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15,277 results for “GENETICS”
Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)
The honeybee (Apis mellifera) has been threatened by multiple factors, including pests and pathogens, pesticides, and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A.m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify purebred A.m. mellifera colonies. Microsatellites have been preferred for identification of A.m. mellifera stocks across conservation centers. However, owing to high-throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite dataset to detect structure and introgression with that of different datasets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellites. Contrary to every SNP dataset, microsatellites were unable to clearly separate the two European lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level microsatellites' performance was relatively poor at the upper range of introgression, a result reflected by their lower precision. Although mean accuracy was relatively high across datasets (>91%), microsatellites were the least accurate and the top-ranked informative 144 SNPs were the most accurate. Comparisons amongst the SNP datasets showed that those combining SNPs flanking microsatellites performed worst. Our results suggest that SNPs are more powerful for identification of A.m. mellifera colonies, especially when they are selected by information content.
Data from: Developmental instability is genetically correlated with phenotypic plasticity, constraining heritability, and fitness
Although adaptive plasticity would seem always to be favored by selection, it occurs less often than expected. This lack of ubiquity suggests that there must be trade-offs, costs, or limitations associated with plasticity. Yet, few costs have been found. We explore one type of limitation, a correlation between plasticity and developmental instability, and use quantitative genetic theory to show why one should expect a genetic correlation. We test that hypothesis using the Landsberg erecta × Cape Verde Islands recombinant inbred lines (RILs) of Arabidopsis thaliana. RILs were grown at four different nitrogen (N) supply levels that span the range of N availabilities previously documented in North American field populations. We found a significant multivariate relationship between the cross-environment trait plasticity and the within-environment, within-RIL developmental instability across 13 traits. This genetic covariation between plasticity and developmental instability has two costs. First, theory predicts diminished fitness for highly plastic lines under stabilizing selection, because their developmental instability and variance around the optimum phenotype will be greater compared to nonplastic genotypes. Second, empirically the most plastic traits exhibited heritabilities reduced by 57% on average compared to nonplastic traits. This demonstration of potential costs in inclusive fitness and heritability provoke a rethinking of the evolutionary role of plasticity.
Data from: Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines
The wild grapevine, Vitis vinifera L. ssp sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain natural populations of Vitis vinifera ssp sylvestris can still be found along river banks. In this work we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analyzed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated and wild germplasm are genetically divergent with low level of introgression. Using a model-based approach implemented in the software STRUCTURE we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships among wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current western cultivars.
Data from: Spatial genetic and morphologic structure of wolves and coyotes in relation to environmental heterogeneity in a Canis hybrid zone
Eastern wolves have hybridized extensively with coyotes and gray wolves and are listed as a 'species of special concern' in Canada. However, a distinct population of eastern wolves has been identified in Algonquin Provincial Park (APP) in Ontario. Previous Canis studies have not linked genetic analysis with field data to investigate genotype-specific morphology or determine how resident animals of different ancestry are distributed across the landscape in relation to heterogeneous environmental conditions. Accordingly, we studied resident wolves and coyotes in and adjacent to APP to identify distinct Canis types, clarify the occurrence of eastern wolves adjacent to APP, and investigate spatial genetic structure and landscape-genotype associations in the hybrid zone. We documented 3 genetically distinct Canis types that also differed morphologically, corresponding to putative gray wolves, eastern wolves, and coyotes. We also documented a substantial number of hybrid individuals (36%). Breeding eastern wolves were less common outside of APP, but occurred in some unprotected areas. We identified a steep cline extending west from APP where the dominant genotype shifted abruptly from eastern wolves to coyotes and hybrids. The genotypic pattern to the south and northwest was a more complex mosaic of alternating genotypes. We modeled genetic ancestry in response to prey availability and human disturbance and found positive and negative associations between wolf ancestry and 1) moose density and 2) road densities, respectively. Our results clarify the structure of the Canis hybrid zone adjacent to APP and provide unique insight into environmental conditions influencing hybridization dynamics between wolves and coyotes.
Data from: Demographic history influences spatial patterns of genetic diversity in recently expanded coyote (Canis latrans) populations
Human-mediated range expansions have increased in recent decades and represent unique opportunities to evaluate genetic outcomes of establishing peripheral populations across broad expansion fronts. Over the past century, coyotes (Canis latrans) have undergone a pervasive range expansion and now inhabit every state in the continental United States. Coyote expansion into eastern North America was facilitated by anthropogenic landscape changes and followed two broad expansion fronts. The northern expansion extended through the Great Lakes region and southern Canada, where hybridization with remnant wolf populations was common. The southern and more recent expansion front occurred approximately 40 years later and across territory where gray wolves have been historically absent and remnant red wolves were extirpated in the 1970s. We conducted a genetic survey at 10 microsatellite loci of 482 coyotes originating from 11 eastern U.S. states to address how divergent demographic histories influence geographic patterns of genetic diversity. We found that population structure corresponded to a north-south divide, which is consistent with the two known expansion routes. Additionally, we observed extremely high genetic diversity, which is atypical of recently expanded populations and is likely the result of multiple complex demographic processes, in addition to hybridization with other Canis species. Finally, we considered the transition of allele frequencies across geographic space and suggest the mid-Atlantic states of North Carolina and Virginia as an emerging contact zone between these two distinct coyote expansion fronts.
Data from: Scanning SNPs from a large set of expressed genes to assess the impact of artificial selection on the undomesticated genetic diversity of white spruce
A scan involving 1134 single-nucleotide polymorphisms (SNPs) from 709 expressed genes was used to assess the potential impact of artificial selection for height growth on the genetic diversity of white spruce. Two case populations of different sizes simulating different family selection intensities (K = 13% and 5%, respectively) were delineated from the Quebec breeding program. Their genetic diversity and allele frequencies were compared with those of control populations of the same size and geographic origin to assess the effect of increasing the selection intensity. The two control populations were also compared to assess the effect of reducing the sampling size. On one hand, in all pairwise comparisons, genetic diversity parameters were comparable and no alleles were lost in the case populations compared with the control ones, except for few rare alleles in the large case population. Also, the distribution of allele frequencies did not change significantly (P ≤ 0.05) between the populations compared, but ten and nine SNPs (0.8%) exhibited significant differences in frequency (P ≤ 0.01) between case and control populations of large and small sizes, respectively. Results of association tests between breeding values for height at 15 years of age and these SNPs supported the hypothesis of a potential effect of selection on the genes harboring these SNPs. On the other hand, contrary to expectations, there was no evidence that selection induced an increase in linkage disequilibrium in genes potentially affected by selection. These results indicate that neither the reduction in the sampling size nor the increase in selection intensity was sufficient to induce a significant change in the genetic diversity of the selected populations. Apparently, no loci were under strong selection pressure, confirming that the genetic control of height growth in white spruce involves many genes with small effects. Hence, selection for height growth at the present intensities did not appear to compromise background genetic diversity but, as predicted by theory, effects were detected at a few gene SNPs harboring intermediate allele frequencies.
Data from: Postglacial range expansion shaped the spatial genetic structure in a marine habitat-forming species: implications for conservation plans in the Eastern Adriatic Sea
Aim: Understanding how historical and contemporary processes shaped and maintain spatial patterns of genetic diversity is a major goal for conservation biologists. Here, we characterized the pattern of neutral genetic diversity and we inferred underlying processes in the habitat-forming octocoral Paramuricea clavata in the Adriatic Sea, a peculiar phylogeographic region of the Mediterranean Sea. Location: Eastern coast of the Adriatic Sea. Methods: We genotyped seven microsatellites in 454 individuals of P. clavata from 13 populations recolonized after the last glacial maximum (LGM). We estimated the levels of contemporary connectivity and genetic drift and we reconstructed the demographic history of these populations. Results: The pattern of spatial genetic structure resulted from the combination of hierarchical genetic clusters and isolation by distance (IBD). A significant decrease in genetic diversity and an increase of the frequencies of individual alleles likely due to allele surfing from the south to the north of the area were observed as expected after a postglacial sequential recolonization. Based on maximum likelihood analyses, the foundation of these populations was not linked to dramatic change in population size. Main conclusion: Oceanographic barriers to gene flow combined to the restricted dispersal of P. clavata likely maintain the hierarchical structure and the IBD pattern. We suggest that the latitudinal genetic gradient results from a northward 'serial founder events' recolonization. By integrating patterns and processes, we bridge the gap between the evolutionary and the conservation biology of P. clavata, providing management guidelines, which will benefit the associated coralligenous biodiversity.
Data from: Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae
Both historical and contemporary processes influence the genetic structure of species, but the relative roles of such processes are still difficult to access. Population genetic studies of species with recent evolutionary histories such as the New Zealand endemic scallop Pecten novaezelandiae (<1 Ma) permit testing of the effects of recent processes affecting gene flow and shaping genetic structure. In addition, studies encompassing the entire distributional range of species can provide insight into colonization processes. Analyses of genetic variation in P. novaezelandiae (952 individuals from 14 locations, genotyped at 10 microsatellite loci) revealed a weak but significant regional structure across the distributional range of the species, as well as latitudinal gradients of genetic diversity and differentiation: estimates of migration rates supported these patterns. Our results suggest that the observed genetic structure and latitudinal gradients reflect a stepping-stone model of colonization (north to south) and emerging divergence of populations as a result of ongoing limitations to gene flow and insufficient time to reach migration–drift equilibrium. The low levels of interpopulation and interregional genetic differentiation detected over hundreds of kilometres reflect the recent evolutionary history of P. novaezelandiae and stand in contrast to patterns reported for other evolutionary older species at the same spatial scale. The outcomes of this study contribute to a better understanding of evolutionary processes influencing the genetic variation of species and provide vital information on the genetic structure of P. novaezelandiae.
Data from: Conservation genetics of the scalloped hammerhead shark in the Pacific coast of Colombia
Previous investigations of the population genetics of the scalloped hammerhead sharks (Sphyrna lewini) in the Eastern Tropical Pacific have lacked information about nursery areas. Such areas are key to promoting conservation initiatives that can protect young sharks from threats such as overfishing. Here, we investigated the genetic diversity, phylogeography, and connectivity of S. lewini found in 3 areas of Colombia's Pacific coast: around Malpelo Island and in 2 National Natural Parks on the Colombian Pacific mainland (Sanquianga and Ensenada de Utría). We analyzed mtDNA control region (CR) sequences and genotyped 15 microsatellite loci in 137 samples of adults and juveniles. The mtDNA analyses showed haplotypes shared between the Colombian Pacific individuals sampled in this investigation and other areas in the Eastern Tropical Pacific, the Indo-Pacific, and with sequences previously reported in Colombia (Buenaventura Port), as well as 4 unique haplotypes. Population assignment and paternity analyses detected 3 parent–offspring pairs between Malpelo and Sanquianga and 1 between Malpelo and Utría. These results indicate high genetic connectivity between Malpelo Island and the Colombian Pacific coast, suggesting that these 2 areas are nurseries for S. lewini. This is, to our knowledge, the first evidence of nursery areas identified for the scalloped hammerhead shark anywhere in the world. Additional conservation planning may be required to protect these nursery habitats of this endangered shark species.
Data from: Fine-scale genetic structure and helping decisions in a cooperatively breeding bird
In animal societies, characteristic demographic and dispersal patterns may lead to genetic structuring of populations, generating the potential for kin selection to operate. However, even in genetically structured populations, social interactions may still require kin discrimination for cooperative behaviour to be directed towards relatives. Here, we use molecular genetics and long-term field data to investigate genetic structure in an adult population of long-tailed tits Aegithalos caudatus, a cooperative breeder in which helping occurs within extended kin networks, and relate this to patterns of helping with respect to kinship. Spatial autocorrelation analyses reveal fine-scale genetic structure within our population, such that related adults of either sex are spatially clustered following natal dispersal, with relatedness among nearby males higher than that among nearby females, as predicted by observations of male-biased philopatry. This kin structure creates opportunities for failed breeders to gain indirect fitness benefits via redirected helping, but crucially, most close neighbours of failed breeders are unrelated and help is directed towards relatives more often than expected by indiscriminate helping. These findings are consistent with the effective kin discrimination mechanism known to exist in long-tailed tits, and support models identifying kin selection as the driver of cooperation.
Data from: Individuals' expected genetic contributions to future generations, reproductive value, and short-term metrics of fitness in free-living song sparrows (Melospiza melodia)
Appropriately defining and enumerating 'fitness' is fundamental to explaining and predicting evolutionary dynamics. Yet, general theoretical concepts of fitness are often hard to translate into quantities that can be measured in wild populations experiencing complex environmental, demographic, genetic and selective variation. While the 'fittest' entities might be widely understood to be those that ultimately leave most descendants at some future time, such long-term legacies can rarely be measured, impeding evaluation of the degree to which tractable short-term metrics of individual fitness could potentially serve as useful direct proxies. One opportunity for conceptual and empirical convergence stems from the principle of individual reproductive value (Vi), defined as the number of copies of each of an individual's alleles that is expected to be present in future generations given the individual's realised pedigree of descendants. Since Vi tightly predicts an individual's longer-term genetic contribution, quantifying Vi provides a tractable route to quantifying what, to date, has been an abstract theoretical fitness concept. We used complete pedigree data from free-living song sparrows (Melospiza melodia) to demonstrate that individuals' expected genetic contributions stabilise within an observed 20-year (i.e. ~8 generation) time period, allowing estimation of individual Vi. Considerable among-individual variation in Vi was evident in both sexes. Standard metrics of individual lifetime fitness, comprising lifespan, lifetime reproductive success and projected growth rate, typically explained less than half the variation. We thereby elucidate the degree to which fitness metrics observed on individuals concur with measures of longer-term genetic contributions, and consider the degree to which analyses of pedigree structure could provide useful complementary insights into evolutionary outcomes.
Data from: Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide SNP genotyping
Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and candidate SNPs tagging adaptive genomic regions. Based on evenly distributed SNPs, the phylogeographic pattern differs substantially from the disjunct pattern previously observed between two highly divergent mtDNA lineages. The SNP tree instead shows extensive within watershed population clustering and different watersheds separated by short branches deep in the tree. These data are consistent with separate colonizations of most watersheds, despite underlying genetic connections between some independent drainages. This supports previous suppositions that morphological diversity observed between watersheds has been shaped independently, with populations exhibiting complete loss of lateral plates and giant size each occurring in several distinct clades. Throughout the archipelago, we see repeated selection of SNPs tagging candidate freshwater adaptive variants at several genomic regions differentiated between marine–freshwater populations on a global scale (e.g. EDA, Na/K ATPase). In estuarine sites, both marine and freshwater allelic variants were commonly detected. We also found typically marine alleles present in a few freshwater lakes, especially those with completely plated morphology. These results provide a general model for postglacial colonization of freshwater habitat by sticklebacks and illustrate the tremendous potential of genome-wide SNP data sets hold for resolving patterns and processes underlying recent adaptive divergences.
Data from: Mating system and genetic diversity of progenies before and after logging: a case study of Bagassa guianensis (Moraceae), a low-density dioecious tree of the Amazonian forest
The logging of large trees in tropical forests causes a decrease in the density of reproductive individuals, which likely affects the pattern of pollen dispersal and the mating system of the remaining trees in the population. Here, we investigate the impact of logging on mating system and genetic diversity of the low-density, thrip-pollinated, dioecious tree Bagassa guianensis within a 500-ha plot at Tapajós National Forest, Pará State, Brazil. Mating system parameters of the logged population were estimated using mixed-mating model. Six microsatellite loci were used to genotype 232 seeds from ten remnant female trees over three seasons (2006, 2007, and 2008). The data were compared with the mating system of the unlogged population of B. guianensis (18 female trees, 488 seeds) in the same plot. The overall number of alleles found in the open-pollinated progenies decreased after logging (K = 71 before logging and K = 57 after logging, considering the three after logging seasons pooled), as well as the average number of alleles per locus (A = 11.8 and 9.5, respectively). Similarly, the number of private alleles, which is defined in the context of this study as the number of alleles observed in the population exclusively before or after logging, also decreased after logging (15 and 1, respectively). However, the average number of alleles per locus and the observed and expected heterozygosities were not significantly higher before logging than after logging. Logging also did not affect the inbreeding of progenies in the population. Somewhat unexpectedly, the effective number of pollen donors was consistently higher after (N ep = 14.5 in 2006, 8.1 in 2007, and 6.3 in 2008) than before logging (N ep = 3.4), suggesting that the loss of alleles in the population was compensated by the higher heterogeneity in the pollen pool after the removal of the largest trees by logging. Potential causes explaining the patterns found here include the maintenance of large patches of forest around the logged plot and the species' ability to perform long-distance pollination by airborne thrips. Maintenance of landscape integrity as logged and unlogged forests around the exploited areas is recommended to enhance pollen migration and to avoid long-term losses in genetic diversity.
Data from: Plant dispersal in the sub-Antarctic inferred from anisotropic genetic structure
Climatic conditions and landscape features often strongly affect species' local distribution patterns, dispersal, reproduction and survival, and may therefore have considerable impacts on species' fine-scale spatial genetic structure (SGS). In this paper we demonstrate the efficacy of combining fine-scale SGS analyses with isotropic and anisotropic spatial autocorrelation techniques to infer the impact of wind patterns on plant dispersal processes. We genotyped 1304 Azorella selago (Apiaceae) specimens, a wind-pollinated and wind-dispersed plant, from four populations distributed across sub-Antarctic Marion Island. SGS was variable with Sp values ranging from 0.001 to 0.014, suggesting notable variability in dispersal distance and wind velocities between sites. Nonetheless, the data supported previous hypotheses of a strong NW – SE gradient in wind strength across the island. Anisotropic autocorrelation analyses further suggested that dispersal is strongly directional, but varying between sites depending on the local prevailing winds. Despite the high frequency of gale-force winds on Marion Island, gene dispersal distance estimates (σ) were surprisingly low (< 10 m), most likely because of a low pollen dispersal efficiency. An SGS approach in association with isotropic and anisotropic analyses provides a powerful means to assess the relative influence of abiotic factors on dispersal, and allow inferences that would not be possible without this combined approach.
Data from: Insights into the introduction history and population genetic dynamics of the Nile monitor (Varanus niloticus) in Florida
Invasive species are widely recognized as important drivers of the ongoing biodiversity crisis. The US state of Florida is especially susceptible to the proliferation of invasive reptiles, and nonnative lizards currently outnumber native lizard species. At present, there are three documented breeding populations of the Nile monitor (Varanus niloticus) in different regions of Southern Florida, and these populations are considered potential dangers to threatened, fossorial endemics, such as burrowing owls, American crocodiles, and gopher tortoises. Nevertheless, at present, both the introduction histories of these populations and the degree to which they are connected by gene flow are not known. To address these issues, we genotyped V. niloticus from Cape Coral, Homestead Air Reserve Base, and West Palm Beach at 17 microsatellite loci and conducted a variety of analyses to assess both intra-population genetic diversity, the degree of gene flow between populations, and the most likely introduction scenario. The results of our analyses demonstrate that all three populations have limited genetic diversity (mean number of effective alleles across loci in all three populations ~ 2.00) and are highly differentiated from one another (GST = 0.268; G''ST = 0.628). Our results also suggest that these populations resulted from independent introduction events that occurred within the past few decades. Consequently, we advise that wildlife managers focus management efforts on containment of existing populations and intensification of monitoring efforts on potential migration corridors.
Data from: Conservation genetics of the Philippine tarsier: cryptic genetic variation restructures conservation priorities for an island archipelago primate
Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier.
Data from: The role of geography and ecology in shaping repeated patterns of morphological and genetic differentiation between European minnows (Phoxinus phoxinus) from the Pyrenees and the Alps
Neutral and selective processes can drive repeated patterns of evolution in different groups of populations experiencing similar ecological gradients. In this paper, we used a combination of nuclear and mitochondrial DNA markers, as well as geometric morphometrics, to investigate repeated patterns of morphological and genetic divergence of European minnows in two mountain ranges: the Pyrenees and the Alps. European minnows (Phoxinus phoxinus) are cyprinid fish inhabiting most freshwater bodies in Europe, including those in different mountain ranges that could act as major geographical barriers to gene flow. We explored patterns of P. phoxinus phenotypic and genetic diversification along a gradient of altitude common to the two mountain ranges, and tested for isolation by distance (IBD), isolation by environment (IBE) and isolation by adaptation (IBA). The results indicated that populations from the Pyrenees and the Alps belong to two well differentiated, reciprocally monophyletic mtDNA lineages. Substantial genetic differentiation due to geographical isolation within and between populations from the Pyrenees and the Alps was also found using rapidly evolving AFLPs markers (isolation by distance or IBD), as well as morphological differences between mountain ranges. Also, morphology varied strongly with elevation and so did genetic differentiation to a lower extent. Despite moderate evidence for IBE and IBA, and therefore of repeated evolution, substantial population heterogeneity was found at the genetic level, suggesting that selection and population specific genetic drift act in concert to affect genetic divergence.
Data from: Conservation genetics of Australasian sailfin lizards: flagship species threatened by coastal development and insufficient protected area coverage
Despite rampant coastal development throughout Southeast Asia and the Pacific, studies of conservation genetics and ecology of vulnerable, coastal species are rare. Large bodied vertebrates with highly specialized habitat requirements may be at particular risk of extinction due to habitat degradation and fragmentation, especially if these habitats are naturally patchily distributed, marginal, or otherwise geographically limited, or associated in space with high human population densities or heavy anthropogenic disturbance. Particularly telling examples of these conservation challenges are large Australasian reptiles with obligate habitat requirements for lowland, coastal and mangrove forests. Plagued by habitat destruction due to high human densities along coastlines, sprawling rural development, and rapidly developing estuarine fisheries industry, coastal forest reptiles are experiencing rapid declines. And yet studies of population biology, genetics, and habitat requirements of species depending on these environments are few. We undertook the present study in order to take a multifaceted approach to understanding a poignant conservation problem. We identify significant evolutionary units for conservation in large-bodied Sailfin Lizards (genus Hydrosaurus), model suitable habitat in the Philippines from extensive occurrence data and evaluate the efficacy of the current protected area network, and identify the source of hydrosaurs in the illegal pet trade. We determine that the extent of the species' habitat coincident with protected areas is low. Our forensic evaluation of the illegal pet trade in the Philippines determines the existence of a natural population that is at risk of systematic exploitation by traders. Together, this integrative study characterizes a conservation urgency of particular significance: the genetically distinct Sailfin lizards of the Bicol faunal region, with suitable habitat virtually unprotected, and clear evidence of heavy exploitation for illegal trade. To the best of our knowledge, our study is the first conservation genetic study to evaluate the potential effectiveness of the protected landscape coverage in the Philippines, a Megadiverse nation and Biodiversity Hotspot.
Data from: Polyandry and the decrease of a selfish genetic element in a wild house mouse population
Despite deleterious effects on individuals, the t haplotype is a selfish genetic element present in many house mouse populations. By distorting the transmission ratio, +/t males transmit the t haplotype to up to 90% of their offspring. However, t/t individuals perish in utero. Theoretical models based on these properties predict a much higher t frequency than observed, leading to the t paradox. Here, we use empirical field data and theoretical approaches to investigate whether polyandry is a female counterstrategy against the negative fitness consequences of such distorters. We found a significant decrease of the t frequency over a period of 5.5 years that cannot be explained by the effect of transmission ratio distortion and recessive lethals, despite significantly higher life expectancy of +/t females compared to +/+ females. We quantified life history data and homozygous and heterozygous fitness effects. Population subdivision and inbreeding were excluded as evolutionary force influencing the t system. The possible influence of polyandry on the t system was then investigated by applying a stochastic model to this situation. Simulations show that polyandry can explain the observed t dynamics, making it a biologically plausible explanation for low t frequencies in natural populations in general.
Data from: Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries
Estuarine organisms grow in highly heterogeneous habitats and their genetic differentiation are driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and it's adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate-high level of genetic differentiation among populations (range FST: 0.0310-0.3325) was showed despite large ongoing dispersal. FLOCK assigned all individuals to 13 clusters and revealed a complex genetic structure. Some genetic clusters were limited in peripheries compared with very mixing constitution in centre populations, suggesting local adaptation was more likely to occur in peripheral populations. 21 candidate outliers under positive selection were detected, and further, the differentiation patterns correlated with geographic distance, salinity difference and colonization history were analyzed with or without the outliers. Combined results of AMOVA and IBD based on different dataset, it was found that the effects of geographic distance and population colonization history on isolation seemed to be promoted by divergent selection. However, none-liner IBE pattern indicates the effects of salinity were overwhelmed by spatial distance or other ecological process in certain areas, and also suggests that salinity was not the only selective factor driving population differentiation. These results together indicate that geographic distance, salinity difference and colonization history co-contributed in shaping the genetic structure of S. mariqueter, and that their relative importance was correlated with spatial scale and environment gradient.
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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.