Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
227
datasets available to search
ShareScore release 0.7.1
Dataset results
227 results for “demographic history”
Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros
<p>The Arctic is warming <span>at an unprecedented rate,</span> with unknown consequences for endemic fauna. However, Earth has experienced severe climatic oscillations in the past, and understanding how species responded to them might provide insight into their resilience to near-future climatic predictions. Little is known about the responses of Arctic marine mammals to past climatic shifts, but narwhals (<i>Monodon monoceros</i>) are considered one of the endemic Arctic species most vulnerable to environmental change. Here, we analyze 121 complete mitochondrial genomes from narwhals sampled across their range, and use them in combination with species distribution models to elucidate the influence of past and ongoing climatic shifts on their population structure and demographic history. We find low levels of genetic diversity and limited geographic structuring of genetic clades. We show that narwhals experienced a long-term low effective population size, which increased after the Last Glacial Maximum (LGM), when the amount of suitable habitat expanded. Similar post-glacial habitat release has been a key driver of population size expansion of other Polar marine predators. Our analyses indicate that habitat availability has been critical to the success of narwhals, raising concerns for their fate in an increasingly warming Arctic.</p>
Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe
<p>Understanding the biological processes involved in genetic differentiation and divergence between populations within species is a pivotal aim in evolutionary biology. One particular phenomenon that requires clarification is the maintenance of genetic barriers despite the high potential for gene flow in the marine environment. Such patterns have been attributed to limited dispersal or local adaptation, and to a lesser extent to the demographic history of the species. The corkwing wrasse (<i>Symphodus melops</i>) is an example of a marine fish species where regions of particular strong divergence are observed. One such genetic break occurred at a surprisingly small spatial scale (<i>F</i><sub>ST</sub> ~0.1), over a short coastline (<60 km) in the North Sea-Skagerrak transition area in southwestern Norway. Here, we investigate the observed divergence and purported reproductive isolation using genome resequencing. Our results suggest that historical events during the post-glacial recolonization route can explain the present population structure of the corkwing wrasse in the northeast Atlantic. While the divergence across the break is strong, we detected ongoing gene flow between populations over the break suggesting recent contact or negative selection against hybrids. Moreover, we found few outlier loci and no clear genomic regions potentially being under selection. We concluded that neutral processes and random genetic drift e.g., due to founder events during colonization have shaped the population structure in this species in Northern Europe. Our findings underline the need to take into account the demographic process in studies of divergence processes.</p>
Genomic data reveal the biogeographic and demographic history of Ammospiza sparrows in northeast tidal marshes
<p><b><i>Aim: </i></b>Shaped by both climate change and sea-level rise, tidal salt marshes represent ephemeral systems that are home to only a few, highly specialized species. The dynamic ecological histories and spatial complexities of these habitats, however, render it challenging to reconstruct the complete biogeographic histories of their endemic taxa. Here, we leverage three species of North American <i>Ammospiza </i>sparrows that inhabit tidal marshes ( <i>Ammospiza caudacuta</i>, <i>A. maritima</i>, and <i>A. n. subvirgatus</i>) and closely related freshwater species to demonstrate the utility of whole-genome data in resolving demographic and evolutionary history as it relates to divergence and dispersal events in ephemeral ecosystems. We employ a combination of demographic and biogeographic reconstructions to shed new light on the colonization history of freshwater-saline environments in this system.</p> <p><b><i>Location: </i></b>North America</p> <p><b><i>Taxon: </i></b> <i>Ammospiza Sparrows</i></p> <p><b><i>Methods: </i></b>We sequenced whole genomes from <i>Ammospiza </i>sparrows to address our objectives. We conducted phylogenomic analyses and reconstructed the demographic and biogeographic history of this clade based on 21 million SNPs from 54 total individuals.</p> <p><b><i>Results: </i></b>Phylogenies based on several million SNPs supported several well-resolved clades that predominantly corresponded to their prior species designations. Phylogenetic and biogeographic reconstructions suggest a series of saltwater to freshwater colonization events within this group, with some endemic taxa exhibiting associations with tidal marsh habitat over longer evolutionary time scales and some habitat transitions occurring as recently as 5,000 years ago. </p> <p><b><i>Main Conclusions: </i></b>Our reconstructions support a biogeographic hypothesis with fewer vicariance and dispersal events among <i>Ammospiza </i>sparrows that is in contrast with the currently supported evolutionary scenario. Biogeographic reconstructions further suggest saltwater to freshwater transitions in <i>A. n. subvirgatus </i>as opposed to the long hypothesized freshwater origin. Our results highlight the fact that reconstructing biogeographic and evolutionary dynamics in ephemeral systems poses challenges given the propensity for high turnover. This reinforces the importance of a multifaceted approach to biogeographic reconstructions in historically dynamic ecosystems.</p>
Data from: Estimating relatedness and inbreeding using molecular markers and pedigrees: the effect of demographic history
Estimates of inbreeding and relatedness are commonly calculated using molecular markers, although the accuracy of such estimates has been questioned. As a further complication, in many situations, such estimates are required in populations with reduced genetic diversity, which is likely to affect their accuracy. We investigated the correlation between microsatellite- and pedigree-based coefficients of inbreeding and relatedness in laboratory populations of Drosophila melanogaster that had passed through bottlenecks to manipulate their genetic diversity. We also used simulations to predict expected correlations between marker- and pedigree-based estimates and to investigate the influence of linkage between loci and null alleles. Our empirical data showed lower correlations between marker- and pedigree-based estimates in our control (nonbottleneck) population than were predicted by our simulations or those found in similar studies. Correlations were weaker in bottleneck populations, confirming that extreme reductions in diversity can compromise the ability of molecular estimates to detect recent inbreeding events. However, this result was highly dependent on the strength of the bottleneck and we did not observe or predict any reduction in correlations in our population that went through a relatively severe bottleneck of N = 10 for one generation. Our results are therefore encouraging, as molecular estimates appeared robust to quite severe reductions in genetic diversity. It should also be remembered that pedigree-based estimates may not capture realized identity-by-decent and that marker-based estimates may actually be more useful in certain situations.
Data from: Genome-wide analysis reveals demographic and life history patterns associated with habitat modification in land-locked, deep-spawning sockeye salmon (Oncorhynchus nerka)
<p>Human-mediated habitat fragmentation in freshwater ecosystems can negatively impact genetic diversity, demography and life history of native biota, while disrupting the behaviour of species that are dependent on spatial connectivity to complete their life cycles. In the Alouette River system (British Columbia, Canada), dam construction in 1928 impacted passage of anadromous sockeye salmon (<i>Oncorhynchus nerka</i>), with the last records of migrants occurring in the 1930's. Since that time, <i>O. nerka</i> persisted as a resident population in Alouette Reservoir until experimental water releases beginning in 2005 created conditions for migration; two years later, returning migrants were observed for the first time in ~70 years, raising important basic and applied questions regarding life history variation and population structure in this system. Here, we investigated the genetic distinctiveness and population history of Alouette Reservoir <i>O. nerka</i> using genome-wide SNP data (n=7,709 loci) collected for resident and migrant individuals, as well as for neighbouring anadromous sockeye salmon and resident kokanee populations within the Fraser River drainage (n=312 individuals). Bayesian clustering and principal components analyses based on neutral loci revealed five distinct clusters, largely associated with geography, and clearly demonstrated that Alouette Reservoir resident and migrant individuals are genetically distinct from other <i>O. nerka</i> populations in the Fraser River drainage. At a finer-level, there was no clear evidence for differentiation between Alouette Reservoir residents and migrants; although we detected eight high-confidence outlier loci, they all mapped to sex chromosomes suggesting that differences were likely due to uneven sex ratios rather than life history. Taken together, these data suggest that contemporary Alouette Reservoir <i>O. nerka</i> represents a landlocked sockeye salmon population, constituting the first reported instance of deep-water spawning behaviour associated with this life history form. This finding punctuates the need for re-assessment of conservation status and supports on-going fisheries management activities in Alouette Reservoir. </p>
Data from: Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers
The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.
Data from: Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae) in Western Ghats, India: implications for conservation in a biodiversity hotspot
The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, one of the world's eight most important biodiversity hotspots. As D. malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-wide genetic structure of twelve D. malabaricum populations was evaluated to assess the impact of human activities on genetic diversity and infer the species' evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (FIS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred before the last glacial maximum. Finally we discussed the implications of these results, in particular the presence of a clear pattern of historical genetic subdivision, on conservation policies.
An unexpected genetic diversity pattern and a complex demographic history of a rare medicinal herb, Chinese asparagus (Asparagus cochinchinensis) in Korea
Range-wide population studies of wide spread species are often associated with complex diversity patterns resulting from genetically divergent evolutionary significant units (ESUs). The compound evolutionary history creating such a pattern of diversity can be inferred through molecular analyses. Asparagus cochinchinensis, a medicinally important perennial herb, is in decline due to overharvesting in Korea. Eight A. cochinchinensis populations in Korea and three neighboring countries (China, Japan and Taiwan) were examined using nine nuclear microsatellite loci and three chloroplast microsatellite loci to characterize molecular diversity patterns. The average within-population diversity was limited likely due to long-term bottlenecks observed in all eight populations. High pairwise FST values indicated that the populations have largely diverged, but the divergences were not correlated with geographic distances. Clustering analyses revealed a highly complex spatial structure pattern associated with two ESUs. Approximate Bayesian Computation (ABC) suggest that the two ESUs split about 21,000 BP, were independently introduced to Korea approximately 1,800 years ago, and admixed in secondary contact zones. The two ESUs found in our study may have different habitat preferences and growth conditions, implying that the two genetically divergent groups should be considered not only for conservation and management but also for breeding programs in agricultural areas.
Demographic History and Genomic Targets of Positive Selection in Giant Gough Mice
<p>A key challenge in understanding how natural selection operates is to identify the mutations and genes that make it possible. Positive selection on beneficial mutations distorts linked variation by altering the site frequency spectrum, the configuration of haplotypes, and population differentiation. By comparing patterns of sequence variation to neutral predictions across genomes, the targets of positive selection can be located. We applied this logic to an unusual population of house mice that shows phenotypic and ecological hallmarks of selection. Mice from Gough Island are twice the body size of mainland mice, eat live seabirds, maintain a very high population density, and inhabit an environment without predators or humans. We used massively parallel short-read sequencing to survey the genomes of 14 Gough Island mice. We computed a set of summary statistics to capture diverse aspects of variation across these genome sequences, used approximate Bayesian computation to reconstruct a null demographic model, and then applied machine learning to estimate the posterior probability of positive selection in each region of the genome. We conducted parallel analyses on genome sequences from 8 mice from Germany, treating them as representatives of a mainland reference population. A few thousand 5kb windows show strong evidence for positive selection in Gough Island mice but not in German mice. Genic regions and the X chromosome contain disproportionate shares of these selection windows. Over-represented gene ontologies in selection windows emphasize neurological themes. Inspection of genomic regions harboring many selection windows with high posterior probabilities pointed to genes with known effects on exploratory behavior and body size as potential targets. Some genes in these regions have missense mutations and/or putative regulatory mutations with large differences between Gough Island mice and German/French mice in the frequency of the derived allele; these are candidates for adaptive variants. Our results provide a genomic portrait of adaptation to island conditions and position Gough Island mice as a powerful system for understanding the genetic component of natural selection.</p>
Figure 3 in Phylogeography and demographic history of the Andean degu, Octodontomys gliroides (Rodentia: Octodontidae)
Figure 3. Map of cluster membership and posterior probability for each cluster based on the GENELAND analysis. A, the estimated cluster membership represents the modal cluster assignment of each pixel, and the rest of the inset maps show the posterior probability of individuals of Octodontomys gliroides in Argentina, Bolivia, and Chile. Black dots represent sampling localities. The three clusters are: B, populations of northern and central Bolivia; C, populations from northern Chile, central and southern Bolivia, and northern Argentina; and D, the remaining Argentinian populations and one population from southern Bolivia. The white area represents a probability between 90 and 100% for sampling localities to belong to their respective cluster.
Figure 5 in Phylogeography and demographic history of the Andean degu, Octodontomys gliroides (Rodentia: Octodontidae)
Figure 5. Map, showing the putative barriers (major rivers, lakes, salt flats, the Atacama Desert, and the mountain chains of the Andes) that separate the populations of Octodontomys gliroides.
Figure 4 in Phylogeography and demographic history of the Andean degu, Octodontomys gliroides (Rodentia: Octodontidae)
Figure 4. Pairwise mismatch distribution (left) and Bayesian skyline plots (right), depicting the demographic history for the entire sample (A and B), lineage A (C and D), and lineage B (E and F). For mismatch distributions, black circles represent the observed distribution of pairwise differences and white circles represent the theoretical expected distribution under a population expansion model. For the skyline plot, black lines represent median estimates, whereas the dotted lines represent the upper and lower 95% credible intervals. The x-axis of Bayesian skyline figures is the time per million years before the present and the y-axis is the estimated effective population size (Ne).
Figure 2. A in Phylogeography and demographic history of the Andean degu, Octodontomys gliroides (Rodentia: Octodontidae)
Figure 2. A, geographical location of the sampled populations along its distributional range (for abbreviations of localities, see Table 1), and results of the BARRIER analysis. Pie charts display the frequency of occurrence of each haplotype in each locality; the size of the pie chart is proportional to population size. The genetic barriers in red are numbered (in Roman numerals) and the thickness is proportional to the ratio between genetic distance values between populations on both sides of each barrier to the average genetic distance among populations in the whole data set. The populations inside unfilled irregular shapes are the populations pooled by the BARRIER analysis (for more detail, see Material and methods). B, the four major genetic boundaries (thick colored lines) detected by BARRIER 2.2 using FST values. The order of the numerical pairs represents the sequence of the boundary formation. The black dots correspond to the population numbers plotted along the ordination (some populations were pooled by the analysis). The dashed lines and solid lines represent the Voronoi tessellation and the Delaunay triangulation, respectively.
Figure 1. A in Phylogeography and demographic history of the Andean degu, Octodontomys gliroides (Rodentia: Octodontidae)
Figure 1. A, phylogenetic relationships within the principal nodes for Octodontomys gliroides, based on Bayesian analysis of mtDNA control region haplotypes. Divergence dates of the most recent common ancestor in million years (above the branches), 95% credible intervals (below the branches), and nodes with high posterior probability (below the 95% credible intervals) are shown. The two main lineages are indicated by black and red lines, and the sublineages found in lineage A, referred to in the text as A1 and A2, respectively, are coloured as follow: sublineage A1, blue; sublineage A2, green. B, haplotype network recovered by statistical parsimony analysis. Each circle represents a different haplotype with size proportional to frequencies, with the largest circles representing the most abundant haplotypes. The coloration pattern of each haplotype represents the lineages and sublineages recovered in the phylogenetic analysis. White circles denote the number of mutational steps between haplotypes. For geographical details of sampling populations and haplotype codes, see Table 1.
Data from: The demographic history of micro-endemics: Have rare species always been rare?
<p>Extinction has increased as human activities impact ecosystems. Conservation assessments for the IUCN red list are a fundamental tool in aiding the prevention of further extinction, yet, relatively few species have been thoroughly assessed. To increase the efficiency of assessments, novel approaches are needed to highlight threatened species that are currently data deficient. Many Madagascan plant species currently have extremely narrow ranges, but this may not have always been the case. To assess this, we used high-throughput DNA sequencing for 2-5 individuals of each species - reflecting the paucity of samples available for rare species. We estimated effective population size (<em>N</em><sub><em>e</em></sub>) for each species and compared this to census population <em>(N</em><sub><em>c</em></sub>) sizes when known. In each case, <em>N</em><sub><em>e</em></sub> was an order of magnitude larger than <em>N</em><sub><em>c</em></sub> – a signature of rapid, recent population decline. We then estimated the demographic history of each species, tracking changes in <em>N</em><sub><em>e</em></sub> over time. Five out of ten species displayed significant population declines towards the present (68–90% decreases). Our results for palm trees indicate that it is possible to predict extinction risk, particularly in the most threatened species. We performed simulations to show that our approach has the power to detect population decline during the Anthropocene, but performs less well when less data is used. Similar declines to those in palms were observed in data deficient species or those assessed as of least concern. These analyses reveal that Madagascar's narrow endemics were not always rare, having experienced rapid decline in their recent history. Our approach offers the opportunity to target species in need of conservation assessment with little prior information, particularly in regions where human modification of the environment has been rapid.</p>
Demographic changes and life-history strategies predict the genetic diversity in crabs
<p>Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analyzed across 150 species (16,992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predicting GD, with species that have undergone bottlenecks followed by population expansion showing lower GD. Egg size, pelagic larval duration, and habitat might play a role probably because of their association with how species respond to disturbances. Ultimately, K-strategists that have undergone bottlenecks are the species showing lower GD. Some variables do not show an association with GD as expected, most likely due to the taxon-specific role of some predictors, which should be considered in further investigations and generalizations. This work highlights the complexity underlying the predictors of GD and adds results from a marine invertebrate group to the current understanding of this topic.</p>
Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent gray fox lineages?
Open the record for dataset details and reuse information.
Data from: Comparative genetic structure and demographic history in endemic Galápagos weevils
Open the record for dataset details and reuse information.
Data from: Estimating relatedness and inbreeding using molecular markers and pedigrees: the effect of demographic history
Open the record for dataset details and reuse information.
Data from: The demographic history of micro-endemics: Have rare species always been rare?
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.