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15,277 results for “GENETICS”
Contribution of genetic versus plastic responses to adaptive patterns in a widespread butterfly along a latitudinal cline
<p>Understanding how organisms adapt to complex environments is a central goal of evolutionary biology and ecology. This issue is of special interest in the current era of rapidly changing climatic conditions. Here, we investigate clinal variation and plastic responses in life history, morphology, and physiology in the butterfly <i>Pieris napi</i> along a pan-European gradient by exposing butterflies raised in captivity to different temperatures. We found clinal variation in body size, growth rates and concomitant development time, wing aspect ratio, wing melanisation, and heat tolerance. Individuals from warmer environments were more heat-tolerant, had less melanised wings and a shorter development but still they were larger than individuals from cooler environments. These findings suggest selection for rapid growth in the warmth and for wing melanisation in the cold, and thus fine-tuned genetic adaptation to local climates. Irrespective of the origin of butterflies, the effects of higher developmental temperature were largely as expected, speeding up development, reducing body size, potential metabolic activity, and wing melanisation, while increasing heat tolerance. At least in part, these patterns likely reflect adaptive phenotypic plasticity. In summary, our study revealed pronounced plastic and genetic responses, which may indicate high adaptive capacities in our study organism. Whether this may help such species though to deal with current climate change needs further investigation, as clinal patterns have typically evolved over long periods.</p>
Functional genetic diversity of domestic and wild American mink (Neovison vison )
<p>The release of domestic organisms to the wild threatens biodiversity because the introduction of domestic genes through interbreeding can negatively impact wild conspecifics via outbreeding depression. In North America, farmed American mink (<i>Neovison vison</i>) frequently escape captivity, yet the impact of these events on functional genetic diversity of wild mink populations is unclear. We characterized domestic and wild mink in Ontario at 17 microsatellites located in functional genes and in a promoter region that is non-coding but thought to be associated with traits affected by domestication. We found low functional genetic diversity in both mink types, as only 4 of 17 genes were variable, and the number of alleles per locus were generally lower in captive mink than in wild mink. To determine if allele frequencies of wild populations were affected by domestic release events, we performed redundancy analysis and spatial analysis of principal components on four polymorphic loci (AR, ATN1, IGF-1, and TOB1). We found evidence to suggest domestic release events are affecting the functional genetic diversity of wild mink, as sPCA showed clear distinctions between wild individuals near mink farms and those located in areas without mink farms. This is further substantiated through RDA, where spatial location was associated with genetic variation of AR, ATN1, and IGF1.</p>
Data from: Genetic population structure and variation at phenology-related loci in anadromous Arctic char (Salvelinus alpinus)
The Arctic will be especially affected by climate change, resulting in altered seasonal timing. Anadromous Arctic char (Salvelinus alpinus) is strongly influenced by sea surface temperature (SST) delimiting time periods available for foraging in the sea. Recent studies of salmonid species have shown variation at phenology-related loci associated with timing of migration and spawning. We contrasted genetic population structure at 53 SNPs versus four phenology-related loci among 15 anadromous Arctic char populations from Western Greenland and three outgroup populations. Among anadromous populations, the time period available for foraging at sea (> 2oC) ranges from a few weeks to several months, motivating two research questions: 1) Is population structure compatible with possibilities for evolutionary rescue of anadromous populations during climate change? 2) Does selection associated with latitude or SST regimes act on phenology-related loci? In Western Greenland, strong isolation-by-distance at SNPs was observed and spatial autocorrelation analysis showed genetic patch size up to 450 km, documenting contingency and gene flow among populations. Outlier tests provided no evidence for selection at phenology-related loci. However, in Western Greenland, mean allele length at OtsClock1b was positively associated with the time of year when SST first exceeded 2oC and negatively associated with duration of the period where SST exceeded 2oC. This is consistent with local adaptation for making full use of the time period available for foraging in the sea. Current adaptation may become maladaptive under climate change, but long-distance connectivity of anadromous populations could redistribute adaptive variation across populations and lead to evolutionary rescue.
The impact of local population genetic background on the spread of the selfish element Medea-1 in red flour beetles
<p>Selfish genetic elements have been found in the genomes of many species, yet our understanding of their evolutionary dynamics is only partially understood. A number of distinct selfish <i>Medea</i> elements are naturally present in many populations of the red flour beetle (<i>Tribolium castaneum</i>). Although these <i>Medea</i> elements are predicted by models to increase in frequency within populations because any offspring of a <i>Medea</i>-bearing mother that do not inherit at least one <i>Medea</i> allele will die, experiments demonstrating an increase in a naturally occuring <i>Medea</i> element are lacking. Our survey of the specific <i>Medea </i>element<i>, </i>M<sup>1</sup>, in the United States showed that it had a patchy geographic distribution. From the survey it could not be determined if this distribution was caused by a slow process of M<sup>1</sup> colonization of discrete populations or if some populations lacked M<sup>1</sup> because they had genetic factors conferring resistance to the <i>Medea </i>mechanism. We show that populations with naturally low to intermediate M<sup>1</sup> frequencies likely represent transient states during the process of <i>Medea</i> spread. Furthermore, we find no evidence that genetic factors are excluding M<sup>1</sup> from US populations where the element is not presently found. We also show how a known suppressor of <i>Medea</i> can impair the increase of M<sup>1</sup> in populations and discuss the implications of our findings for pest-management applications of <i>Medea</i> elements.</p>
Conservation genetics of native and European-introduced Chinese Water Deer (Hydropotes inermis)
<p><span><span><span><span><span><span><span><span><span><span><span>The Chinese water deer (<i>Hydropotes inermis</i>) belongs to a relatively early-divergence lineage of Cervidae and is thought to have retained some ancestral features of the group. This species is classified as Vulnerable on the IUCN Red List (accessed 2020), and populations in its native range have declined drastically in recent years. However, a number of individuals were introduced to the UK about a century ago; these have flourished and now make up over 40% of global numbers. To infer the population genetic structure and genetic diversity of Chinese water deer both in their native China and in populations introduced to the UK and France, mitochondrial DNA sequence variation was investigated (control region and cytochrome B) for near 100 individuals. The distribution of haplotypes among the regions shows distinct geographic structure, and only one cytochrome B haplotype was common to both China and European populations. Our results reveal lower levels of genetic diversity in the British populations, differentiation between native and introduced populations, and that the source population of British deer is likely to be extinct. Some recommendations are made for the conservation of different populations.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Genetic identity and herbivory drive the invasion of a common aquatic microbial invader - phytoplankton and zooplankton abundance
<p>Despite the increasing number of species invasions, the factors driving invasiveness are still under debate. This is particularly the case for 'invisible' invasions by aquatic microbial species. Since in many cases only a few individuals or propagules enter a new habitat, their genetic variation is low and might limit their invasion success, known as the genetic bottleneck. Thus, a key question is, how genetic identity and diversity of invading species influences their invasion success and, subsequently, affect the resident community.</p> <p>We conducted invader-addition experiments using genetically different strains of the globally invasive, aquatic cyanobacterium <i>Raphidiopsis raciborskii</i> (formerly: <i>Cylindrospermopsis raciborskii</i>) to determine the role of invader identity and genetic diversity (strain richness) at four levels of herbivory. We tested the invasion success of solitary single strain invasions against the invader genetic diversity, which was experimentally increased up to ten strains (multi-strain populations). By using amplicon sequencing we determined the strain-specific invasion success in the multi-strain treatments and compared those with the success of these strains in the single-strain treatments. Furthermore, we tested for the invasion success under different herbivore pressures.</p> <p>We showed that high grazing pressure by a generalist herbivore prevented invasion, whereas a specialist herbivore enabled coexistence of consumer and invader. We found a weak effect of diversity on invasion success only under highly competitive conditions. When invasions were successful, the magnitude of this success was strain-specific and consistent among invasions performed with single-strain or multi-strain populations. A strain-specific effect was also observed on the resident phytoplankton community composition, highlighting the strong role of invader genetic identity.</p> <p>Our results point to a strong effect of the genetic identity on the invasion success under low predation pressure. The genetic diversity of the invader population, however, had little effect on invasion success in our study, in contrast to most previous findings. Instead, it is the interaction between the consumer abundance and type together with the strain identity of the invader that defined invasion success. This study underlines the importance of strain choice in invasion research and in ecological studies in general.</p>
Species-specific effects of thermal stress on the expression of genetic variation across a diverse group of plant and animal taxa under experimental conditions
<p>Assessing the genetic adaptive potential of populations and species is essential for better understanding evolutionary processes. However, the expression of genetic variation may depend on environmental conditions, which may speed up or slow down evolutionary responses. Thus, the same selection pressure may lead to different responses. Against this background, we here investigate the effects of thermal stress on genetic variation, mainly under controlled laboratory conditions. We estimated additive genetic variance (<i>V<sub>A</sub></i>), narrow-sense heritability (<i>h</i><sup>2</sup>), and the coefficient of genetic variation (<i>CV<sub>A</sub></i>) under both benign control and stressful thermal conditions. We included six species spanning a diverse range of plant and animal taxa and a total of 25 morphological and life-history traits. Our results show that (1) thermal stress reduced fitness components, (2) the majority of traits showed significant genetic variation, and that (3) thermal stress affected the expression of genetic variation (<i>V<sub>A</sub></i>, <i>h</i><sup>2</sup> or <i>CV<sub>A</sub></i>) in only one third of the cases (25 of 75 analyses, mostly in one clonal species). Moreover, effects were highly species-specific, with genetic variation increasing in 11 and decreasing in 14 cases under stress. Our results hence indicate that thermal stress does not generally affect the expression of genetic variation under laboratory conditions but, nevertheless, increases or decreases genetic variation in specific cases. Consequently, predicting the rate of genetic adaptation might not be generally complicated by environmental variation, but requires a careful case-by-case consideration.</p>
Genetic connectivity and population structure of African savanna elephants (Loxodonta africana) in Tanzania
<p>Increasing human population growth, exurban development, and associated habitat fragmentation is accelerating the isolation of many natural areas and wildlife populations across the planet. In Tanzania, rapid and ongoing habitat conversion to agriculture has severed many of the country's former wildlife corridors between protected areas. To identify historically-linked protected areas, we investigated the genetic structure and gene flow of African savanna elephants in Tanzania using microsatellite and mitochondrial DNA markers in 688 individuals. Our results indicate distinct population genetic structure within and between ecosystems across Tanzania, and reveal important priority areas for connectivity conservation. Elephants sampled from the Tarangire-Manyara ecosystem appear marginally, yet significantly isolated from elephants sampled from the greater Serengeti ecosystem (mean FST = 0.03), where two distinct subpopulations were identified.Unexpectedly, elephants in the Lake Manyara region appear to be more closely related to those across the East African Rift wall in the Ngorongoro Conservation Area than they are to the neighboring Tarangire subpopulations. We concluded that the Rift wall has had a negligible influence on genetic differentiation up to this point, but differentiation may accelerate in the future because of ongoing loss of corridors in the area. Interestingly, relatively high genetic similarity was found between elephants in Tarangire and Ruaha although they are separated by >400 km. In southern Tanzania, there was little evidence of female-mediated gene flow between Ruaha and Selous, probably due to the presence of the Udzungwa Mountains between them. Despite observing evidence of significant isolation, the populations of elephants we examined generally exhibited robust levels of allelic richness (mean AR = 9.96), heterozygosity (mean µHE = 0.73), and effective population sizes (mean Ne = 148). Our results may inform efforts to restore wildlife corridors between protected areas in Tanzania in order to facilitate gene flow for long-term survival of elephants and other species.</p>
Datasets of the study: "Describing variability in pig genes involved in coronavirus infections: towards a One Health perspective in conservation of animal genetic resources"
<p><strong>Dataset description</strong></p> <p>Sequencing data (*.bam files) of four pig genes (<em>ACE2</em>, <em>ANPEP</em>, <em>DPP4</em> and <em>TMPRSS2</em>)<em> </em>that can serve as receptors or protease for priming the infection of coronaviruses.</p> <p>The datasets are related to 22 European pig breeds and wild boars (Alentejana, AL; Apulo-Calabrese, AC; Basque, BA; Bísara, BI; Black Slavonian, BS; Casertana, CA; Cinta Senese, CS; Gascon, GA; Krškopolje, KR; Lithuanian Indigenous Wattle, LIW; Lithuanian White Old Type, LWOT; Majorcan Black, MB; Mora Romagnola, MR; Moravka, MO; Nero Siciliano, NS; Sarda, SA; Schwäbisch-Hällisches Schwein, SHS; Swallow-Bellied Mangalitsa, SBMA; Turopolje, TU; Italian Duroc, IDU; Italian Large White, ILW; Italian Landrace, ILA; Wild Boar, WB). This work took advantage of a study design developed within the Horizon 2020 TREASURE project.</p> <p>Each folder contains *.bam files and the related indexes *.bai. The name of the investigated breed and gene is part of the file name (e.g. ILW.ACE2.bam identifies the sequencing data related to the ACE2 gene in the Italian Large White pig breed). Details of sequencing and the bioinformatic pipeline are below reported.</p> <p><strong>Sequencing data</strong></p> <p>A total of 22 DNA pools were constructed from the European pig breeds and one DNA pool was constructed from European wild boars, including in each pool 30 or 35 individual DNA samples pooled at equimolar concentration. For the 22 DNA pools, libraries were prepared and fed into an Illumina HiSeq X Ten sequencer for paired-end sequencing, obtaining 150 bp length reads. The wild boar DNA pool was sequenced from 250 bp fragment libraries, with 100 bp long paired-end reads, on the BGISeq 500 platform, following the provider’s procedures.</p> <p><strong>Data processing</strong></p> <p>Reads that were obtained from the sequenced libraries were cleaned by removing adapter sequences and filtering out sequences presenting more than 10% unknown bases (N) and/or containing low-quality bases (Q ≤ 5) over 50% of the total sequenced bases. Then, filtered high-quality reads were mapped on the latest version of the <em>Sus scrofa</em> reference genome (Sscrofa11.1; https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.fna.gz) using the BWA-MEM algorithm v.0.7.17 and the parameters for paired-end data. Picard v.2.1.1 (https://broadinstitute.github.io/picard/) was used to remove duplicated reads. Whole sequence data are available in the EMBL-EBI European Nucleotide Archive (ENA) repository (http://www.ebi.ac.uk/ena), under the study accession PRJEB36830. </p> <p>Reads covering the four genes (ACE2: NC_010461.5:12094853-12156275; ANPEP: NC_010449.5:55346083-55378881; DPP4: NC_010457.5:68655849-68748818; TMPRSS2: NC_010455.5:204871561-204907561) were extracted with samtools v.1.7 and exported as aligned, sorted and indexed *.bam files. Gene length includes UTRs and flanking regions of 5 kbp upstream [flanking (5’-UTR)] and downstream [flanking (3’-UTR)].</p>
Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs
<p>The New World Screwworm fly, <i>Cochliomyia hominivorax</i>, is a major pest of livestock in South America and Caribbean. However, few genomic resources have been available for this species. A genome of 534 Mb was assembled from long read PacBio DNA sequencing of DNA from a highly inbred strain. Analysis of molecular evolution identified 40 genes that are likely under positive selection. Developmental RNA-seq analysis identified specific genes associated with each stage. We identify and analyze the expression of genes that are likely important for host-seeking behavior (chemosensory), development of larvae in open wounds in warm-blooded animals (heat shock protein, immune response) and for building transgenic strains for genetic control programs including gene drive (sex determination, germline). This study will underpin future experiments aimed at understanding the parasitic lifestyle of the screwworm fly and greatly facilitate future development of strains for efficient systems for genetic control of screwworm.</p>
Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers
Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.
Data from: Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species
<p>The world's second largest expanse of tropical rain forest is in Central Africa and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across central African rain forest plants, in particular a North-South genetic discontinuity around the equatorial line, in a continuous expanse of rain forest but where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rain forest tree species Annickia affinis (Annonaceae). We showed for the first time that the North-South divide is the result of a single, major colonisation event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly-developed genomic tools can provide invaluable insights into our understanding of tropical rain forest evolutionary dynamics.</p>
Data from: Restricted connectivity and population genetic fragility in a globally endangered hammerhead shark
Vagile, large-bodied marine organisms frequently have wide range dispersion but also dependence on coastal habitats for part of their life-history. These characteristics may induce complex population genetic structure patterns, with resulting implications for the management of exploited populations. The scalloped hammerhead, Sphyrna lewini, is a cosmopolitan, migratory shark in tropical and warm temperate waters, inhabiting coastal bays during parturition and juvenile development and the open ocean as adults. Here, we investigated the genetic connectivity and diversity of S. lewini in the western Atlantic using large sample coverage (N=308), and data from whole mitochondrial control region (mtCR) sequences and ten nuclear microsatellite loci. We detected significant population genetic structure with both mtCR and microsatellites markers (mtCR: ΦST = 0.60; p < 0.001; microsatellites: Dest 0.0794, p = 0.001, FST = 0.046, p < 0.05), and isolation by distance (mtCR r = 0.363, p = 0.009; microsatellites r = 0.638, p = 0.007). The migration and gene flow patterns, based on mtCR and microsatellites were asymmetric, and female reproductive philopatry is postulated to explain such population subdivision patterns. The notable population differentiation at microsatellites markers indicates low-levels of male-mediated gene flow in the western Atlantic. The overall effective population size was estimated as 299 (215 – 412 Confidence Interval), and there was no evidence of strong or recent bottleneck effects. Findings of at least three management units, moderate genetic diversity, and low effective population size in the context of current overfishing calls for intensive management aimed at short and long-term conservation for this endangered species in the western Atlantic Ocean.
Monitoring and traceability of genetically modified soybean event GTS 40-3-2 during soybean protein concentrate and isolate preparation
To evaluate DNA fragmentation and GMO quantification during soybean protein concentrate and isolate preparation, genetically modified soybean event GTS 40-3-2 (RRS) was blended with conventional soybeans at mass percentages of 0.9%, 2%, 3%, 5%, and 10%. Qualitative PCR and real-time PCR were used to monitor the taxon-specific lectin and exogenous cp4 epsps target levels in all of the main products and by-products, which has practical significance for RRS labelling threshold and traceability. Along the preparation chain, the majority of DNA was distributed in main products, and the DNA degradation was noticed. From a holistic perspective, the lectin target degraded more than cp4 epsps target during both of the two soybean proteins preparations. Therefore, the transgenic contents in the final protein products were higher than the actual mass percentages of RRS in raw materials. Our results are beneficial to the improvement of GMO labelling legislation and the protection of consumer rights.
Data from: Wintering grounds, population size and evolutionary history of a cryptic passerine species from isotopic and genetic data
<p>Cryptic species pose a particular challenge to biologists in the context of life history investigations because of the difficulty in their field discrimination. Additionally, there is normally a lag in their widespread acceptance by the scientific community once they are formally recognised. These two factors might constrain our ability to properly assess the conservation status of the different species conforming a cryptic complex. In this study, we analysed isotopic and genetic data to shed light into the still unclear wintering grounds, population size and evolutionary history of the Iberian chiffchaff (<i>Phylloscopus ibericus</i>), a species included within the Common chiffchaff (<i>Phylloscopus collybita</i>) until two decades ago due to their phenotypic similarity. We used molecular methods to identify spring-migrating <i>Phylloscopus</i> species captured in northern Iberia, and by comparing the Hydrogen isotopic ratios of their claw tips (δ<sup>2</sup>H<sub>c</sub>; which would reflect the signatures of their wintering grounds), we detected that δ<sup>2</sup>H<sub>c</sub> values of Iberian chiffchaffs were similar to Willow warblers (<i>Phylloscopus trochilus</i>; a renowned trans-Saharan migrant), and higher than Common chiffchaffs (mostly a pre-Saharan migrant). These results strongly support the idea that Iberian chiffchaffs winter in tropical Africa. We additionally reconstructed the phylogeny and evolutionary history of the Iberian chiffchaff's clade using mitochondrial and nuclear markers. Our results revealed relatively high values of nucleotide diversity (and, hence, high N<sub>e</sub>) for the species that were greater than the values of the Common/Iberian most recent common ancestor. This suggests that the Iberian chiffchaff did not experience strong bottlenecks after diverging from the Common chiffchaff approximately one million years ago. Ultimately, our study provides another illustrative example of how isotopic and genetic analysis tools can help to enhance our understanding of avian ecology and evolution.</p>
More than meets the eye: syntopic and morphologically similar mangrove killifish species show different mating systems and patterns of genetic structure along the Brazilian coast
<p><a name="_Hlk40344892">Different mating systems can strongly affect the extent of genetic diversity and population structure among species. Given the increased effects of genetic drift on reduced population size, theory predicts that species undergoing self-fertilization should have greater population structure than outcrossed species, however demographic dynamics may affect this scenario. </a>The mangrove killifish clade is composed of the two only known examples of self-fertilising species among vertebrates (<i>Kryptolebias marmoratus </i>and <i>K</i>. <i>hermaphroditus</i>). A third species in this clade, <i>K. ocellatus, </i>inhabits mangrove forests in southeast Brazil, however its mating system and patterns of genetic structure have been rarely explored. Here, we examined the genetic structure and phylogeographic patterns of <i>K</i>. <i>ocellatus</i> along its distribution, using mitochondrial DNA and microsatellites to compare its patterns of genetic structure with the predominantly selfing and often syntopic, <i>K</i>. <i>hermaphroditus.</i> Our results indicate that <i>K</i>. <i>ocellatus</i> reproduces mainly by outcrossing across much of its known range, with no current evidence of selfing, despite being an androdioecious species. Our results also reveal a stronger population subdivision in <i>K</i>. <i>ocellatus </i>compared to <i>K</i>. <i>hermaphroditus</i>, contrary to the theoretical predictions based on reproductive biology of the two species. Our findings indicate that, although morphologically similar, <i>K</i>. <i>ocellatus </i>and <i>K</i>. <i>hermaphroditus</i> had remarkably different evolutionary histories when colonising the same mangrove areas in south-eastern Brazil, with other factors (e. g. time of colonisation, dispersal/establishment capacity) having more profound effects on the current population structuring of those species than differences in mating systems.</p>
Cryptic species and genetic connectivity among populations of the coral Pocillopora damicornis (Scleractinia) in the tropical southwestern Pacific
<p>Studying population genetic connectivity (i.e., identifying gene flow among populations and understanding their impacts on the genetic structure and diversity of populations) is first a matter of knowing what we work on, that is, accurately delimiting evolutionary units. Here, we focused on <em>Pocillopora damicornis</em> sensu stricto (or <em>Pocillopora </em>PSH04 sensu Gélin et al. in Mol Phylogenet Evol 109:430–446. http://dx.doi.org/10.1016/j.ympev.2017.01.018, 2017). From 458 colonies sampled within the tropical southwestern Pacific [Chesterfield Islands and New Caledonia (Grande Terre and Loyalty Islands)], Bayesian assignments and network analyses were conducted with 11-microsatellite loci to first evaluate the genetic partitioning of the colonies in distinct Secondary Species Hypotheses (SSHs), then in distinct clusters. Population genetic connectivity was then assessed for each cluster separately. <em>Pocillopora </em>PSH04 was partitioned into two highly differentiated SSHs (SSH04a and SSH04b), regularly found in sympatry. Furthermore, SSH04a was subdivided into two clusters (SSH04a-1 and SSH04a-2). This pattern of genetic structuring seems not related to clonality, but rather to the establishment of reproductive barriers. Nevertheless, considering each cluster separately, the populations appeared highly differentiated, suggesting relatively weak gene flow. This low connectivity among populations, coupled with the existence of cryptic species, brings new insights to the connectivity pattern of this understudied Pacific region.</p> <p>This dataset contains the microsatellite genotypes analysed (458 <em>Pocillopora</em> PSH04 colonies × 13 loci).</p>
Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites
<p>STRUCTURE remains the most applied tool aimed at recovering the true, but unknown, population structure from observed microsatellite data or other genetic markers. About 30% of <span class="Program"><span>STRUCTURE</span></span>-based studies could not be reproduced (Gilbert et al., 2012). Here we use a large set of data from 2323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellite markers, to evaluate how program settings, in particular the so far insufficiently evaluated number of replicates, impact the estimation of the optimal number of population clusters <i>K</i><sub>opt</sub> that best describe the observed data. Domestic horses are suited as a test case as there is extensive knowledge of the history of many breeds, extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (<span class="Program"><span>DAPC</span></span>, <span class="Program"><span>FLOCK</span></span>, PCoA and <span class="Program"><span>STRUCTURE</span></span> with different run scenarios) all revealed the general, broad-scale relationships among the breeds that largely reflect known breed histories but diverged largely how they characterized small-scale patterns. <span class="Program"><span>STRUCTURE</span></span> failed to consistently identify <i>K</i><sub>opt</sub> using the most widespread approach, the ΔK method, despite very large numbers of MCMCs (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of<i> K</i>, without assuming a <i>K</i><sub>opt</sub>, was consistent with known breed histories. The over-reliance on <i>K</i><sub>opt</sub> should be replaced by a qualitative description of clustering over increasing <i>K</i>, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.</p>
Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts
<p>Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (<i>Populus angustifolia</i>) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) <i>P. angustifolia</i> is differentiated into six genetic groups across its range from México to Canada, and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically-informed ecological niche models (gENMs) outperformed the standard species-level ENM (3-14% increase in AUC; 1-23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change, and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species' capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, <i>P. fremontii</i>. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly "adaptive management" approach to support conservation genetic management of species facing global change.</p>
Data from: Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula
The introduction of non-native species can have long-term effects on native plant and animal communities. Introduced populations are occasionally not well understood and offer opportunities to evaluate changes in genetic structure through time and major population changes such as bottleneck and or founder events. Invasive species can often evolve rapidly in new and novel environments, which could be essential to their long-term success. Sika deer are native to East Asia, and their introduction and establishment to the Delmarva Peninsula, USA is poorly documented, but probably involved ≥1 founder and/or bottleneck events. We quantified neutral genetic diversity in the introduced population and compared genetic differentiation and diversity to the presumed source population from Yakushima Island, Japan, and a captive population of sika deer in Harrington, Delaware, USA. Based on data from 10 microsatellite DNA loci, we observed reduced genetic variation attributable to founder events, support for historic hybridization events, and evidence that the population did originate from Yakushima Island stocks. Estimates of population structure through Bayesian clustering and demographic history derived from Approximate Bayesian Computation (ABC), were consistent with the hypothesized founder history of the introduced population in both timing and effective population size (approximately 5 effective breeding individuals, an estimated 36 generations ago). Our ABC results further supported a single introduction into the wild happening before sika deer spread throughout the Delmarva. We conclude that free-ranging sika deer on Delmarva are descended from ca. 5 individuals introduced about 100 years ago from captive stocks of deer maintained in the United Kingdom. Free-ranging sika deer on Delmarva have lost neutral diversity due to founder and bottleneck events, yet populations have expanded in recent decades and show no evidence of abnormalities associated with inbreeding. We suggest management practices including increasing harvest areas and specifically managing sika deer outside of Maryland.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.