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.
79
datasets available to search
ShareScore release 0.9.0
Dataset results
79 results for “Genetic admixture”
Data from: Range expansion of house sparrows (Passer domesticus) in Kenya: evidence of genetic admixture and human-mediated dispersal
Introduced species offer an opportunity to study the ecological process of range expansions. Recently, 3 mechanisms have been identified that may resolve the genetic paradox (the seemingly unlikely success of introduced species given the expected reduction in genetic diversity through bottlenecks or founder effects): multiple introductions, high propagule pressure, and epigenetics. These mechanisms are probably also important in range expansions (either natural or anthropogenic), yet this possibility remains untested in vertebrates. We used microsatellite variation (7 loci) in house sparrows (Passer domesticus), an introduced species that has been spreading across Kenya for ~60 years, to determine if patterns of variation could explain how this human commensal overcame the genetic paradox and expresses such considerable phenotypic differentiation across this new range. We note that in some cases, polygenic traits and epistasis among genes, for example, may not have negative effects on populations. House sparrows arrived in Kenya by a single introduction event (to Mombasa, ~1950) and have lower genetic diversity than native European and introduced North American populations. We used Bayesian clustering of individuals (n = 233) to detect that at least 2 types of range expansion occurred in Kenya: one with genetic admixture and one with little to no admixture. We also found that genetic diversity increased toward a range edge, and the range expansion was consistent with long-distance dispersal. Based on these data, we expect that the Kenyan range expansion was anthropogenically influenced, as the expansions of other introduced human commensals may also be.
Data from: Genetic structure, admixture, and invasion success in a Holarctic defoliator, the gypsy moth (Lymantria dispar, Lepidoptera: Erebidae)
Characterizing the current population structure of potentially invasive species provides a critical context for identifying source populations and for understanding why invasions are successful. Non-native populations inevitably lose genetic diversity during initial colonization events, but subsequent admixture among independently introduced lineages may increase both genetic variation and adaptive potential. Here we characterize the population structure of the gypsy moth (Lymantria dispar Linnaeus), one of the world's most destructive forest pests. Native to Eurasia and recently introduced to North America, the current distribution of gypsy moth includes forests throughout the temperate region of the northern hemisphere. Analyses of microsatellite loci and mitochondrial DNA sequences for 1738 individuals identified four genetic clusters within L. dispar. Three of these clusters correspond to the three named subspecies; North American populations represent a distinct fourth cluster, presumably a consequence of the population bottleneck and allele frequency change that accompanied introduction. We find no evidence that admixture has been an important catalyst of the successful invasion and range expansion in North America. However, we do find evidence of ongoing hybridization between subspecies and increased genetic variation in gypsy moth populations from Eastern Asia, populations that now pose a threat of further human-mediated introductions. Finally, we show that current patterns of variation can be explained in terms of climate and habitat changes during the Pleistocene, a time when temperate forests expanded and contracted. Deeply diverged matrilines in Europe imply that gypsy moths have been there for a long time and are not recent arrivals from Asia.
Data from: Genetic structure reveals a history of multiple independent origins followed by admixture in the allopolyploid weed Salsola ryanii
It has recently become clear that many invasive species have evolved in situ via hybridization or polyploidy from progenitors which themselves are introduced species. For species formed by hybridization or polyploidy, genetic diversity within the newly formed species is influenced by the number of independent evolutionary origins of the species. For recently formed species, an analysis of genetic structure can provide insight into the number of independent origin events involved in the formation of the species. For a putative invasive allopolyploid species, the number of origins involved in the species formation, the genetic diversity present within these origins, and the level of gene flow between independent origins determines the genetic composition of the neospecies. Here we analyze the genetic structure of the newly formed allopolyploid species, Salsola ryanii, a tumbleweed which evolved within the last 20–100 years in California. We utilize the genetic structure analysis to determine that this new species is the result of at least three independent allopolyplodization events followed by gene flow between the descendants of independent origins.
Data from: Genetic admixture and heterosis may enhance the invasiveness of common ragweed
Biological invasions are often associated with multiple introductions and genetic admixture of previously isolated populations. In addition to enhanced evolutionary potential through increased genetic variation, admixed genotypes may benefit from heterosis, which could contribute to their increased performance and invasiveness. To deepen our understanding of the mechanisms and management strategies for biological invasions, we experimentally studied whether intraspecific admixture causes heterosis in common ragweed (Ambrosia artemisiifolia) by comparing the performance of crosses (F1) between populations relative to crosses within these populations for each range (native, introduced) under different ecologically relevant conditions (control, drought, competition, simulated herbivory). Performance of admixed genotypes was highly variable, ranging from strong heterotic effects to weak outbreeding depression. Moreover, heterosis was not uniformly observed among between-population crosses, but certain native population crosses showed considerable heterosis, especially under simulated herbivory. In contrast, heterosis was largely absent in crosses from the introduced range, possibly implying that these populations were already admixed and benefit little from further mixing. In conclusion, these results support the hypothesis that heterosis may contribute to biological invasions, and indicate the need to minimize new introductions of exotic species, even if they are already present in the introduced range.
Data from: Genetic diversity, breed composition and admixture of Kenyan domestic pigs
The genetic diversity of African pigs, whether domestic or wild has not been widely studied and there is very limited published information available. Available data suggests that African domestic pigs originate from different domestication centers as opposed to international commercial breeds. We evaluated two domestic pig populations in Western Kenya, in order to characterize the genetic diversity, breed composition and admixture of the pigs in an area known to be endemic for African swine fever (ASF). One of the reasons for characterizing these specific populations is the fact that a proportion of indigenous pigs have tested ASF virus (ASFv) positive but do not present with clinical symptoms of disease indicating some form of tolerance to infection. Pigs were genotyped using either the porcine SNP60 or SNP80 chip. Village pigs were sourced from Busia and Homabay counties in Kenya. Because bush pigs (Potamochoerus larvatus) and warthogs (Phacochoerus spp.) are known to be tolerant to ASFv infection (exhibiting no clinical symptoms despite infection), they were included in the study to assess whether domestic pigs have similar genomic signatures. Additionally, samples representing European wild boar and international commercial breeds were included as references, given their potential contribution to the genetic make-up of the target domestic populations. The data indicate that village pigs in Busia are a non-homogenous admixed population with significant introgression of genes from international commercial breeds. Pigs from Homabay by contrast, represent a homogenous population with a "local indigenous' composition that is distinct from the international breeds, and clusters more closely with the European wild boar than African wild pigs. Interestingly, village pigs from Busia that tested negative by PCR for ASFv genotype IX, had significantly higher local ancestry (>54%) compared to those testing positive, which contained more commercial breed gene introgression. This may have implication for breed selection and utilization in ASF endemic areas. A genome wide scan detected several regions under preferential selection with signatures for pigs from Busia and Homabay being very distinct. Additionally, there was no similarity in specific genes under selection between the wild pigs and domestic pigs despite having some broad areas under similar selection signatures. These results provide a basis to explore possible genetic determinants underlying tolerance to infection by ASFv genotypes and suggests multiple pathways for genetically mediated ASFv tolerance given the diversity of selection signatures observed among the populations studied.
Data from: Non-random patterns of genetic admixture expose the complex historical hybrid origin of unisexual leaf beetle species in the genus Calligrapha
Many unisexual animal lineages supposedly arose from hybridization. However, support for their putative hybrid origins mostly comes from indirect methodologies, which are rarely confirmatory. Here we provide compelling data indicating that tetraploid unisexual Calligrapha are true genetic mosaics obtained via analysis of mitochondrial DNA (mtDNA) and allelic variation and coalescence times for three single-copy nuclear genes (CPS, HARS, and Wg) in five of six unisexual Calligrapha and a representative sample of bisexual species. Nuclear allelic diversity in unisexuals consistently segregates in the gene pools of at least two but up to three divergent bisexual species, interpreted as putative parentals of interspecific hybridization crosses. Interestingly, their mtDNA diversity derives from an additional yet undiscovered older evolutionary lineage that is possibly the same for all independently originated unisexual species. One possibly extinct species transferred its mtDNA to several evolutionary lineages in a wave of hybridization events during the Pliocene, whereby descendant species retained a polymorphic mtDNA constitution. Recent hybridizations, in the Pleistocene and always involving females with the old introgressed mtDNA, seemingly occurred in the lineages leading to unisexual species, decoupling mtDNA introgression (and inferences derived from these data, such as timing and parentage) from subsequent acquisition of the new reproductive mode. These results illuminate an unexpected complexity in possible routes to animal unisexuality, with implications for the interpretation of ancient unisexuality. If the origin of unisexuality requires a mechanism where (1) hybridization is a necessary but insufficient condition and (2) multiple bouts of hybridization involving more than two divergent lineages are required, then the origins of several classical unisexual systems may have to be reassessed.
Data from: Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries
PREMISE OF THE STUDY: Hybrid zones provide 'natural laboratories' for understanding the processes of selection, reinforcement and speciation. We sought to gain insight into the degree of introgression and the extent of ecological/phenotypic intermediacy in the natural hybrid strawberry, Fragaria × ananassa subsp. cuneifolia. METHODS: We used whole plastome sequencing to identify parental species-specific (Fragaria chiloensis and F. virginiana) chloroplast SNPs, and combined the use of these with nuclear microsatellite markers to genetically characterize the hybrid zone. We assessed the potential role of selection in the observed geographic patterns by bioclimatically characterizing the niche of the hybrid populations and phenotypically characterizing hybrid individuals of known genomic constitution. KEY RESULTS: Significant admixture and little overall maternal bias in chloroplast or nuclear genomes suggest a high degree of inter-fertility among the parental and hybrid species and point to a long history of backcrossing and genetic mixing in the hybrid zone. Even though hybrids were phenotypically intermediate to the parental species there was still a discernible fingerprint of the parental genotype within hybrid individuals. Thus, while the pattern of introgression observed suggests geographic limitations to gene flow, it may be reinforced by selection for specific parental traits in the bioclimatically-intermediate habitat occupied by the hybrid. CONCLUSION: This work uncovered the genetic complexity underlying the hybrid zone of the wild relatives of the cultivated strawberry. It lays the foundation for experimental dissection of the causes of genomic introgression and nuclear-cytoplasmic disassociation, and understanding other parts of the Fragaria evolutionary history.
Data from: Hybrid speciation in sparrows I: phenotypic intermediacy, genetic admixture and barriers to gene flow
Homoploid hybrid speciation is thought to require unusual circumstances to yield reproductive isolation from the parental species, and few examples are known from nature. Here we present genetic evidence for this mode of speciation in birds. Using Bayesian assignment analyses of 751 individuals genotyped for 14 unlinked, nuclear microsatellite loci, we show that the phenotypically intermediate Italian sparrow (Passer italiae) does not form a cluster of its own, but instead exhibits clear admixture (over its entire breeding range) between its putative parental species, the house sparrow (P. domesticus) and the Spanish sparrow (P. hispaniolensis). Further, the Italian sparrow possesses mitochondrial (mt) DNA haplotypes identical to both putative parental species (although mostly of house sparrow origin), indicating a recent hybrid origin. Today, the Italian sparrow has a largely allopatric distribution on the Italian peninsula and some Mediterranean islands separated from its suggested parental species by the Alps and the Mediterranean Sea, but occurs sympatrically with the Spanish sparrow on the Gargano peninsula in southeast Italy. No evidence of interbreeding was found in this sympatric population. However, the Italian sparrow hybridizes with the house sparrow in a sparsely populated contact zone in the Alps. Yet, the contact zone is characterized by steep clines in species-specific male plumage traits, suggesting that partial reproductive isolation may also have developed between these two taxa. Thus, geographic and reproductive barriers restrict gene flow into the nascent hybrid species. We propose that an origin of hybrid species where the hybrid lineage gets geographically isolated from the parental species, as seems to have happened here, might be more common in nature than previously assumed.
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>
Introgression, admixture and selection facilitate genetic adaptation to high-altitude environments in Chinese cattle
<p>Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of <em>Bos grunniens</em> and <em>Bos javanicus</em> on the formation of Chinese indicine breeds that led to their divergence from India-origin Zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (>1800m) and low-altitude adapted breeds (<1500m) revealed candidate genes (<em>ACSS2</em>, <em>ALDOC,</em> <em>EPAS1</em>,<em> EGLN1, NUCB2</em>) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 <em>ACSS2</em>-knockout analyses suggests that the up-regulation of <em>ACSS2</em> expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted Yaks into Chinese <em>B. t. taurus </em>prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.</p>
Data from: Northern range expansion of European populations of the wasp spider Argiope bruennichi is associated with global warming correlated genetic admixture and specific temperature adaptations
Poleward range expansions are observed for an increasing number of species, which may be an effect of global warming during the past decades. However, it is still not clear in how far these expansions reflect simple geographical shifts of species ranges, or whether new genetic adaptations play a role as well. Here, we analyse the expansion of the wasp spider Argiope bruennichi into Northern Europe during the last century. We have used a range-wide sampling of contemporary populations and historical specimens from museums to trace the phylogeography and genetic changes associated with the range shift. Based on the analysis of mitochondrial, microsatellite and SNP markers, we observe a higher level of genetic diversity in the expanding populations, apparently due to admixture of formerly isolated lineages. Using reciprocal transplant experiments for testing overwintering tolerance, as well as temperature preference and tolerance tests in the laboratory, we find that the invading spiders have possibly shifted their temperature niche. This may be a key adaptation for survival in Northern latitudes. The museum samples allow a reconstruction of the invasion's genetic history. A first, small-scale range shift started around 1930, in parallel with the onset of global warming. A more massive invasion of Northern Europe associated with genetic admixture and morphological changes occurred in later decades. We suggest that the latter range expansion into far Northern latitudes may be a consequence of the admixture that provided the genetic material for adaptations to new environmental regimes. Hence, global warming could have facilitated the initial admixture of populations and this resulted in genetic lineages with new habitat preferences.
Data from: Genetic structure of Omani goats reveals admixture among populations from geographically proximal sites
The genetic diversity of most global goat populations has been assessed in recent decades using nuclear markers but remains unstudied in the south Arabian Peninsula, particularly in Sultanate of Oman, despite the importance of these animals for the local economy and food supply. Therefore, the present study provides a comparative analysis of the genetic diversity of five native Omani goat populations and evaluates possible admixture rates with the four most frequently imported goat populations from geographically proximal countries. Quality control of 15 loci was conducted and molecular characterization of nine populations was performed with 11 microsatellite markers. Accordingly, a data set based on 11 high informative microsatellites loci genotypes from nine populations was used to estimate the population genetic parameters. The summary statistics for the parameters depicted relatively highly diverse populations (Ho = 0.667, He = 0.663) with relatively low and mostly non-significant levels of inbreeding (FIS). Furthermore, the population substructure estimators (AMOVA) and population differentiation coefficient (FST) were indicated weak genetic differentiation among populations (P < 0.001).A finer analysis of the population substructure and differentiation using STRUCTURE, discriminant analyses of principal components (DAPCs) and a neighbor-joining (NJ) tree were supported a scenario that a high level of gene flow between populations from close geographical locations are the main evolutionary driving force. Thus, any future conservation strategy and breeding programs should include to preserve unique alleles that might be contributing to with stand the limited feed and requirement in desert ecosystems as well as economic traits.
Data for: Invasion history of Lycium ferocissimum in Australia – the impact of admixture on genetic diversity and differentiation
<p class="MsoNormal"><strong><span>Aim:</span></strong><span> We investigated the invasion history of <em>Lycium ferocissimum</em>, a spine-covered shrub native to South Africa that has developed into a damaging invasive plant of undisturbed landscapes and pastures across southern and eastern Australia. In addition to identifying the provenance of the Australian plants, we tested for evidence of admixture, and contrasted genetic diversity and structuring across the native and introduced ranges.</span></p> <p class="MsoNormal"><strong><span>Location: </span></strong><span>Samples were collected across South Africa (24 localities) and Australia (26 localities).</span></p> <p class="MsoNormal"><strong><span>Methods:</span></strong><span> We used genotyping-by-sequencing (3,130 SNPs across 381 individuals) to assess population genetic structuring in <em>L. ferocissimum </em>across Australia and South Africa. Coalescent analyses were used to explicitly test contrasting invasion scenarios.</span></p> <p class="MsoNormal"><strong><span>Results:</span></strong><span> Clear geographic genetic structuring was detected across South Africa, with distinct clusters in the Eastern and Western Cape provinces. The <em>L. ferocissimum</em> plants in Australia form their own genetic cluster, with a similar level of genetic diversity as plants in South Africa. Coalescent analyses demonstrated that the lineage in Australia was formed by admixture between Eastern Cape and Western Cape plants, with analyses suggesting that plants from both African regions were originally introduced to South Australia. We detected little evidence of geographic genetic structure across Australia, although many of the populations were genetically distinct from one another.</span></p> <p class="MsoNormal"><strong><span>Main conclusions</span></strong><span>: Our results illustrate how admixture can result in genetically diverse and distinct invasive populations. The complex invasion history of <em>L. ferocissimum </em>in Australia poses particular challenges for biological control. We suggest potential biological control agents should be screened against admixed plants (in addition to plants from the Eastern and Western Cape) to test whether they provide effective control of the genetically distinct invasive lineage.</span></p>
Figure 3 in Rare genetic admixture and unidirectional gene flow between Vipera aspis and Vipera berus at their contact zone in western France
Figure 3. Principal Coordinates Analysis (PCoA) based on 10 microsatellite markers showing the distribution of morphologically intermediate individuals in between the pure V. aspis and pure V. berus individuals in the Loire Atlantique department (France). Individual 4.14 was morphologically intermediate but genetically assigned to pure V. aspis.
Figure 1 in Rare genetic admixture and unidirectional gene flow between Vipera aspis and Vipera berus at their contact zone in western France
Figure 1. Structure analysis (K = 2) of V. aspis and V. berus samples collected in the Loire Atlantique department (France). Morphologically intermediate individuals include individual 4.14 which was genetically assigned to V. aspis. The hybridization level of individuals 14 and 71 could not be clearly assigned.
Mapping of End Stage Renal Disease Genetic Susceptibility in African Americans by Admixture Linkage Disequilibrium
ClinicalTrials.gov study NCT00559767. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Introgression, admixture and selection facilitate genetic adaptation to high-altitude environments in Chinese cattle
Open the record for dataset details and reuse information.
Data from: Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)
Open the record for dataset details and reuse information.
Data from: Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries
Open the record for dataset details and reuse information.
Data from: Genetic admixture and heterosis may enhance the invasiveness of common ragweed
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.