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80 results for “Historical structures”
Data from: Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography
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Data from: Historical and contemporary factors shape the population genetic structure of the broadcast spawning coral, Acropora millepora, on the Great Barrier Reef
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Data from: Spatiotemporally explicit demographic modelling supports a joint effect of historical barriers to dispersal and contemporary landscape composition on structuring genomic variation in a red-listed grasshopper
Inferring the processes underlying spatial patterns of genomic variation is fundamental to understand how organisms interact with landscape heterogeneity and to identify the factors determining species distributional shifts. Here, we employ genomic data (ddRADSeq) to test biologically-informed models representing historical and contemporary demographic scenarios of population connectivity for the Iberian cross-backed grasshopper Dociostaurus hispanicus, a species with a narrow distribution that currently forms highly fragmented populations. All models incorporated biological aspects of the focal taxon that could hypothetically impact its geographical patterns of genomic variation, including (a) spatial configuration of impassable barriers to dispersal defined by topographic landscapes not occupied by the species, (b) distributional shifts resulted from the interaction between the species bioclimatic envelope and Pleistocene glacial cycles, and (c) contemporary distribution of suitable habitats after extensive land clearing for agriculture. Spatiotemporally-explicit simulations under different scenarios considering these aspects and statistical evaluation of competing models within an Approximate Bayesian Computation (ABC) framework supported spatial configuration of topographic barriers to dispersal and human-driven habitat fragmentation as the main factors explaining the geographical distribution of genomic variation in the species, with no apparent impact of hypothetical distributional shifts linked to Pleistocene climatic oscillations. Collectively, this study supports that both historical (i.e., topographic barriers) and contemporary (i.e., anthropogenic habitat fragmentation) aspects of landscape composition have shaped major axes of genomic variation in the studied species and emphasizes the potential of model-based approaches to gain insights into the temporal scale at which different processes impact the demography of natural populations.
Data from: Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus)
Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequence data from one mitochondrial and five nuclear loci to assess the potential influence of Pleistocene climatic changes on the phylogeography and demographic history of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Population samples representing the three major morphotypes of Delphinus were obtained from ten oceanic regions. Our results suggest that short-beaked common dolphins are likely to have originated in the eastern Indo-Pacific Ocean during the Pleistocene and expanded into the Atlantic Ocean through the Indian Ocean. On the other hand, long-beaked common dolphins appear to have evolved more recently and independently in several oceans. Our results also suggest that short-beaked common dolphins had recurrent demographic expansions concomitant with changes in sea surface temperature during the Pleistocene and its associated increases in resource availability, which differed between the North Atlantic and Pacific Ocean basins. By proposing how past environmental changes had an effect on the demography and speciation of a widely distributed marine mammal, we highlight the impacts that climate change may have on the distribution and abundance of marine predators and its ecological consequences for marine ecosystems.
Data from: Population structure, gene flow, and historical demography of a small coastal shark (Carcharhinus isodon) in US waters of the Western Atlantic Ocean
Patterns of population structure, genetic demographics, and gene flow in the small coastal shark Carcharhinus isodon (finetooth shark) sampled from two discrete nurseries along the southeastern US coast (Atlantic) and three nurseries in the northern Gulf of Mexico (Gulf), were assessed using 16 nuclear-encoded microsatellites and 1077 base pairs of the mitochondrial DNA (mtDNA) control region. Significant heterogeneity in microsatellite allele distributions was detected among all localities except between the two in the Atlantic. Significant heterogeneity in mtDNA haplotypes was not detected, a result likely due to extremely low mtDNA diversity. The genetic discontinuities combined with seasonal movement patterns, a patchy distribution of appropriate nursery habitat, the apparent absence of sex-biased gene flow, and the occurrence of mating in the vicinity of nursery areas, suggest that both male and female finetooth sharks display regional philopatry to discrete nursery areas. Global and local tests of neutrality, using mtDNA haplotypes, and demographic model testing, using Approximate Bayesian Computation of microsatellite alleles, supported a range-wide expansion of finetooth sharks into US waters occurring less than ∼9000 years ago. These findings add to the growing number of studies in a variety of coastally distributed marine fishes documenting significant barriers to gene flow around peninsular Florida and in the eastern Gulf. The findings also provide further evidence that the traditional model of behavioural ecology, based on large coastal sharks, may not be appropriate for understanding and conserving small coastal sharks.
Data from: Genetic structure and diversity among historic and modern populations of the Sumatran rhinoceros (Dicerorhinus sumatrensis)
The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed two sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, while an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore two overriding priorities for the species: (1) translocation of wild rhinos to ex situ facilities, and (2) collection and storage of gametes and cell lines from every surviving captive and wild individual.
SNP matrices and vcf files for phylogenetic, genetic structure and historical demographic analyses of Podocarpus from Hispaniola
<p><b>Aim</b><span>: </span>Hispaniola is the second largest island in the Caribbean and a hotspot of biodiversity. The island was formed by the fusion of a northern and southern palaeo-islands during the mid-Miocene (15 Ma). The historical split of Hispaniola together with repeated marine incursions during the Pleistocene are known to have influenced lineage divergence and genetic structure in a few birds and mammals, but the effect on vascular plants is less understood. The conifer genus <i>Podocarpus </i>has two species, <i>P. hispaniolensis </i>and <i>P. buchii, </i>that are endemic to the mountains of Hispaniola and are IUCN endangered. The former occurs in the mountains of the north, and the latter in the south, with a region of sympatry in the Central Cordillera. Here we evaluate the historical split of the two palaeo-islands, and repeated marine incursions as dispersal barriers to the geographical distribution of genetic diversity, genetic structure, divergence patterns, and the historical demography of the two species.</p> <p><b><span>Location</span></b><span>: Hispaniola island, Caribbean.</span></p> <p><b><span>Methods</span></b><span>: </span>Using Genotyping by Sequencing in 47 <i>Podocarpus</i> samples we identified two sets of single nucleotide polymorphisms for our analyses (74,260 and 22,657 SNPs).</p> <p><b><span>Results</span></b><span>: </span>The results show a population genetic structure that corresponds to the geographic distribution of the species in mountainous areas. <i>Podocarpus </i>in Hispaniola followed a stepping-stone colonization pattern with bottlenecks at each mountain colonization event.</p> <p><b><span>Main conclusions</span></b><span>:</span> The historical events in question did not seem to have influenced the genetic structure, diversity, or demography of <i>Podocarpus</i>, instead the current geographic barriers imposed by lowland xeric valleys did. The clear divergence between species together with the elevated within-population genetic diversity and significant genetic structure call for a multi-population <i>in situ</i> conservation of each species.</p>
FIGURE 4 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features
FIGURE 4. Bayesian inference skyline plot of the mtDNA control region of D. ensatus.
Genotype and individual data for genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture
<p><b><span>Premise: </span></b><span>When divergent lineages come into secondary contact reproductive isolation may be incomplete, thus providing an opportunity to investigate how speciation is manifested in the genome. The Louisiana Irises (<i>Iris</i>, series <i>Hexagonae</i>) comprise a group of three or more ecologically and reproductively divergent lineages that can produce hybrids where they come into contact. In this study we sought to estimate standing genetic variation to understand the current distribution of population structure in the Louisiana Irises.</span></p> <p><b><span>Methods:</span></b><span> We used genotyping-by-sequencing techniques to sample the genomes of Louisiana Iris species across their ranges. Twenty populations were sampled (total n=632) across 11,249 loci. Population genetic data were assessed using ENTROPY and PCA models. </span></p> <p><b><span>Results: </span></b><span>We discovered evidence for interspecific gene flow in parts of the range and revealed patterns of population structure at odds with widely accepted nominal taxonomy. Undescribed hybrid populations were discovered that were designated as belonging to the <i>I. brevicaulis</i> lineage. <i>Iris nelsonii </i>shared significant ancestry with only one of the purported parent species, <i>I. fulva, </i>evidence inconsistent with a hybrid origin.</span></p> <p><b><span>Conclusions: </span></b><span>This study provides several key findings important to the investigation of standing genetic variation in the Louisiana Iris species complex. <i>Iris brevicaulis</i> has a large amount of genetic diversity within it relative to the other nominal species. In addition, this study has discovered a previously unknown hybrid zone between <i>I. brevicaulis </i>and <i>I. hexagona</i> along the Texas coast. Finally, <i>I. nelsonii</i> does not appear to have mixed ancestry from three parental taxa as has been the longstanding hypothesis. </span></p>
SNP matrices and vcf files for phylogenetic, genetic structure and historical demographic analyses of Podocarpus from Hispaniola
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Data from: Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus)
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Data from: Genetic structure and diversity among historic and modern populations of the Sumatran rhinoceros (Dicerorhinus sumatrensis)
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Data from: Population structure, gene flow, and historical demography of a small coastal shark (Carcharhinus isodon) in US waters of the Western Atlantic Ocean
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Data from: Spatiotemporally explicit demographic modelling supports a joint effect of historical barriers to dispersal and contemporary landscape composition on structuring genomic variation in a red-listed grasshopper
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Genotype and individual data for genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture
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Data from: Historical and anthropogenic factors affecting the population genetic structure of Ontario’s inland lake populations of walleye (Sander vitreus)
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Data from: Population structure and historical demography of Dipteronia dyeriana (Sapindaceae), an extremely narrow palaeoendemic plant from China: implications for conservation in a biodiversity hot spot
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Figure 2 in Contemporary genetic structure reflects historical drainage isolation in an Australian snapping turtle, Elseya albagula
Figure 2. Minimum spanning tree depicting haplotype relationships for concatenated control region/nicotinamide adenine dinucleotide dehydrogenase subunit 4 (ND4) mtDNA from Elseya albagula across ten locations. Circles represent unique haplotypes and are connected to one another by mutational changes (lines). Crossbars indicate additional mutational steps and circle size is proportional to the number of individuals sharing that haplotype. Colours indicate geographical source of haplotypes. B, Burnett, F, Fitzroy; M, Mary.
Figure 3. A in Historical demography and spatial genetic structure of the subterranean rodent Ctenomys magellanicus in Tierra del Fuego (Argentina)
Figure 3. A, minimum spanning tree of nine mtDNA haplotypes of Ctenomys magellanicus from Tierra del Fuego, Argentina. Areas are proportional to haplotype frequencies, shading indicates populations, and cross hatches represent nucleotide differences between haplotypes. Haplotype numbers correspond to those of Table 1. Abbreviations for populations are given in Figure 1. B, observed and expected mismatch distributions for C. magellanicus (south + north). Dashed line, observed distribution; solid line, theoretical expected distribution under a population expansion model.
Figure 4 in Historical demography and spatial genetic structure of the subterranean rodent Ctenomys magellanicus in Tierra del Fuego (Argentina)
Figure 4. Relationship between pairwise geographical distances and Fst for Ctenomys magellanicus from Tierra del Fuego, based on Fst from mitochondrial control region sequences. The relationship between variables was non-significant (see Results).
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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.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.