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1,598 results for “genetic diversity”
High sexual display trait diversity without measured genetic divergence in a montane hybrid zone involving young species (Habronattus americanus subgroup, Araneae, Salticidae)
<p>Genetic introgression, allele exchange across species boundaries, is a commonly recognized feature of animal evolution. Under such a paradigm contemporary contact zones provide first-hand and complementary insight into the geographic, phenotypic, and genetic details of introgression. Also, when mate choice phenotypes are conspicuous and variable in hybrids, contact zones provide potential insight into how sexual selection interacts with species boundary maintenance, particularly when postzygotic reproductive isolation is weak. The <em>Habronattus</em> <em>americanus</em> subgroup includes several recently evolved jumping spider species, with an estimated age of about 200,000 years, and substantial evidence for hybridization and introgression. We explored a contact zone involving <em>H. americanus</em> (Keyserling, 1885) and <em>H. kubai</em> (Griswold, 1979) on Mount Shasta, California, in alpine habitats that would have been unavailable (under ice) at the Last Glacial Maximum. We characterized morphological diversity within the contact zone, including the fine-scale geographic distribution of hybrid and parental individuals, and assessed genetic variation using ddRADseq data. Combined results indicate a lack of measured genomic differentiation between specimens with distinct morphologies, including individuals with phenotypes of the parental species. We identified a diverse array of hybrid morphologies, with phenotypic evidence for backcrossing, essentially forming a phenotypic bridge between parental taxa. The study area is characterized by more hybrid than parental individuals, with a significantly larger number of red-palped morphologies than white and/or yellow-palped morphologies; the novel, white-palped phenotype is perhaps transgressive. Overall, these results contribute to a better understanding of the expected ebb and flow of lineage interactions during the early stages of speciation.</p>
Different photoperiodic responses in diapause induction can promote the maintenance of genetic diversity via the storage effect in Daphnia pulex
<p>Understanding mechanisms that promote the maintenance of biodiversity (genetic and species diversity) has been a central topic in evolution and ecology. Previous studies have revealed that dormancy can contribute to coexistence of competing genotypes or species in fluctuating environments via the storage effect. However, they tended to focus on differences in reproductive success (e.g., seed yield) and diapause termination (e.g., germination) timing. Here we tested whether different photoperiodic responses in diapause induction can promote coexistence of two parthenogenetic (asexual) genotypes of <em>Daphnia pulex </em>in Lake Fukami-ike, Japan. Through laboratory experiments, we confirmed that short day length and low food availability induced the production of diapausing eggs. Furthermore, we found that one genotype tended to produce diapausing eggs in broader environmental conditions than the other. Terminating parthenogenetic reproduction earlier decreases total clonal production, but the early-diapausing genotype becomes advantageous by assuring reproduction in "short" years where winter arrival is earlier than usual. Empirically parameterized theoretical analyses suggested that different photoperiodic responses can promote coexistence via the storage effect with fluctuations of the growing season length. Therefore, timing of diapause induction may be as important as diapause termination timing for promoting the maintenance of genetic diversity in fluctuating environments.</p>
Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii
<p>Understanding the processes that underlie the development of population genetic structure is central to the study of evolution. Patterns of genetic structure can reveal signatures of isolation by distance, barriers to gene flow, or even the genesis of speciation. However, it is unclear how severe range restriction might impact the processes that dominate the development of genetic structure. In narrow endemic species, is population structure likely to be adaptive in nature, or rather the result of genetic drift? In this study, we investigated patterns of genetic diversity and structure in the narrow endemic Hayden's ringlet butterfly. Specifically, we asked to what degree genetic structure in the Hayden's ringlet can be explained by isolation by distance, isolation by resistance (in the form of geographic or ecological barriers to migration between populations), and isolation by environment (in the form of differences in host plant availability and preference). We employed a genotyping-by-sequencing (GBS) approach coupled with host preference assays, Bayesian modeling, and population genomic analyses to answer these questions. Our results suggest that despite their restricted range, levels of genetic diversity in the Hayden's ringlet are comparable to those seen in more widespread butterfly species. Hayden's ringlets showed a strong preference for feeding on grasses relative to sedges, but neither larval preference nor potential host availability at sampling sites correlated with genetic structure. We conclude that geography, in the form of isolation by resistance and simple isolation by distance, was the major driver of contemporary patterns of differentiation in this narrow endemic species.</p>
Parallel evolution despite low genetic diversity in three-spined sticklebacks
<p>The three-spined stickleback (<em>Gasterosteus aculeatus</em>) is a model organism for studies of parallel evolution in the wild; marine stickleback populations have repeatedly colonized and adapted to different brackish and freshwater habitats. Population genetic studies of European three-spined sticklebacks have usually been conducted only in high-latitude areas. Here, we analysed southern and northern European samples of marine and freshwater three-spined stickleback to test two hypotheses. First, southern European freshwater populations – which currently lack or have limited connection to marine populations – have lost genetic diversity due to population bottlenecks and inbreeding compared to their northern European counterparts. Second, the degree of genetic parallelism in response to freshwater colonisation is higher among northern than southern European populations as the latter have been isolated and likely subjected to strong genetic drift. The results show that southern populations exhibit lower genetic diversity but a higher degree of genetic parallelism than northern populations. Hence, they confirm the hypothesis that southern populations have lost genetic diversity, but this loss likely happened after they had already adapted to freshwater conditions, explaining the high degree of genetic parallelism in the south.</p>
Demography and environment modulate the effects of genetic diversity on extinction risk in a butterfly metapopulation
<p>Linking genetic diversity to extinction is a common goal in genomic studies. Recently, a debate has arisen regarding the importance of genetic variation in conservation as some studies have failed to find associations between genome-wide genetic diversity and extinction risk. However, only rarely are genetic diversity and fitness measured together in the wild, and typically variation in demographic history or environment are ignored. It is therefore difficult to infer whether a lack of an association is real or obscured by confounding factors. To address these shortcomings, we analysed genetic data from 7,501 individuals with extinction data from 279 meadows and mortality of 1,742 larval nests in a butterfly metapopulation. We found strong negative associations between genetic diversity and extinction when heterozygosity was included alone in models. However, this association was no longer present when ecological covariates were included. Interactions between heterozygosity and demographic variables revealed that associations are context-dependent or only detectable when confounding factors are controlled. For example, extinction declined with increasing heterozygosity in large but not currently small populations, although negative associations between heterozygosity, extinction, and mortality were detected in populations with a recent history of decline. We conclude that low genetic diversity is an important predictor of extinction, predicting >25% increase in extinction beyond ecological factors in certain contexts. This highlights that inferences about the importance of genetic diversity should not rely on genomic data alone but requires investments in obtaining demographic and environmental data from natural populations to jointly assess their impact on population extinction risk.</p>
Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow
<p><span><span>Red deer (</span><span><em>Cervus elaphus</em></span><span>) throughout central Europe are</span> impacted by different anthropogenic activities including habitat fragmentation, selective hunting, and translocations<span>. This has substantial influences on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess the genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. </span></span><span><span>We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, and anthropogenic infrastructures) has led to comparably low levels of genetic diversity. The mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. </span></span><span><span>Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. </span></span></p> <p><span><span>Based on these findings, we suggest that connectivity among existing management units needs to be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.</span></span></p>
First insights into population structure and genetic diversity versus host specificity in trypanorhynch tapeworms using multiplexed shotgun genotyping
<p>Theory predicts relaxed host specificity and high host vagility should contribute to reduced genetic structure in parasites while strict host specificity and low host vagility should increase genetic structure. Though these predictions are intuitive, they have never been explicitly tested in a population genomic framework. Trypanorhynch tapeworms, which parasitize sharks and rays (elasmobranchs) as definitive hosts, are the only order of elasmobranch tapeworms that exhibit considerable variability in their definitive host specificity. This allows for unique combinations of host use and geographic range, making trypanorhynchs ideal candidates for studying how these traits influence population-level structure and genetic diversity. Multiplexed shotgun genotyping (MSG) datasets were generated to characterize component population structure and infrapopulation diversity for a representative of each trypanorhynch suborder: the ray-hosted <em>Rhinoptericola megacantha</em> (Trypanobatoida) and the shark-hosted Callitetrarhynchus gracilis (Trypanoselachoida). Adults of <em>R. megacantha</em> are more host-specific and less broadly distributed than adults of <em>C. gracilis</em>, allowing correlation between these factors and genetic structure. Replicate tapeworm specimens were sequenced from the same host individual, from multiple conspecific hosts within and across geographic regions, and from multiple definitive host species. For <em>R. megacantha</em>, population structure coincided with geography rather than host species. For <em>C. gracilis</em>, limited population structure was found, suggesting a potential link between degree of host specificity and structure. Conspecific trypanorhynchs from the same host individual were found to be as, or more, genetically divergent from one another as from conspecifics from different host individuals. For both species, high levels of homozygosity and positive FIS values were documented.</p>
Populations restored using regional seed are genetically diverse and similar to natural populations in the region
<p>Ecological restoration and plant re-introductions aim to create plant populations that are genetically similar to natural populations to preserve the regional gene pool, yet genetically diverse to allow adaptation to a changing environment. For this purpose, seeds for restoration are increasingly sourced from multiple populations in the target region. However, it has only rarely been tested whether using regional seed indeed leads to genetically diverse restored populations which are genetically similar to natural populations.</p> <p>We used single nucleotide polymorphism (SNP) markers to investigate genetic diversity within and differentiation among populations of <em>Centaurea jacea</em> and <em>Betonica officinalis</em> on restored and natural meadows in the White Carpathians, Czech Republic. The restoration took place 20 years ago using regional seeds propagated from a mix of multiple regional source populations. We included original regional seeds in our analysis to compare the restored populations with their origin (only in <em>C. jacea</em>). Additionally, we analysed conventional seeds without certified origin because these would have constituted a common alternative for restoration seeding in the absence of regional seeds.</p> <p>The differentiation between restored and natural populations (mean pairwise <em>F<sub>ST</sub></em> = 0.018 in <em>Centaurea</em> and 0.021 in <em>Betonica</em>) was similar to the differentiation among natural populations (<em>F<sub>ST</sub></em> = 0.023 and 0.021), and the restored populations were slightly more genetically diverse than the natural populations. In addition, restored populations were relatively similar to their origin, the regional seeds (<em>F<sub>ST</sub></em> = 0.015). In contrast, conventional seeds were strongly differentiated from all regional populations (<em>F<sub>ST</sub></em> = 0.100 and 0.059, in <em>Centaurea</em> and <em>Betonica</em>, respectively) and harboured substantially lower genetic diversity. We also found signs of gene flow via pollen or seed dispersal from natural to restored populations but not <em>vice versa</em>.</p> <p><em>Policy implications</em>. Regionally sourced seeds can produce genetically diverse populations at natural levels of genetic differentiation.</p>
Data from: Genetic diversity and divergence in the fountain darter (Etheostoma fonticola): implications for conservation of an endangered species
<p>The endangered fountain darter Etheostoma fonticola is found only in the Comal and San Marcos rivers in the Guadalupe River basin in central Texas, USA. Comal River fountain darters were believed to be extir- pated following a severe drought in the 1950s and were reintroduced in the early 1970s using 457 darters from the San Marcos River. In this study we used 23 microsatellite loci to describe and evaluate the genetic diversity, population structure and effective population size (Ne) of fountain darters. We also evaluated the genetic effect of the Comal River reintroduction and the influence of low-head dams (dams) on dispersal in both rivers. Bayesian analysis of individual genotypes and Analysis of Molecular Variation supported two distinct populations concordant with the two rivers. Estimates of Ne were much smaller (<10 %) than census size (Nc) in both rivers but did not indicate the populations are at risk of an immediate and rapid loss of genetic diversity. Coalescent-based estimates of the genetically effective number of founders (Nf) for the Comal River averaged about 49 darters and, together with the indices of genetic diversity and the bottleneck test (heterozygosity excess) results, were consistent with a founder event following the reintroduction in the Comal River. Finally, our results regarding the influence of dams on fountain darter dispersal were equivocal and did not support a conclusion. We recommend this issue be examined further as part of the fountain darter recovery program.</p>
The genetic diversity of triploid Celtis pumila and its diploid relatives C. occidentalis and C. laevigata (Cannabaceae)
<p>The genus <i>Celtis</i> in eastern North America shows puzzling patterns of variation. While three species are generally recognized, many authors have suggested hybridization may be blurring the boundaries among them. Suspected hybridization between <i>C. occidentalis</i> and <i>C. pumila</i> has hampered conservation planning for the latter, which is a Threatened species in Canada. Using microsatellite markers and flow cytometry, we assessed the relationship between genetic diversity, ploidy, and morphology in this group. We confirmed the presence of two diploid species, <i>C. occidentalis</i> and <i>C. laevigata</i>, and that they do hybridize where they co-occur in southern Missouri and Illinois. We found two triploid genetic groups. These groups had distinct geographic ranges, but were morphologically very similar, corresponding to <i>C. pumila</i>. Furthermore, the triploid groups were characterized by a small number of heterozygous multi-locus genotypes. A single genotype dominated populations across Ontario, Michigan, Ohio and Pennsylvania, indicating apomictic reproduction is common in these groups. While the triploid clusters were distinct from each other, they did have strong associations with sympatric diploid species, and also with the western triploid species <i>C. reticulata</i>. The triploid <i>Celtis pumila</i> demonstrates remarkable phenotypic plasticity, with the same genotype variously presenting as dwarf shrubs in xeric, exposed sites, and subcanopy tree in mesic forests.</p>
Evolution of selfing syndrome and its influence on genetic diversity and inbreeding: A range-wide study in Oenothera primiveris.
<p><strong>Premise of the study:</strong> To avoid inbreeding depression plants have evolved diverse breeding systems to favor outcrossing such as self-incompatibility. However, changes in biotic and abiotic conditions can result in selective pressures that lead to a breakdown in self-incompatibility. The shift to increased selfing is commonly associated with reduced floral features, lower attractiveness to pollinators, and increased inbreeding. In this study, we tested the hypothesis that the loss of self-incompatibility, a shift to self-fertilization (autogamy), and concomitant evolution of the selfing syndrome (reduction in floral traits associated with cross-fertilization) will lead to increased inbreeding and population differentiation in <em>Oenothera primiveris</em>. Across its range, this species exhibits a shift in its breeding system and floral traits from a self-incompatible population with large flowers to self-compatible populations with smaller flowers.</p> <p><strong>Methods:</strong> We conducted a breeding system assessment, evaluated floral traits in the field and under controlled conditions, and measured population genetic parameters using RADseq data. </p> <p><strong>Key results:</strong> Our results reveal a bimodal transition to the selfing syndrome from the west to the east of the range of <em>O. primiveris</em>. This shift includes variation in the breeding system, mating system, a reduction in floral traits (flower diameter, herkogamy, and scent production), a shift to greater autogamy, reduced genetic diversity, and increased inbreeding.</p> <p><strong>Conclusions:</strong> The observed variation highlights the importance of range-wide studies to understand breeding system variation and the evolution of the selfing syndrome within populations and species.</p>
Archived data for: Balancing selection, genetic drift, and human mediated-introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout
<p>The extraordinary polymorphism of Major Histocompatibility Complex (MHC) genes is considered a paradigm of pathogen-mediated balancing selection, although empirical evidence is still scarce. Furthermore, the relative contribution of balancing selection to shape MHC population structure and diversity, compared to that of neutral forces, as well as its interaction with other evolutionary processes such as hybridization, remains largely unclear. To investigate these issues, we analysed adaptive (MHC-DAB gene) and neutral (11 microsatellite loci) variation in 156 brown trout (<i>Salmo trutta </i>complex) from six wild populations in central Italy exposed to introgression from domestic hatchery lineages (assessed with the LDH gene). MHC diversity and structuring correlated with those at microsatellites, indicating the substantial role of neutral forces. However, individuals carrying locally rare MHC alleles/supertypes (regardless of the zygosity status and degree of sequence dissimilarity of MHC) were in better body condition (a proxy of individual fitness/parasite load), hence supporting balancing selection under rare allele advantage, but not heterozygote advantage or divergent allele advantage. The association between specific MHC supertypes and body condition confirmed in part this finding. Across populations, MHC allelic richness increased with increasing admixture between native and domestic lineages, indicating introgression as a source of MHC variation. Furthermore, introgression across populations appeared more pronounced for MHC than microsatellites, possibly because initially-rare MHC variants are expected to introgress more readily under rare allele advantage. Providing evidence for the complex interplay among neutral evolutionary forces, balancing selection and human-mediated introgression in shaping the pattern of MHC (functional) variation, our findings contribute to a deeper understanding of the evolution of MHC genes in wild populations exposed to anthropogenic disturbance.</p>
Reduced genetic diversity associated with the northern expansion of an amphibian species with high habitat-specialization, Ascaphus truei, resolved using two types of genetic markers
<p>Reconstruction of historical relationships between geographic regions within a species' range can indicate dispersal patterns and help predict future responses to shifts in climate. <em>Ascaphus truei </em>(coastal tailed frog) is an indicator species of the health of forests and perennial streams in the Coastal and Cascade Mountains of the Pacific Northwest of North America. We used two genetic techniques — microsatellite and genotype-by-sequencing (GBS) — to compare the within region genetic diversity of populations near the northern extent of the species' range (British Columbia, Canada) to two geographic regions in British Columbia and two in Washington, USA, moving towards the core of the range. Allelic richness and heterozygosity declined substantially as latitude increased. The northernmost region had the lowest mean expected heterozygosities for both techniques (microsatellite, M = 0.20, SE = 0.080; GBS, M = 0.025, SE = 0.0010) and the southernmost region had the highest (microsatellite, M = 0.88, SE = 0.054; GBS, M = 0.20, SE = 0.0029). The northernmost regions (NC and MC) clustered together in population structure models for both genetic techniques. Our discovery of reduced diversity may have important conservation and management implications for population connectivity and the response of <em>A. truei</em> to climate change.</p>
Genetic diversity and lifespan of transplanted colonies
<p>Selection may favour traits throughout an individuals lifetime or at a particular life stage. In many species of social insects, established colonies that are more genetically diverse outperform less diverse colonies with respect to a variety of traits that contribute to fitness, but whether selection favours high diversity in small colonies is unknown. We tested the hypothesis that selection favours genetically diverse colonies during the juvenile period using a multi-year field experiment with the harvester ant, <em>Pogonomyrmex occidentalis</em>. We used controlled matings to generate colonies that varied in genetic diversity and transplanted them into the field. We monitored their survival for seven (the 2015 cohort, <em>N</em> = 149) and six (the 2016 cohort, <em>N</em> = 157) years. Genetically more diverse colonies had greater survival, resulting in significant viability selection. However, in both cohorts survival was not influenced by genetic diversity until colonies were three years old. We suggest that changes in their internal organization enabled colonies to use the benefits of multiple genotypes, and discuss possible mechanisms that can generate this pattern.</p> <p>The accompanying data give the number of patrilines, the date of transplant and the number of years that the colony survived. </p>
Assessing population structure and genetic diversity in U.S. Suffolk sheep to define a framework for genomic selection
<p>Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the U.S. was evaluated in four ways: 1) using genetic relationships from pedigree data [(n=64,310 animals recorded in the U.S. National Sheep Improvement Program (NSIP)]; 2) using molecular data (n=304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n=109) and Irish (n=55) Suffolk sheep to those in the U.S. using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n=18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size (N<sub>e</sub>) ranged from 27.5 to 244.2 based on pedigree and was 79.5 based on molecular data. Expected (H<sub>E</sub>) and observed (H<sub>O</sub>) heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. From Principal Component Analysis, countries separated into distinct populations. Within the U.S. population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by F<sub>ST</sub>. Using these measures of genetic diversity, a framework for establishing a genomic reference population in U.S. Suffolk sheep engaged in NSIP was proposed.</p>
Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator
<p><span>Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔFST, respectively) and assess the effective population size (Ne-indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harbored more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne≤500) in 20 populations with five showing Ne<100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity.</span></p>
Supporting data and code for: Host plant and insecticides shape the evolution of genetic and clonal diversity in a major aphid crop pest
<p>This is the first release of the final data and code for the article accepted for publication in <em>Evolutionary Applications</em> journal. It contains the necessary scripts to produce most of the analyses and figures of the manuscript. All the necessary data can be found in the 'data' folder.</p>
Genetic diversity and differentiation of populations of Anthyllis vulneraria along elevational and latitudinal gradients
<p>The abundant centre model (ACM) predicts that the suitability of environmental conditions for a species decreases from the centre of its distribution towards its range periphery and consequently its populations will become scarcer, smaller and more isolated, resulting in lower genetic diversity and increased differentiation. However, little is known about whether genetic diversity shows similar patterns along elevational and latitudinal gradients with similar changes in important environmental conditions. Using microsatellite markers we studied the genetic diversity and structure of 20 populations each of <em>Anthyllis vulneraria </em>along elevational gradients in the Alps from the valleys to the elevational limit (2500 m), and along a latitudinal gradient (2500 km) from Central Europe to the range margin in northern Scandinavia. Both types of gradients corresponded to a 11.5 °C difference in mean annual temperature. Genetic diversity strongly declined and differentiation increased with latitude in line with the predictions of the ACM. However, as population size did not decline with latitude and genetic diversity was not related to population size in <em>A. vulneraria</em>, this pattern is not likely to be due to less favourable conditions in the North, but due to serial founder effects during the post-glacial recolonization process. Genetic diversity was not related to elevation, but we found significant isolation by distance along both gradients, although the elevational gradient was shorter by orders of magnitude. Subarctic populations differed genetically from alpine populations indicating that the northern populations did not originate from high elevational Alpine ones. Our results support the notion that postglacial latitudinal colonization over large distances resulted in a larger loss of genetic diversity than elevational range shifts. The lack of genetic diversity in subarctic populations may threaten their long-term persistence in the face of climate change, whereas alpine populations could benefit from gene flow from low-elevation populations.</p>
The Atlas of mitochondrial genetic diversity for Western Palearctic butterflies
<p>Abstract: Motivation<br>Butterflies represent a model in biology and a flagship group for invertebrate conservation. We provide four new resources for the Western-Palearctic butterflies: 1) An updated checklist comprising 552 species; 2) a curated dataset of 32,129 mitochondrial COI sequences for 532 species, including a de novo reference library for the Maghreb (Morocco and northern Algeria and Tunisia) and Macaronesia (Azores, Madeira and Canary Islands); 3) seven indexes of intraspecific genetic variation (IGV): observed and expected number of haplotypes, haplotype and nucleotide diversity, two fixation indexes, and maximum p-distance; 4) species-level maps illustrating the distribution of COI variability and haplotype networks. The updated checklist will be fundamental for any application dealing with butterfly diversity in Western Palearctic. IGV indexes provide measures for genetic polymorphism and spatial structure and represent proxies for dispersal capacity. These resources will facilitate comparative studies of macrogenetics, will foster integrative taxonomy, and will aid conservation strategies.</p> <p>Main types of variables contained<br>A complete species checklist in table format, 32,129 mitochondrial DNA-barcodes provided with metadata (species membership, WGS84 coordinates, sequence length), and a book in PDF format including the IGV atlas and indexes.</p> <p>Spatial location and grain<br>The checklist encompasses Europe up to Urals in the east, north Macaronesia (Azores, Madeira and Canary Islands), as well as the Maghreb (Morocco and northern Algeria and Tunisia). DNA-barcodes have been retained in the geographic interval of -31.3–67.5 degrees of longitude and 27.5–71.2 degrees of latitude.</p> <p>Time period and grain<br>DNA-barcodes originate from studies published between 1998-2022 and from de novo sequencing of 2,608 specimens done between 2007-2022.</p> <p>Major taxa and level of measurement<br>Butterflies (Lepidoptera, Papilionoidea), analysed from individual to species level.</p> <p>Software format<br>Data and functions to manage the dataset are provided in the iodatabase R package (<a href="https://github.com/leondap/iodatabase" rel="noopener noreferrer">https://github.com/leondap/iodatabase</a>) and in Dryad</p>
Nuclear genetic diversity and structure of Anastrepha ludens wild populations evidenced by microsatellite markers
<p class="MsoNormal"><span>The Mexican fruit fly, <em>Anastrepha ludens </em>is an important pest that causes widespread damage to a number of fruit crops in Mexico. The Sterile Insect Technique (SIT) is commonly used for its control. However, the existence of natural barriers can give rise to a population structure in neutral loci and possibly behavioral or adaptive traits that interfere with SIT. For this reason, it is important to understand the genetic diversity and structure of<em> A. ludens </em>populations and to better understand the evolutionary ecology and population processes in view of possible expansions and possible host shifts due to climate change. We genotyped nine nuclear DNA (nDNA) microsatellite loci among fruit fly populations collected from five biogeographic areas within Mexico, Mexican Plateau, the Northeastern Coastal Plain, the Pacific Coast, the Gulf Coast of Mexico, the Soconusco and a laboratory strain. The nuclear genetic diversity was moderate (from <em>H</em>e = 0.34 to <em>H</em>e = 0.39) within the wild mexfly population. We found that populations were clustered in three genetic groups (<em>K</em>=3). The diversity and genetic structure of <em>A. ludens</em> are produced by environmental and geological conditions as well as local conditions like anthropogenic perturbation which would produce population expansion and the existence of possible predators that would affect the population density. Gene flow showed recent migration among populations. The laboratory strain showed less diversity than the wild samples. Large values of current and ancestral population size suggest high resistance to climatic changes, probably due to biological attributes, such as its polyphagous, multivoltine and high dispersal characteristics. In particular ecosystem fragmentation and perturbation as well as the existence of new plant hosts all of which would probably increase the abundance of flies.</span></p>
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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.