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15 results for “Isolation Migration”
FIGURE 4. Isolated left P4 in Endemism and migration in the Kochkor Basin? Identification and description of Adcrocuta eximia (Mammalia: Carnivora: Hyaenidae) and c.f. Paramachaerodus (Mammalia: Carnivora: Felidae) fossils at the Miocene locality of Ortok, Kyrgyzstan
FIGURE 4. Isolated left P4 of UOMNH F-70508, Adcrocuta eximia. A, schematic of preserved features in occlusal view; B, occlusal view of specimen displaying minimal wear on metastylar blade; C, lingual view of specimen. Note reduced protocone that does not extend anterior to the anterior face of the parastyle. Scale bar equals 10 mm.
Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
<p>Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus <em>Arvicola</em>, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of <em>A. scherman</em> present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, <em>A. amphibius</em>, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.</p>
Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
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Data from: Migration and isolation during the turbulent Ponto-Caspian Pleistocene create high diversity in the crustacean Paramysis lacustris
The Ponto-Caspian brackish-water fauna inhabits estuaries and rivers of the Black, Azov and Caspian seas and is fragmented by higher salinity waters and a major interbasin watershed. The fauna is known for the high levels of endemism, complex zoogeographic histories, and as a recent source of successful invasive species. It remains debated whether the Black and Azov Sea brackish-water populations survived unfavourable Pleistocene conditions in multiple separate refugia or whether the two seas were (repeatedly) recolonized from the Caspian. Using microsatellite and mtDNA markers, we demonstrate deep among- and within-basin subdivisions in a widespread Ponto-Caspian mysid crustacean Paramysis lacustris. Five genetic clusters were identified, but their relationships did not reflect the geography of the region. The Azov cluster was the most distinct (4–5% COI divergence), despite its geographic position in the corridor between Black and Caspian seas, and may represent a new species. In the northern Black Sea area, the Dnieper cluster was closer to the Caspian cluster than to the neighbouring Danube–Dniester–Bug populations, suggesting separate colonizations of the Black Sea. Overall, the data implied a predominant gene flow from the east to the Black Sea and highlight the importance of Caspian Sea transgressions in facilitating dispersal. Yet, the presence of distinct lineages in the Black Sea points to the persistence of isolated refugial populations that have gained diagnostic differences under presumably high mutation rates and large population sizes. The unfavourable Pleistocene periods in the Black Sea therefore appear to have promoted diversification of the brackish-water lineages, rather than extirpated them.
Data from: Identifying loci under selection against gene flow in isolation with migration models
When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).
Data from: Migration and isolation during the turbulent Ponto-Caspian Pleistocene create high diversity in the crustacean Paramysis lacustris
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Data from: Identifying loci under selection against gene flow in isolation with migration models
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Resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories
The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus , and Mus musculus musculus, are estimated to have diverged ~325-500KYA. Resolution of the details of their evolutionary history is complicated by their relatively recent divergence, ongoing gene flow among the subspecies, and complex demographic histories. Previous studies have been limited to some extent by the number of loci surveyed and/or by the scope of the method used. Here we apply a method (IMa3) that provides an estimate of a population phylogeny while allowing for complex histories of gene exchange. Results strongly support a topology with M. m. domesticus as sister to M. m. castaneus and M. m. musculus . In addition, we find significant evidence of reciprocal gene flow between all pairs of subspecies. Our estimates of another key set of parameters, effective population size ( N e ), support previous results that the N e of M. m. castaneus is larger than that of the other two subspecies.
Data from: Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex
Background: Determining the presence or absence of gene flow between populations is the target of some statistical methods in population genetics. Until recently, these methods either avoided the use of recombining genes, or treated recombination as a nuisance parameter. However, genes with recombination contribute additional information for the detection of gene flow (i.e. through linkage disequilibrium). Methods: We present three summary statistics based on the spatial arrangement of fixed differences, and shared and exclusive polymorphisms that are sensitive to the presence and direction of gene flow. Power and false positive rate for tests based on these statistics are studied by simulation. Results: The application of these tests to populations from the Drosophila simulans species complex yielded results consistent with migration between D. simulans and its two endemic sister species D. mauritiana and D. sechellia, and between populations D. mauritiana on the islands of the Mauritius and Rodrigues. Conclusions: We demonstrate the sensitivity of the developed statistics to the presence and direction of gene flow, and characterize their power as a function of differentiation level and recombination rate. The properties of these statistics make them especially suitable for analyzing high-throughput sequencing data or for their integration within the approximate Bayesian computation framework.
Data from: Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex
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Data from: Maximum likelihood implementation of an isolation-with-migration model for three species
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Resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories
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Data from: On the occurrence of false positives in tests of migration under an isolation with migration model
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Regulation of gene expression in splenic cDC1 isolated from WT vs XCR1-/- miceNK cells orchestrate cDC1 migration to potentiate antiviral protective CD8+ T cell responses
GEO Series GSE142402. Mus musculus. 8 samples. Type: Expression profiling by array.
Analysis of gene expression in primary murine OPC isolated from cerebrum and spinal cord to identify differentially regulated genes important for OPC migration
GEO Series GSE178301. Mus musculus. 6 samples. Type: Expression profiling by array.
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