Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,100
datasets available to search
ShareScore release 0.9.0
Dataset results
3,100 results for “recent”
Weather dataset (Typical Downscaled Year, Extreme Cold Year, Extreme Warm Year) for building energy simulations (.epw format) in recent past climate, Leuven City centre, Belgium
<p>Typical Downscaled Year (TDY), Extreme Cold Year and Extreme Warm Year based on the methodology of Nik (2016), is extracted for the location of city centre of Leuven (50°52'48"N, 4°42'0"E) from the EC-Earth driven convection-permitting climate model COSMO-CLM for the Belgian domain extended with land-surface scheme TERRA_URB(v2.0) making use of the SURY (Semi-empirical URban canopY) parameterization ( Wouters et al. 2016). The integrations are identical to the ones which are described in Vanden Broucke et al. (2019). The climate model has a spatial resolution of 2.8 km and an hourly temporal resolution and is available for the recent past (1976-2004) and future (2070-2098) as 30-year datasets. For this dataset, the TDY, ECY, and EWY are extracted for the recent past period. A bias correction is applied for the following variables: temperature (as described in Ramon et al. 2020), solar radiation and relative humidity as described in Ramon et al. (202X).</p>
Reproduction package for the paper "Completing the X-ray view of the recently discovered supernova remnant G54.41+0.03"
<p>This is a basic reproduction package for the paper "Completing the X-ray view of the recently discovered supernova remnant G54.41+0.03" by V. Domček et al. (2021). It provides raw, intermediate and final data sets, including figures and scripts to allow the reproduction of the work performed in this paper. It also lists software used and data archives containing the public observational data. </p> <p>An open access version of the paper can be found at https://arxiv.org/abs/</p>
Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics.
<p>The crustacean marine isopod species <i>Haploniscus bicuspis</i> (G.O. Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as to investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using Confocal Laser Scanning Microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably characterize different male developmental stages.</p>
Recent estimate of Asian elephants in Borneo reveals a smaller population
<p>Asian elephants occurring in northern Borneo form a geographically isolated and genetically distinct population. Of this, the subpopulation of Central Sabah holds the greatest opportunity for long-term survival, due to a relatively large population size and occurrence over a vast, contiguous, and protected habitat. We surveyed this subpopulation in 2015 using advanced methods to obtain a population size estimate. We used the distance-sampling framework and laid out transects following a stratified random design for counting elephant dung piles; measured dung decay following the 'retrospective' method; and used Bayesian analysis to estimate dung decay rate and dung pile density. Thus, we estimated a posterior mean dung decay rate of 212 days (95% BCI: 133–319), an overall elephant density of 0.07 per km<sup>2</sup> (95% BCI: 0.03–0.11), and a population size of 387 elephants (95% BCI: 169–621). These estimates were far lower than the population size of 1132 individuals and density of 1.18 per km<sup>2 </sup>estimated in 2008. It is unlikely that there has been a steep population decline, as there were no drastic land-use changes between 2008 and 2015, nor were there other identifiable causes for a population decline. Therefore, it appears that the methodological and analytical flaws in the previous estimate are the most plausible reason for this observed difference. Given that the new estimate suggests a much smaller population, it is prudent and precautionary to use the new estimate as the basis for all policy decisions and conservation actions for elephants in Sabah.</p>
Evaluating refugia in recent human evolution in Africa: Supplementary information
<p><em>Homo sapiens</em> have adapted to an incredible diversity of habitats around the globe. This capacity to adapt to different landscapes is clearly expressed within Africa, with Late Pleistocene <em>Homo sapiens</em> populations occupying savannahs, woodlands, coastlines and mountainous terrain. As the only area of the world where <em>Homo sapiens</em> have clearly persisted through multiple glacial-interglacial cycles, Africa is the only continent where classic refugia models can be formulated and tested to examine and describe changing patterns of past distributions and human phylogeographies. The potential role of refugia has frequently been acknowledged in the Late Pleistocene palaeoanthropological literature, yet explicit identification of potential refugia has been limited by the patchy nature of palaeoenvironmental and archaeological records, and the low temporal resolution of climate or ecological models. Here, we apply potential climatic thresholds on human habitation, rooted in ethnographic studies, in combination with high resolution model datasets for precipitation and biome distributions to identify persistent refugia spanning the Late Pleistocene (130-10 thousand years ago). We present two alternate models suggesting that between 27-66% of Africa may have provided refugia to Late Pleistocene human populations, and examine variability in precipitation, biome, and ecotone distributions within these refugial zones.</p>
Figure 2. Three brooding Brettus cingulatus females. 1, Female guarding recently deposited eggs. 2 in Do female Brettus cingulatus (Araneae: Salticidae: Spartaeini) feed their young?
Figure 2. Three brooding Brettus cingulatus females. 1, Female guarding recently deposited eggs. 2, Female with first instar young, still with little pigmentation of the opisthosoma. Note that almost all covering silk, white flecks, and eggshell fragments were absent at this stage. 3, Later first instar young with full pigmentation of the prosoma and opisthosoma, as well as pigmentation of each femur I. The female (not shown) was still guarding the brood at this stage. Photographs by Arundathi Sambayya taken at Bhimanakone, Sangara taluk, Shimoga District, Karnataka, India.
Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus
<p>Rapid speciation is an important aspect of adaptive radiations, but can obfuscate phylogenetic relationships among taxa. For recent radiations, there are challenges to reconstructing the relationships among the species due to often shorter branch lengths. Resolution of these relationships is further confounded when studies only use a few genetic markers. Double digest restriction-site associated DNA sequencing (ddRADseq) is a method of next generation sequencing that identifies many single nucleotide polymorphisms (SNPs) throughout the genome. This increases statistical power to resolve close phylogenetic relationships like those found within an adaptive radiation. We used this approach to understand the evolutionary history of the rockfishes of the genus <em>Sebastes</em>, which experienced an adaptive radiation between 3 to 5 mya. Here, we reconstructed the phylogenetic relationships among six species of rockfish within the subgenus <em>Sebastosomus</em> using over 11,600 SNPs. This reconstruction includes the two recently diverged species, <em>Sebastes</em> mystinus and <em>S. diaconus</em>, that were first described genetically in 2008 using mtDNA control region sequence data and six microsatellite loci. We confirmed the relationship of these cryptic species as sister-taxa and found evidence that <em>S. melanops</em> and <em>S. flavidus</em> were also sister-taxa. The latter contradicts prior studies but is supported by our reconstruction using nuclear DNA and measures of genetic differentiation tests and a discriminant analysis of principal components. The relationships between the species of <em>Sebastosomus</em> are further supported by morphological, biological, and ecological justifications.</p>
A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird
<p>The dark-eyed junco (<i>Junco hyemalis</i>) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior and evolutionary biology for over a century. It is composed by at least six distinct, geographically structured forms of recent evolutionary origin presenting remarkable variation in phenotypic traits, migratory behavior and habitat. Here we report a high-quality genome assembly and annotation of the dark-eyed junco generated using a combination of shotgun libraries and proximity ligation Chicago<sup>TM</sup> and Dovetail HiC<sup>TM</sup> libraries. The final assembly is 1,031,523,571 bp long, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 71,3 Mb/5 scaffolds. We identified 19,026 functional genes combining gene prediction and similarity approaches, of which 15,967 were associated to GO terms. Genome assembly and annotated set of genes yielded 95.4% and 96.2% completeness scores, respectively, when compared with the BUSCO avian dataset. This new assembly for <i>J. hyemalis </i>provides a valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.</p>
Fig. 1. Spanish slug from Kyiv, August 2017 in Fast Recent Expansion Of The Spanish Slug (Gastropoda, Stylommatophora, Arionidae) Across Ukraine
Fig. 1. Spanish slug from Kyiv, August 2017 (photo I. Balashov).
Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae:Coregonus spp.)
<p>Groups of sympatric taxa with low inter-specific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes (<em>Coregonus</em> spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the <em>Coregonus artedi</em> complex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the latter was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified as <em>C. hoyi</em> and <em>C. zenithicus</em>, which could be evidence of incomplete lineage sorting or recent hybridization between the two groups. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent datasets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.</p>
Mesocosm experiments reveal the loss of migratory tendencies in a recently isolated population of three-spined sticklebacks
<p>In the 1970s, water management in the Netherlands resulted in numerous isolated populations of three-spined sticklebacks, which can no longer migrate from freshwater to the sea. We tested whether ~50 years of isolation resulted in reduced migratory tendencies in these resident sticklebacks. Lab-based individual testing showed behavioural divergence between residents and migrants, but also produced counter-intuitive results, especially with regards to movement tendencies. To detect differences in migration tendencies, we set up a semi-natural mesocosm, consisting of connected ponds, where movements of numerous individuals could continually be tracked at larger spatial scales. We found that wild-caught residents and migrants exhibited no differences in movement tendencies within ponds, but residents moved significantly less between ponds than migrants. Between-pond movements were consistent and the observed differences were robust across contexts (changes in water flow and group size). Our study reveals that larger-scale movement tendencies can diverge over short time scales in response to human-induced isolation, and highlights the importance of observing behaviour in ecologically relevant setups that bridge the gap between lab and field studies.</p>
Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris Sea Urchins
<p>Changes in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life, but the evolutionary mechanisms that operate on interactions with these networks remain poorly understood. Closely related species with extreme phenotypic divergence provide a valuable window into the genetic and molecular basis for changes in dGRNs and their relationship to adaptive changes in organismal traits. Here we analyze genomes, epigenomes, and transcriptomes during early development in two sea urchin species in the genus <em>Heliocidaris </em>that exhibit highly divergent life histories and in an outgroup species. Signatures of positive selection and changes in chromatin status within putative gene regulatory elements are both enriched on the branch leading to the derived life history, and particularly so near core dGRN genes; in contrast, positive selection within protein-coding regions have at most a modest enrichment in branch and function. Single-cell transcriptomes reveal a dramatic delay in cell fate specification in the derived state, which also has far fewer open chromatin regions, especially near dGRN genes with conserved roles in cell fate specification. Experimentally perturbing the function of three key transcription factors reveals profound evolutionary changes in the earliest events that pattern the embryo, disrupting regulatory interactions previously conserved for ~225 million years. Together, these results demonstrate that natural selection can rapidly reshape developmental gene expression on a broad scale when selective regimes abruptly change and that even highly conserved dGRNs and patterning mechanisms in the early embryo remain evolvable under appropriate ecological circumstances.</p>
Description of two new species and phylogenetic placement of recent taxonomic novelties in the Chilean endemic genus Miersia (Gilliesieae, Allioideae, Amaryllidaceae)
<p>Abstract: Two new species in the Chilean endemic genus <em>Miersia</em> (Gilliesieae, Allioideae, Amaryllidaceae) are introduced: <em>M. stellata</em> and <em>M. raucoana</em>. A morphological description, distribution map, illustration, and the assessment of their conservation status are provided for each new taxon, along with an updated key to all species in <em>Miersia</em>. Additionally, analyses of DNA sequences were performed to inquire the evolutionary affinities of both new species and the recently described, <em>M. putaendensis</em>, within Gilliesieae phylogenetic framework. Data from multiple single-copy nuclear genes, as well as the inclusion of <em>Trichlora</em> and <em>Schickendantziella</em>, are necessary to corroborate the tribe’s phylogeny and reassess its generic classification.</p> <p>Dataset description: Two phylip alignment files were uploaded: 1) Miersia_nov_ITS_3.0.phy, includes sequences of nrDNA ITS (nrITS) region, and 2) Miersia_nov_cpDNA_3.0.phy, includes concatenated sequences of two chloroplast (cpDNA) markers, <em>trnL-F</em> and <em>rbcL</em>. Sequences were aligned using MAFFT v.1.4.0.</p> <p>Three *.bestTree.tre files for 1) nrITS, 2) cpDNA, and 3) concatenated dataset of all loci (nrITS, <em>trnL-F</em>, <em>rbcL</em>). All were inferred using RAxML-NG v.1.1.0 (Kozlov et al. 2019), GTR+Γ as the model of molecular evolution (--model GTR+G), and partitioned by locus. nrITS and cpDNA analyses were performed conducting 50 tree searches using 25 random and 25 parsimony-based starting trees to pick the best-scoring topology (--tree pars{25},rand{25}), and the concatenated analysis included 100 tree searches using 50 random and 50 parsimony-based starting trees (--tree pars{50},rand{50}). </p> <p>Also, the respective boostrap trees (*.bootstraps.tre) were uploaded for each analysis. Likelihood bootstrap analyses were conducted in RAxML-NG v.1.1.0 with 1,000 pseudoreplicates (--bs-trees 1000).</p> <p>We also uploaded two Nexus files which correspond to sequence data from Escobar et al. (2020, Bot. J. Linn. Soc. 194: 84–99), considering that these are currently not available in TreeBase.</p>
Dataset from: Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification
<p><strong>Premise</strong>: To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target-enriched nuclear data to improve our understanding of phylogenetic relationships in the family. </p> <p><strong>Methods</strong>: We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in <em>Brunellia</em>, and several outgroup taxa. We removed loci that indicated biased relationships and applied concatenated and coalescent methods to infer <em>Brunellia</em> phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage-sorting events and assessed their impact on the phylogeny. Finally, we performed ancestral-state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in <em>Brunellia</em>.</p> <p><strong>Results</strong>: <em>Brunellia</em> comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses.</p> <p><strong>Conclusions</strong>: Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene-tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in <em>Brunellia</em>, the relationships among subclades remain incompletely understood.</p>
Pre-processed data for "Does host plant drive variation in microbial gut communities in a recently shifted pest?"
<p>Pre-processed fastqs files generated by Illumina sequencing associated with the publication by Javal et al. entitled "Does host plant drive variation in microbial gut communities in a recently shifted pest?".</p>
Demographic modelling helps tracking the rapid and recent divergence of a conifer species pair from central Mexico
<p>Secondary contact of recently diverged species may have several outcomes, ranging from rampant hybridization to reinforced reproductive isolation. In plants, selfing tolerance and disjunct reproductive phenology may lead to reproductive isolation at contact zones. However, they can evolve under both allopatric or parapatric frameworks and originate from adaptive and/or neutral forces. Inferring the historical demography of diverging taxa is thus a crucial step to identify those factors that may lead to putative reproductive isolation. We explored various competing hypotheses to account for the rapid divergence of a fir species complex (<em>Abies flinckii - A. religiosa</em>) distributed in 'sky-islands' across central Mexico (i.e., along the Trans-Mexican Volcanic Belt; TMVB). Despite co-occurring in two independent sympatric regions (west and center), these taxa rarely interbreed because of disjunct reproductive phenologies. We genotyped 1,147 SNPs, generated by GBS, across 23 populations, and compared multiple demographic scenarios based on the geological history of the TMVB. The best-fitting model revealed one of the most rapid and complete speciation cases for a conifer species-pair, dating back to ~1.2 Ma. Coupled with the lack of support for stepwise colonization, our coalescent inferences point to an early cessation of interspecific gene flow under parapatric speciation; ancestral gene flow during divergence was asymmetrical (mostly from western firs into A. religiosa) and exclusive to the most ancient (i.e., central) contact zone. Factors promoting rapid reproductive isolation should be explored in other slowly-evolving species complexes as they may account for the large tropical and subtropical diversity.</p>
Data from: Patterns and drivers of recent land cover change on two trailing-edge forest landscapes
<p>Climate change is altering the distribution of woody plants by influencing demographic processes and modifying disturbance regimes. Trailing-edge forests may be particularly vulnerable to these effects because they exist at warm, dry margins of tree distributions. To better understand recent climate-driven changes in trailing-edge forests, we used Landsat time series and 1,558 field reference plots to develop annual land cover maps from 1985 to 2020 in two large, biodiverse landscapes in central Arizona, USA. We then combined annual land cover maps with tree ring records and spatial data describing interannual climate, terrain, bark beetle (Curculionidae: Scolytinae) activity, wildfire, and harvest to quantify drivers of forest change. Throughout the two landscapes, forest extent declined by 0.3% and 0.8% from 1985 to 2020. However, considerable variation occurred within the study period, with abrupt (ca. 1–2 years) declines in forest extent followed by gradual (ca. 10 years) recovery on each landscape. Pinyon-juniper (<em>Pinus</em> <em>edulis</em>, <em>Pinus</em> <em>monophylla</em>, and/or <em>Juniperus</em> spp.) cover increased from 1985 to ca. 2000 but declined after 2000, a period of extreme drought and regional tree die-off. In contrast, pine-oak (<em>Pinus</em> <em>ponderosa</em> and <em>Quercus</em> spp.) cover increased from 2000 to 2020, primarily due to declines in ponderosa pine and mixed conifer cover over the same period. Wildfire was a key driver of transitions from forest to non-forest cover in our study area, with the occurrence of multiple compounded drought years playing an important role in unburned areas. By driving transitions to alternative forest types or non-forest cover, disturbance and drought will increasingly shape forest dynamics and ecosystem transformations throughout the southwestern US.</p>
A field test of mechanisms underpinning animal diversity in recently burned landscapes
<p>1. Planned burning generates different types of pyrodiversity, however, experimental tests of how alternative spatial patterns of burning influence animal communities remain rare. Field tests are needed to understand the mechanisms through which spatial variation in planned fire affects fauna, and how fire can be applied to benefit biodiversity.</p> <p>2. We tested five hypotheses of how fire-driven variation in habitat composition and configuration affects fauna at fine scales. Small mammal, reptile and invasive predator activity was monitored at 12 burnt and eight unburnt sites through the year following a large, planned burn in semi-arid 'mallee' woodlands of southern Australia. We explored measures of burnt or unburnt habitat ("habitat status"); amount of unburnt vegetation ("habitat amount"); interspersion of burnt and unburnt patches ("habitat complementation"); distance to external or internal unburnt vegetation ("habitat connectivity"); and unburnt patch size and local vegetation cover ("habitat refuge"). Generalized linear models were used to test the influence of each variable on capture rate of three small mammal and 11 reptile species; activity of the introduced red fox (Vulpes vulpes); and species richness of native animals.</p> <p>3. We found strong support for the habitat status hypothesis and moderate support for four hypotheses relating to spatial patterns of fire. Reptile assemblages varied between burnt and unburnt sites, and relationships were identified between abundance of one or more reptile species and each measure of spatial variation. Reptile species richness was higher at unburnt sites and at sites with more unburnt vegetation in the surrounding area. Sites that were less connected to unburnt vegetation had fewer reptile species. Mammals did not have clear relationships with fine-scale fire patterns.</p> <p>4. Synthesis and applications: Application of planned fire to promote biodiversity is globally important. We show that retaining unburnt areas and well-connected habitat refuges is important for reptile diversity. We also found that several species of small mammals and reptiles appear resilient to the fine-scale patterns of planned fire experienced in this study, despite activity of introduced predators. The diversity of animals can remain relatively high in areas subject to planned fire, provided that internal and external habitat refuges are retained.</p>
Supplementary data for: Hybridisation has shaped a recent radiation of grass-feeding aphids
<p><strong>Orthogroups and species tree</strong></p> <p>Proteomes included in the analysis: proteomes.tar.gz<br> Orthogroups: Orthogroups.txt<br> Gene counts per orthogroup, per species: Orthogroups.GeneCount.tsv<br> Single copy conserved orthogroups used for species tree: Orthogroups_SingleCopyOrthologues.txt<br> Protein alignment used for species tree reconstruction: SpeciesTreeAlignment.fa<br> Species tree: SpeciesTree_rooted.txt</p> <p><strong>Whole genome alignment of <em>S. avenae</em>, <em>S. miscanthi,</em> <em>M. dirhodum</em> and <em>A. pisum</em></strong></p> <p>Cactus whole genome alignment (hal format): Siave_Simis_Medir_Acpis.hal.gz</p> <p><strong>Haplotype divergence analysis (whole genome sequences)</strong></p> <p>VCF files of HapCUT2 phased variants for <em>S. miscanthi </em>Langfang-1 chromosomes (Simis_v2 assembly scaffolds 1 to 9):<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_1.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_2.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_3.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_4.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_5.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_6.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_7.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_8.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_9.hap.phased.VCF.gz</p> <p>VCF files of HapCUT2 phased variants for <em>S. avenae </em>JIC1<em> </em>chromosomes (Siave_v2.1 assembly scaffolds 1 to 9):<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_1.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_2.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_3.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_4.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_5.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_6.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_7.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_8.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_9.hap.phased.VCF.gz</p> <p>Haplotype resolved assemblies of <em>S. avenae</em> JIC1 and <em>S. miscanthi </em>Langfang-1 based on HapCUT2 phasing results:<br> JIC1_H1.Hapcut2.fa<br> JIC1_H2.Hapcut2.fa<br> Langfang1_H1.Hapcut2.fa<br> Langfang1_H2.Hapcut2.fa</p> <p>SibeliaZ whole genome alignment of <em>S. avenae </em>JIC1 and <em>S. miscanthi </em>Langfang-1 haplotypes: alignment.filtered.ordered.stranded.sorted.maf</p> <p><strong>Filtered VCF files used for population genomics analysis</strong></p> <p><em>S. avenae</em> and <em>S. miscanthi</em> GBS samples + JIC1 and Langfang1 WGS samples variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.vcf<br> <em>S. avenae</em> and <em>S. miscanthi</em> GBS samples + JIC1 and Langfang1 WGS samples phased variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.fix_mis.beagle.vcf<br> <em>S. avenae</em> and <em>S. miscanthi</em> GBS samples + JIC1, Langfang1 and <em>M. dirhodum </em>WGS samples variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.vcf<br> <em>S. avenae</em> and <em>S. miscanthi </em>GBS samples + JIC1, Langfang1 and <em>M. dirhodum</em> WGS samples phased variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf<br> <em>S. miscanthi </em>GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.vcf<br> <em>S. miscanthi </em>GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf</p> <p><strong>SNAPP phylogenetic analysis configuration file and trees</strong></p> <p>SNAPP configuration file: snapp.xml<br> SNAPP log file: ut.log<br> SNAPP posterior sample of trees: ut.trees<br> SNAPP maximum clade credibility tree with 10% burn in: ut.trees.max_cred_burn_10pc</p> <p> </p> <p> </p>
Figure 5. Female Neobrettus tibialis with their broods. 1, Female tending recently deposited eggs covered with flecked silk. 2, Female with emergent instar 1 spiderlings, showing little pigmentation. 3, Female tending instar 1 spiderlings with more eye pigmentation. 4-5, Females with older instar 1 spiderlings. 6-7, Females with mixed instar 1 and 2 in New observations of the jumping spider Neobrettus tibialis (Araneae: Salticidae: Spartaeini) in West Bengal, India
Figure 5. Female Neobrettus tibialis with their broods. 1, Female tending recently deposited eggs covered with flecked silk. 2, Female with emergent instar 1 spiderlings, showing little pigmentation. 3, Female tending instar 1 spiderlings with more eye pigmentation. 4-5, Females with older instar 1 spiderlings. 6-7, Females with mixed instar 1 and 2 spiderlings.
ScienceDex guides
Understand access before you commit
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.