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Dataset results
17 results for “demographic history inference”
Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses
<p>The present-day population structure of a species reflects the combination of oceanographic currents, life-history traits, and historical events. However, little is known about the mechanisms that have shaped the gene lineage distribution of marine species inhabiting the Southeast Pacific. Here we provide a comprehensive phylogeographical study of a species distributed along the Southeast Pacific coastal region by analyzing the endemic gastropod Thaisella chocolata (Duclos, 1832). Sequencing of mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S rRNA revealed strikingly high haplotypic nucleotide and genetic diversity but a lack of significant population differentiation within the survey area. In addition, a star-shaped phylogeny and significantly negative Tajima's D and Fu's Fs tests of neutrality suggested historical occurrence of rapid demographic expansion. Mismatch distributions and Bayesian inference analyses also confirmed T. chocolata to have undergone two ancestral demographic expansions. Calculations suggested that these expansions began in the lower and middle Pleistocene epoch, likely due to continental shelf development and climatic conditions. These findings could help establish a genetic baseline for T. chocolata as the first step toward sustainable spatial management of this species, as well as understand this species' response to future climate change.</p>
Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses
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Data from: Genetic structure and demographic history of house mice in Western Europe inferred using whole genome sequences
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Data from: Demographic history and inbreeding in two declining sea duck species inferred from whole genome sequence data
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Data from: Demographic history inferred from genome-wide data reveals two lineages of sheldgeese endemic to a glacial refugium in the southern Atlantic
Aim: The Malvinas/Falkland Islands (MFI) constitute the largest archipelago in the southern Atlantic, and harbour endemic lineages that presumably evolved after sea-level rise, associated with glacial periods, isolated ancestral populations. We investigate the role of the MFI in isolating populations from continental counterparts of two highly vagile species: the sheldgeese Chloephaga picta and Chloephaga rubidiceps. Location: Patagonia and the Malvinas/Falkland Islands. Methods: We sampled C. picta and C. rubidiceps on the continent and MFI. Using a reduced-representation genomic approach, we quantified the genetic differentiation between insular and continental populations of both species, and used coalescent-based analyses to model their demography. Results: The MFI harbour independently evolving lineages of C. picta and C. rubidiceps, which diverged from their continental counterparts during the Middle-Late Pleistocene and have since experienced negligible gene flow. Main conclusions: The c. 450 km that separate the archipelago from the continent are sufficient to isolate populations of these putatively highly vagile species. Ancestral lineages may have reached the MFI refugium during glacial cycles. Without conservation measures, the drastic decline of the morphologically, behaviourally and ecologically distinct continental population of C. rubidiceps, to < 1000 individuals, may lead to the extinction of an independently evolving taxon.
Data from: Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield
How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rainfall and temperature changes during and/or immediately after the last glacial maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the eastern Guiana Shield over a timescale of several thousand generations, through the application of approximate Bayesian computation and maximum-likelihood methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contraction, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rainforests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demographic events, with a trend towards the increase in frequency of light-demanding, disturbance-associated species.
Data from: Phylogenomics at the tips: inferring lineages and their demographic history in a tropical lizard, Carlia amax
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Data from: Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA
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Data from: Demographic history inferred from genome-wide data reveals two lineages of sheldgeese endemic to a glacial refugium in the southern Atlantic
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Data from: Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield
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Data from: Inferring the demographic history of European Ficedula flycatcher populations
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Data from: Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species
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Data from: Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions
Drosophila subobscura presents a rich and complex chromosomal inversion polymorphism. It can thus be considered a model system i) to study the mechanisms originating inversions and how inversions affect the levels and patterns of variation in the inverted regions, and ii) to study adaptation at both the single-gene and chromosomal inversion levels. It is therefore important to infer its demographic history since previous information indicated that its nucleotide variation is not at mutation-drift equilibrium. For that purpose, we sequenced 16 non-coding regions distributed across those parts of the J chromosome not affected by inversions in the studied population and possibly either by other selective events. The pattern of variation detected in these 16 regions is similar to that previously reported within different chromosomal arrangements, suggesting that the latter results would, thus, mainly reflect recent demographic events rather than the partial selective sweep imposed by the origin and frequency increase of inversions. Among the simple demographic models considered in our ABC analysis of variation at the 16 regions, the model best supported by the data implies a population size expansion soon after the penultimate glacial period. This model constitutes a better null model and it is therefore an important resource for subsequent studies aiming among others to uncover selective events across the species genome. Our results also highlight the importance of introducing the possibility of multiple hits in the coalescent simulations with an outgroup.
Demographic inferences and climatic niche modeling shed light on the evolutionary history of the emblematic cold-adapted Apollo butterfly at regional scale
<p>Cold-adapted species escape climate warming by latitudinal and/or altitudinal range shifts, and currently occur in Southern Europe in isolated mountain ranges within 'sky islands.</p> <p>Here we studied the genetic structure of the Apollo butterfly in five such alpine islands (above 1000 m) in France, and infer its demographic history since the last interglacial, using single nucleotide polymorphisms (ddRADseq SNPs). The Auvergne and Alps populations show strong genetic differentiation but not alpine massifs, although separated by deep valleys. Combining three complementary demographic inference methods and species distribution models (SDMs) we show that the LIG period was highly defavorable for Apollo that probably survived in small population in the highest summits of Auvergne. The population shifted downslope and expanded eastward between LIG and LGM throughout the large climatically suitable Rhône valley between the glaciated summits of Auvergne and Alps. The Auvergne and Alps populations started diverging before the LGM but remained largely connected till the mid-Holocene. Population decline in Auvergne was more gradual but started before (~7 kya versus 800 ya), and was much stronger with current population size ten times lower than in the Alps. In the Alps, the low genetic structure and limited evidence for isolation by distance suggest a non-equilibrium metapopulation functioning. The core Apollo population experienced cycles of contraction-expansion with climate fluctuations with largely inter-connected populations over time according to a 'metapopulation-pulsar' functioning. This study demonstrates the power of combining demographic inferences and SDMs to determine past and future evolutionary trajectories of an endangered species at a regional scale.</p>
Demographic inferences and climatic niche modeling shed light on the evolutionary history of the emblematic cold-adapted Apollo butterfly at regional scale
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Data from: Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes
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Data from: Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.