mindanao Region (NMR) and Northern Zamboanga Peninsula (NZP), yielding conflicting results. Phenotypic variation suggests distinct stocks between the two regions, while mitochondrial DNA did not detect evidence of genetic differentiation for this high gene flow species. This paper tested the hypothesis of regional structuring using genome-wide single nucleotide polymorphisms (SNPs) acquired through restriction-site associated DNA sequencing (RADseq). We examined patterns of population genomic structure using a full panel of 3,573 loci, which was then partitioned into a neutral panel of 3,348 loci and an outlier panel of 31 loci. Similar inferences were obtained from the full and neutral panels, which were contrary to the inferences from the outlier panel. While the full and neutral panels suggested a panmictic population (global F<sub>ST</sub> ~ 0, p > 0.05), the outlier panel revealed genetic differentiation between the two regions (global F<sub>ST</sub> = 0.161, p = 0.001; F<sub>CT</sub> = 0.263, p < 0.05). This indicated that while gene flow is apparent, selective forces due to environmental heterogeneity between the two regions play a role in maintaining adaptive variation. Annotation of the outlier loci returned five genes that were mostly involved in organismal development. Meanwhile, three unannotated loci had allele frequencies that correlated with sea surface temperature. Overall, our results provided support for local adaptation despite high levels of gene flow in <em>S. lemuru</em>. Management therefore should not only focus on demographic parameters (e.g., stock size, catch volume), but also consider the preservation of adaptive variation.</p>
Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures
Genome sequencing of spatially distributed individuals sheds light on how evolution structures genetic variation. Populations of <i>Phellopilus nigrolimitatus</i>, a red-listed wood-inhabiting fungus associated with old-growth coniferous forests, have decreased in size over the last century due to a loss of suitable habitats. We assessed the population genetic structure and investigated local adaptation in<i> P. nigrolimitatus</i>, by establishing a reference genome and genotyping 327 individuals sampled from 24 locations in Northern Europe by RAD sequencing. We revealed a shallow population genetic structure, indicating large historical population sizes and high levels of gene flow. Despite this weak sub-structuring, two genetic groups were recognized; a western group distributed mostly in Norway and an eastern group covering most of Finland, Poland and Russia. This sub-structuring may reflect co-immigration with the main host, Norway spruce (<i>Picea abies</i>), into Northern Europe after the last ice age. We found evidence of low levels of genetic diversity in southwestern Finland, which has a long history of intensive forestry and urbanization. Numerous loci were significantly associated with one or more environmental factors, indicating adaptation to specific environments. These loci clustered into two groups with different associations with temperature and precipitation. Overall, our findings indicate that the current population genetic structure of P. nigrolimitatus results from a combination of gene flow, genetic drift and selection. The acquisition of similar knowledge especially over broad geographic scales, linking signatures of adaptive genetic variation to evolutionary processes and environmental variation, for other fungal species will undoubtedly be useful for assessment of the combined effects of habitat fragmentation and climate change on fungi strongly bound to old-growth forests. --
Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges
<p>The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, e.g., when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species <em>Formica polyctena</em> and <em>F. aquilonia</em>. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent-based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (ca. 500 kya) and occurred with continuous asymmetrical gene flow from <em>F. aquilonia</em> to <em>F. polyctena</em> until a recent time, when migration became negligible (2-19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.</p>
Asymmetric song recognition does not influence gene flow in an emergent songbird hybrid zone
<p>Hybrid zones can be used to examine the mechanisms affecting reproductive isolation and speciation, like song. Song has equivocal support as a driver of speciation; we did not find song to cause reproductive isolation. We examined an emerging secondary contact zone between White-crowned Sparrow subspecies <em>pugetensis </em>and <em>gambelii </em>by measuring song variation, song recognition, plumage, morphology and mtDNA. Plumage and morphological characters provided evidence of hybridization in the contact zone, with some birds possessing plumage and song characteristics intermediate between the subspecies. Playback experiments revealed asymmetric song recognition: male <em>pugetensis </em>displayed greater response to their own song than <em>gambelii </em>song, whereas <em>gambelii </em>did not discriminate significantly. If female choice operates similarly to male song discrimination, we predicted asymmetric gene flow, resulting in a greater number of hybrids with <em>gambelii </em>mitochondrial DNA (mtDNA). Contrary to our prediction, more <em>gambelii </em>and putative hybrids in the contact zone possessed <em>pugetensis </em>mtDNA haplotypes, possibly due to greater <em>pugetensis </em>abundance and female-biased dispersal.</p>
Data from: Inversion Invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow
<p><span></span></p> <p>Across many species where inversions have been implicated in local adaptation, genomes often evolve to contain multiple, large inversions that arise early in divergence. Why this occurs has yet to be resolved. To address this gap, we built forward-time simulations in which inversions have flexible characteristics and can invade a metapopulation undergoing spatially divergent selection for a highly polygenic trait. In our simulations, inversions typically arose early in divergence, captured standing genetic variation upon mutation, and then accumulated many small-effect loci over time. Under special conditions, inversions could also arise late in adaptation and capture locally adapted alleles. Polygenic inversions behaved similarly to a single supergene of large effect and were detectable by genome scans. Our results show that characteristics of adaptive inversions found in empirical studies (e.g., multiple large, old inversions that are FST outliers, sometimes overlapping with other inversions) are consistent with a highly polygenic architecture, and inversions do not need to contain any large-effect genes to play an important role in local adaptation. By combining a population and quantitative genetic framework, our results give a deeper understanding of the specific conditions needed for inversions to be involved in adaptation when the genetic architecture is polygenic.</p>
Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations
<p><span>Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven <em>Quercus canariensis</em> and four <em>Q. faginea</em> rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.</span></p>
Data from: Understanding species boundaries that arise from complex histories: Gene flow across the speciation continuum in the spotted whiptail lizards
<p>Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus <em>Aspidoscelis </em>(<em>A. gularis </em>complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a two species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.</p>
Beyond gene flow: (non)-parallelism of secondary contact in a pair of highly differentiated sibling species
<p>Replicated secondary contact zones can provide insights on the barriers to gene flow that are important during speciation and can reveal to which degree secondary contact may result in similar evolutionary outcomes. Here, we studied two secondary contact zones between highly differentiated Alpine butterflies<em> </em>of the genus <em>Erebia</em> using whole-genome re-sequencing data. We assessed the genomic relationships between populations and species and find hybridization to be rare, with no to little current or historical introgression in either contact zone. There are large similarities between the contact zones, consistent with an allopatric origin of interspecific differentiation, with no indications for ongoing reinforcing selection. Consistent with expected reduced effective population size, we further find that scaffolds related to the Z-chromosome show increased differentiation compared to the already high levels across the entire genome, which could also hint towards a contribution of the Z chromosome to species divergence in this system. Finally, we detected the presence of the endosymbiont <em>Wolbachia</em>, which can cause reproductive isolation between its hosts, in all <em>E. cassioides</em>, while it appears to be fully or largely absent in contact zone populations of <em>E. tyndarus</em>. We discuss how this rare pattern may have arisen and how it may have affected the dynamics of speciation upon secondary contact.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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