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1,492 results for “species delimitation”
Data from: Re-examination of species limits in Aspergillus section Flavipedes using advanced species delimitation methods and description of four new species
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Data from: Transcriptome analysis of two radiated Cycas species and its utilization on species delimitation in Cycas taiwaniana complex
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Data from: Delimiting species of marine gastropods (Turridae, Conoidea) using RAD-sequencing in an integrative taxonomy framework
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Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)
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Data from: Bayesian species delimitation can be robust to guide tree inference errors
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Data from: Species detection and individual assignment in species delimitation: can integrative data increase efficacy?
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Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)
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Data from: Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)
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Data from: Delimiting species-poor datasets using single molecular markers: a study of barcode gaps, haplowebs and GMYC
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Data from: Species delimitation with gene flow
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Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)
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Integrative taxonomy and geographic sampling underlie successful species delimitation
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Figure 1 from: Yu H-J, Lin X-L, Zhang R-L, Wang Q, Wang X-H (2020) Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes. ZooKeys 975: 79-86. https://doi.org/10.3897/zookeys.957.54668
Figure 1 Larva of Propsilocerus taihuensis (Wen, Zhou & Rong, 1994).
Data from: Delimiting species in recent radiations with low levels of morphological divergence: a case study in Australian Gehyra geckos
Recent conceptual and methodological advances have increased the ability to apply multifaceted approaches to species delimitation, which is particularly useful in delimiting recently diversified species where single lines of evidence lead to incorrect species delimitation or assignment of individuals to species (e.g. cryptic, morphological species and paraphyletic, hybridizing species). Species of the Australian Gehyra gecko radiation have historically proven difficult to delimit due the group's uniform, almost continent-wide geographic distribution and conservative morphology, contrasting high chromosomal and genetic diversity. Using an integrated approach to species delimitation taking advantage of morphological, geographic distributional and multi-locus genetic data, we investigate the diversity within three Gehyra species from the Australian arid zone. Our results show that these species represent eight distinct phylogenetic lineages, which display different patterns of morphological distinction and reproductive isolation. Using a recently developed Bayesian species delimitation method, we also find different levels of support for putative species dependent on priors for population size and timing of diversification assumed. Our results show that the current taxonomy does not adequately account for the diversity of the group. Discrepancies between lines of evidence indicate that diversification of the group is recent and ongoing, thus posing challenges for both species concepts and delimitation.
Data from: Limitations of species delimitation based on phylogenetic analyses: a case study in the (Hypogymnia hypotrypa) group (Parmeliaceae, Ascomycota)
Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences) to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida clade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the "Automatic Barcode Gap Discovery" (ABGD), the Poisson tree process model (PTP), the General Mixed Yule Coalescent (GMYC), and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (FST). The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain. This study reveals the potential limitations of relying on distinct reproductive strategies as diagnostic taxonomic characters for Hypogymnia and also the challenges of using popular sequence-based species delimitation methods in groups with recent diversification histories.
Figure 6 from: Bergsten J, Weingartner E, Hájek J (2017) Species delimitation of the Hyphydrus ovatus complex in western Palaearctic with an update of species distributions (Coleoptera, Dytiscidae). ZooKeys 678: 73-96. https://doi.org/10.3897/zookeys.678.12886
Figure 6 - Hyphydrus head. a H. anatolicus b H. ovatus c H. sanctus. Not in scale.
Figure 1 from: Zhu X-C, Chen J, Chen R, Jiang L-Y, Qiao G-X (2017) DNA barcoding and species delimitation of Chaitophorinae (Hemiptera, Aphididae). ZooKeys 656: 25-50. https://doi.org/10.3897/zookeys.656.11440
Figure 1 - Continue.
Figure 10 from: Urgiles VL, Székely P, Székely D, Christodoulides N, Sanchez-Nivicela JC, Savage AE (2019) Genetic delimitation of Pristimantis orestes (Lynch 1979) and P. saturninoi Brito et al., 2017 and the description of two new terrestrial frogs from the Pristimantis orestes species group (Anura, Strabomantidae). ZooKeys 864: 111-146. https://doi.org/10.3897/zookeys.864.35102
Figure 10 Holotype of Pristimantisquintanai sp. nov. in life.
Figure 5 from: Urgiles VL, Székely P, Székely D, Christodoulides N, Sanchez-Nivicela JC, Savage AE (2019) Genetic delimitation of Pristimantis orestes (Lynch 1979) and P. saturninoi Brito et al., 2017 and the description of two new terrestrial frogs from the Pristimantis orestes species group (Anura, Strabomantidae). ZooKeys 864: 111-146. https://doi.org/10.3897/zookeys.864.35102
Figure 5 Holotype of Pristimantiscajanuma sp. nov. in life. A dorsolateral view B ventral view.
Comparative evaluation of species delimitation methods and phylogeny of the genus Agrilus (Coleoptera: Buprestidae) from China
<p><span>Table S1. Primer information. Table S2. PCR reaction conditions for COI.<span> Table S3. PCR reaction conditions for CYTB. </span>Table S4.<span> Information of <em>Agrilus</em> species collected from China. Figure S1. Comparison of results of four methods (ABGD, ASAP, jMOTU, bPTP) based on COI. Figure S2. Comparison of results of four methods (ABGD, ASAP, jMOTU, bPTP) based on CYTB. Figure S3. ML tree based on the concatenated sequences of three genes (COI, CYTB and 28S).</span> The DNA sequences of COI, CYTB and 28S used in this study are also provided.</span></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.