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.
2,185
datasets available to search
ShareScore release 0.9.0
Dataset results
2,185 results for “integrated taxonomy”
Data from: Integrative taxonomy and species delimitation in harvestmen: a revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea)
Alpha taxonomy, and specifically the delimitation of species, is becoming increasingly objective and integrative. The use of coalescent-based methods applied to genetic data is providing new tools for the discovery and delimitation of species. Here, we use an integrative approach via a combination of discovery-based multivariate morphological analyses to detect potential new species. These potential species are then used as a priori species in hypothesis-driven validation analyses with genetic data. This research focuses on the harvestmen genus Sclerobunus found throughout the mountainous regions of western North America. Based on our analyses, we conduct a revision of Sclerobunus resulting in synonymy of Cyptobunus with Sclerobunus including transfer of S. cavicolens comb. nov. and elevation of both subspecies of S. ungulatus: S. ungulatus comb. nov. and S. madhousensis comb. nov., stat. nov. The three subspecies of S. robustus are elevated, S. robustus, S. glorietus stat. nov., and S. idahoensis stat. nov. Additionally, five new species of Sclerobunus are described from New Mexico and Colorado, including S. jemez sp. nov., S. klomax sp. nov., S. skywalkeri sp. nov., S. speoventus sp. nov., and S. steinmanni sp. nov. Several of the newly described species are single-cave endemics, and our findings suggest that further exploration of western North American cave habitats will likely yield additional new species.
Data from: Integrative taxonomy recognizes evolutionary units despite widespread mitonuclear discordance: evidence from a rotifer cryptic species complex
Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relation to, for instance, complex introgression scenarios involving many species. Here, we report remarkably widespread mitonuclear discordance between about 15 mitochondrial and four nuclear Brachionus calyciflorus groups identified using different species delimitation approaches. Using coalescent-, Bayesian admixture-, and allele sharing-based methods with DNA sequence or microsatellite data, we provide strong evidence in support of hybridization as a driver of the observed discordance. We then describe our combined molecular, morphological, and ecological approaches to resolving phylogenetic conflict and inferring species boundaries. Species delimitations based on the ITS1 and 28S nuclear DNA markers proved a more reliable predictor of morphological variation than delimitations using the mitochondrial COI gene. A short-term competition experiment further revealed systematic differences in the competitive ability between two of the nuclear-delimited species under six different growth conditions, independent of COI delimitations; hybrids were also observed. In light of these findings, we discuss the failure of the COI marker to estimate morphological stasis and morphological plasticity in the B. calyciflorus complex. By using B. calyciflorus as a representative case, we demonstrate the potential of integrative taxonomy to guide species delimitation in the presence of mitonuclear phylogenetic conflicts.
Data from: Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation of Mesocarabus (Coleoptera: Carabidae)
In species differentiation, characters do not usually diverge synchronously and there are also processes that effectively shuffle character states present in lineages descendant from a common ancestor. Species are thus expected to show some degree of incongruence among characters, and we argue that taxonomic delimitation actually benefits from integrative approaches and objective strategies dealing with character conflict. We illustrate the potential of exploiting conflict for species delimitation in a study-case of ground beetles of the subgenus Carabus (Mesocarabus), where traditional taxonomy fails to accurately delimit species. The molecular phylogenies of four mitochondrial and three nuclear genes, cladistic analysis of the aedeagus, ecological niche divergence, and morphometry of pronotal shape in altogether more than 500 specimens of Mesocarabus, show that none of these character sets are fully congruent with each other. For these data, a three-steps operational strategy is proposed for species delimitation by (1) delineating candidate species based on the integration of incongruence among conclusive lines of evidence, (2) corroborating candidate species with inconclusive lines of evidence, and (3) refining a final species proposal based on an integrated characterization of candidate species based on the evolutionary analysis of incongruence. This procedure provided a general understanding of the reticulate process of hybridization and introgression acting on Mesocarabus and generated the hypothesis of seven Mesocarabus species, including two putative hybrid lineages. Our work emphasizes the importance of incorporating critical analyses of character and phylogenetic conflict to infer both the evolutionary history and species boundaries through an integrative taxonomic approach.
Data from: Taking the discovery approach in integrative taxonomy: decrypting a complex of narrow-endemic Alpine harvestmen (Opiliones: Phalangiidae: Megabunus)
Species delimitation is fundamental for biological studies, yet precise delimitation is not an easy task, and every involved approach has an inherent failure rate. Integrative taxonomy, a method that merges multiple lines of evidence, can profoundly contribute to reliable alpha taxonomy and shed light on the processes behind speciation. In this study, we explored and validated species limits in a group of closely related Megabunus harvestmen (Eupnoi, Phalangiidae) endemic to the European Alps. Without a priori species hypotheses, we used multiple sources of inference, including mitochondrial and multilocus nuclear DNA, morphometrics, and chemistry. The results of these discovery approaches revealed morphological crypsis and multiple new species within two of the five hitherto known species. Based on our analyses, we discussed the most plausible evolutionary scenarios, invoked the most reasonable species hypotheses, and validated the new species limits. Building upon the achieved rigour, three new species, M. cryptobergomas Muster & Wachter sp. nov., M. coelodonta Muster & Steiner sp. nov., and M. lentipes Muster & Komposch sp. nov., are formally described. In addition, we provide a dichotomous morphological key to the Megabunus species of the Alps. Our work demonstrates the suitability of integrative, discovery-based approaches in combination with validation approaches to precisely characterise species and enabled us to implement nomenclatural consequences for this genus.
Data from: Integrative taxonomy refutes a species hypothesis: the asymmetric hybrid origin of Arsapnia arapahoe (Plecoptera, Capniidae)
Molecular tools are commonly directed at refining taxonomies and the species that constitute their fundamental units. This has been especially insightful for groups for which species hypotheses are ambiguous and have largely been based on morphological differences between certain life stages or sexes, and has added importance when taxa are a focus of conservation efforts. Here we examine the taxonomic status of Arsapnia arapahoe, a winter stonefly in the family Capniidae that is a species of conservation concern because of its limited abundance and restricted range in northern Colorado, USA. Phylogenetic analyses of sequences of mitochondrial and nuclear genes of this and other capniid stoneflies from this region and elsewhere in western North America indicated extensive haplotype sharing, limited genetic differences, and a lack of reciprocal monophyly between A. arapahoe and the sympatric A. decepta, despite distinctive and consistent morphological differences in the sexual apparatus of males of both species. Analyses of autosomal and sex-linked single nucleotide polymorphisms detected using genotyping by sequencing, however, indicated that all individuals of A. arapahoe consisted of F1 hybrids between female A. decepta and males of another sympatric stonefly, Capnia gracilaria. Rather than constitute a self-sustaining evolutionary lineage, A. arapahoe appears to represent the product of nonintrogressive hybridization in the limited area of syntopy between two widely distributed taxa. This offers a cautionary tale for taxonomists and conservation biologists working on the less-studied components of the global fauna.
Data from: Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales: Jungermanniopsida), including two reinstated and five new species
Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph. and R. notabilis sp. nov. are endemic to the Wet Tropics Bioregion of north-east Queensland, suggesting high diversity and high endemism might characterise the bryoflora of this relatively isolated wet-tropical region. Radula demissa sp. nov. is endemic to southern temperate Australasia, and like R. strangulata occurs on both sides of the Tasman Sea. Radula imposita sp. nov. is a twig and leaf epiphyte found in association with waterways in New South Wales and Queensland. Another species, R. pugioniformis sp. nov., has been confused with Radula buccinifera but was not included in the molecular phylogeny. Morphological data suggest it may belong to subg. Odontoradula. Radula buccinifera is endemic to Australia including Western Australia and Tasmania, and to date is known from south of the Clarence River on the north coast of New South Wales. Nested within R. buccinifera is a morphologically distinct plant from Norfolk Island described as R. anisotoma sp. nov. Radula australiana is resolved as monophyletic, sister to a species occurring in east coast Australian rainforests, and nesting among the R. buccinifera lineages with strong support. The molecular phylogeny suggests several long-distance dispersal events may have occurred. These include two east-west dispersal events from New Zealand to Tasmania and south-east Australia in R. strangulata, one east-west dispersal event from Tasmania to Western Australia in R. buccinifera, and at least one west-east dispersal from Australia to New Zealand in R. australiana. Another west-east dispersal event from Australia to Norfolk Island may have led to the budding speciation of R. anisotoma. In contrast, Radula demissa is phylogeographically subdivided into strongly supported clades either side of the Tasman Sea, suggesting long distance dispersal is infrequent in this species.
Data from: Integrative taxonomy at work: DNA barcoding of taeniids harbored by wild and domestic cats
In modern taxonomy, DNA barcoding is particularly useful where biometric parameters are difficult to determine or useless due to the poor quality of samples. These situations are frequent in parasitology. Here we present an integrated study, based on both DNA barcoding and morphological analysis, on cestodes belonging to the genus Taenia, for which biodiversity is still largely underestimated. In particular, we characterized cestodes from Italian wildcats (Felis silvestris silvestris), free-ranging domestic cats (F. s. catus) and their hybrids populations. Adult taeniids were collected by post-mortem examinations of the hosts, and morphologically identified as Taenia taeniaeformis. We produced the cox1 barcode sequences for all the analyzed specimens and we compared them with reference sequences of individuals belonging to the genus Taenia retrieved from GenBank. In order to evaluate the performance of a DNA barcoding approach to discriminate these parasites, the strength of correlation between species identification based on classical morphology-based approaches and the molecular divergence of cox1 sequences was measured. Our study provides clear evidence that DNA barcoding is highly efficient to reveal the presence of cryptic lineages within already described taeniid species. Indeed, we detected three well-defined molecular lineages within the whole panel of specimens morphologically identified as T. taeniaeformis. Two of these molecular groups were already identified by other authors and should be ranked at species level. The third molecular group encompasses only samples collected in Italy during this study, and it represents a third candidate species, still morphologically undescribed.
Data from: How diverse is Mitopus morio? Integrative taxonomy detects cryptic species in a small-scale sample of a widespread harvestman
Mitopus morio is a widespread harvestman species occurring in most of Europe and in moderate and cold-moderate zones of Asia and North America. The species is characterized by extreme variability in body size and leg length. As leg length is correlated with habitat temperature, M. morio has been considered as an example of Allen's rule. Recently, observations for a single location in Tyrol, Austria, indicated the absence of mating between short- and long-legged individuals. This study examines for signs of putative cryptic species in M. morio using an integrative approach that combines mating trials, amplified fragment length polymorphism whole-genome scans, mitochondrial sequences and morphometrics. The mating trials did not corroborate the initial hypothesis of a reproductive barrier associated with leg size. Both types of genetic data revealed the existence of three distinct groups, in line with the mating results but largely unrelated to leg morphology and geographical origin of specimens. Morphometric characters supporting the findings of the other disciplines were identified using a supervised approach. We infer from all data together the existence of strongly diverged cryptic lineages among the analysed individuals, cautiously interpret them as three sympatric species and conclude that in these harvestmen Allen's rule applies at different levels. Due to the unexpected amount of differentiation found within a geographical scale very small compared with the distribution of M. morio, we suggest a thorough revision of the genus prior to formal taxonomic changes. Our case study underlines the general applicability of the integrative taxonomic protocol used and highlights the relevance of several rationales implemented in the protocol.
FIGURE 2 in Species status of Centrolene lema Duellman and Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy
FIGURE 2. Ventral view of Centrolene gorzulae showing the distribution of iridophores on viscera. (A) MHNLS 17326 from Auyan-tepui; (B) MHNLS 17267 from Sierra de Lema. Photos by S. Castroviejo-Fisher.
FIGURE 1 in Species status of Centrolene lema Duellman and Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy
FIGURE 1. Dorsal and ventral view of Centrolene gorzulae from Sierra de Lema (A, B; CVULA 7013; photos by C. L. Barrio-Amorós) and Auyan-tepui (C, D; MHNLS 17325; photos by S. Castroviejo-Fisher).
FIGURE 5 in Species status of Centrolene lema Duellman and Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy
FIGURE 5. Egg clutch of Centrolene gorzulae deposited on moss, on a branch overhanging water (ca. 2.0 m high). Photograph by P. J. R. Kok.
FIGURE 4 in Species status of Centrolene lema Duellman and Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy
FIGURE 4. Neighbor-joining tree based on a 16S rDNA fragment. Support is indicated at the node when bootstrap values are> 70%. Terminals are labeled according to their species identification, distribution, and museum number (Gen- Bank accession number in the case of Allophryne ruthveni). The topology supports the hypothesis that Centrolene lema is a synonym of C. gorzulae.
FIGURE 3 in Species status of Centrolene lema Duellman and Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy
FIGURE 3. Audiospectograms (top) and oscillograms of the advertisement calls of Centrolene gorzulae. (A) MHNLS 17326 from Auyan-tepui; (B) MHNLS 17142 from Sierra de Lema. Air temperature at recordings ~ 19°.
FIGURE 6 in Species status of Centrolene lema Duellman and Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy
FIGURE 6. Map of northeastern South America showing known localities of Centrolene gorzulae (red dots). 1 = Auyan-tepui (type locality of C. gorzulae and C. auyantepuiana); 2 = Parque Nacional Canaima, Cuenca alta del río Cucurital, Atapare; 3 = Sierra de Lema (type locality of C. lema); 4 = Peters Mountain (type locality of C. papillahallicum); 5 = Southeast slope of Maringma tepui; 6 = Kaieteur National Park.
FIGURES 5–7 in Alobevania, a new genus of neotropical ensign wasps (Hymenoptera: Evaniidae), with three new species: integrating taxonomy with the World Wide Web
FIGURES 5–7. Alobevania lateral mesosoma; scale bars = 0.5 mm. 5) A. gattiae (Morphbank), 6) A. longisaeta (Morphbank), 7) A. tavaresi (Morphbank).
FIGURES 2–4 in Alobevania, a new genus of neotropical ensign wasps (Hymenoptera: Evaniidae), with three new species: integrating taxonomy with the World Wide Web
FIGURES 2–4. Alobevania head, anterior view; scale bars = 0.25 mm. 2) A. gattiae (Morphbank), 3) A. longisaeta (Morphbank), 4) A. tavaresi (Morphbank).
FIGURE 1 in Alobevania, a new genus of neotropical ensign wasps (Hymenoptera: Evaniidae), with three new species: integrating taxonomy with the World Wide Web
FIGURE 1. Partial phylogeny of Evaniidae from Deans et al. (2006; bootstrap values from their Fig. 3 and posterior probabilities from their Fig. 6) showing position of Alobevania gattiae (gray branch) outside of Evaniella (dashed branches) with relatively strong support (circled values). Numbers represent Bayesian posterior probabilities / parsimony bootstrap. A. gattiae lacks the 2c-2 helix/non-helix combination found in the other taxa belonging to this lineage (i.e., Evaniella Bradley, Acanthinevania Bradley, Szepligetella Bradley).
FIGURES 8–9 in Alobevania, a new genus of neotropical ensign wasps (Hymenoptera: Evaniidae), with three new species: integrating taxonomy with the World Wide Web
FIGURES 8–9. Alobevania lateral habitus, showing sexual dimorphism; scale bars = 1.0 mm. 8) A. gattiae male (Morphbank), 9) A. longisaeta female (Morphbank).
FIGURES 10–12 in Alobevania, a new genus of neotropical ensign wasps (Hymenoptera: Evaniidae), with three new species: integrating taxonomy with the World Wide Web
FIGURES 10–12. Alobevania dorsal mesosoma and head; scale bars = 0.5 mm. 10) A. gattiae (Morphbank), 11) A. longisaeta (Morphbank), 12) A. tavaresi (Morphbank).
FIGURE 13 in Integrative taxonomy identifies new (and old) species in the Lasioglossum (Dialictus) tegulare (Robertson) species group (Hymenoptera, Halictidae)
FIGURE 13. Dorsal surface of the propodeum showing surface sculpture of the metapostnotum in (A) L. lepidii and (B) L. tegulare.
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.