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124 results for “Genetic distance”
Data from: Does genetic distance between parental species influence outcomes of hybridisation among coral reef butterflyfishes?
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Data from: Genetic structure in parasitic Rhinanthus angustifolius is determined by geographical distance rather than habitat – implications for taxonomy and conservation
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Data from: Multi-level patterns of genetic structure and isolation by distance in the widespread plant Mimulus guttatus
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Data from: The extended consequences of genetic conductivity: mating distance affects community phenotypes in Norway spruce
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Data from: Combined genetic and telemetry data reveal high rates of gene flow, migration, and long-distance dispersal potential in Arctic ringed seals (Pusa hispida)
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An evaluation of isolation by distance (IBD) and isolation by resistance (IBR) on genetic structure of the Persian squirrel (Sciurus anomalus) in the Zagros forests of Iran
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Data from: Indirect estimates of natal dispersal distance from genetic data in a stream-dwelling fish (Mogurnda adspersa)
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Data from: Regression commonality analyses on hierarchical genetic distances.
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Data from: Multi-level patterns in population genetics: variogram series detects a hidden isolation-by- distance- dominated structure of Scandinavian brown bears Ursus arctos
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Isolation by geographical distance after release from Pleistocene refugia explains genetic and phenotypic variation in Xylotrupes siamensis (Coleoptera: Scarabaeidae)
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Plasmodium falciparum genomic surveillance reveals spatial and temporal trends, association of genetic and physical distance, and household clustering
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Data from: Competitive consequences determined by phenotypic but not genetic distance: a study with asexual Daphnia genotypes
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Influence of voltine ecotype and geographic distance on genetic and haplotype variation in the Asian corn borer
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Data from: Variation in the level of aggression, chemical and genetic distance among three supercolonies of the Argentine ant in Europe
In their invasive ranges, Argentine ant populations often form one geographically vast supercolony, genetically and chemically uniform within which there is no intraspecific aggression. Here we present regional patterns of intraspecific aggression, cuticular hydrocarbons and population genetics of 18 nesting-sites across Corsica and the French mainland. Aggression tests confirm the presence of a third European supercolony, the Corsican supercolony, which exhibits moderate to high levels of aggression, depending on nesting-sites, with the Main supercolony, and invariably high levels of aggression with the Catalonian supercolony. The chemical analyses corroborated the behavioral data, with workers of the Corsican supercolony showing moderate differences in cuticular hydrocarbons compared to workers of the European Main supercolony and strong differences compared to workers of the Catalonian supercolony. Interestingly, there were also clear genetic differences between workers of the Catalonian supercolony and the two other supercolonies at both nuclear and mitochondrial markers, but only very weak genetic differentiation between nesting-sites of the Corsican and Main supercolonies (FST = 0.06). A detailed comparison of the genetic composition of supercolonies also revealed that, if one of the last two supercolonies derived from the other, it is the Main supercolony that derived from the Corsican supercolony rather than the reverse. Overall, these findings highlight the importance of conducting more qualitative and quantitative analyses of the level of aggression between supercolonies, which has to be correlated with genetic and chemical data.
Data from: Isolation-by-distance in landscapes: considerations for landscape genetics
In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern). We investigated if landscape configuration influenced the rate at which a case-IV pattern changed to a case-I pattern. We also determined at what interdeme distance the highest correlation was measured between genetic differentiation and geographic distance and whether this distance corresponded to the maximum migration distance. We set up a population genetic simulation study and assessed the development of IBD patterns for several habitat configurations and maximum migration distances. We show that the rate and likelihood of the transition of case-IV to case-I FST–distance relationships was strongly influenced by habitat configuration and maximum migration distance. We also found that the maximum correlation between genetic differentiation and geographic distance was not related to the maximum migration distance and was measured across all deme pairs in a case-I pattern and, for a case-IV pattern, at the distance where the FST–distance curve flattens out. We argue that in landscape genetics, separate analyses should be performed to either assess IBD or the landscape effects on gene flow.
Data from: Genetic distance as an alternative to physical distance for definition of gene units in association studies
Background: Some association studies, as the implemented in VEGAS, ALIGATOR, i-GSEA4GWAS, GSA-SNP and other software tools, use genes as the unit of analysis. These genes include the coding sequence plus flanking sequences. Polymorphisms in the flanking sequences are of interest because they involve cis-regulatory elements or they inform on untyped genetic variants trough linkage disequilibrium. Gene extensions have customarily been defined as ± 50 Kb. This approach is not fully satisfactory because genetic relationships between neighbouring sequences are a function of genetic distances, which are only poorly replaced by physical distances. Results: Standardized recombination rates (SRR) from the deCODE recombination map were used as units of genetic distances. We searched for a SRR producing flanking sequences near the ± 50 Kb offset that has been common in previous studies. A SRR ≥ 2 was selected because it led to gene extensions with median length = 45.3 Kb and the simplicity of an integer value. As expected, boundaries of the genes defined with the ± 50 Kb and with the SRR ≥2 rules were rarely concordant. The impact of these differences was illustrated with the interpretation of top association signals from two large studies including many hits and their detailed analysis based in different criteria. The definition based in genetic distance was more concordant with the results of these studies than the based in physical distance. In the analysis of 18 top disease associated loci form the first study, the SRR ≥2 genes led to a fully concordant interpretation in 17 loci; the ± 50 Kb genes only in 6. Interpretation of the 43 putative functional genes of the second study based in the SRR ≥2 definition only missed 4 of the genes, whereas the based in the ± 50 Kb definition missed 10 genes. Conclusions: A gene definition based on genetic distance led to results more concordant with expert detailed analyses than the commonly used based in physical distance. The genome coordinates for each gene are provided to maintain a simple use of the new definitions.
Data from: Parasite genetic distance and local adaptation in coevolving bacteria-bacteriophage populations
Antagonistic coevolution between hosts and parasites can lead to local adaptation (LA), such that parasite fitness is greatest in sympatric hosts (or vice versa). The magnitude of LA typically increases with geographic distance, which is assumed to be because genetic (and hence phenotypic) distance increases with geographic distance. Here we explicitly test the relationships between parasite genetic and phenotypic distance and LA using isolates of coevolved viral parasites (lytic bacteriophage ϕ2) and the host bacterium Pseudomonas fluorescens SBW25. We find positive relationships between parasite genotype and infectivity phenotype, but the strength of the relationship was greater when infectivity was defined by the identity of hosts that could be infected rather than the actual number of hosts infected (host range), and when measurements were compared within rather than among populations. Crucially, we find a monotonic relationship between LA and genetic distance across phage isolates from different populations, although in contrast to many geographic studies, parasite LA decreased with genetic distance. These results can be explained by the fact that bacteria can rapidly adapt to phage infectivity mutations, but that evolved resistance has a degree of specificity to the local phage population. Our results show that antagonistic coevolution alone can result in predictable links between genetic distance and host-parasite local adaptation.
Data from: Current approaches using genetic distances produce poor estimates of landscape resistance to interindividual dispersal
Landscape resistance reflects how difficult it is for genes to move across an area with particular attributes (e.g., land cover, slope). An increasingly popular approach to estimate resistance uses Mantel and partial Mantel tests or causal modeling to relate observed genetic distances to effective distances under alternative sets of resistance parameters. Relatively few alternative sets of resistance parameters are tested, leading to relatively poor coverage of the parameter space. Although this approach does not explicitly model key stochastic processes of gene flow, including mating, dispersal, drift, and inheritance, bias and precision of the resulting resistance parameters have not been assessed. We formally describe the most commonly used model as a set of equations and provide a formal approach for estimating resistance parameters. Our optimization finds the maximum Mantel r when an optimum exists, and identifies the same resistance values as current approaches when the alternatives evaluated are near the optimum. Unfortunately, even where an optimum existed, estimates from the most commonly used model were imprecise and were typically much smaller than the simulated true resistance to dispersal. Causal modeling using Mantel significance tests also typically failed to support the true resistance to dispersal values. For a large range of scenarios, current approaches using a simple correlational model between genetic and effective distances do not yield accurate estimates of resistance to dispersal. We suggest that analysts consider the processes important to gene flow for their study species, model those processes explicitly, and evaluate the quality of estimates resulting from their model.
Data from: Genetic uniformity and long-distance clonal dispersal in the invasive androgenetic Corbicula clams
The clam genus Corbicula is an interesting model system to study the evolution of reproductive modes since it includes both sexual and asexual (androgenetic) lineages. While the sexual populations are restricted to the native Asian areas, the androgenetic lineages are widely distributed being also found in America and Europe where they form a major aquatic invasive pest. We investigated the genetic diversity of native and invasive Corbicula populations through a worldwide sampling. The use of mitochondrial and nuclear (microsatellite) markers revealed an extremely low diversity in the invasive populations with only four, undiversified, genetic lineages distributed across Europe and America. On the contrary, in the native populations, both sexual and androgenetic lineages exhibited much higher genetic diversity. Remarkably the most abundant and widely distributed invasive forms, the so-called form A and form R found in America and Europe respectively, are fixed for the same single COI (cytochrome c oxydase subunit I) haplotype and same multilocus genotype. This suggests that form R, observed in Europe since the 1980s, derived directly from form A found in America since the 1920s. In addition, this form shares alleles with some Japanese populations indicating a Japanese origin for this invasive lineage. Finally, our study suggests that few androgenetic Corbicula individuals successfully invaded the non-native range and then dispersed clonally. This is one striking case of genetic paradox raising the issue of invasive and evolutionary success of genetically undiversified populations.
Figure 4 in Effects of genetic relatedness, spatial distance, and context on intraspecific aggression in the red wood ant Formica pratensis (Hymenoptera: Formicidae)
Figure 4. Neighbor-joining tree of genetic distances of the COI gene for F. pratensis sampled from nine colonies. Numbers on the nodes show the bootstrap values (>50%) and the numbers and the abbreviations at the end of the branches denote the localities and the nest IDs, respectively.
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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.