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1,467 results for “Genetic structure”
Data from: Genetic structure of the Painted Bunting and its implications for conservation of migratory populations
The Painted Bunting Passerina ciris is a Neotropical songbird which breeds primarily in the United States during the summer and migrates to Mexico, Central America, southern Florida, and the Caribbean over the winter. Male Painted Buntings are brightly coloured, which makes them highly sought after as pets, particularly in Mexico, Central America and Europe. We used short sequence repeats (microsatellite DNA) to investigate the population genetic structure of the Painted Bunting and its implications in conservation management of migratory populations. We found a detectable level of population differentiation as revealed by pairwise FST and RST comparisons and Bayesian clustering analyses, with strong support for differentiation between eastern and western Painted Buntings (e.g. Oklahoma and Georgia FST = 0.1; P = 0.005; RST = 0.18; P = 0.04) in accordance with previous mitochondrial DNA analysis. We recovered additional support for two sub‐groups within the western clade. While linking migrant songbirds captured outside of the United States to their breeding populations remains a challenge, we show that natural levels of population genetic differentiation can be detected via microsatellite DNA markers and exploited in migratory connectivity studies. We also demonstrate the potential utility of our low‐cost markers for population identification of birds recovered from the pet trade by screening a small subset of samples (n = 5) collected as part of wildlife tracking. We discuss the implications of our results for future efforts to understand patterns of population decline in Painted Buntings more generally, as well as how we might expand this methodology to combat illegal pet‐trade activity in this and other songbird species.
Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species
<p>Most Central African rainforest canopies consist of light-demanding tree species that hold high commercial value but also suffer locally from regeneration deficits, raising concerns about the sustainability of logging. Regeneration is influenced by factors such as past perturbations (including human activity), mating systems, and seed/pollen dispersal processes that impact demographic, spatial, and genetic structures within populations. To gain a better understanding of these interactions, we studied the spatial distribution and trunk diameter structure of <em><span>Cylicodiscus gabunensis</span></em> (Fabaceae) - a wind-dispersed, insect-pollinated, timber species - in three plots ranging from 400 to 839<span> </span>ha situated in various environmental contexts (e.g. forest types and elephant densities) across Central Africa. We also genotyped adults and juveniles using microsatellite markers to analyze the spatial genetic structure of each population and infer the selfing rate, seed and pollen dispersal capacities and selection gradients using the <span>'</span>neighborhood model<span>'</span>. The selfing rate was low (3 <span>–</span> 4<span> </span>%), and seed dispersal distances (<em><span>ds</span></em><span> </span>=<span> </span>184<span> </span>m) were much shorter than pollen dispersal distances (<em><span>dp</span></em><span> </span>><span> </span>2<span> </span>km). The three populations displayed contrasted spatial, demographic and genetic structures. One population showed no spatial aggregation or genetic structure, and a multimodal diameter structure indicating pulses of regeneration events. Two populations showed strong spatial aggregation and genetic structures. One exhibited a unimodal diameter structure indicating one ancient pulse of regeneration, while the other displayed a 'reverse J-shaped' diameter structure, typical of ongoing regeneration. In the latter, reproductive success appeared leptokurtic, three mother trees accounting for over 90<span> </span>% of the regeneration and no tree below the minimum cutting diameter implemented by logging companies had offspring. The idiosyncratic nature of population characteristics observed in <em><span>C. gabunensis</span></em> suggests that, for sustainable management, a nuanced approach is needed. This involves protecting productive seed trees in areas where natural regeneration is occurring and actively supporting regeneration in areas exhibiting deficits, especially in contexts with low elephant densities.</p>
Data from: Relict stands of Central European oaks: unravelling autochthony and genetic structure based on a multi-population study
<p><span>Central European white oaks expanded rapidly after the last glacial period and reached their current distribution range during the early Holocene. They have been an important resource of timber, fuelwood and animal feed for humans, who actively promoted their presence in forests and other landscape types at least since the early historical times. Besides stands with intensive management, putatively relict populations of three native oak species can be found on unproductive sites with restricted accessibility. Here, we apply chloroplast and nuclear microsatellite markers in order to address the autochthony of relict and managed stands and compare the spatial distribution of genetic variation between them. Based on data from more than 150 populations, we demonstrate that oak autochthony was preserved throughout historical times which is likely the result of traditional silvicultural treatment. This is supported by the fact that the spatial pattern of chloroplast haplotype distribution still reflects the post-glacial recolonization in both relict and old managed stands. We observed significant admixture of haplotypes only in stands established after the Second World War, which is attributable to the transfer of reproductive material used for afforestation. In terms of nuclear genetic variation, we observed marked differences among species. <em>Quercus</em> <em>pubescens</em> exhibited a pronounced genetic structure. Genetic drift and limited gene flow among its small and isolated populations in our study area might have contributed to this pattern. Varying extent of genetic introgression with other sympatric oak species could offer an additional explanation. On the contrary, the gene pools of <em>Q. petraea </em>and<em> Q. robur</em> are highly homogenous, displaying only weak isolation-by-distance. We found no significant differences of genetic diversity and differentiation between relict and managed stands. This suggests that seed transfer mostly occurred within our study area, even in those stands established in post-war times, verifying previous findings that point out limited human interference. We recommend consideration of population genetic structure for gene conservation, with a finer resolution of gene conservation units needed for <em>Q. pubescens </em>due to its spatial genetic structure. Both relict and old managed stands, species-pure or mixed, are suitable for conservation, as they host autochthonous gene pools. Coppice-with-standard management could contribute to preservation of autochthony. In the face of climate change, it is also important to maintain the evolutionary potential of the stands, by facilitating generative reproduction and allowing for hybridization in mixed stands.</span></p>
Data from: Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants
<p><span><strong>Premise</strong>:</span><span> Density-dependent pollinator visitation can lead to density-dependent mating patterns and within-population genetic structure. In Gymnadenia conopsea, individuals in low-density patches receive more self-pollen than individuals in high-density patches, suggesting higher relatedness at low density. Ongoing fragmentation is also expected to cause more local matings, potentially leading to biparental inbreeding depression.</span></p> <p><span><strong>Methods</strong>: </span><span>To evaluate whether relatedness decreases with local density, we analysed 1315 SNP loci in 113 individuals within two large populations. We quantified within-population genetic structure in one of the populations, recorded potential habitat barriers, and visualized gene flow using estimated effective migration surfaces (EEMS). We further estimated the magnitude of biparental inbreeding depression that would result from matings restricted to within 5 m.</span></p> <p><span><strong>Results</strong>: </span><span>There was no significant relationship between local density and relatedness in any population. We detected significant fine-scale genetic structure consistent with isolation-by-distance, with positive kinship coefficients at distances below 10 m. Kinship coefficients were low, and predicted biparental inbreeding depression resulting from matings within the closest 5 m was a modest 1–3%.</span> <span>EEMS suggested that rocks and bushes may act as barriers to gene flow within a population.</span></p> <p><span><strong>Conclusions</strong>: </span><span>The results suggest that increased self-pollen deposition in sparse patches does not necessarily cause higher selfing rates, or that inbreeding depression results in low establishment success of inbred individuals. The modest relatedness suggests that biparental inbreeding depression is unlikely to be an immediate problem following fragmentation of large populations. The results further indicate that habitat structure may contribute to governing fine-scale genetic structure in <em>G. conopsea</em>.</span></p>
Patterns in the genetic structure of 49 lowland rain forest tree species co-distributed on opposite sides of the Northern Andes
<p>The Andes are a major dispersal barrier for lowland rain forest plants and animals, yet hundreds of lowland tree species are distributed on both sides of the Northern Andes, raising questions about how the Andes influenced their biogeographic histories and population genetic structure. To explore these questions, we generated standardized datasets of thousands of SNPs from paired populations of 49 tree species co-distributed in rain forest tree communities located in Panama and Amazonian Ecuador and calculated genetic diversity (<em>π</em>) and absolute genetic divergence (<em>d</em><sub>XY</sub>) within and between populations, respectively. We predicted (1) higher genetic diversity in the ancestral source region (east or west of the Andes) for each taxon, and (2) correlation of genetic statistics with species attributes, including elevational range and life-history strategy. We found that genetic diversity was higher in putative ancestral source regions, possibly reflecting founder events during colonization. We found little support for a relationship between genetic divergence and species attributes except that species with higher elevational range limits exhibited higher <em>d</em><sub>XY</sub>, implying older divergence times. One possible explanation for this pattern is that dispersal through mountain passes declined in importance relative to dispersal via alternative lowland routes as the Andes experienced uplift. We found no difference in mean genetic diversity between populations in Central America and the Amazon. Overall, our results suggest that dispersal across the Andes has left enduring signatures in the genetic structure of widespread rain forest trees. We outline additional hypotheses to be tested with species-specific case studies.</p>
Shared and distinct patterns of genetic structure in two sympatric large decapods
<p><em>Aim: </em>Comparing genetic structure in species with shared spatial ranges and ecological niches can help identify how dissimilar aspects of biology can shape differences in population connectivity. Similarly, where species are widely distributed across heterogeneous environments and major topographic barriers, knowledge of the structuring of populations can help reveal the impacts of factors that limit dispersal and/or drive divergence, aiding conservation management.</p> <p><em>Location: </em>European seas of the northeast Atlantic and Mediterranean.</p> <p><em>Taxa:</em> European clawed lobster (<em>Homarus gammarus</em>) and European crawfish (<em>Palinurus elephas</em>), two sympatric, heavily-fished decapods with extensive dispersal potential.</p> <p><em>Methods: </em>By RAD-sequencing 214 <em>H. gammarus </em>from 32 locations, and 349 <em>P. elephas </em>from 15 locations, we isolated 6,340 and 7,681 SNP loci, respectively. Using these data to characterise contemporary population structuring, we investigate potential spatial and environmental drivers of genomic heterogeneity.</p> <p><em>Results: </em>We found higher levels of differentiation among clawed lobsters than crawfish, both globally and within basins, and demonstrate where known hydrographic and topographic barriers generate shared patterns of divergence, such as a genetic break between the Atlantic and Mediterranean basins. Genetic structure not common to both species is principally apparent in the Atlantic portions of their range, where clawed lobster exhibits a genetic cline and increased differentiation towards range margins, while crawfish appear effectively panmictic throughout this region.</p> <p><em>Main Conclusions: </em>We attribute the comparative lack of crawfish population structuring to their greater dispersal tendencies via a longer pelagic larval duration and sporadic adult movements. In contrast, genetic connectivity in clawed lobster is relatively restricted, with the correlation of site of origin and temperature to geographic heterogeneity at many divergent loci indicative of both neutral and adaptive processes. Our results help inform how contemporary management can account for likely demographic connectivity and marry the conservation of genomic variation with sustainable fisheries in these ecologically and economically important crustaceans.</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>
Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance
<p>Declines in bumblebee species ranges and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumblebee (<em>Bombus affinis</em>) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of <em>B. affinis</em> from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range wide male diploidy rate of ~15%. Our results suggest the Appalachians represents a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for <em>B. affinis</em> compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies suggesting B. affinis has undergone a recent decline and exhibits substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where <em>B. affinis</em> is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and can help set clear recovery targets for this and other threatened bumblebee species.</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>
Pinpointing genetic breaks in the southeastern Pacific: phylogeography and genetic structure of Pyura chilensis, a commercially important tunicate
<p><strong>Aim</strong>: Accurate characterization of evolutionary units (species or populations) underlies all ecological and evolutionary studies and is crucial to conservation planning. Seascapes have long been thought to be highly permeable to gene flow, yet over the last decade building evidence has shown that barriers to gene flow in marine environments are much more common than previously thought. Here, we precisely characterize barriers to gene flow in the tunicate Pyura chilensis across 26° of latitude in the southeastern Pacific, assess the magnitude of said barriers, and explore their congruence with current biogeographic patterns of this region.</p> <p><strong>Location</strong>: The southeastern Pacific (SEP), from Ilo, Perú (17ºS) to Chiloe, Chile (43ºS).</p> <p><strong>Taxon: </strong><em>Pyura chilensis</em></p> <p><strong>Methods</strong>: We used a combination of highly polymorphic microsatellite markers and a 540 bp fragment of the Cytochrome Oxidase subunit I (COI) to compare individuals sampled at 26 localities spanning approximately 2500 km of the SEP. Genetic diversity was analyzed using Bayesian clustering, haplotype networks, Isolation by Distance, and cline models. Coalescent simulators were used to estimate migration rates.</p> <p><strong>Results</strong>: The results from both the microsatellite and COI markers indicate the presence of two genetic discontinuities: one at 34°S and one at 39°S which coincide with genetic breaks reported for other species. Interestingly, we were able to determine that genetic transitions occur abruptly and within short geographic distances (~ 30 km) compared with previous studies of this tunicate. Coalescent simulations indicate the 34ºS break is less permeable than the 39ºS break, and gene flow appears to be mostly unidirectional from north to south.</p> <p><strong>Main conclusions</strong>: Our results support other studies that show that seascapes are complex, and also highlight the importance of accurately sampling distribution ranges when making conclusions about gene flow. Overall, the two main biogeographic barriers to gene flow characterized in the southeastern Pacific are not homogenously permeable and can be narrow (< 30 km). These results are relevant for the management of fisheries in this region and specifically for this commercially important species.</p>
Even more oak species in Mexico? Genetic structure and morphological differentiation support the presence of at least two specific entities within Quercus laeta
<p>Differentiation among populations, sometimes despite ongoing gene exchange, is a key step in speciation. Therefore, comparison of intra- and interspecific differentiation patterns is of great significance to understanding speciation. The genus <em>Quercus </em>is an interesting system to test speciation models in the presence of gene flow, due to its weak interspecific reproductive barriers. The aim of the present study was to characterize the degree and pattern of morphological and genetic differentiation among different morphotypes in the white oak <em>Quercus laeta</em>, some corresponding to the previously described species <em>Q</em>. <em>centralis</em>, <em>Q</em>. <em>laeta</em>, <em>Q</em>. <em>prinopsis </em>and <em>Q</em>. <em>transmontana</em>, as well as geographically structured variation within <em>Q</em>. <em>transmontana </em>not previously described. Our goal was to evaluate if some of these can be considered distinct specific entities or are rather part of a continuum of variation. Nine microsatellite loci and two intergenic regions of chloroplast DNA were analyzed. Morphological differences were evaluated using geometric morphometrics. Chloroplast DNA showed low differentiation, suggesting introgression or sharing of ancestral haplotypes among the <em>Q</em>. <em>laeta </em>morphotypes. Nuclear microsatellites indicated differentiation into two distinct main genetic groups, which were congruent with morphological differentiation. In conclusion, nuclear markers and morphological variation suggest the existence of at least two different entities within <em>Q</em>. <em>laeta</em>.</p>
Loricarioid catfish evolved skin denticles that recapitulate teeth at the structural, developmental, and genetic levels (raw RNAseq reads)
<p>The first vertebrate mineralized skeleton was an external bony armor coated with dental structures. The subsequent emergence of a mineralized endoskeleton and of teeth are considered key innovations in the diversification of vertebrates. Although time clouds our understanding of the initial evolution of these mineralized structures, recent re-emergences may shed light on the underlying processes. Loricarioid catfishes are a lineage that, much like the ancestral vertebrates, bear denticle-clad bony armor from head to tail. Loricarioid denticles (LDs) and oral teeth are very similar in superstructure. We show here that other extra-oral dental structures are found as ancestral characters only in lineages that are distantly related to loricarioids such as sharks or coelacanth, indicating that LDs have independently re-emerged in loricarioid catfishes. We investigate whether the similarities between LDs and teeth extend to their developmental and genetic context, and how their development compares to that of other vertebrate integument structures. Our detailed study of the development of LDs, and gene expression analyses through in situ hybridization confirm that all 12 genes from the tooth-forming gene regulatory network (oGRN) are expressed in developing LDs in a similar way as they are expressed in developing teeth. We then compare the developmental, structural, and genetic aspects of LD and teeth with that of other integument appendages such as fish scales, shark dermal denticles, feathers and hairs. We find that LDs share all developmental cues with teeth and, to a lesser extent, with the other vertebrate integument structures. Taken together, our results indicate that denticles have re-emerged on the trunk of loricarioid catfishes through the ectopic co-option of the oGRN rather than the resurrection of an ancestral trunk-specific denticle genetic pathway.</p>
Dataset for: Rio de Janeiro and other paleodrainages evidenced by the genetic structure of an Atlantic Forest catfish
<p><strong>Aim</strong>: The disjunct distributions of freshwater organisms along coastal drainages are usually explained by paleodrainages formed during sea-level retreats that connected currently isolated basins, or by river capture from tectonic adjustments between adjoining watersheds. We evaluate the relative importance of these events on the genetic variation of freshwater fishes inhabiting the Serra do Mar in eastern Brazil, a region with steep mountains and pronounced bays.<br> Location: Coastal river drainages in southeastern Brazil.</p> <p><br> <strong>Taxon</strong>: Catfishes of the Trichomycterus alternatus group.</p> <p><br> <strong>Methods</strong>: We tested the effects of paleolandscape connections (GIS-reconstructed paleodrainages and putative river captures) on the genetic structure (mitochondrial and nuclear markers) of T. alternatus from 15 drainages using phylogenetic reconstructions, lineage delimitation methods and analyses of molecular variance.<br> Results: Trichomycterus alternatus is monophyletic and comprised of three main lineages: two restricted to the basin at its northernmost distribution and another broadly distributed to the south. In the latter, seven major cytb clades were geographically compatible with the eight paleodrainages, with three incongruences matching river captures previously described for the Guanabara Bay (GB). Shared haplotypes among isolated rivers flowing into GB provide the first molecular evidence of the 'Rio de Janeiro' paleoriver.</p> <p><br> <strong>Main conclusions</strong>: Dispersal via paleorivers is an important process, but it is not enough to recover the most recent dispersive events. Therefore, integrating both paleo-riverine configuration (GIS-based) and localized river captures (geological studies) is crucial to reveal the role of past geological and climatic events on the distribution of freshwater organisms. Taken together, these two factors significantly explained a high portion T. alternatus genetic structure along coastal drainages, revealing a paleolandscape scenario that may have been used by other freshwater Atlantic Forest taxa.</p>
Ecological traits drive genetic structuring in two open-habitat birds from the morphologically cryptic genus Elaenia (Aves: Tyrannidae)
<p>Understanding the relative contributions of the many factors that shape population genetic structuring is a central theme in evolutionary and conservation biology. Historically, abiotic or extrinsic factors (such as geographic barriers or climatic shifts) have received greater attention than biotic or intrinsic factors (such as dispersal or migration). This focus stems in part from the logistical difficulties in taking a comparative phylogeographic approach that contrasts species that have experienced similar abiotic conditions during their evolution yet differ in the intrinsic attributes that might shape their genetic structure. To explore the effects of intratropical migration on the genetic structuring of Neotropical birds, we chose two congeneric species, the Lesser Elaenia (<em>Elaenia chiriquensis</em>) and the Plain-crested Elaenia (<em>E. cristata</em>), that are largely sympatric, and which have similar plumage, habitat preferences, and breeding phenology. Despite these many commonalities, they differ in migratory behavior: <em>E. chiriquensis</em> is an intratropical migratory species while <em>E. cristata</em> is sedentary. We used a reduced representation genomic approach to test whether migratory behavior is associated with increased gene flow and therefore lower genetic population structure. As predicted, we found notably stronger genetic structuring in the sedentary species than in the migratory ones. <em>E. cristata</em> comprises genetic clusters with geographic correspondence throughout its distribution, while there are no geographic groups within Brazil for <em>E. chiriquensis</em>. This comparison adds to the growing evidence about how intrinsic traits like migration can shape the genetic structuring of birds, and advances our understanding of the diversification patterns of the understudied, open habitat species from South America.</p>
Environmental differences explain subtle yet detectable genetic structure in a widespread pollinator
<p><strong>Background</strong><br>The environment is a strong driver of genetic structure in many natural populations, yet often neglected in population genetic studies. This may be a particular problem in vagile species, where subtle structure cannot be explained by limitations to dispersal. Consequently, these species might falsely be considered quasi-panmictic and hence potentially mismanaged. A species this might apply to, is the buff-tailed bumble bee (<em>Bombus terrestris</em>), an economically important and widespread pollinator, which is considered to be quasi-panmictic at mainland continental scales. Here we aimed to (i) quantify genetic structure in 21+ populations of the buff-tailed bumble bee, sampled throughout two Eastern European countries, and (ii) analyse the degree to which structure is explained by environmental differences, habitat permeability and geographic distance. Using 12 microsatellite loci, we characterised populations of this species with Fst analyses, complemented by discriminant analysis of principal components and Bayesian clustering approaches. We then applied generalized dissimilarity modelling to simultaneously assess the informativeness of geographic distance, habitat permeability and environmental differences among populations in explaining divergence.</p> <p><br><strong>Results</strong><br>Genetic structure of the buff-tailed bumble bee quantified by means of Fst was subtle and not detected by Bayesian clustering. Discriminant analysis of principal components suggested insignificant but still noticeable structure that slightly exceeded estimates obtained through Fst analyses. As expected, geographic distance and habitat permeability were not informative in explaining the spatial pattern of genetic divergence. Yet, environmental variables related to temperature, vegetation and topography were highly informative, explaining between 33 and 39% of the genetic variation observed.</p> <p><br><strong>Conclusions</strong><br>In contrast to previous studies reporting quasi-panmixia in continental populations of this species, we demonstrated the presence of subtle population structure related to environmental heterogeneity. Environmental data proved to be highly useful in unravelling the drivers of genetic structure in this vagile and opportunistic species. We highlight the potential of including these data to obtain a better understanding of population structure and the processes driving it in species considered to be quasi-panmictic.</p>
Genetic structure in the nonbreeding range of rufa Red Knots suggests distinct Arctic breeding populations
<p>An understanding of the migratory connectivity between breeding and nonbreeding areas is fundamental to the management of long-distance migrants under pressure from habitat change along their flyways. Here we describe evidence for genetic structure within the nonbreeding range of the endangered Arctic-Canadian rufa subspecies of Red Knots (Calidris canutus). Using blood and tissue samples from the major nonbreeding regions in Argentina (Tierra del Fuego and Río Negro), northern Brazil (Maranhão), and southeastern USA (Florida), we estimated genetic structure in 514 amplified fragment length polymorphism (AFLP) loci, applying cluster assignment analyses in DAPC, assignPOP, and STRUCTURE. Using a priori location information, individuals could be correctly re-assigned to their nonbreeding regions, which validated that the assignment accuracy of the data was sufficient. Without using a priori location information, we detected 3–5 genotype clusters, and posterior assignment probabilities of samples to these genotype clusters varied among the three regions. Lastly a chi-square test confirmed that allele frequencies varied significantly among nonbreeding regions, rejecting the hypothesis that samples were drawn from a single gene pool. Our findings hint at undescribed structure within the Red Knot rufa breeding range in the Canadian Arctic and indicate that each rufa nonbreeding area in this study hosts a different subsample of these breeding populations. The observation that nonbreeding sites of rufa Red Knots contain different genetic pools argues for separate conservation management of these sites.</p>
Gene flow between wild trees and cultivated varieties shapes the genetic structure of sweet chestnut (Castanea sativa Mill.) populations
<p>The sweet chestnut orchards (<em>Castanea sativa</em> Mill.) are traditionally planted in the northern Adriatic region. This study investigates their population structure, as well as the genetic background of three toponymous clonal varieties. Six genomic simple sequence repeat (gSSR) and nine EST-derived SSR (EST-SSR) loci were utilized in this study. We have identified five closely related clones, which represent a singular, polyclonal marron variety, found in all three cultivation areas, acompanied by many hybrids, resulting from the breeding between cultivated and wild chestnuts. </p>
Lack of spatial and temporal genetic structure of Japanese eel (Anguilla japonica) populations
Japanese eel (Anguilla japonica) is an important food source in East Asia whose population has dramatically declined since the 1970s. Despite past analysis with DNA sequencing, microsatellite and isozyme methods, management decisions remain hampered by contradictory findings. For example, it remains unresolved whether Japanese eels are a single panmictic population or whether they harbor significant substructure. Accurate assessment of population genetic substructure, both spatial and temporal, is essential for determining the relevant number of distinct management units appropriate for this species. In the present study, we assayed genetic variation genome-wide using Restriction Site Associated DNA Sequencing (RAD-seq) technology to analyze the population genetic structure of Japanese eels. For analysis of temporal isolation, five "cohort" samples were collected yearly from 2005 to 2009 in the Yangtze River Estuary. For analysis of spatial structure, five "arrival wave" samples were collected in China in 2009, and two arrival wave samples were collected in Japan in 2001. In each cohort of each arrival wave, five individuals were collected for a total of 55 eels sampled. In total, 214,210 loci were identified from these individuals, 106,652 of which satisfied quality checks and were retained for further analysis. There was relatively little population differentiation between arrival waves and cohorts collected either at different locations during the same year (Fst = 0.077) or at the same location collected over subsequent years (Fst = 0.082), and locations displayed no consistent isolation-by-distance.
Landscape connectivity and genetic structure in a mainstem and a tributary stonefly (Plecoptera) species using a novel reference genome
<p>Abstract Understanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modelling to investigate how climatic and habitat variables relate to patterns of genetic variation in two stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO &gt; 95% using "insecta_ob9" reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis. but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.</p>
ScienceDex guides
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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.