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27 results for “Historical Demography”
Genetic structure and historic demography of endangered unarmored threespine stickleback at southern latitudes signals a need for new management directives
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Data from: Historical demography and climate driven distributional changes in a widespread Neotropical freshwater species with high economic importance
The Neotropical region exhibits the greatest worldwide diversity and the diversification history of several clades is related to the puzzling geomorphologic and climatic history of this region. The freshwater Amazon ecoregion contains the main hydrographic basins of the Neotropical region that are highly dendritic and ecologically diverse. It contains a rich and endemic fish fauna, including one of its most iconic and economically important representatives, the bony-tongue Arapaima gigas (Teleostei, Osteoglossiformes). Here, we evaluated the projected distribution of the genus in different historical periods (Present, Last Glacial Maximum, Last Interglacial Maximum and Near Future) and interpreted these results in light of the genomic diversity and modeled historical demography. For that, we combined species distribution models, population genetic analysis using SNPs and deep learning model selection. We analyzed a representative sample of the genus from the two basins where it naturally occurs, four localities in the Amazon (Am) and three in the Tocantins-Araguaia (To-Ar) basin, as well as individuals from three fish farms. We inferred a potentially smaller distribution in the glacial period, with a possible refuge in central Am. Our genetic data agrees with this result, suggesting a higher level of genetic diversity in the Am basin, compared to that observed in To-Ar. Our deep learning model comparison indicated that the To-Ar basin was colonized by the population from the Am basin. Considering a global warming scenario in the near future, A. gigas could reach an even larger range, especially if anthropogenic related dispersal occurs, potentially invading new areas and impacting their communities.
Data from: One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark
With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost-effectiveness.
Data from: Historical demography of four gecko species specializing in boulder cave habitat – its implications in the evolutionary dead end hypothesis and conservation
Specialization in narrow ecological niches might not only help species to survive in competitive or unique environments but also contribute to their extermination over evolutionary time. Although the "evolutionary dead end" hypothesis has long been debated, empirical evidence from species with detailed information on niche specialization and evolutionary history is still rare. Here we used a group of four closely related Cnemaspis gecko species that highly depend on granite boulder caves in the Mekong Delta to illuminate the potential impact of ecological specialization on their evolution and population dynamics. Isolated by the unsuitable habitat of a flood plain, these boulder-dwelling geckos are among the most narrowly distributed Squamata species in the world. We applied several coalescence-based approaches combined with the RAD-seq technique to estimate their divergence times, gene flow and demographic fluctuations during the speciation and population differentiation processes. Our results showed long-term population shrinkage in the four geckos and limited gene flow during their divergence. The results suggest that the erosion and fragmentation of the granite boulder hills have had great impacts on these populations' divergences and population declines. We argue that the specialist gecko's habitat specialization has facilitated the fine-scaled speciation in these granite rocky hills; in contrast, specialization might also have pushed these species toward the edge of extinction. Our study also emphasizes the conservation urgency of these vulnerable, cave-dependent geckos.
Original FASTQ files of: Global genetic diversity and historical demography of the Bull Shark
<p><strong>Aim</strong></p> <p>Biogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (N<sub>e</sub>) temporal variations, a key genetics parameter. We reconstructed the historical demography and divergence history of a vulnerable coastal high-trophic shark using population genomics and assessed our ability to detect recent bottlenecks events.</p> <p><strong>Location</strong></p> <p>Western and Central Indo-Pacific (IPA), Western Tropical Atlantic (WTA), Eastern Tropical Pacific (EPA)</p> <p><strong>Taxon</strong></p> <p>Carcharhinus leucas (Müller & Henle, 1839)</p> <p><strong>Methods</strong></p> <p>A <a>DArTcap</a><sup>TM</sup> approach was used to sequence 475 samples and assess global genetic structuring. Three demographic models were tested on each population, using an ABC-RF framework coupled with coalescent simulations, to investigate within-cluster structure. Divergence times between clusters were computed, testing multiple scenarios, with <em>fastsimcoal</em>. N<sub>e</sub> temporal variations were reconstructed with STAIRWAYPLOT. Coalescent simulations were performed to determine the detectability of recent bottleneck under the estimated historical trend for datasets of this size.</p> <p><strong>Results</strong></p> <p>Three genetic clusters corresponding to the IPA, WTA and EPA regions were identified, agreeing with previous studies. The IPA presented the highest genetic diversity and was consistently identified as the oldest. No significant within-cluster structuring was detected. N<sub>e </sub>increased globally, with an earlier onset in the IPA, during the last glacial period. Coalescent simulations showed that weak and recent bottlenecks could not be detected with our dataset, while old and/or strong bottlenecks would erase the observed ancestral expansion.</p> <p><strong>Main conclusions</strong></p> <p>This study further confirms the role of marine biogeographic breaks in shaping the genetic history of large mobile marine predator. N<sub>e </sub>Historical increases of N<sub>e</sub> are potentially linked to extended coastal habitat availability. The limited within-cluster population structuring suggests that Ne can be monitored over ocean basins. Due to insufficient amount of available genetic data, it cannot be concluded whether overfishing is impacting Bull Shark genetic diversity, calling for whole genome sequencing.</p>
Long-distance dispersal drives the genetic variation and historical demography of Quercus magnoliifolia and Quercus resinosa (Fagaceae) in the Mexican highlands
<p>Genotypes of chloroplast microsatellites used in Albarrán-Lara et al. Data comprises six loci from 61 localities sampling in Mexico</p>
Data from: Historical demography and climate driven distributional changes in a widespread Neotropical freshwater species with high economic importance
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Original FASTQ files of: Global genetic diversity and historical demography of the Bull Shark
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Data from: One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark
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Data from: Historical demography of four gecko species specializing in boulder cave habitat – its implications in the evolutionary dead end hypothesis and conservation
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Data from: Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population
Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.
Figure 2 in Historical demography and spatial genetic structure of the subterranean rodent Ctenomys magellanicus in Tierra del Fuego (Argentina)
Figure 2. Bayesian inference trees of Ctenomys genus. A, tree derived from the D-loop marker. B, tree derived from Cyt b. Numbers next to branches are bootstrap support values and Bayesian posterior probabilities, respectively.
Figure 1 in Historical demography and spatial genetic structure of the subterranean rodent Ctenomys magellanicus in Tierra del Fuego (Argentina)
Figure 1. Geographical distribution of Ctenomys magellanicus sampling sites along the study area. Squares show the two regions: north (steppe, chromosome form 2n = 34) and south (ecotone, chromosome form 2n = 36). Each region was subdivided into subpopulations: two for the north (subpopulations A and B) and four for the south (subpopulations C–F).
Data from: Inferring responses to climate dynamics from historical demography in neotropical forest lizards
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Data from: Historical changes in grassland area determined the demography of semi-natural grassland butterflies in Japan
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Data from: Climate, not Aboriginal landscape burning, controlled the historical demography and distribution of fire-sensitive conifer populations across Australia
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Data from: Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population
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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)
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: 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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