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2,445 results for “Genetics: population”
Data from: Evidence of neutral and adaptive genetic divergence between European trout populations sampled along altitudinal gradients
Species with a wide geographical distribution are often composed of distinct subgroups which may be adapted to their local environment. European trout (Salmo trutta species complex) provide an example of such a complex consisting of several genetically and ecologically distinct forms. However, trout populations are strongly influenced by human activities, and it is unclear to what extent neutral and adaptive genetic differences have persisted. We sampled 30 Swiss trout populations from heterogeneous environments along replicated altitudinal gradients in three major European drainages. More than 850 individuals were genotyped at 18 microsatellite loci which included loci diagnostic for evolutionary lineages and candidate markers associated with temperature tolerance, reproductive timing and immune defence. We find that the phylogeographic structure of Swiss trout populations has not been completely erased by stocking. Distinct genetic clusters corresponding to the different drainages could be identified, although nonindigenous alleles were clearly present, especially in the two Mediterranean drainages. We also still detected neutral genetic differentiation within rivers which was often associated with the geographical distance between populations. Five loci showed evidence of divergent selection between populations with several drainage-specific patterns. Lineage-diagnostic markers, a marker linked to a quantitative trait locus for upper temperature tolerance in other salmonids and a marker linked to the major histocompatibility class I gene were implicated in local adaptation and some patterns were associated with altitude. In contrast, tentative evidence suggests a signal of balancing selection at a second immune relevant gene (TAP2). Our results confirm the persistence of both neutral and potentially adaptive genetic differences between trout populations in the face of massive human-mediated dispersal.
Data from: Comparing G: multivariate analysis of genetic variation in multiple populations
The additive genetic variance–covariance matrix (G) summarizes the multivariate genetic relationships among a set of traits. The geometry of G describes the distribution of multivariate genetic variance, and generates genetic constraints that bias the direction of evolution. Determining if and how the multivariate genetic variance evolves has been limited by a number of analytical challenges in comparing G-matrices. Current methods for the comparison of G typically share several drawbacks: metrics that lack a direct relationship to evolutionary theory, the inability to be applied in conjunction with complex experimental designs, difficulties with determining statistical confidence in inferred differences and an inherently pair-wise focus. Here, we present a cohesive and general analytical framework for the comparative analysis of G that addresses these issues, and that incorporates and extends current methods with a strong geometrical basis. We describe the application of random skewers, common subspace analysis, the 4th-order genetic covariance tensor and the decomposition of the multivariate breeders equation, all within a Bayesian framework. We illustrate these methods using data from an artificial selection experiment on eight traits in Drosophila serrata, where a multi-generational pedigree was available to estimate G in each of six populations. One method, the tensor, elegantly captures all of the variation in genetic variance among populations, and allows the identification of the trait combinations that differ most in genetic variance. The tensor approach is likely to be the most generally applicable method to the comparison of G-matrices from any sampling or experimental design.
Data from: Seed germination schedule and environmental context shaped the population genetic structure of subtropical evergreen oaks on the Yun-Gui Plateau, Southwest China
<p>The evergreen broadleaved forests (EBLFs) of Southwest China have a long-term stable environment and support a diverse flora, thus forming a global biodiversity hotspot. However, the key drivers that have shaped the genetic diversity patterns of species in these EBLFs are not well understood. <i>Quercus delavayi</i>, <i>Q. schottkyana</i>,<i> </i>and<i> Q. kerrii </i>are sympatric oak species with different seed biological traits that are typical for these EBLFs. This study combined multilocus phylogeography and ecological niche modeling to screen 33 <i>Q. delavayi</i> populations. Their population genetic structure was inferred in comparison with previous studies on <i>Q. schottkyana</i> and <i>Q. kerrii</i>. The seed germination traits of all three species were also investigated. cpDNAs showed a significant phylogeographic structure in <i>Q. delavayi</i>, which was not detected in <i>Q. schottkyana</i> or <i>Q. kerrii</i>. <i>Quercus delavayi</i>, <i>Q. kerrii</i>, and <i>Q. schottkyana </i>exhibited different pollen-to-seed migration ratios (r = 219, 117, and 22, respectively), which are linked to the germination schedules of acorns. The distributions of <i>Q. delavayi</i> and <i>Q. schottkyana</i> remained long-term stable since the last glacial maximum (LGM) with a similar nSSR genetic gradient change along latitude. Instead, <i>Q. kerrii</i> experienced a prominent range expansion since the LGM with genetic diversification between the East and the West of the Tanaka line due to environmental heterogeneity. These results identify seed traits and environmental heterogeneity as two key drivers that shape the population genetic structure of EBLF trees in Southwest China. These should be considered in regional forestry conservation and management.</p>
Data from: Microsatellite analysis of genetic diversity and population structure of Arabian horse populations
The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here we explore seven different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya-Arabian and Polish-Arabian) and America (American-Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, AMOVA, factorial correspondence analysis and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source of among populations variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American-Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses, and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.
Data from: Fire increases genetic diversity of populations of Six-lined Racerunner
Wildfires are highly variable and can disturb habitats, leading to direct and indirect effects on the genetic characteristics of local populations. Florida scrub is a fire-dependent, highly fragmented, and severely threatened habitat. Understanding the effect of fire on genetic characteristics of the species that use this habitat is critically important. We investigated one such lizard, the Six-lined Racerunner (Aspidoscelis sexlineata), which has a strong preference for open areas. We collected Six-lined Racerunners (n=154) from 11 sites in Highlands County Florida and defined two time-since-last-fire categories: recently burned and long unburned. We screened genetic variation at six microsatellites to estimate genetic differentiation and compare genetic diversity among sites to determine the relationship with time-since-last-fire. A clear pattern exists between genetic diversity and time-since-last-fire in the absence of strong genetic differentiation. Genetic diversity was greater and inbreeding was lower in sites with more recent time-since-last-fire, and genetic characteristics had significantly larger variance in long unburned sites compared to more recently burned sites. Our results suggest that fire suppression increases variance in genetic characteristics of the Six-lined Racerunner. More generally, fire may benefit genetic characteristics of some species that use fire dependent habitats and management efforts for such severely fragmented habitat will be challenged by the presence of multiple species with incompatible fire preferences.
Data from: A single migrant enhances the genetic diversity of an inbred puma population
Migration is essential for maintaining genetic diversity among populations, and pumas (Puma concolor) provide an excellent model for studying the genetic impacts of migrants on populations isolated by increasing human development. In densely populated southern California, USA, puma populations on the east and west side of interstate highway 15 (I-15) have become fragmented into a small inbred population on the west side (Santa Ana Mountains) and a relatively larger, more diverse population on the east side (Eastern Peninsular Range). From 146 sampled pumas, genetic analyses indicate seven pumas crossed I-15 over the last 15 years, including four males from west to east, and three males from east to west. However, only a single migrant (named M86) was detected to have produced offspring and contribute to gene flow across the I-15 barrier. Prior to the M86 migration, the Santa Ana population exhibited inbreeding and had significantly lower genetic diversity than the Eastern Peninsular Range population. After M86 emigrated, he sired 11 offspring with Santa Ana females, decreasing inbreeding measures and raising heterozygosity to levels similar to pumas in the Eastern Peninsular Range. The emigration of M86 also introduced new alleles into the Santa Ana population, although allelic richness still remained significantly lower than the Eastern Peninsular population. Our results clearly show the benefit of a single migrant to the genetics of a small, isolated population. However, ongoing development and habitat loss on both sides of I-15 will increasingly strengthen the barrier to successful migration. Further monitoring, and potential human intervention, including minimizing development effects on connectivity, adding or improving freeway crossing structures, or animal translocation, may be needed to ensure adequate gene flow and long-term persistence of the Santa Ana puma population.
Data from: Self-limiting population genetic control with sex-linked genome editors
In male heterogametic species the Y chromosome is transmitted solely from fathers to sons, and is selected for based only on its impacts on male fitness. This fact can be exploited to develop efficient pest control strategies that use Y-linked editors to disrupt the fitness of female descendants. With simple population genetic and dynamic models we show that Y-linked editors can be substantially more efficient than other self-limiting strategies and, while not as efficient as gene drive approaches, are expected to have less impact on non-target populations with which there is some gene flow. Efficiency can be further augmented by simultaneously releasing an autosomal X-shredder construct, in either the same or different males. Y-linked editors may be attractive option to consider when efficient control of a species is desired in some locales but not others.
Data from: Genetic diversity and population structure of wild sunflower (Helianthus annuus L.) in Argentina: reconstructing its invasion history
Studying the levels and patterns of genetic diversity of invasive populations is important to understand the evolutionary and ecological factors promoting invasions and for better designing preventive and control strategies. Wild sunflower (Helianthus annuus L.) is native to North America and was introduced, and has become invasive, in several countries, including Argentina (ARG). Here, using classical population genetic analyses and Approximate Bayesian Computation (ABC) modelling, we studied the invasion history of wild sunflower in ARG. We analyzed 115 individuals belonging to 15 populations from ARG (invasive range) and United States (US, native range) at 14 nuclear and three chloroplast simple sequence repeat markers along with 23 phenotypic variables. Populations from ARG showed similar levels of nuclear genetic diversity to US populations and higher genetic diversity in the chloroplast genome, indicating no severe genetic bottlenecks during the invasion process. Bayesian clustering analysis, based on nuclear markers, suggests the presence of three genetic clusters, all present in both US and ARG. Discriminant analysis of principal components (DAPC) detected an overall low population structure between central US and ARG populations but separated two invasive populations from the rest. ABC modelling supports multiple introductions but also a southward dispersal within ARG. Genetic and phenotypic data support the central US as a source of introduction while the source of secondary introductions could not be resolved. Finally, using genetic markers from the chloroplast genome, we found lower population structure in ARG when compared to US populations, suggesting a role for seed-mediated gene flow in Argentina.
Data from: Climate effects on growth, body condition and survival depend on the genetic characteristics of the population
Climatic change is expected to affect individual life-histories and population dynamics, potentially increasing vulnerability to extinction. The importance of genetic diversity has been highlighted for adaptation and population persistence. However, whether responses of life-history traits to a given environmental condition depend on the genetic characteristics of a population remains elusive. Here we tested this hypothesis in the lizard Zootoca vivipara, by simultaneously manipulating habitat humidity, a major climatic predictor of Zootoca's distribution, and adult male colour morph frequency, a trait with genome-wide linkage. Interactive effects of humidity and morph frequency had immediate effects on growth and body condition of juveniles and yearlings, and on adult survival, and delayed effects on offspring size. In yearlings, higher humidity led to larger female body size, and lower humidity led to higher male compared to female survival. In juveniles and yearlings, some treatment effects were compensated over time. The results show that individual responses to environmental conditions depend on the population's colour morph frequency, age class and sex, and that these affect intra- and inter-age class competition. Moreover, humidity affected the competitive environment, rather than imposing trait-based selection on specific colour morphs. This indicates that species' responses to changing environments, e.g. to climate change, are highly complex, and difficult to accurately reconstruct and predict without information on the genetic characteristics and demographic structure of populations.
Data from: Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish
How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA) and trait differentiation (QST) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made.
Data from: Testing for a genetic response to sexual selection in a wild Drosophila population
In accordance with the consensus that sexual selection is responsible for the rapid evolution of display traits on macroevolutionary scales, microevolutionary studies suggest sexual selection is a widespread and often strong form of directional selection in nature. However, empirical evidence for the contemporary evolution of sexually selected traits remains weak. In this study we used a novel application of quantitative genetic breeding designs to test for a genetic response to sexual selection on eight chemical display traits in a field population of the fly, Drosophila serrata. Using our quantitative genetic approach, we were able to detect a genetically-based difference in means between groups of males descended from either successful or random wild males for one of these display traits, the diene (Z,Z)-5,9-C27:2. Our experimental results, in combination with previous lab studies on this system, suggest that both natural selection and sexual selection may be influencing the evolutionary trajectories of these traits in nature, limiting the capacity for a contemporary evolutionary response.
Genetic diversity and population structure in Chrysolepis chrysophylla (golden chinquapin; Fagaceae): SSRs vs SNPs
<p>Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) genotypes on the same plant samples of <i>Chrysolepis chrysophylla</i> (Fagaceae; golden chinquapin) from 22 sites were used to determine genetic diversity and population structure. One site of <i>C. sempervirens</i> allowed <i>inter</i>specific vs.<i> intra</i>specific comparison. SSRs and SNPs yielded many similar results. Among-site variation contributed 13% to 17% of the genetic variation and Fst estimates of 0.14 to 0.17 were in the range expected among Fagaceae species rather than among populations within a species. The northern sites tended to group separately on the first two axes of multivariate scatterplots from southern sites. Sites in two geographically isolated areas were divergent: 1) the Hood Canal, Washington population was relatively more genetically distant from other golden chinquapin sites than was our <i>C. sempervirens</i> site; 2) three coastal southern California sites were moderately diverged. The Hood Canal site had a negative inbreeding coefficient, fewer alleles, lower heterozygosity, and differed from the Skamania County, Washington site as well as all other sites. Hood Canal trees are distinguished by disjunct geography and by these molecular results. This suggests that the golden chinquapin near Hood Canal be treated as a management unit, and potential conservation actions are discussed.</p>
Data from: Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load
Mutations are the ultimate source of heritable variation for evolution. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should be minimized for well-adapted populations living in stable environments, whereas hypermutators may evolve if conditions change. However, the long-term fate of hypermutators is unknown. Using a phylogenomic approach, we found that an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was later invaded by two independent lineages with mutY mutations that reduced genome-wide mutation rates. Applying neutral theory to synonymous substitutions, we dated the emergence of these mutations and inferred that the mutT mutation increased the point-mutation rate by ~150-fold, while the mutY mutations reduced the rate by ~40-60%, with a corresponding decrease in the genetic load. Thus, the long-term fate of the hypermutators was governed by the selective advantage arising from a reduced mutation rate as the potential for further adaptation declined.
Data from: Fixation of mutators in asexual populations: the role of genetic drift and epistasis
We study the evolutionary dynamics of an asexual population of nonmutators and mutators on a class of epistatic fitness landscapes. We consider the situation in which all mutations are deleterious and mutators are produced from nonmutators continually at a constant rate. We find that in an infinitely large population, a minimum nonmutator-to-mutator conversion rate is required to fix the mutators but an arbitrarily small conversion rate results in the fixation of mutators in a finite population. We calculate analytical expressions for the mutator fraction at mutation-selection balance and fixation time for mutators in a finite population when the difference between the mutation rate for mutator and nonmutator is smaller (regime I) and larger (regime II) than the selection coefficient. Our main result is that in regime I, the mutator fraction and the fixation time are independent of epistasis but in regime II, mutators are rarer and take longer to fix when the decrease in fitness with the number of deleterious mutations occurs at an accelerating rate (synergistic epistasis) than at a diminishing rate (antagonistic epistasis). Our analytical results are compared with numerics and their implications are discussed.
Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])
Bactrocera carambolae Drew and Hancock and B. dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same pathway. Molecular markers can be used for both species identification and pathway analysis. We analyzed 1601 individuals from 18 populations using 765 base pairs of the mitochondrial cytochrome oxidase I (COI) gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges. We analyzed these samples by either grouping by species or geographic populations due to the genetic similarity in the mitochondrial genome. We found no genetic structure between B. dorsalis and B. carambolae and our findings suggest recent and most likely ongoing, genetic exchange between these two species in the wild. Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation rates. Only 52% of the haplotypes found in the trap captures from California are shared with haplotypes from flies found in our global survey, indicating significant genetic diversity in the native range that is missing from our samples. However, these results provide a foundation for the accurate determination of the provenance of invasive populations around the world.
Data from: Genetic drift outweighs natural selection at toll-like receptor (TLR) immunity loci in a reintroduced population of a threatened species
During population establishment, genetic drift can be the key driver of changes in genetic diversity, particularly while the population is small. However, natural selection can also play a role in shaping diversity at functionally important loci. We used a well-studied, re-introduced population of the threatened Stewart Island robin (N = 722 pedigreed individuals) to determine whether selection shaped genetic diversity at innate immunity toll-like receptor (TLR) genes, over a 9-year period of population growth following establishment with 12 genetic founders. We found no evidence for selection operating with respect to TLR diversity on first-year overwinter survival for the majority of loci, genotypes and alleles studied. However, survival of individuals with TLR4BE genotype was significantly improved: these birds were less than half as likely to die prior to maturity compared with all other TLR4 genotypes. Furthermore, the population frequency of this genotype, at a two-fold excess over Hardy–Weinberg expectation, was increased by nonrandom mating. Near-complete sampling and full pedigree and reproductive data enabled us to eliminate other potential causes of these patterns including inbreeding, year effects, density dependence, selection on animals at earlier life history stages or genome-level association of the TLR4E allele with 'good genes'. However, comparison of observed levels of gene diversity to predictions under simulated genetic drift revealed results consistent with neutral expectations for all loci, including TLR4. Although selection favoured TLR4BE heterozygotes in this population, these effects were insufficient to outweigh genetic drift. This is the first empirical study to show that genetic drift can overwhelm natural selection in a wild population immediately following establishment.
Data from: Genetic and physiological data suggest demographic and adaptive responses in complex interactions between populations of figs (Ficus pumila) and their pollinating wasps (Wiebesia pumilae)
To study interactions between host figs and their pollinating wasps and the influence of climatic change on their genetic structures, we sequenced cytoplasmic and nuclear genes and genotyped nuclear microsatellite loci from two varieties of Ficus pumila, the widespread creeping fig and endemic jelly fig, and from their pollinating wasps, Wiebesia pumilae, found in Taiwan and on nearby offshore islands. Great divergence in the mitochondrial cytochrome c oxidase subunit I (mtCOI) with no genetic admixture in nuclear markers indicated that creeping- and jelly-fig wasps are genetically distinct. Compared with creeping-fig wasps, jelly-fig wasps also showed better resistance under cold (20 °C) than warm (25 and 30 °C) conditions in a survival test, indicating their adaptation to a cold environment, which may have facilitated population expansion during the ice age as shown by a nuclear intron and 10 microsatellite loci. An excess of amino acid divergence and a pattern of too many rare mtCOI variants of jelly-fig wasps as revealed by computer simulations and neutrality tests implied the effect of positive selection, which we hypothesize was associated with the cold-adaptation process. Chloroplast DNA of the two fig plants was completely segregated, with signs of genetic admixture in nuclear markers. As creeping- and jelly-fig wasps can pollinate creeping figs, occasional gene flow between the two figs is thus possible. Therefore, it is suggested that pollinating wasps may be playing an active role in driving introgression between different types of host fig.
Data from: The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis
The inference of population genetic structures is essential in many research areas in population genetics, conservation biology and evolutionary biology. Recently, unsupervised Bayesian clustering algorithms have been developed to detect a hidden population structure from genotypic data, assuming among others that individuals taken from the population are unrelated. Because of this hypothesis, markers in a sample taken from a subpopulation can be considered to be in Hardy-Weinberg and linkage equilibrium. However, close relatives might be sampled from the same subpopulation, and consequently, might cause Hardy-Weinberg and linkage disequilibrium and thus bias a population genetic structure analysis. In this study, we used simulated and real data to investigate the impact of close relatives in a sample on Bayesian population structure analysis. We also showed that, when close relatives were identified by a pedigree reconstruction approach and removed, the accuracy of a population genetic structure analysis can be greatly improved. The results indicate that unsupervised Bayesian clustering algorithms cannot be used blindly to detect genetic structure in a sample with closely related individuals. Rather, when closely related individuals are suspected to be frequent in a sample, these individuals should be first identified and removed before conducting a population structure analysis.
Data from: Toward the genetic origins of a potentially non-native population of threespine stickleback (Gasterosteus aculeatus) in Alberta
Disentangling the origin of putatively introduced/invasive species is of increasing priority in conservation biology. The presence of a previously undocumented species may be due to an undetected recent population or range expansion associated with environmental change, or due to an introduction by humans. We used molecular tools to address the origin of a population of threespine stickleback (Gasterosteus aculeatus) first identified in central Alberta, Canada in 1980 from a single lake. We characterized this inland, high elevation Alberta population in comparison to samples from five representative geographic regions worldwide, using mtDNA and nine microsatellite loci to elucidate genetic structure and estimate divergence times. We found significantly lower levels of genetic variation in the Alberta population, which could reflect either a recent colonization or periodic bottlenecks associated with winterkills. While we did find that the Alberta samples were most closely related to the North American West Coast populations, we did not uncover a putative source population. Alberta samples formed a clade in phylogenetic analyses, with divergence time estimates between the Alberta and British Columbia samples ca. 250–750 kya. The hypothesis that the Alberta population represents a natural colonization during North America's last glacial recession could not be rejected. Collectively, these data suggest that the genetic signature of colonizing populations following introductions may be similar to populations at their range limit, contributing to difficulties establishing population origins.
Data from: Genetic ancestry and population differences in levels of inflammatory cytokines in women: role for evolutionary selection and environmental factors
Background: Selection pressure due to exposure to infectious pathogens endemic to Africa may explain distinct genetic variations in immune response genes. However, the impact of those genetic variations on human immunity remains understudied, especially within the context of modern lifestyles and living environments, which are drastically different from early humans in sub Saharan Africa. There are few data on population differences in constitutional immune environment, where genetic ancestry and environment are likely two primary sources of variation. Methods and Findings: In a study integrating genetic, molecular and epidemiological data, we examined population differences in plasma levels of 14 cytokines involved in innate and adaptive immunity, including those implicated in chronic inflammation, and possible contributing factors to such differences, in 914 AA and 855 EA women. We observed significant differences in 7 cytokines, including higher plasma levels of CCL2, CCL11, IL4 and IL10 in EAs and higher levels of IL1RA and IFNα2 in AAs. Analyses of a wide range of demographic and lifestyle factors showed significant impact, with age, education level, obesity, smoking, and alcohol intake, accounting for some, but not all, observed population differences for the cytokines examined. Levels of two pro-inflammatory chemokines, CCL2 and CCL11, were strongly associated with percent of African ancestry among AAs. The signal was pinpointed through admixture mapping to local ancestry at 1q23, with fine-mapping analysis refined to the Duffy-null allele of rs2814778. In AA women, this variant was a major determinant of systemic levels of CCL2 (p=1.1e-58) and CCL11 (p=2.2e-110), accounting for 19% and 40% of the phenotypic variance, respectively. Conclusion: Our data reveal strong ancestral footprints in inflammatory chemokine regulation. The Duffy-null allele may indicate a loss of the buffering function for chemokine levels. The substantial immune differences by ancestry may have broad implications to health disparities between AA and EA populations.
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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.