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1,598 results for “genetic diversity”
Linked collectors and determiners for: First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches.
Natural history specimen data linked to collectors and determiners held within, "First record of Limnatis paluda (Hirudinida, Arhynchobdellida, Praobdellidae) from Kazakhstan, with comments on genetic diversity of Limnatis leeches". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/0bb8a532-1b00-45e6-99ea-774b47eae650">https://bionomia.net/dataset/0bb8a532-1b00-45e6-99ea-774b47eae650</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/0bb8a532-1b00-45e6-99ea-774b47eae650">https://gbif.org/dataset/0bb8a532-1b00-45e6-99ea-774b47eae650</a>. Formatted as a Frictionless Data package.
Data from: On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity
A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, though these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analyzing the relationship among intraspecies diversity, interspecies divergence, and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centered on long non-coding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms.
Data from: Effects of complex life cycles on genetic diversity: cyclical parthenogenesis
Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).
Data from: The legend of the Canadian horse: genetic diversity and breed origin
The Canadian breed of horse invokes a fascinating chapter of North American history and as such it is now a heritage breed and the national horse of Canada. The aims of this study were to determine the level of genetic diversity in the Canadian, investigate the possible foundation breeds and the role it had in the development of the US horse breeds, such as Morgan Horse. We tested a total of 981 horses by using 15 microsatellite markers. We found that Canadian horses have high values of genetic diversity indices and show no evidence of a serious loss of genetic diversity and the inbreeding coefficient was not significantly different from zero. Belgian, Percheron, Breton and Dales Pony, unlike the light French horses, may have common ancestries with the Canadian and could be important founders. However, the Shire and Clydesdale influenced the Canadian to a lesser extent than French and Belgian draft breeds. Furthermore, our finding indicated that there was no evidence of a clear relationship between Canadian and Oriental or Iberian breeds. Also, the Canadian likely contributed to the early development of the Morgan. Finally, these findings support the ancient legends of the Canadian Horse as North America's first equine breed and the foundation bloodstock to many American breeds and may help in the management and breeding program of this outstanding breed in North America.
Data from: Broad-scale genetic diversity of Cannabis for forensic applications
Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide.
Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: patterns, processes and conservation implications.
<p><span><span><span><span><span><span><span><span><span><span><span>The aim of this study was to determine how historical and contemporary eco-evolutionary processes shape the patterns of genetic diversity and differentiation across species' distribution range remains an open question with strong conservation implications. Focusing on the orange stony coral, <i>Astroides calycularis</i>, we i) characterized the pattern of neutral genetic diversity across the distribution range; ii) gave insights into the underlying processes; and iii) discussed conservation implications with emphasis on a national park located on a hotspot of genetic diversity.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Location:</b> South Mediterranean Sea and Zembra National Park.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>We combined new data from 12 microsatellites in 13 populations located in the Centre and in the Western Periphery of the distribution range with a published dataset including 16 populations from the Western and Eastern Peripheries. We analysed the relationship among parameters of genetic diversity (<i>H<sub>e</sub></i>, <i>Ar<sub>(g)</sub></i>) and structure (population-specific <i>F<sub>ST</sub></i>) and two measures of geographic peripherality. We compared two estimators of pairwise genetic structure (<i>G<sub>ST</sub></i>, <i>D<sub>EST</sub></i>) across the distribution range. The evolutionary and demographic history of the populations following the Last Glacial Maximum was reconstructed using approximate Bayesian computations and Maximum Likelihood analyses. We inferred the contemporary connectivity among populations from Zembra National Park and with the neighbouring area of Cap Bon. </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>We demonstrate a decrease of genetic diversity and an increase of genetic differentiation from the Centre to the Eastern and Western Peripheries of the distribution range<i>. </i>Populations from Zembra show the highest genetic diversity reported in the species. We identified a spillover effect towards Cap Bon. </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>The patterns of genetic diversity and differentiation are most likely explained by "the postglacial range expansion hypothesis" rather than the "central-peripheral hypothesis". Enforcement of conservation measures should be considered to protect this genetic diversity pattern, in particular when considering the low effective population size inferred at many sites.</span></span></span></span></span></span></span></span></span></span></span></p>
Genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations
<p>Rufiji tilapia (<em>Oreochromis urolepis urolepis</em>) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth-rate, salinity tolerance, and the production of all-male hybrids when crossed with Nile tilapia (<em>Oreochromis niloticus</em>). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices.</p>
Figure 2 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 2 Phylogenetic trees of the mtDNA control region haplotypes in C. guichenoti reconstructed with Bayesian inference. Numbers at nodes represent Bayesian posterior probabilities and neighbor-joining tree. At the right side of the figure, the numbers represent the total of individuals from different sampling locations in each haplotype.
Figure 3 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 3 Median-joining network of the mtDNA control region haplotypes of C. guichenoti. The size of each circle indicates the relative frequency of the corresponding haplotype in the whole data set.
Supplementary material 1 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Tables S1, S2, Figures S1, S2
Figure 4 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 4 Isolation by distance (IBD) relationship among C. guichenoti wild populations in five populations collected in 2009 a and seven populations collected in 2019 b.
Figure 1 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 1 Sampling localities of China (solid triangles indicate sites in 2009; solid circle indicate sites in 2019) of C. guichenoti. For full names of populations, see Table 1.
Figure 2 in Genetic diversity of Atherina hepsetus (Osteichthyes: Atherinidae) populations as determined by RFLP analysis of three mtDNA regions
Figure 2. Neighbor-joining (Saitou and Nei 1987) cladogram, based on the net nucleotide divergence.
Data from: In situ glacial survival maintains high genetic diversity of Mussaenda kwangtungensis on continental islands in subtropical China
<p>Generally, island populations are predicted to have less genetic variation than their mainland relatives. However, there has been exceptions, indicating that the relationships were impacted by several factors, e.g historical processes. In the present study, we chose a group of subtropical islands located in South China as the study system, which are quite younger and much closer to the mainland than most of the previous studied island systems, to test the hypothesis that<i> in situ</i> glacial survival contributes to high levels of genetic diversity in island populations. We conducted a comparison of genetic variation between 12 island and 11 nearby mainland populations of <i>Mussaenda kwangtungensis</i> using eleven nuclear microsatellite and three chloroplast markers, evaluated effects of the island area and distance to mainland on genetic diversity of island populations, and simulated the potential distribution over the past by ecological niche modelling, together with the genetic data to detect the role of islands during the glacial periods. The island populations displayed comparable levels of genetic diversity and differentiation with mainland populations, overall high levels of unique polymorphisms, and the greatest values of specific within-population genetic diversity. No significant correlation was detected between genetic diversity of island populations and distance to mainland, as well as area of islands, except that allelic richness was significantly positively correlated with the area of islands. Nuclear microsatellites revealed two main clusters, largely corresponding to islands and inland populations, which divergence dated to a time of island formation by ABC analysis. Ecological Niche Modelling predicted a highly climatic suitability on islands during the Last Glacial Maximum (LGM). Our results suggest that the islands have acted as refugia during the LGM and highlight the role of <i>in situ</i> glacial survival in maintaining high levels of genetic diversity of <i>M. kwangtungensis</i> in continental islands of subtropical China.</p>
Figure 2 in Genetic diversity, population structure and demographic history of Dugesia japonica in Taihang Mountains
Figure 2. Mismatch distribution of Dugesia japonica from Taihang Mountains based on mitochondrial COI.
Figure 1 in Species diversity and endemism in the Daphnia of Argentina: a genetic investigation
Figure 1. Collection sites for Argentine populations belonging to the subgenus Daphnia. Photographs are included for a single individual of each species. Species were identified based on genetic analyses (see text and Fig. 2). Animals are not shown to scale. In some cases, multiple collections of the same species within a small geographical region are not shown (see Appendix 1 for the complete list of collection localities).
Host genotype and genetic diversity shape the evolution of a novel bacterial infection
<p><span><span><span><span><span><span><span><span><span><span><span>Pathogens continue to emerge from increased contact with novel host species. Whilst these hosts can represent distinct environments for pathogens, the impacts of host genetic background on how a pathogen evolves post-emergence are unclear. In a novel interaction, we experimentally evolved a pathogen (<i>Staphylococcus aureus</i>) in populations of wild nematodes (<i>Caenorhabditis elegans</i>) to test whether <span><span>host genotype and genetic diversity affect pathogen evolution</span></span>. After 10 rounds of selection, we found that pathogen virulence evolved to vary across host genotypes, with differences in host metal ion acquisition detected as a possible driver of increased host exploitation. Diverse host populations selected for the highest levels of pathogen virulence, but infectivity was constrained, unlike in host monocultures. We hypothesize that population heterogeneity might pool together individuals that contribute disproportionately to the spread of infection or to enhanced virulence. The genomes of evolved populations were sequenced, and it was revealed that pathogens selected in distantly-related host genotypes diverged more than those in closely-related host genotypes. <i>S. aureus </i>nevertheless maintained a broad host range. Our study provides unique empirical insight into the evolutionary dynamics that could occur in other novel infections of wildlife and humans.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Landscape, colonization and life history: their effects on genetic diversity in four sympatric species inhabiting a dendritic system
To what degree are patterns of genetic structure in fragmented systems the result of contemporary landscape vs. history? We examined the distribution of genetic diversity as a function of colonization history and contemporary landscape in four fish species inhabiting a hierarchically fragmented, unaltered system, the Kogaluk drainage (Labrador): lake trout, longnose sucker, round whitefish, and lake chub. The footprint of colonization history was still observable in the three species where this issue was examined regardless of the generations since their arrival. ABC analyses suggest colonization took place from the southwest. The species exhibit similar diversity patterns despite different Nes and generation intervals. Contemporary gene flow was largely negligible except for gene flow from a centrally located lake. These results suggest landscape has driven colonization history, which still has influence on genetic structuring. The species are widespread. Understanding how they behave in the pristine Kogaluk provides a baseline against which to evaluate how other anthropogenically perturbed systems are performing. Improved understanding of historical and contemporary processes is required to fully explain diversity patterns in complex metapopulations
Figure 7 from: Kuznetsova V, Aguin-Pombo D (2015) Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review. In: Lukhtanov VA, Kuznetsova VG, Grozeva S, Golub NV (Eds) Genetic and cytogenetic structure of biological diversity in insects. ZooKeys 538: 63-93. https://doi.org/10.3897/zookeys.538.6724
Figure 7 - Histogram showing the distribution of female diploid chromosome numbers in Cicadomorpha at species and generic levels, based on analysis of 511 species and 335 genera of the families Cicadellidae, Membracidae, Ulopidae, Ledridae, Aetalionidae, Cercopidae, Aphrophoridae, Machaerotidae, Clastopteridae, Cicadidae, and Myerslopiidae.
Figure 5 from: Kuznetsova V, Aguin-Pombo D (2015) Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review. In: Lukhtanov VA, Kuznetsova VG, Grozeva S, Golub NV (Eds) Genetic and cytogenetic structure of biological diversity in insects. ZooKeys 538: 63-93. https://doi.org/10.3897/zookeys.538.6724
Figure 5 - Histogram showing the distribution of female diploid chromosome numbers in Cercopoidea at species and generic levels, based on analysis of 50 species and 23 genera of the families Cercopidae, Aphrophoridae, Machaerotidae, and Clastopteridae.
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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.