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191 results for “Vicariance”
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>
Supplementary material for: Phylogeny and biogeography of the ancient spider family Filistatidae (Araneae) is consistent both with long-distance dispersal and vicariance following continental drift
<p>Raw data and input files for phylogenetic and biogeographic analysis of the article "<strong>Phylogeny and biogeography of the ancient spider family Filistatidae (Araneae) is consistent both with long-distance dispersal and vicariance following continental drift</strong>".</p> <p><strong>Supplementary material S1. </strong>Matrix of phenotypic characters in .ss format.</p> <p><strong>Supplementary material S2. </strong>Alignment of COI sequences in fasta format..</p> <p><strong>Supplementary material S3. </strong>Alignment of H3 sequences in fasta format.</p> <p><strong>Supplementary material S4. </strong>Alignment of 16S sequences in fasta format before trimming with gblocks.</p> <p><strong>Supplementary material S5. </strong>Alignment of 28S sequences in fasta format before trimming with gblocks.</p> <p><strong>Supplementary material S6. </strong>Input for running parsimony analysis using TNT (phenotypic data only).</p> <p><strong>Supplementary material S7. </strong>Input for running Bayesian inference using MrBayes (phenotypic data only).</p> <p><strong>Supplementary material S8. </strong>Input for running parsimony analysis using TNT (sequence data only).</p> <p><strong>Supplementary material S9. </strong>Input for running Bayesian inference using MrBayes (sequence data only).</p> <p><strong>Supplementary material S10. </strong>Input for running parsimony analysis using TNT (total evidence).</p> <p><strong>Supplementary material S11. </strong>Input for running Bayesian inference using MrBayes (total evidence).</p> <p><strong>Supplementary material S12. </strong>Input for running parsimony analysis using TNT (total evidence, dataset with reduced number of terminals).</p> <p><strong>Supplementary material S13. </strong>Input for running Bayesian inference using MrBayes (total evidence, dataset with reduced number of terminals).</p> <p><strong>Supplementary material S14. </strong>Input for running Bayesian inference using MrBayes (total evidence) and estimating node ages using tip-dating.</p> <p><strong>Supplementary material S15. </strong>Input for running Bayesian inference using Beast (sequence data only) and estimating node ages using node-dating.</p> <p><strong>Supplementary material S16. </strong>Raw geographic distances among areas in each time slice and dispersal probability matrices for each biogeographic model.</p> <p><strong>Supplementary material S17. </strong>Inputs for estimating ancestral ranges and performing biogeographic stochastic maps for our dataset.</p> <p><strong>Supplementary material S18. </strong>Consensus tree found with parsimony analysis using TNT (phenotypic data only).</p> <p><strong>Supplementary material S19. </strong>Consensus tree found with Bayesian inference using MrBayes (phenotypic data only).</p> <p><strong>Supplementary material S20. </strong>Consensus tree found with parsimony analysis using TNT (sequence data only).</p> <p><strong>Supplementary material S21. </strong>Consensus tree found with Bayesian inference using MrBayes (sequence data only).</p> <p><strong>Supplementary material S22. </strong>Consensus tree found with parsimony analysis using TNT (total evidence).</p> <p><strong>Supplementary material S23. </strong>Consensus tree found with Bayesian inference using MrBayes (total evidence).</p> <p><strong>Supplementary material S24. </strong>Consensus tree found with parsimony analysis using TNT (total evidence, dataset with reduced number of terminals).</p> <p><strong>Supplementary material S25. </strong>Consensus tree found with Bayesian inference using MrBayes (total evidence, dataset with reduced number of terminals).</p> <p><strong>Supplementary material S26. </strong>Consensus tree found with Bayesian inference using MrBayes (total evidence) and with node ages estimated using tip-dating.</p> <p><strong>Supplementary material S27. </strong>Maximum clade credibility tree found with Bayesian inference using Beast (sequence data only) and with node ages estimated using node-dating.</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>
Figure 1 in Discovery of a Nearctic vicariant bumblebee (Hymenoptera: Apidae) in Eurasia uncovers secondary trans-Beringian exchanges of insect faunas
Figure 1. Distribution map of Bombus kirbiellus Curtis 1835. The red circles indicate new samples from Asia (this study; N = 3); the blue circles indicate published records from North America (GBIF Secretariat 2023; GBIF Occurrence Download: https://doi.org/10.15468/dl.ck3xk3; N = 185). Map: Mikhail Y. Gofarov.
Figure 2 in Discovery of a Nearctic vicariant bumblebee (Hymenoptera: Apidae) in Eurasia uncovers secondary trans-Beringian exchanges of insect faunas
Figure 2. Morphology of Bombus kirbiellus Curtis 1835 from north-eastern Asia (Chukotka Peninsula). (A) Lateral view of a female. (B) Hind view of a female. (C) Lateral view of a male. (D) Hind view of a male. (E) Male genitalia. Scale bars = 5 mm (A, B, C, D) and 2 mm (E). (Photos: Grigory S. Potapov).
Data from: The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago
A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the so-called ''species-pump'' model, in which repeated bouts of co-speciation is driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with the glacial cycles. This repeated climate-driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. Given the significance and conceptual impact the model has shown, surprisingly few tests of this prediction have been provided. We collected comparative genomic data from 16 pairs of insular gecko populations to test the prediction of temporally clustered divergences. Specifically, we analyze these data in a full-likelihood, Bayesian model-choice framework to test for shared divergence times among the pairs. Our results provide support against the species-pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate-driven landscape fragmentation has not been an important mechanism of speciation for gekkonid lizards on the Philippine Islands. Interpretations of shared mechanisms of diversification historically have been pervasive in biogeography, often advanced on the basis of taxonomy-based depictions of species distributions. Our results call for possible re-evaluation of other, classic co-diversification studies in a variety of geographic systems.
Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations
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The key role of vicariance for soil animal biogeography in a biodiversity hotspot region
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Data from: The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago
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Mapped read data and files and scripts from: Vicariance followed by secondary gene flow in a young gazelle species complex
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Data from: Cycles of trans‐Arctic dispersal and vicariance, and diversification of the amphi‐boreal marine fauna
<p>The amphi‐boreal faunal element comprises closely related species and conspecific populations with vicarious distributions in the North Atlantic and North Pacific basins. It originated from an initial trans‐Arctic dispersal in the Pliocene after the first opening of the Bering Strait, and subsequent vicariance through the Pleistocene when the passage through the Arctic was severed by glaciations and low sea levels. Opportunities for further dispersal have risen at times however, and molecular data now expose more complex patterns of inter‐oceanic affinities and dispersal histories. For a general view on the trans‐Arctic dynamics and of the roles of potential dispersal‐vicariance cycles in generating systematic diversity we produced new phylogeographic data sets for amphi‐boreal taxa in 21 genera of invertebrates and vertebrates, and combined them with similar published data sets of mitochondrial coding gene variation, adding up to 89 comparisons involving molluscs, crustaceans, echinoderms, polychaetes, fishes and mammals. Only 39% of the cases correspond with a simple history of Pliocene divergence; in most taxonomical groups, the range of divergence estimates implies connections through the entire Pliocene–Pleistocene‐Holocene time frame. Repeated inter‐oceanic exchange was inferred for 23 taxa, and the latest connection was usually post‐glacial. Such repeated invasions have usually led to secondary contacts and occasionally to widespread hybridization between the different invasion waves. Late‐ or post‐glacial exchange was inferred in 50% of the taxa, stressing the importance of the relatively recent invasions to the current diversity in the Northern Atlantic. Individual taxa also showed complex idiosyncratic patterns and histories, and several instances of cryptic speciation were recognized. In contrast to a simple inter‐oceanic vicariance scenario underlying amphi‐boreal speciation, the data expose complex patterns of reticulation and introgression that complicate the interpretation of taxon boundaries in the region.</p>
Data from: Biogeographical evidence for common vicariance and rare dispersal in a southern Appalachian harvestman (Sabaconidae, Sabacon cavicolens)
Aim: Species or higher taxa that are obviously dispersal-limited, but which occupy large geographical distributions, represent a biogeographical paradox. Dispersal must have happened, likely under special and infrequent environmental conditions, but details have been lost to history. The overarching goal of our research is to understand the details of a 'common vicariance, rare dispersal' biogeographical history in a widespread but habitat-specialized harvestman species (Sabacon cavicolens) with a southern Appalachian centre of distribution. Location: Eastern North America, southern Appalachians. Methods: We assessed cryptic speciation using mitochondrial and nuclear gene DNA sequence data, testing alternative delimitation hypotheses using multispecies coalescent analyses. We also tested whether riverine barriers are associated with mitochondrial genealogical structuring, focusing on multiple rivers in the southern Blue Ridge physiographical province. Finally, we conducted population genetic analyses to assess female-based range expansion out of the southern Blue Ridge. Results: Genetic analyses suggest a large number of species-level lineages within S. cavicolens, although we prefer a more conservative three-species hypothesis. These putative species are geographically cohesive and allopatric (Ozarks, Cumberland Plateau, southern Blue Ridge), with the Blue Ridge species including multiple divergent mitochondrial haplogroups. Several genealogical breaks in the Blue Ridge species coincide with riverine barriers, separating mostly allopatric mitochondrial lineages. Contrasting with evidence for constrained gene flow and vicariance, two Blue Ridge haplogroups reveal extensive range expansion both northwards and westwards, resulting in the widespread distribution of closely related haplotypes, and occasional sympatry of dispersive haplotypes. Main Conclusions: Hidden beneath the apparently widespread distribution of a single species is a history of old vicariance separating geographically disjunct cryptic species. How these lineages came to occupy such disparate geographies is illustrated by dynamics within the Blue Ridge species, where both in situ vicariance and long-distance dispersal have shaped a 'common vicariance, rare dispersal' biogeographical history.
UCE phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) elucidates genus boundaries, species boundaries, and the vicariant history of a temperate-tropical disjunction
<p><span><span><span><span><span><span><span><span><span><span><span>The genus <i>Cryptopone</i> Emery contains 25 species of litter and soil ants, 5 of which occur in the Americas. <i>Cryptopone</i><i>gilva </i>occurs in the southeastern U.S.A. and cloud forests of Mesoamerica, exhibiting an uncommon biogeographic disjunction observed most often in plants. We used phylogenomic data from ultraconserved elements (UCEs), as well as mitogenomes and legacy markers, to investigate phylogenetic relationships, species boundaries, and divergence dates among New World <i>Cryptopone</i>. Species delimitation was conducted using a standard approach and then tested using model-based molecular methods (SNAPP, BPP, SODA, and bPTP). We found that <i>Cryptopone</i> as currently constituted is polyphyletic, and that all the South American species belong to <i>Wadeura</i> Weber, a separate genus unrelated to <i>Cryptopone</i>. A single clade of true <i>Cryptopone</i> occurs in the Americas, restricted to North and Central America. This clade is composed of four species that originated ~4.2 million years ago. One species from the mountains of Guatemala is sister to the other three, favoring a vicariance hypothesis of diversification. The taxonomy of the New World <i>Cryptopone</i>and <i>Wadeura</i> are revised. Taxonomic changes are: <i>Wadeura</i> Weber is <b>resurrected</b>, with <b>new combinations</b> <i>W. guianensis</i>Weber, <i>W. holmgreni</i> (Wheeler), and <i>W. pauli</i> (Fernandes & Delabie); <i>C. guatemalensis</i> (Forel) (<b>rev. stat.</b>) is raised to species, and includes <i>C. obsoleta</i> (Menozzi) (<b>syn. nov.</b>). The following <b>new species</b> are described: <i>Cryptopone gilvagrande</i>, <i>C. gilvatumida</i>, and <i>Wadeura holmgrenita</i>. <i>Cryptopone hartwigi</i> is transferred to <i>Fisheropone</i> (<b>n. comb.</b>). <i>Cryptopone mirabilis</i> (Mackay & Mackay 2010) is a junior synonym of <i>Centromyrmex brachycola</i> (Roger) (<b>syn. nov.</b>).</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance
<p>The separation of closely-related terrestrial or freshwater species by vast marine barriers represents a biogeographic riddle. Such cases can provide evidence for vicariance, a process whereby ancient geological events like continental rifting divided ancestral geographic ranges. With an evolutionary history extending tens of millions of years, freshwater ecology, and distribution encompassing widely separated southern landmasses, osteoglossid bonytongue fishes are a textbook case of vicariance attributed to Mesozoic fragmentation of the Gondwanan supercontinent. Largely overlooked fossils complicate the clean narrative invoked for extant species by recording occurrences on additional continents and in marine settings. Here we present a new total-evidence hypothesis for bonytongue fishes combined with quantitative models of range evolution and show that the last common ancestor of extant osteoglossids was likely marine, and that the group colonized freshwater settings at least four times when both extant and extinct lineages are considered. The correspondence between extant osteoglossid relationships and patterns of continental fragmentation therefore represents a striking example of biogeographic pseudocongruence. Contrary to arguments against vicariance hypotheses that rely only on temporal or phylogenetic evidence, these results provide direct palaeontological support for enhanced dispersal ability early in the history of a group with widely separated distributions in the modern day.</p>
Data from: Environmental heterogeneity and not vicariant biogeographic barriers generate community wide population structure in desert adapted snakes
Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic dataset. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers.
Genome-wide RAD sequencing data suggest predominant role of vicariance in Sino-Japanese disjunction of the monotypic genus Conandron (Gesneriaceae)
<p>Disjunct distribution is a key issue in biogeography and ecology, but it is often difficult to determine relative roles of dispersal vs. vicariance in disjunctions. We studied phylogeographic pattern of the monotypic <em>Conandron</em> <em>ramondioides</em> (Gesneriaceae), which shows Sino-Japanese disjunctions, with ddRAD sequencing based on a comprehensive sampling of 11 populations from mainland China, Taiwan Island, and Japan. We found a very high degree of genetic differentiation among these three regions, with very limited gene flow and a clear Isolation by Distance pattern. Mainland China and Japan clades diverged first from a widespread ancestral population in the middle Miocene, followed by a later divergence between mainland China and Taiwan Island clades in the early Pliocene. Three current groups have survived in various glacial refugia during the Last Glacial Maximum (LGM), and experienced contraction and/or bottlenecks since their divergence during Quaternary glacial cycles, with strong niche divergence between mainland China + Japan and Taiwan Island ranges. Thus, we verified a predominant role of vicariance in the current disjunction of the monotypic genus <em>Conandron</em>. The sharp phylogenetic separation, ecological niche divergences among these three groups and the great number of private alleles in all populations sampled indicate a considerable time of independent evolution and suggest the need for a taxonomic survey to detect potentially overlooked taxa.</p>
The presence of a guard vicariously drives split sex ratios in a facultatively social bee
<p>Split sex ratios provide broad insights into how reproductive strategies evolve and historically have special relevance to the evolution of eusociality. Yet almost no attention has been directed to situations where split sex ratios may potentially decrease the payoffs for worker-like behaviour, increasing selective thresholds for eusociality. We examined sex ratios in a facultatively social colletid bee, <em>Amphylaeus morosus</em>. Sex ratios in this bee vary strongly with the presence of a nest guard and in a pattern that does not conform to assumptions of previous models in which split sex ratios facilitate altruism. While the production of daughters was constant across social and solitary nests, mothers produced more brood when a non-reproductive guard was present, but these extra brood were all male. This leads to split sex ratios, vicariously driven by guards that are unable to manipulate sex ratios in their favour. Importantly, if guarding becomes more common in a population this would lead to an excess of males and lower the genetic value of these extra males to guards, effectively putting a brake on selection for worker-like behaviour.</p>
How did subterranean amphipods cross the Adriatic Sea? Phylogenetic evidence for the dispersal-vicariance interplay mediated by marine regression-transgression cycles
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Data from: Environmental heterogeneity and not vicariant biogeographic barriers generate community wide population structure in desert adapted snakes
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UCE phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) elucidates genus boundaries, species boundaries, and the vicariant history of a temperate-tropical disjunction
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