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.
141
datasets available to search
ShareScore release 0.9.0
Dataset results
141 results for “population genetics analysis”
Data from: Comparing the performance of microsatellites and RADseq in population genetic studies: analysis of data for pike (Esox lucius) and a synthesis of previous studies
<p>Population genetic studies reveal biodiversity patterns and inform about drivers of evolutionary differentiation and adaptation, including gene flow, drift and selection. This can advance our understanding and aid decision making regarding management and conservation efforts. Microsatellites have long been used in population genetic studies.Thanks to the development of newer techniques, sequencing approaches such as restriction site associated DNA sequencing (RADseq) are on their way to replace microsatellites for some applications. However, the performance of these two marker types in population genetics have rarely been systematically compared. We utilized three neutrally and adaptively differentiated populations of anadromous pike (<i>Esox lucius</i>) to assess the relative performance of microsatellites and RADseq with respect to resolution and conclusiveness of estimates of population differentiation and genetic structure. To this end, the same set of individuals (<i>N</i> = 64) were genotyped with both RADseq and microsatellite markers. To assess effects of sample size, the same subset of 10 randomly chosen individuals from each population (<i>N</i> = 30 in total) were also genotyped with both methods. Comparisons of estimated genetic diversity and structure showed that both markers were able to uncover genetic structuring. The full RADseq dataset provided the clearest detection of the finer scaled genetic structuring, and the other three datasets (full and subset microsatellite, and subset RADseq) provided comparable results. A search for outlier loci performed on the full SNP dataset poninted to signs of selection potentially associated with salinity and temperature, exemplifying the utility of RADseq to inform about the importance of different environmental factors. To evaluate whether performance differences between the markers are general or context specific, the results of previous studies that have investigated population structure using both marker types were synthesized. The synthesis revealed that RADseq performed as well as, or better than microsatellites in detecting genetic structuring in the included studies. The differences in the ability to detect population structure, both in the present and the previous studies, are likely explained by the higher number of loci typically utilized in RADseq compared to microsatellite analysis, as increasing the number of markers will (regardless of the marker type) increase power and allow for clearer detection and higher resolution of genetic structure.</p>
Genetic consequences of plant edaphic specialisation to solfatara fields; phylogenetic and population genetic analysis of Carex angustisquama (Cyperaceae)
<p>Edaphic specialisation is one of the main drivers of plant diversification and has multifaceted effects on population dynamics. Carex angustisquama is a sedge plant growing only on heavily acidified soil in solfatara fields, where only extremophytes can survive. Because of the lack of closely related species in similar habitats and its disjunct distribution, the species offers ideal settings to investigate the effects of adaptation to solfatara fields and historical biogeography on genetic consequences of plant edaphic specialisation to solfatara fields. Here, genome-wide single-nucleotide polymorphisms were used to reveal the phylogenetic origin of C. angustisquama, and 16 expressed sequence tag–simple sequence repeat markers were employed to infer population demography of C. angustisquama. Molecular phylogenetic analysis strongly indicated that C. angustisquama formed a monophyletic clade with C. doenitzii, a species growing on non-acidified soil in sympatric sub-alpine zone. The result of population genetic analysis showed that C. angustisquama possesses much lower genetic diversity than the sister species, and notably, all 16 loci were completely homozygous in most individuals of C. angustisquama. Approximate Bayesian computation analysis supported the model that assumed hierarchical declines of population size through its evolutionary sequence. We propose that the edaphic specialist in solfatara fields has newly attained the adaptation to solfatara fields in the process of speciation. Furthermore, we found evidence of a drastic reduction in genetic diversity in C. angustisquama, suggesting that the repeated founder effects associated with edaphic specialisation and subsequent population demography bring the loss of genetic diversity to the extremophyte in solfatara fields.</p>
Data from: Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations
Following almost 10 years of no reported cases, Guinea worm disease (GWD or dracunculiasis) reemerged in Chad in 2010 with peculiar epidemiological patterns and unprecedented prevalence of infection among non-human hosts, particularly domestic dogs. Since 2014, animal infections with Guinea worms have also been observed in the other three countries with endemic transmission (Ethiopia, Mali, and South Sudan), causing concern and generating interest in the parasites' true taxonomic identity and population genetics. We present the first extensive population genetic data for Guinea worm, investigating mitochondrial and microsatellite variation in adult female worms from both human and non-human hosts in the four endemic countries to elucidate the origins of Chad's current outbreak and possible host-specific differences between parasites. Genetic diversity of Chadian Guinea worms was considerably higher than that of the other three countries, even after controlling for sample size through rarefaction, and demographic analyses are consistent with a large, stable parasite population. Genealogical analyses eliminate the other three countries as possible sources of parasite reintroduction into Chad, and sequence divergence and distribution of genetic variation provide no evidence that parasites in human and non-human hosts are separate species or maintain isolated transmission cycles. Both among and within countries, geographic origin appears to have more influence on parasite population structure than host species. Guinea worm infection in non-human hosts has been occasionally reported throughout the history of the disease, particularly when elimination programs appear to be reaching their end goals. However, no previous reports have evaluated molecular support of the parasite species identity. Our data confirm that Guinea worms collected from non-human hosts in the remaining endemic countries of Africa are Dracunculus medinensis and that the same population of worms infects both humans and dogs in Chad. Our genetic data and the epidemiological evidence suggest that transmission in the Chadian context is currently being maintained by canine hosts.
Data from: Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean
Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933–0.987, π=0.763–0.996% and Rs=4.22–4.37, He=0.624–0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat.
Data from: Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci
Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high-gene-flow marine species off the west coast of North America that experienced strong population decline over the past three decades. We used 18 anonymous and 13 gene associated simple sequence repeat loci (EST-SSRs) to characterize range-wide population structure with temporal replicates. No FST-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between FST and variation or marker class was observed. General Linear Model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates, but did not affect the observed pattern of population structure.
Data from: Influence of parameter settings in automated scoring of AFLPs on population genetic analysis
The use of procedures for the automated scoring of AFLP fragments has recently increased. Corresponding software does not only automatically score the presence or absence of AFLP fragments, but also allows an evaluation of how different settings of scoring parameters influence subsequent population genetic analyses. In this study, we used the automated scoring package RAWGENO to evaluate how five scoring parameters influence the number of polymorphic bins and estimates of pairwise genetic differentiation between populations (Fst). Steps were implemented in R to automatically run the scoring process in RAWGENO for a set of different parameter combinations. While we found the scoring parameters minimum bin width and minimum number of samples per bin to have only weak influence on pairwise Fst values, maximum bin width and bin reproducibility had much stronger effects. The minimum average bin fluorescence scoring parameter affected Fst values in an only moderate way. At a range of scoring parameters around the default settings of RAWGENO, the number of polymorphic bins as well as pairwise Fst values stayed rather constant. This study thus shows the particularities of AFLP scoring, be it either manual or automatical, can have profound effects on subsequent population genetic analysis.
FIGURE 5 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure
FIGURE 5. Unrooted phylogenetic tree constructed with Freqpars (Swofford & Berlocher 1987) on the basis of allele frequencies.
FIGURE 4 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure
FIGURE 4. UPGMA dendrogram showing evolutionary relationships between populations based on genetic identity values (Nei 1978).
FIGURE 3 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure
FIGURE 3. Map of collecting sites. See Table 1 for abbreviations. Solid boxes are sites where only D. ornata was found; solid circles are sites where only D. saundersi was found; asterisks are sites where both species live sympatrically.
Data from: Genetic analysis of life-history constraint and evolution in a wild ungulate population
Trade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.
Genetic admixture and population structure analysis of Indian water buffaloes (Bubalus bubalis) using STR markers
<p><span>We generated genetic diversity data for 10 different buffalo populations of India using 20 highly polymorphic microsatellite markers. The buffalo populations of Odisha were the primary focus, viz. Chilika, Paralakhemundi, Kalahandi, Sambhalpuri, and Manda. The total observed number of alleles ranged between 143 (Manda) and 301 (Paralakhemundi) with an average of 204 alleles per breed. The minimal spanning network based on Bruvo's distance, PCA based on the Fst values, and genetic admixture analysis using both the STRUCTURE and 'snapclust' could identify the Manda population distinct from other Odisha buffalo breeds as well as Chhattisgarhi buffalo breed. The Sambhalpuri buffalo population also clustered into two separate subpopulations, half of the unique sub-population located geographically south-wards displayed no admixture with any of the adjacent buffalo populations. The Sambhalpuri population requires elaborate analysis to confirm the existence of two distinct sub-populations and if they could be recognized as separate breeds. The limited number of sires in the Manda population has resulted in excess of heterozygosity. Furthermore, the Manda population is left with very little allelic richness and this poses a huge threat to the population's existence. In another way, the study has led to the identification of the Manda buffalo as a distinct population, and the germplasm has been registered based on the study.</span></p>
Fig. 1 in Multilocus population analysis of Gavia immer (Aves: Gaviidae) mtDNA reveals low genetic diversity and lack of differentiation across the species breeding range
Fig. 1 Haplotype network constructed using the median joining method. Haplotype numbers are indicated. Circle patterns represent coastal sampling locations: GZ Galicia, Spain, MX Mexico, GE Germany, NJ New Jersey, US, MI Michigan, US, CA Canada, FL Florida, US. Circle surfaces are roughly proportional to the number of individuals with each haplotype (Table 3)
FIGURE 1 in Combining morphology and population genetic analysis uncover species delimitation in the widespread African tree genus Santiria (Burseraceae)
FIGURE 1. Genetic clusters (GC) detected in Santiria samples from western Central Africa. Bayesian clustering analyses were performed on 479 individuals genotyped at 10 microsatellites loci. A. Variation in means of Ln (likelihood) of the data as a function of the number of hypothetical genetic clusters (K), showing a plateau at K=3. B. Histogram of genetic assignment of the 481 individuals at K = 3. C. Distribution of the three genetic clusters in western Central Africa, and delimitation of the distribution of each genetic cluster (dotted line: GC1, solid line: GC2, dashed line: GC3). We extended the distribution ranges of GC2 and GC3 because morphotypes of both genetic clusters were observed in the south of the Republic of the Congo. Note: Interm. GCx and GCy = intermediate individuals between GCx and GCy.
FIGURE 2 in Combining morphology and population genetic analysis uncover species delimitation in the widespread African tree genus Santiria (Burseraceae)
FIGURE 2. Extended Principal Component Analysis (the Hill-Smith ordination) of quantitative and qualitative traits assessed in 103 Santiria herbarium samples assigned to GC1 (N = 46, open circles), GC2 (N = 21, stars) and GC3 (N = 36, open triangles). Note: NL = number of leaflets per leaf; LL = length of leaves; LP = length of petiole; WP = width of petiole; LP/WP = ratio between LP and WP; TPeL = terminal petiolule length; TLL = terminal leaflet length; TLW = terminal leaflet width; TLL/TLW = ratio between TLL and TLW; TLWe = terminal leaflet weight dry portion; AL = apex length; GD = glandular dots; Le = lenticels.
Data from: Population genetic analysis of white sturgeon (Acipenser transmontanus) in the Fraser River
White sturgeon (Acipenser transmontanus) in the Fraser River are listed as imperiled (the second highest possible rating) by the British Columbia Conservation Data Centre. A difficulty in trying to protect this species in the Fraser River and elsewhere is the lack of knowledge regarding their population biology. Variation in the mitochondrial DNA control region and at four microsatellite loci was examined in order to characterize white sturgeon samples from throughout the Fraser River mainstem and from a major tributary, the Nechako River. Samples from the adjacent Columbia River were analyzed for comparison. In contrast to previous work, present data indicate that white sturgeon population structure in this region reflects post-glacial dispersal more than it does recent anthropogenic effects. The data divided the Fraser into four biogeographic regions: (i) the lower Fraser, below Hell's Gate; (ii) the middle Fraser, between Hell's Gate and river km 553; (iii) the upper Fraser, above the Nechako confluence; and (iv) the Nechako River. These four groups are concordant with those suggested by tag and recapture and catch per unit effort data, and are separated by what have been identified as barriers to white sturgeon migration. Based on concordance between these different types of data, it is argued that the four groups identified here merit evolutionarily significant unit (ESU) status.
Data from: Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines
Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyze 21 microsatellite loci in historical (archived scales from 1927-1956) and contemporary samples of brown trout (Salmo trutta) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with non-local strains of hatchery trout. We show that all populations have been strongly affected by stocking, with admixture proportions ranging from 14 to 64%. Historical population genetic structure was characterized by isolation-by-distance and by positive correlations between historical effective population sizes and habitat area within river systems. Contemporary population genetic structure still showed isolation-by-distance, but also reflected differences among populations in hatchery trout admixture proportions. Despite significant changes to the genetic composition within populations over time, dispersal rates among populations were roughly similar before and after stocking. We also assessed whether population declines or introgression by hatchery strain trout should be the most significant conservation concern in this system. Based on theoretical considerations, we argue that population declines have had limited negative effects for the persistence of adaptive variation, but admixture with hatchery trout may have resulted in reduced local adaptation. Collectively, our study demonstrates the usefulness of analyzing historical samples for identifying the most important consequences of human activities on the genetic structure of wild populations.
Figure 1 in Genetic diversity of Atherina hepsetus (Osteichthyes: Atherinidae) populations as determined by RFLP analysis of three mtDNA regions
Figure 1. Sampling sites: Monastiraki (MON), Panagopoula (PAN), Kiparissi (KIP), Tinos (TIN), Naxos (NAX), Samos (SAM), Nissiros (NIS), Leipsi (LEI), Kos (KOS), Lesvos (MYT) and Evvoia (EVV).
Figure 3 in Genetic diversity of Atherina hepsetus (Osteichthyes: Atherinidae) populations as determined by RFLP analysis of three mtDNA regions
Figure 3. Dollo parsimony (Farris 1977) dendrogram showing the relationships between the 15 mtDNA haplotypes detected. Numbers indicate the bootstrap support (10,000 replicates) of each node of the majority-rule consensus tree.
Oxytenanthera abyssinica (A. Rich.) Munro; lowland bamboo (Poaceae, Bambusinea) in Ethiopia: Genetic diversity, population structure and gene flow analysis
<p><span>As one of the most important non-timber forest resources, a potential alternative to wood and wood product and fastest-growing plant in the world (91 cm (35 in) per day), bamboo is a member of the grass family (Poaceae) and constitutes a single subfamily Bambusoideae. 67% of total area of bamboo in Africa and 7% of world total is contributed by Ethiopia giving more than 1.44 million hectares. Silica gel dried young fresh leaves from 130 individuals of O. abyssinica were collected for DNA extraction and PCR amplification. Each of the PCR amplified ISSR fragments using 19 ISSR primers were used to study band pattern and heterozigosity, level of polymorphism, calculating marker efficiency, Nei`s (H) and Shannon (I) genetic diversity, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA) and admixture results. High genetic variation at species level was observed with the percentage of the polymorphic loci (PPL) = 84.48%. The H, I, observed number of alleles (Na) and effective number of alleles (Ne) at species level was 0.2702, 0.4061, 1.8448, and 1.4744, respectively, showing a relatively high level of genetic diversity. However, the genetic differentiation at the population level was relatively low. AMOVA using grouped populations revealed that, most of the diversity was distributed within the populations (61.05%) with F<sub>ST</sub> = 0.38949, F<sub>SC</sub> = 0.10486 and F<sub>CT</sub> = 0.31797. Cluster analysis grouped the populations into sharply distinct clusters, which could be attributed to cross pollination nature of the plant and long lived to the area. STRUCTURE analyses for all population and excluding Gambella population gives different result K = 2 and K = 11. Using these markers, we find strong evidence linking geographic origin of diversity and samples from Gambella Region found different from others and might tell the availability of additional bamboo species in the country.</span></p>
Fig. 4 in An analysis of variations in morphological characteristics, essential oil content, and genetic sequencing among and within major Iranian Juniper (Juniperus spp.) populations
Fig. 4. (A) A map of Iran showing the relative geographic location of each habitat, (B) Representative of DNA fragments generated by the UBC807 primer in the nine juniper populations. The left-most (L) column corresponds to the biological ruler (Ladder) and the right-most column () is a negative control., (C) Dendrogram obtained from five ISSR primers using UPGMA method by Dice similarity coefficient for 27 juniper genotypes (D) Principal Component Analysis based on Dice matrix for 27 juniper genotypes.
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.