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.
33
datasets available to search
ShareScore release 0.9.0
Dataset results
33 results for “genetic homogeneity”
Data from: Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley
<p>Direct observation is central to our understanding of the process of adaptation, but evolution is rarely documented in a large, multicellular organism for more than a few generations. Here, we observe genetic and phenotypic evolution across a century-scale competition experiment, barley composite cross II (CCII). CCII was founded in 1929 with tens of thousands of unique genotypes and has been adapted to local conditions in Davis, CA, USA for 58 generations. We find that natural selection has massively reduced genetic diversity leading to a single clonal lineage constituting most of the population by generation F50. Selection favored alleles originating from similar climates to that of Davis, and targeted genes regulating reproductive development, including some of the most well-characterized barley diversification loci, Vrs1, HvCEN, and Ppd-H1. We chronicle the dynamic evolution of reproductive timing in the population and uncover how parallel molecular pathways are targeted by stabilizing selection to optimize this trait. Our findings point to selection as the predominant force shaping genomic variation in one of the world's oldest ongoing biological experiments.</p>
Data from: Losing cichlid fish biodiversity: genetic and morphological homogenization of tilapia following colonization by introduced species
Open the record for dataset details and reuse information.
Data from: Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley
Open the record for dataset details and reuse information.
Data from: Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi
Genetic differentiation is characteristically weak in marine species making assessments of population connectivity and structure difficult. However the advent of genomic methods have increased genetic resolution, enabling studies to detect weak, but significant population differentiation within marine species. With an increasing number of studies employing high resolution genome-wide techniques, we are realising the connectivity of marine populations is often complex and quantifying this complexity can provide an understanding of the processes shaping marine species genetic structure and to inform long-term, sustainable management strategies. This study aims to assess the genetic structure, connectivity and local adaptation of the Eastern Rock Lobster (Sagmariasus verreauxi), which has a maximum pelagic larval duration of 12 months and inhabits both subtropical and temperate environments. We used 645 neutral and 15 outlier SNPs to genotype lobsters collected from the only two known breeding populations and a third episodic population — encompassing S. verreauxi's known range. Through examination of the neutral SNP panel, we detected genetic homogeneity across the three regions, which extended across the Tasman Sea encompassing both Australian and New Zealand populations. We discuss differences in neutral genetic signature of S. verreauxi and a closely-related, co-distributed rock lobster, Jasus edwardsii, determining a regional pattern of genetic disparity between the species, which have largely similar life histories. Examination of the outlier SNP panel detected weak genetic differentiation between the three regions. Outlier SNPs showed promise in assigning individuals to their sampling origin and may prove useful as a management tool for species exhibiting genetic homogeneity.
Data from: Homogenous population genetic structure of the non-native raccoon dog (Nyctereutes procyonoides) in Europe as a result of rapid population expansion
The extent of gene flow during the range expansion of non-native species influences the amount of genetic diversity retained in expanding populations. Here, we analyse the population genetic structure of the raccoon dog (Nyctereutes procyonoides) in north-eastern and central Europe. This invasive species is of management concern because it is highly susceptible to fox rabies and an important secondary host of the virus. We hypothesized that the large number of introduced animals and the species' dispersal capabilities led to high population connectivity and maintenance of genetic diversity throughout the invaded range. We genotyped 332 tissue samples from seven European countries using 16 microsatellite loci. Different algorithms identified three genetic clusters corresponding to Finland, Denmark and a large 'central' population that reached from introduction areas in western Russia to northern Germany. Cluster assignments provided evidence of long-distance dispersal. The results of an Approximate Bayesian Computation analysis supported a scenario of equal effective population sizes among different pre-defined populations in the large central cluster. Our results are in line with strong gene flow and secondary admixture between neighbouring demes leading to reduced genetic structuring, probably a result of its fairly rapid population expansion after introduction. The results presented here are remarkable in the sense that we identified a homogenous genetic cluster inhabiting an area stretching over more than 1500km. They are also relevant for disease management, as in the event of a significant rabies outbreak, there is a great risk of a rapid virus spread among raccoon dog populations.
Data from: Genetic homogenization of indigenous sheep breeds in Northwest Africa
Northwest-African sheep represent an ideal case-study for assessing the potential impact of genetic homogenization as a threat to the future of traditional breeds that are adapted to local conditions. We studied ten Algerian and Moroccan breeds of sheep, including three transboundary breeds, distributed over a large part of the Maghreb region, which represents a geographically and historically coherent unit. Our analysis of the dataset that involved carrying out Genome-wide SNP genotyping, revealed a high level of homogenization (ADMIXTURE, NetView, fineSTRUCTURE and IBD segments analyses), in such a way that some breeds from different origins appeared genetically undistinguished: by grouping the eight most admixed populations, we obtained a mean global FST value of 0.0024. The sPCA analysis revealed that the major part of Morocco and the Northern part of Algeria were affected by the phenomenon, including most of the breeds considered. Unsupervised cross-breeding with the popular Ouled-Djellal breed was identified as a proximate cause of this homogenization. The issue of transboundary breeds was investigated, and the Hamra breed in particular was examined via ROH fragments analysis. Genetic diversity was considered in the light of historical archives and anthropological works. All of these elements taken together suggest that homogenization as a factor affecting the Maghrebin sheep stock, has been particularly significant over the last few decades, although this process probably started much earlier. In particular, we have identified the policies set by the French administration during the colonial period of the region's history as a causal factor that probably contributed significantly to this process. The genetic homogenization that we have observed calls into question the integrity of the farm animal genomic resources represented by these local breeds, whose conservation is of critical importance to the future of the livestock sector.
Data from: The curious case of Hermodice carunculata (Annelida: Amphinomidae): evidence for genetic homogeneity throughout the Atlantic Ocean and adjacent basins
Over the last few decades, advances in molecular techniques have led to the detection of strong geographic population structure and cryptic speciation in many benthic marine taxa, even those with long-lived pelagic larval stages. Polychaete annelids, in particular, generally show a high degree of population divergence, especially in mitochondrial genes. Rarely have molecular studies confirmed the presence of 'cosmopolitan' species. The amphinomid polychaete Hermodice carunculata was long considered the sole species within its genus, with a reported distribution throughout the Atlantic and adjacent basins. However, recent studies have indicated morphological differences, primarily in the number of branchial filaments, between the East and West Atlantic populations; these differences were invoked to re-instate Hermodice nigrolineata, formerly considered a junior synonym of H. carunculata. We utilized sequence data from two mitochondrial (cytochrome c oxidase subunit I, 16S rDNA) markers and one nuclear (internal transcribed spacer) marker to examine the genetic diversity of Hermodice throughout its distribution range in the Atlantic Ocean, including the Mediterranean Sea, the Caribbean Sea, the Gulf of Mexico and the Gulf of Guinea. Our analyses revealed generally low genetic divergences among collecting localities and between the East and West Atlantic, although phylogenetic trees based on mitochondrial data indicate the presence of a private lineage in the Mediterranean Sea. A re-evaluation of the number of branchial filaments confirmed differences between East and West Atlantic populations; however, the differences were not diagnostic and did not reflect the observed genetic population structure. Rather, we suspect that the number of branchial filaments is a function of oxygen saturation in the environment. Our results do not support the distinction between H. carunculata in the West Atlantic and H. nigrolineata in the East Atlantic. Instead, they re-affirm the older notion that H. carunculata is a cohesive species with a broad distribution across the Atlantic Ocean.
FIGURE 3 in Global genetic homogeneity in the deep-sea foraminiferan Epistominella exigua (Rotaliida: Pseudoparrellidae)*
FIGURE 3. ITS sequences network performed by TCS software: schema of genetic relationships between each haplotype (1 node represents a difference of 1 nucleotide or indel). Geographic origin of haplotypes is indicated by the color of the boxes: yellow for Pacific, red for Antarctic, blue for Arctic and green for North Atlantic.
FIGURE 2 in Global genetic homogeneity in the deep-sea foraminiferan Epistominella exigua (Rotaliida: Pseudoparrellidae)*
FIGURE 2. In Background. Map with position of Epistominella exigua sampling sites (red anchors for Antarctic, green for Atlantic, blue for Arctic and yellow for Pacific). In Foreground. E. exigua ITS rDNA sequence divergences. Minimum and maximum values of divergences within each geographic population (DiP) as well as maximum values of intraspecimen divergences (DiS) are indicated in color according the sampling sites. Minimum and maximum values of divergences between each geographic population (DIP) are indicated above black arrows. Inset. Epistominella exigua specimen collected off Japan.
FIGURE 1 in Global genetic homogeneity in the deep-sea foraminiferan Epistominella exigua (Rotaliida: Pseudoparrellidae)*
FIGURE 1. Phylogenetic tree inferred from SSU rDNA sequences showing the position of E. exigua among other Epistominella species and the lack of differentiation between populations of E, exigua from different regions. This tree has been obtained using the ML method with 1000 bootstrap replicates. The support values at internal nodes correspond to ML (left) and Bayesian (right) analyses. Only values over 50% were indicated. Within the genus Epistominella, first letters of the Epistominella sequence names indicate their geographical origin (ARK: Arctic, WED: Weddell Sea, ATL: North Atlantic, P: Pacific, McM: Mc Murdo Sound, USH: Ushuaia, KG: King George Island) and colour indicates a range of depths (purple: 0-200 m; green: 200–1200 m; dark blue:>1200 m). New sequences are indicated by a star (*).
Figure 3 in Genetic homogeneity in a Pontocaspian crested newt species (Triturus karelinii) suggests recent isolation of its three allopatric range sections
Figure 3. DISTRUCT plots showing allocation of Triturus karelinii individuals to gene pools (k) based on the different Bayesian clustering programs (noted on the left with the preferred k value). See the main text for details. Population numbers (noted at the top) correspond to fig. 1 and table 1.
Figure 5 in Genetic homogeneity in a Pontocaspian crested newt species (Triturus karelinii) suggests recent isolation of its three allopatric range sections
Figure 5. Species distribution model for Triturus karelinii projected on climate layers for the present, the mid-Holocene (mid-Holo, ∼6 Ka), the Last Glacial Maximum (LGM, ∼22 Ka) and the Last Interglacial (∼130 Ka). For the mid-Holocene and the Last Glacial Maximum projections on data layers based on the CCSM4 (CCSM) and MIROC-ESM (MIROC) model are shown. Warmer colours reflect a higher predicted suitability.
Figure 2 in Genetic homogeneity in a Pontocaspian crested newt species (Triturus karelinii) suggests recent isolation of its three allopatric range sections
Figure 2. Phylogeny (left) and haplotype network for Triturus karelinii mtDNA. Haplotype codes (the prefix 'TkarA' has been excluded in the haplotype network) correspond to supplementary table S1. Colours reflect the three regions where haplotypes originate from. Values at nodes are posterior probability values (<0.5 not shown). The outgroup is not shown.
Figure 1 in Genetic homogeneity in a Pontocaspian crested newt species (Triturus karelinii) suggests recent isolation of its three allopatric range sections
Figure 1. Sampling scheme for Triturus karelinii. Numbered localities were sequenced for nuclear DNA and correspond to table 1. The black squares reflect additional localities for which mtDNA has been sequenced and the white stars reflect localities that were on top of that used to create the species distribution model. Grey background shading reflects elevation with darker colours reflecting higher elevation.
Figure 4 in Genetic homogeneity in a Pontocaspian crested newt species (Triturus karelinii) suggests recent isolation of its three allopatric range sections
Figure 4. Results of a principal component analysis of nuclear genetic data for Triturus karelinii. Population numbers correspond to fig. 1 and table 1.
FIGURE 4 in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia
FIGURE 4. An unrooted Neighbor Joining tree of Lake Tana Labeobarbus species constructed by APE (an R-package) using pair-wise genetic distances among individuals based on analysis of 10 microsatellite loci. Bootstrap percentage values shown at nodes are from 100 pseudo-replicates and indicate the level of support for each group; only bootstrap values higher than 50% are indicated.
FIGURE 3 in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia
FIGURE 3. Scatter plot from Discriminant analysis of Principal Components (DPC; Jombart et al. 2010) of microsatellite data from 161 Lake Tana Labeobarbus individuals. The 95% confidence ellipses of each group based on the common covariance matrix assumption for the multivariate normal distribution are presented. Points represent individual genotypes and symbols represent species (A) or spawning populations (B). A. Using species as grouping factor with asterisks representing the estimated means for each population: Pop A = L. acutirostris, Pop B = L. brevicephalus, Pop C = L. crassibarbus, Pop D = L. gorgorensis, Pop E = L. gorguari, Pop F = L. intermedius, Pop G = L. longissimus, Pop H = L. macrophtalmus, Pop I = L. megastoma, Pop J = L. nedgia, Pop K = L. platydorsus, Pop L = L. surkis, Pop M = L. tsanensis, Pop N = L. truttiformis. B. Using spawning strategy as grouping criteria: ▲riverine spawning population, ●lacustrine spawning population.
FIGURE 2 in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia
FIGURE 2. Bayesian clustering assignment of individuals based on Structure analysis of 10 microsatellite loci of Labeobarbus populations from Lake Tana and adjacent water bodies. A. Analysis of whole dataset without a priori population definitions (K=1–15). B. Lake Tana Labeobarbus populations only with K = 2 inferred clusters. 1. L. acitirostris, 2. L. brevicephalus, 3. L. crassibarbus, 4. L. gorgorensis, 5. L. gorguari, 6. L. longissimus, 7. L. macrophtalmus, 8. L. megastoma, 9. L. nedgia, 10. L. platydorsus, 11. L. surkis, 12. L. truttiformis, 13. L. tsanensis, 14. L. intermedius, 15. L. beso.
FIGURE 1. A in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia
FIGURE 1. A. Map showing major river drainages of Ethiopia; B. Map of Lake Tana. All samples of Lake Tana were drawn from sites (area lying within the red rectangle) located in the Bahir Dar Gulf.
Data from: Genetic homogenization of indigenous sheep breeds in Northwest Africa
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.