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343 results for “genomic divergence”
Assessing changes in genomic divergence following a century of human mediated secondary contact among wild and captive-bred ducks
<p>Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used world-wide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary time scales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (<i>Anas platyrhynchos</i>) throughout North America, and two domestic mallard-types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (<i>A. rubripes</i>) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.</p>
Data from: Genotyping by sequencing and genome–environment associations in wild common bean predict widespread divergent adaptation to drought
Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using Genotyping by Sequencing (GBS) to discover single-nucleotide-polymorphisms (SNPs). The wild beans represented Mesoamerica, Guatemala, Colombia, Ecuador/Northern Peru and Andean groupings. We found high polymorphism with a total of 22,845 SNPs across the 86 accessions loci that confirmed genetic relationships for the groups. As a second objective, we quantified allelic associations with a bioclimatic-based drought index using 10 different statistical models that accounted for population structure. Based on the optimum model, 115 SNPs in 90 regions, widespread in all 11 common bean chromosomes, were associated with the bioclimatic-based drought index. A gene coding for an Ankyrin repeat-containing protein and a phototropic-responsive NPH3 gene were identified as potential candidates. Genomic windows of 1Mb containing associated SNPs had more positive Tajima's D scores than windows without associated markers. This indicates that adaptation to drought, as estimated by bioclimatic variables, has been under natural divergent selection, suggesting that drought tolerance may be favorable under dry conditions but harmful in humid conditions. Our work exemplifies that genomic signatures of adaptation are useful for germplasm characterization, potentially enhancing future marker-assisted selection and crop improvement.
Divergent selection in low recombination regions shapes the genomic islands in two incipient shorebird species
<p>Divergent selection in the face of gene <span>flow is usually associated with</span> a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic island. This conundrum can be solved through examination of the genomic landscapes of species pairs that are still in the early stages of evolution. In this study, population genomics analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (<em>Charadrius alexandrinus</em>) and white-faced plover (<em>C. dealbatus</em>). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on Taiwan Island<span>.</span> <span>Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and recurrent gene flow is still ongoing in mainland coastal populations</span>. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which<span> contain several genes potentially associated with disease resistance, coloration, and regulation of plumage moulting, thus may be connected to the phenotypic and ecological divergence of</span> the two nascent species<span>. Overall, our findings suggest that divergent selection in low recombination regions may be the main force in shaping the genomic islands in two incipient shorebird species.</span></p>
Diverging repeatomes in holoparasitic Hydnoraceae uncover a playground of genome evolution
<p>The present repository provides a FASTA resource with reference sequences of major repetitive DNA sequences from the genomes of <em>Hydnora </em>and <em>Prosopanche </em>species. This sequence list is complemented by a GFF file with detailed annotations for the included retrotransposons. <br><br><br>The nuclear genomes of parasitic plants have undergone unique evolutionary trajectories to adapt to the heterotrophic lifestyle. These adaptations often involve large genomic alterations, potentially driven by repetitive elements. Despite the well-recognized role of repetitive DNAs as evolutionary forces in shaping plant genomes, their role in genome evolution of parasitic plants remains largely unexplored. To address this knowledge gap, we conducted the first analysis of repetitive DNAs in eleven genomes of Hydnoraceae, a family of mostly non-crop parasitizing holoparasites.</p> <p>The observed repeat abundance profiles and presence-absence patterns align with the phylogenetic relationships, geographical distribution, and host shifts, suggesting a key role of repetitive DNAs in shaping Hydnoraceae genomes. The repetitive fraction of the two Hydnoraceae genera, <em>Hydnora</em> and <em>Prosopanche</em>, are fundamentally different: Whereas the eight analyzed <em>Hydnora</em> genomes are largely populated by long terminal repeat retrotransposons, particularly of the Tekay and Ogre type, the three <em>Prosopanche </em>repeatomes differ vastly in individual abundances, including <em>P. bonacinae</em> with massive amplifications of a single DNA transposon and <em>P. panguanensis</em> with over 15% 5S rDNA (as opposed to some Hydnoraceae with <0.1% 5S rDNA). Both extremely low and very high abundance of 5S rDNA challenges our current understanding for chromosome stabilization and rRNA transcription.</p> <p>These genome dynamics suggest rapidly evolving repeat profiles, potentially being enhanced by the adaptation to the parasitic lifestyle. The heterogeneous abundance of rDNAs and DNA transposons in Hydnoraceae genomes needs further attention, with regard to repeat-driven evolution. This study lays the groundwork for future genomic explorations on Hydnoraceae, as well as heterotrophic plants and their nuclear genome composition in general.</p>
Genomic associations with poxvirus across divergent island populations in Berthelot's pipit
<p><span>Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot's pipit (<em>Anthus berthelotii</em>) experiences extensive and consistent spatial heterogeneity in </span><span>avian pox infection pressure across its range of island populations</span><span>, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes </span><span>involved in cellular </span><span>stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses indicates that pathogen-mediated selection may play a role in shaping genomic variation among relatively recently colonised island bird populations and highlights the utility of genotype-environment associations for identifying candidate genes potentially involved in host-pathogen interactions.</span></p>
Genomic and phenotypic divergence‐with‐gene‐flow across an ecological and elevational gradient in a neotropical bird
<p>Aim: Along with environmental gradients, some species show significant differences in morphological, ecological-related traits. Those differences are commonly related to past events of allopatry but, alternatively, could be caused by natural selection in the presence of gene flow. We aimed to explore the prevalence of the divergence-with-gene-flow model across the Chaco-Andes dry forest belt, testing competing models of evolution in a Neotropical bird.</p> <p>Location: Central Andes Mountain range and Chaco region of Argentina and Bolivia. </p> <p>Taxon: Phytotoma rutila (Aves, Cotingidae).</p> <p>Methods: We studied ddRADseq loci (4,893 SNPs) of 21 tissue samples and body size variation of 146 specimens. We evaluated population genetic structure and tested the effects of altitude and distance on genomic divergence. To evaluate allopatry and divergence-with-gene-flow, we compared the divergence on phenotypic traits (bill, tarsus, and wing measurements) versus neutral genomic variation, conducted coalescent analyses to estimate gene flow and divergence time among populations, and calculated relative (FST) versus absolute (DXY) genomic divergence.</p> <p>Results: a) there is a genomic and phenotypic differentiation in P. rutila matched the highland-lowland axis, where the altitude variation explains genomic variation; b) A larger phenotypic than neutral genomic variation was found. c) there is an asymmetric gene flow between populations; d) a pattern of relative and absolute genomic differentiation compatible with divergence-with-gene-flow.</p> <p>Main conclusions: The mechanism behind the morphological and genomic diversification along the Chaco-Andes dry forest belt in P. rutila is divergence‐with‐gene‐flow. Far more complex than we traditionally thought, diversification in South America implicates gene flow between populations and also natural selection along with the environmental gradients, as well as vicariance, contrasting with the idea of tropical speciation primarily based on allopatric models.</p> <p> </p>
Data from: Population genomics reveal deep divergence and strong geographical structuring in the Hengduan Mountains
<p>We used restriction site-associated DNA sequencing to generate 1,907 single nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the <em>Gentiana hexaphylla</em> complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing the diversification of <em>G</em>. <em>hexaphylla</em> in the HM. Here, the SNP data and plastid sequence alignments are provided.</p>
Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex
<p>We investigated genomic divergence, interspecific and intraspecific diversity and population structure, local directional selection, and complex demographic history in a popular freshwater species complex in the Central Interior Highlands, North America. Specifically, we assessed differentiation between the Neosho Bass (<em>Micropterus velox</em>) and Smallmouth Bass (<em>M. dolomieu</em>) where their ranges are parapatric in this ecoregion. We scanned the genome for signatures of local direction and mapped divergence at selected SNPs at the population level. Additionally, we identified stream populations with extensive admixture, and we used a model-testing framework to investigate complex demographic histories between the two species.</p> <p>Raw ddRADseq .fastq sequence files, along with intermediate processing files, finalized VCF files, a data summary report, and other data information, are given in the "smb_ddRAD_rawdata.tar file. Metadata, including sample_id, species designation, and stream population, are given in the "metadata.xlsx" file.</p>
High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan
<p>Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (<em>Coregonus clupeaformis</em>) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management. </p>
Data from: The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system
<p>A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defense, are excellent models to understand the link between vivid color pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which species share a conspicuous phenotype can provide an even better model for understanding the mechanisms of color production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which mimicry is produced in poison frogs. We assembled a 6.02 Gbp genome with a contig N50 of 310 Kbp, a scaffold N50 of 390 Kbp, and 85% of expected tetrapod genes. We leveraged this genome to conduct gene expression analyses throughout development of four color morphs of <em>R. imitator </em>and two color morphs from both <em>R. fantastica </em>and <em>R. variabilis </em>which <em>R. imitator</em> mimics. We identified a large number of pigmentation and patterning genes differentially expressed throughout development, many of them related to melanophores/melanin, iridophore development, and guanine synthesis. We also identify the pteridine synthesis pathway (including genes such as <em>qdpr </em>and <em>xdh</em>) as a key driver of the variation in color between morphs of these species, and identify several plausible candidates for coloration in vertebrates (e.g., <em>cd36, ep-cadherin, perlwapin</em>). Finally, we hypothesize that keratin genes (e.g., <em>krt8</em>) are important for producing different structural colors within these frogs.</p>
Genomic signatures of rapid adaptive divergence in a tropical montane species
<p>This dataset contains data from a study described in the paper: Ericson, P.G.P., Irestedt, M., She, H., and Qu, Y. (2021) "Genomic signatures of rapid adaptive divergence in a tropical montane species". <em>Biology Letters</em> (in print).</p> <p>The study investigates allopatric divergence and selection in Archbold's Bowerbird (<i>Amblyornis papuensis</i>), an iconic bird living in a tropical mountain region in New Guinea, using a novel chromosome-level genome and population genomic comparisons.</p> <p>Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11,800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is likely associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between eastern and western Central Range likely drive adaptive divergence between them.</p>
Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a geographic survey of genomic variation across four sites where apple and hawthorn flies co-occur from north to south in the Midwestern USA. The results demonstrated that the majority of the genome showing significant geographic and host-related variation can be accounted for by initial diapause intensity and eclosion time. Local genomic differences between sympatric apple and hawthorn flies were subsumed within broader geographic clines; allele frequency differences within the races across the Midwest were 2 to 3-fold greater than those between the races in sympatry. As a result, sympatric apple and hawthorn populations displayed more limited genomic clustering compared to geographic populations within the races. The findings suggest that with reduced gene flow and increased selection on diapause equivalent to that seen between geographic sites, the host races may be recognized as different genotypic entities in sympatry, and perhaps species, a hypothesis requiring future genomic analysis of related sibling species to R. pomonella to test. Our findings concerning the way selection and geography interplay could be of broad significance for many cases of earlier stages of divergence-with-gene flow, including (1) where only modest increases in geographic isolation and the strength of selection may greatly impact genetic coupling and (2) the dynamics of how spatial and temporal standing variation is extracted by selection to generate differences between new and discrete units of biodiversity.
Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of the erato-sara group of Heliconius butterflies
<p>Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ the multispecies coalescent (MSC) model with and without gene flow to infer the species phylogeny and cross-species introgression events using genomic data from six members of the <i>erato</i>-<i>sara</i> clade of <i>Heliconius</i> butterflies. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the <i>sara</i> clade and an ancestral population of <i><span>H. telesiphe</span></i>, a likely hybrid speciation origin for <i>H. hecalesia</i>, and gene flow between the sister species <i><span>H. erato</span></i><span> and <i>H. himera</i></span>. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the multispecies coalescent makes it possible to extract rich historical information of species divergence and gene flow from genomic data.</p>
Data from: Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas
<p>Understanding the role of adaptation in species responses to climate change is important for evaluating the evolutionary potential of populations and informing conservation efforts. Population genomics provides a useful approach for identifying putative signatures of selection and the underlying environmental factors or biological processes that may be involved. Here, we employed a population genomic approach within a space-for-time study design to investigate the genetic basis of local adaptation and reconstruct patterns of movement across rapidly changing environments in a thermally-sensitive mammal, the American pika (<i>Ochotona princeps</i>). Using genotypic data at 49,074 single nucleotide polymorphisms (SNPs), we analyzed patterns of genome-wide diversity, structure, and migration along three independent elevational transects located at the northern extent (Tweedsmuir South Provincial Park, British Columbia, Canada) and core (North Cascades National Park, Washington, USA) of the Cascades lineage. We identified 899 robust outlier SNPs within- and among-transects. Of those annotated to genes with known function, many were linked with cellular processes related to climate stress including ATP-binding, ATP citrate synthase activity, ATPase activity, hormone activity, metal ion-binding, and protein-binding. Moreover, we detected evidence for contrasting patterns of directional migration along transects across geographic regions that suggest an increased propensity for American pikas to disperse among lower elevation populations at higher latitudes where environments are generally cooler. Ultimately, our data indicate that fine-scale demographic patterns and adaptive processes may vary among populations of American pikas, providing an important context for evaluating biotic responses to climate change in this species and other alpine-adapted mammals.</p>
Genome sequence and silkomics of the spindle ermine moth, Yponomeuta cagnagella, representing the early diverging lineage of the ditrysian Lepidoptera
<p>Many lepidopteran caterpillars produce silk, cocoons, feeding tubes, or nests for protection from predators and parasites. Yet, the number of lepidopteran species whose silk composition has been studied in detail is very small, because the genes encoding the major structural silk proteins tend to be large and repetitive, making their assembly and sequence analysis difficult. Here we have analyzed the silk of <em>Yponomeuta cagnagella</em>, which represents one of the early diverging lineages of the ditrysian Lepidoptera thus improving the coverage of the order. To obtain a comprehensive list of the <em>Y. cagnagella</em> silk genes, we sequenced, assembled, and annotated the draft genome using Oxford Nanopore and Illumina technologies. The 626 Mb assembly with N50 of 96.5 kb contained 96.9% insect orthologs recovered by BUSCO and 30,003 predicted gene models. We then used a silk-gland transcriptome and a silk proteome to identify major silk components and verified the tissue specificity of the expression of individual genes. </p>
Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence
<p>The brown bear is a textbook example species of the effect of Quaternary glaciation cycles on the present-day geographical distribution of mtDNA haplotypes. We compiled and analysed a range-wide whole-genome dataset of 128 brown bear individuals in order to re-evaluate brown bear population structure and genetic diversity using nuclear markers from autosomes and sex chromosomes. The file 'PLOTCOMMANDS.txt' contains detailed instructions on how to recreate the figures presented within the paper. </p>
Genomic tools for comparative conservation genetics among three recently diverged stag beetles (Lucanus, Lucanidae)
<p>We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedented rate of decline. However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remain challenging. We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex. We found that the three sky-island taxa formed three independently evolving units without detectable post-divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid-Pleistocene, have experienced episodes of demographic decline in the past. More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesized to impact the recent demographic history (< 100 years) differently, we found a shared pattern of continuous decline in effective population size among the three geographical taxa. We argue that future empirical studies should include more taxa, in addition to the focal species, that may or may not be affected by the focal historical events to avoid making biased conservation plans.</p>
Genomes of the extinct Bachman's Warbler show high divergence and no evidence of admixture with other extant Vermivora Warblers
<p>Bachman's Warbler (<em>Vermivora</em> <em>bachmanii</em>) – last sighted in 1988 – is one of the only North American passerines to have gone extinct. Given extensive ongoing hybridization of its two extant congeners – the Blue-Winged Warbler (<em>V. cyanoptera</em>) and Golden-Winged Warbler (<em>V. chrysoptera</em>) – and shared patterns of plumage variation between Bachman's Warbler and hybrids between those extant species, it has been suggested that Bachman's Warbler might have also had a component of hybrid ancestry. Here, we use historic DNA (hDNA) and whole genomes of Bachman's Warblers collected at the turn of the 20th century to address this. We combine these data with the two extant <em>Vermivora</em> species to examine patterns of population differentiation, inbreeding, and gene flow. In contrast to the admixture hypothesis, the genomic evidence is consistent with <em>V. bachmanii</em> having been a highly divergent, reproductively isolated species, with no evidence of introgression. We show that these three species have similar levels of runs of homozygosity (ROH), consistent with effects of a small long-term effective population size or population bottlenecks, with one <em>V. bachmanii</em> outlier showing numerous long ROH and an FROH greater than 5%. We also found—using population branch statistic estimates—previously undocumented evidence of lineage-specific evolution in <em>V. chrysoptera</em> near a pigmentation gene candidate, CORIN, which is a known modifier of ASIP, which is in turn involved in melanic throat and mask coloration in this family of birds. Together, these genomic results also highlight how natural history collections are such invaluable repositories of information about extant and extinct species.</p>
Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge
<p>Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (<em>Euphorbia</em> <em>virgata</em>), across ~500km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.</p>
Genomic divergence and introgression between cryptic species of a widespread North American songbird
<p>Analysis of genomic variation among related populations can sometimes reveal distinct species that were previously undescribed due to similar morphological appearances, and close examination of such cases can provide much insight regarding speciation. Genomic data can also reveal the role of reticulated evolution in differentiation and speciation. White-breasted nuthatches (<em>Sitta carolinensis</em>) are widely distributed North American songbirds that are currently classified as a single species but have been suspected to represent a case of cryptic speciation. Previous genetic analyses suggested four divergent groups, but it was unclear whether these represented multiple reproductively isolated species. Using extensive genomic sampling of over 350 white-breasted nuthatches from across North America and a new chromosome-level reference genome, we asked if white-breasted nuthatches are comprised of multiple species and whether introgression has occurred between divergent populations. Genomic variation of over 300,000 loci revealed four highly differentiated populations (Pacific, n = 45; Eastern, n = 23; Rocky Mountains North, n = 138; and Rocky Mountains South, n = 150) with geographic ranges that are adjacent. We observed a moderate degree of admixture between Rocky Mountain populations but only a small number of hybrids between the Rockies and the Eastern population. The rarity of hybrids together with high levels of differentiation between populations is supportive of populations having some level of reproductive isolation. Between populations, we show evidence for introgression from a divergent ghost lineage of white-breasted nuthatches into the Rocky Mountains South population, which is otherwise closely related to Rocky Mountains North. We conclude that white-breasted nuthatches are best considered at least 3 species and that ghost lineage introgression has contributed to differentiation between the two Rocky Mountain populations. White-breasted nuthatches provide a dramatic case of morphological similarity despite high genomic differentiation, and the varying levels of reproductive isolation among the four groups provide an example of the speciation continuum. </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.