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Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders
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Data from: Seascape genomics of red abalone: Limited range-wide population structure and evidence for local adaptation
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Data from: The contribution of hybridization to range‐wide population genetic structure in a Pacific coastal dune plant
<p>Premise of the study: Interspecific hybridization can cause genetic structure across species ranges if the mating system and degree of sympatry/parapatry with close relatives varies geographically. The coastal dune endemic <em>Camissoniopsis cheiranthifolia</em> (Onagraceae) exhibits genetic subdivisions across its range, some of which are associated with shifts in mating system from outcrossing to selfing, while others are not. For instance, strong differentiation between large-flowered, self-incompatible (LF-SI) and large-flowered, self-compatible (LF-SC) populations occurs without much reduction in outcrossing or obvious barriers to gene flow. We hypothesized that LF-SI diverged from LF-SC via hybridization with the predominantly inland SI sister species <em>C. bistort</em>a.</p> <p>Methods: We analyzed spatial proximity using 1460 herbarium records, and genetic variation at 12 microsatellites assayed for 805 and 404 individuals from 32 <em>C. cheiranthifolia</em> and 18 <em>C. bistorta</em> populations, respectively. We also assayed nine chloroplast microsatellites for 124 and 111 individuals from 27 and 19 populations, respectively. </p> <p>Key results: Closer parapatry was associated with unexpectedly high genetic continuity between LF-SI <em>C. cheiranthifolia</em> and <em>C. bistorta</em>. LF-SI genotypes clustered with <em>C. bistorta</em> exclusive of other <em>C. cheiranthifolia</em> genotypes. Similarly, pairwise FST among SI <em>C. cheiranthifolia</em> and <em>C. bistorta</em>, adjusted for geographic proximity, was not higher between heterospecific than conspecific populations. </p> <p>Conclusions: The lack of genetic differentiation between LF-SI <em>C. cheiranthifolia</em> and <em>C. bistorta</em> populations, even those located away from the zone of parapatry, suggests that LF-SI <em>C. cheiranthifolia</em> instead of hybridizing with <em>C. bistorta</em> is rather an ecotype of <em>C. bistorta</em> that has adapted to coastal dune habitat independent of other lineages in <em>C. cheiranthifolia</em> proper.</p>
Data from: One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark
With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost-effectiveness.
Data from: Population genomic diversity and structure at the discontinuous southern range of the Great Gray Owl in North America
<p>Species' distributions are often discontinuous near the edge of the range where the environment may be more variable than the core of the range. Range discontinuity can reduce or cut off gene flow to small peripheral populations and lead to genetic drift and subsequent loss of genetic diversity. The southern extent of the Great Gray Owl ( Strixnebulosa) range in North America is discontinuous, unlike their northern core range across the boreal forests. We sampled owls from five different locations on the periphery of the range across the western US (Wyoming, Idaho, California, northern Oregon, and southern Oregon) to investigate genetic population structure and genetic diversity. Using a reduced-representation genomic sequencing approach to genotype 123 individuals at 4,817 single nucleotide polymorphic loci, we identified four genetically differentiated populations: California, southern Oregon, northern Oregon, and Wyoming and Idaho grouped together as a single Rocky Mountain population. The four genetically differentiated populations of Great Gray Owls identified in this study display high differentiation and low genetic variation, which is suggestive of long-term isolation and lack of connectivity, potentially caused by range discontinuity. The populations that lack habitat connectivity to the rest of the breeding range (i.e. those in California and Oregon) had lower genetic diversity than the Rocky Mountain population that is connected to the core of the range. These factors and other risks (such as disease and human-caused mortality) heighten susceptibility of these range-edge populations to future habitat and climate changes, genetic diversity erosion, and potential extinction vortex. For these reasons, protecting and monitoring this species on the southern edge of their range is vital.</p>
Data from: Population structure, connectivity and demographic history of an apex marine predator, the bull shark Carcharhinus leucas
Knowledge of population structure, connectivity and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analysing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes (CR, nd4, cytb). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DN A. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC-RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines , highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale.
Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes
Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, inter-population genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.
Dynamic shifts in social network structure and composition within a breeding hybrid population
1. Mating behavior and the timing of reproduction can inhibit genetic exchange between closely related species; however, these reproductive barriers are challenging to measure within natural populations. Social network analysis provides promising tools for studying the social context of hybridization, and the exchange of genetic variation, more generally. 2. We test how social networks within a hybrid population of California (Callipepla californica) and Gambel's quail (Callipepla gambelii) change over discrete periods of a breeding season. We assess patterns of phenotypic and genotypic assortment, and ask whether altered associations between individuals (association rewiring), or changes to the composition of the population (individual turnover) drive network dynamics. We use genetic data to test whether social associations and relatedness between individuals correlate with patterns of parentage within the hybrid population. 3. To achieve these aims, we combine RFID association data, phenotypic data, and genomic measures with social network analyses. We adopt methods from the ecological network literature to quantify shifts in network structure and to partition changes into those due to individual turnover and association rewiring. We integrate genomic data into networks as node-level attributes (ancestry) and edges (relatedness, parentage) to test links between social and parentage networks. 4. We show that rewiring of associations between individuals that persist across network periods, rather than individual turnover, drives the majority of the changes in network structure throughout the breeding season, and that the traits involved in phenotypic/genotypic assortment were highly dynamic over time. Social networks were randomly assorted based upon genetic ancestry, suggesting weak behavioral reproductive isolation within this hybrid population. Finally, we show that the strength of associations within the social network, but not levels of genetic relatedness, predict patterns of parentage. 5. Social networks play an important role in population processes such as the transmission of disease and information, yet there has been less focus on how networks influence the exchange of genetic variation. By integrating analyses of social structure, phenotypic assortment, and reproductive outcomes within a hybrid zone, we demonstrate the utility of social networks for analyzing links between social context and gene flow within wild populations. 08-Jul-2020
Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea
Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of the major human malaria parasites, <i>Plasmodium falciparum</i> (Pf) and <i>Plasmodium vivax</i> (Pv) populations following nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-6) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik: Pf=54.9-8.5%, Pv=35.7-5.6%, Madang: Pf=38.0-9.0%, Pv: 31.8-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, He = 0.77-0.71; Madang: Rs= 8.2-6.1, He = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs=11.4-9.3, He=0.83-0.80; Madang: Rs=12.2-14.5, He=0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium (mLD) post-LLIN was a positive indicator of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.
Data from: Changes in age-structure over four decades were a key determinant of population growth rate in a long-lived mammal
<p>1. A changing environment directly influences birth and mortality rates, and thus population growth rates. However, population growth rates in the short-term are also influenced by population age-structure. Despite its importance, the contribution of age-structure to population growth rates has rarely been explored empirically in wildlife populations with long-term demographic data.</p> <p>2. Here, we assessed how changes in age-structure influenced short-term population dynamics in a semi-captive population of Asian elephants (Elephas maximus).</p> <p>3. We addressed this question using a demographic dataset of female Asian elephants from timber camps in Myanmar spanning 45 years (1970-2014). First, we explored temporal variation in age-structure. Then, using annual matrix population models, we used a retrospective approach to assess the contributions of age-structure and vital rates to short-term population growth rates with respect to the average environment.</p> <p>4. Age-structure was highly variable over the study period, with large proportions of juveniles in the years 1970 and 1985, and made a substantial contribution to annual population growth rate deviations. High adult birth rates between 1970-1980 would have resulted in large positive population growth rates, but these were prevented by a low proportion of reproductive-aged females.</p> <p>5. We highlight that an understanding of both age-specific vital rates and age-structure is needed to assess short-term population dynamics. Furthermore, this example from a human-managed system suggests that the importance of age-structure may be accentuated in populations experiencing human disturbance where age-structure is unstable, such as those in captivity or for endangered species. Ultimately, changes to the environment drive population dynamics by influencing birth and mortality rates, but understanding demographic structure is crucial for assessing population growth.</p>
Population genetic structure of the insular Ryukyu flying fox Pteropus dasymallus
<p>Small isolated populations are vulnerable to both stochastic events and the negative consequences of genetic drift. For threatened species, the genetic management of such populations has therefore become a crucial aspect of conservation. Flying foxes (<i>Pteropus</i> spp, Chiroptera) are keystone species with essential roles in pollination and seed dispersal in tropical and subtropical ecosystems. However, many flying fox species are also threatened, having experienced dramatic population declines driven by habitat loss and hunting. The insular Ryukyu flying fox (<i>Pteropus dasymallus</i>) ranges from the Ryukyu Archipelago of Japan through Taiwan to the northern Philippines and has undergone precipitous population crashes on several islands in recent decades. To assess the population genetic structure and diversity in <i>P. dasymallus</i>, and its likely causes, we analyzed mitochondrial and microsatellite DNA. Both markers showed significant genetic differentiation among most island populations, with mitochondrial haplotypes showing some mixing across the region, likely reflecting historical colonization and/or dispersal events. In contrast, microsatellite markers showed an overall pattern of isolation by distance; however, this pattern appeared to be driven by the presence of deep ocean trenches between geographically distant populations. Thus the current distribution of<i> P. dasymallus</i> and its subspecific diversity appears to have arisen through vicariance coupled with a long history of restricted gene flow across oceanic barriers. We conclude that isolated island subgroups should be managed separately, with efforts directed at reducing further declines in genetic diversity.</p>
Data from: Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes
<p>Single Nucleotide Polymorphisms files and phylogonetic trees of S. miscanthi samples collected in China and S. avenae from the UK used to study the population genetics analyses of these species. These are:</p> <p>China_samples_vcf.zip: dataset of SNPs from S. miscanthi sampled in 10 populations of China obtained using FreeBayes (in vcf format).</p> <p>China_samples_vcf_filtered.zip: SNPs from S. miscanthi after filtering the file China_samples_vcf.zip using vcftools (max-missing 0.75, minDP 3, mac 3, minQ 30, remove-indels, thin 2000, max-missing 0.9, thin 5000). This file was used in all population genetic analyses of the Chinese populations in the paper, transforming to the appropriate formats.</p> <p>China_samples_SNPs.fas: fasta file of phased SNPs used to estimate the phylogeny of S. miscanthi haplotypes using RAxML.</p> <p>China_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with China_samples_SNPs.fas.</p> <p>England_samples_vcf.zip: dataset of SNPs from S. avenae sampled in 12 populations of England obtained using FreeBayes (in vcf format).</p> <p>England_samples_vcf_filtered.zip: SNPs from S. avenae after filtering the file England_samples_vcf.zip using vcftools (max-missing 0.5, mac 3, minQ 30, minDP 3, max-missing 0.5, exclude individuals with 50% missing data, max-missing 0.75, remove-indels, thin 2000). This file was used in all population genetic analyses of the English populations in the paper, transforming the vcf to the corresponding formats.</p> <p>England_samples_SNPs.fas: fasta file of phased SNPs.</p> <p>England_samples_SNPs_polymorphic.fas: fasta file of phased SNPs used in the phylogenetic reconstruction of S. avenae haplotypes using RAxML. This file is the same as England_samples_SNPs.fas after removing sites which were not polymorphic (e.g. a site that contains N and T in different samples is not considered polymorphic for RAxML and has to be removed)</p> <p>England_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with England_samples_SNPs_polymorphic.fas.</p>
Geography, seasonality, and host-associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal
<p>The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture and daylight. Muskoxen (<i>Ovibos moschatus</i>) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season (spring/summer/winter), year (2007-2016), and host genetic structure on population-level microbiome variation in muskoxen from the Canadian Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal microbial communities of 78 male muskoxen encompassing two population genetic clusters.<a name="_Hlk534564036"> These clusters are defined by Arctic Mainland and Island populations, including; 1) two mainland sampling locations of the Northwest Territories and Nunavut; and 2) four locations of Victoria Island. </a>Between these geographic populations, we found that differences in the microbiome reflected host-associated genetic cluster with evidence of migration. Within populations, seasonality influenced bacterial diversity with no significant differences between years of sampling. We found evidence of pathogenic bacteria, with significantly higher presence in mainland samples. Our findings demonstrate the effects of seasonality and the role of host population-level structure in driving fecal microbiome differences in a large Arctic mammal.</p>
Mixed-stock analysis using Rapture genotyping to evaluate stock-specific exploitation of a walleye population despite weak genetic structure
<p>Mixed-stock analyses using genetic markers have informed fisheries management in cases where strong genetic differentiation occurs among local spawning populations, yet many fisheries are supported by multiple spawning stocks that are weakly differentiated. Freshwater fisheries exemplify this problem, with many harvested populations supported by multiple stocks of young evolutionary age and that are isolated across small spatial scales. As a result, attempts to conduct genetic mixed-stock analyses of inland fisheries have often been unsuccessful. Advances in genomic sequencing now offer the ability to discriminate among populations with weak population structure, by providing the necessary resolution to conduct mixed-stock assignment among previously indistinguishable stocks. We demonstrate the use of genomic data to conduct a mixed-stock analysis of Lake Erie's commercial and recreational walleye (<em>Sander vitreus</em>) fisheries and estimate the relative harvest of weakly differentiated stocks. We used RAD-capture (Rapture) to sequence and genotype individuals at 12,081 loci that had been previously determined to be capable of discriminating between western and eastern basin stocks (mean pairwise F<sub>ST</sub> = 0.001) with 95% reassignment accuracy. An outcome not possible in the past with microsatellite markers. Genetic assignment of 1,075 fish harvested from recreational and commercial fisheries in the eastern basin indicated that western basin stocks supported the majority of the harvest during peak harvest (July – September). Composition of harvest changed seasonally, with eastern basin fish comprising much of the early season harvest (May – June). Clear spatial structure in stock-specific harvest existed; more easterly sites contained more individuals of east basin origin than did westerly sites. Our study provides important stock contribution estimates for Lake Erie fishery management and demonstrates the power of genomic data to facilitate mixed-stock analysis in exploited fish populations with weak population structure or limited existing genetic resources.</p>
Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers
<p>Pea (<em>Pisum</em> <em>sativum</em> L.) is an important legume crop that is widely grown worldwide for human consumption and livestock feed. Despite extensive studies, the population genetic structure and classification of cultivated and wild pea (<em>Pisum</em> sp.) are remaining controversial. To characterize patterns of genetic and morphological variation and investigate the classification of <em>Pisum</em>, we conducted comprehensive population genetic analyses for 323 accessions from cultivated and wild pea representing three species of <em>Pisum</em> utilizing 34 morphological traits and 87 polymorphic SSR markers. First, we identified three distinct genetic groups among all samples. Group I was primarily composed of <em>Pisum fulvum</em>, <em>Pisum</em> <em>abyssinicum</em> and some wild <em>P. sativum</em> accessions, whereas groups II and III consisted of the two genetic groups under <em>P. sativum </em>representing different geographic distributions of cultivated pea. Analyses of morphological variation revealed significant differences among the three species. Second, among pea germplasms representing eight taxa of <em>Pisum</em>, <em>P. fulvum</em> and <em>P. abyssinicum</em> possessed unique genetic backgrounds and morphological characteristics, corroborating their independent species status. The intraspecific subdivisions of <em>P. sativum</em> described by some authors were not supported in this study, with the exception of several genotypes of <em>P. sativum</em> subsp. <em>elatius</em> that were clustered with <em>P. fulvum</em> and <em>P. abyssinicum</em>. Finally, we confirmed that the Chinese pea germplasm was genetically distinct and could be divided into two genetic groups, each of which included both spring-sowing and autumn-sowing ecotypes. These results provide a robust foundation for understanding pea domestication and the utilization of wild genetic resources of pea.</p>
Microsatellite genotypes and associated data for: The contribution of clonality to population genetic structure in the sea anemone Diadumene lineata
<p>Ecological and evolutionary processes differ depending on how genetic diversity is organized in space. For clonal organisms, the organization of both genetic and genotypic diversity can influence the fitness effects of competition, the mating system, and reproductive mode, which are key drivers of life cycle evolution. Understanding how individual reproductive behavior contributes to population genetic structure is essential for disentangling these forces, particularly in species with complex and plastic life cycles. The widespread sea anemone <i>Diadumene lineata</i> exhibits temperature-dependent fission which contributes to predictable variation in clonal rate along the Atlantic coast of the United States, part of its non-native range. Because warmer conditions lead to higher rates of clonality, we expected to find lower genotypic and genetic diversity in lower versus higher latitude populations. We developed primers for 11 microsatellite loci and genotyped 207 anemones collected from 8 sites ranging from Florida to Massachusetts. We found clonal influence at all sites, and as predicted, the largest clones were found at lower latitude sites. We also found genetic signatures of sex in the parts of the range where gametogenesis is most common. Evidence of sex outside the native range is novel for this species and provides insights into the dynamics of this successful invader. Our findings also illustrate challenges that partially clonal taxa pose for eco-evolutionary studies, such as difficulty sampling statistically robust numbers of genets and interpretating common population genetic metrics. For example, we found high among-locus variation in F<i><sub>is, </sub></i>which makes the meaning of mean multilocus F<i><sub>is</sub></i> unclear.</p>
Consequences of population structure for sex allocation and sexual conflict
<p class="Standard">Both sex allocation and sexual conflict can be modulated by spatial structure. However, how the interplay between the type of dispersal and the scale of competition simultaneously affects these traits in sub-divided populations is rarely considered.</p> <p>We investigated sex allocation and sexual conflict evolution in meta-populations of the spider mite <i>Tetranychus urticae</i> evolving under budding (pairing females from the same patch) or random (pairing females from different patches) dispersal and either local (fixed sampling from each subpopulation) or global (sampling as a function of subpopulation productivity) competition.</p> <p>Females evolving under budding dispersal produced less female-biased offspring sex ratios than those from the random dispersal selection regimes, contradicting theoretical predictions. In contrast, the scale of competition did not strongly affect sex allocation. Offspring sex ratio and female fecundity were unaffected by the number of mates, but female fecundity was highest when their mates evolved under budding dispersal, suggesting these males inflict less harm than those evolving under random dispersal.</p> <p>This work highlights that population structure can impact the evolution of sex allocation and sexual conflict. Moreover, selection on either trait may reciprocally affect the evolution of the other, for example via effects on fecundity.</p>
Population studies of the wild tomato species Solanum chilense reveal geographically structured major gene-mediated pathogen resistance
<p>Natural plant populations encounter strong pathogen pressure and defense-associated genes are known to be under selection dependent on the pressure by the pathogens. Here we use populations of the wild tomato Solanum chilense to investigate natural resistance against Cladosporium fulvum, a well-known ascomycete pathogen of domesticated tomatoes. Host populations used are from distinct geographical origins and share a defined evolutionary history. We show that distinct populations of S. chilense differ in resistance against the pathogen. Screening for major resistance gene mediated pathogen recognition throughout the whole species showed clear geographical differences between populations and complete loss of pathogen recognition in the south of the species range. In addition, we observed high complexity in a homologues of Cladosporium resistance (Hcr) locus, underlying the recognition of C. fulvum, in central and northern populations. Our findings show that major gene mediated recognition specificity is diverse in a natural plant-pathosystem. We place major gene resistance in a geographical context that also defined the evolutionary history of that species. Data suggest that the underlying loci are more complex than previously anticipated, with small-scale gene recombination being possibly responsible for maintaining balanced polymorphisms in the populations that experience pathogen pressure.</p>
Data from: Isolation by instability: historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna
Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene-flow in areas with high climatic instability promoting isolation of populations, defined here as "isolation by instability", highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.
Tracking invasions of a destructive defoliator, the gypsy moth (Erebidae: Lymantria dispar): population structure, origin of intercepted specimens, and Asian introgression into North America
Genetic data can help elucidate the dynamics of biological invasions, which are fueled by the constant expansion of international trade. The introduction of European gypsy moth (<i>Lymantria dispar dispar</i>) into North America is a classic example of human-aided invasion that has caused tremendous damage to North American temperate forests. Recently, the even more destructive Asian gypsy moth (mainly <i>L. d. asiatica</i> and <i>L. d. japonica</i>) has been intercepted in North America, mostly transported by cargo ships. To track invasion pathways, we developed a diagnostic panel of 60 DNA loci (55 nuclear and 5 mitochondrial) to characterize worldwide genetic differentiation within <i>L. dispar</i> and its sister species <i>L. umbrosa</i>. Hierarchical analyses supported strong differentiation and recovered five geographic groups that correspond to 1) North America, 2) Europe plus North Africa and Middle East, 3) the Urals, Central Asia, and Russian Siberia, 4) continental East Asia, and 5) the Japanese islands. Interestingly, <i>L. umbrosa</i> was grouped with <i>L. d. japonica</i>, and the introduced North American population exhibits remarkable distinctiveness from contemporary European counterparts. Each geographic group, with the exception of North America, shows additional lower-level structures when analyzed individually, which provided the basis for inference of the origin of invasive specimens. Two assignment approaches consistently identified a coastal area of continental East Asia as the major source for Asian invasion during 2014–2015, with Japan being another source. By analyzing simulation and laboratory crosses, we further provided evidence for the occurrence of natural Asian-North American hybrids in the Pacific Northwest, raising concerns for introgression of Asian alleles that may accelerate range expansion of gypsy moth in North America. Our study demonstrates how genetic data contribute to bio-surveillance of invasive species with results that can inform regulatory management and reduce the frequency of trade-associated invasions.
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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.