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89 results for “integrated species delimitation”
Phylogenomic species delimitation in the ants of the Temnothorax salvini Group (Hymenoptera: Formicidae): An integrative approach
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Data from: Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation of Mesocarabus (Coleoptera: Carabidae)
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Data from: Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
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Species delimitation beyond phylogenomics: integrative approaches reveal gentoo penguin speciation
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Data from: An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid.
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Data from: Sex-biased dispersal obscures species boundaries in integrative species delimitation approaches
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Data from: Integrative taxonomy and species delimitation in harvestmen: a revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea)
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Data from: One, two or three? Integrative species delimitation of short-range endemic Hemicycla species (Gastropoda: Helicidae) from the Canary Islands based on morphology, barcoding, AFLP and ddRADseq data
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Data from: Species detection and individual assignment in species delimitation: can integrative data increase efficacy?
Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and individual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological diversity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign individuals to putative species. Our approach recovers a similar number of species recognized using traditional, qualitative taxonomic approaches that are not detected when using purely genetic methods. Furthermore, our approach detects groupings that traditional, qualitative taxonomic approaches do not. This empirical test suggests that our approach to detecting and assigning individuals to putative species could be useful in species delimitation despite varying levels of differentiation across genetic, phenotypic and ecological axes. This work highlights a critical, and often overlooked, aspect of the process of statistical species delimitation—species detection and individual assignment. Irrespective of the species delimitation approach used, all downstream processing relies on how individuals are initially assigned, and the practices and statistical issues surrounding individual assignment warrant careful consideration.
Data from: The species versus subspecies conundrum: quantitative delimitation from integrating multiple data types within a single Bayesian approach in Hercules beetles
With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status.
Data from: Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers
Although resolving phylogenetic relationships and establishing species limits is a primary goal of systematics, these tasks remain challenging at both conceptual and analytical levels. Here, we integrated genomic and phenotypic data and employed a comprehensive suite of coalescent-based analyses to develop and evaluate competing phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers (Chorthippus binotatus group) composed of two species and eight putative subspecies. To resolve the evolutionary relationships within this complex, we first evaluated alternative phylogenetic hypotheses arising from multiple schemes of genomic data processing and contrasted genetic-based inferences with different sources of phenotypic information. Second, we examined the importance of number of loci, demographic priors, number and kind of phenotypic characters, and sex-based trait variation for developing alternative species delimitation hypotheses. The best-supported topology was largely compatible with phenotypic data and showed the presence of two clades corresponding to the nominative species groups, one including three well-resolved lineages and the other comprising a four-lineage polytomy and a well-differentiated sister taxon. Integrative species delimitation analyses indicated that the number of employed loci had little impact on the obtained inferences but revealed the higher power provided by an increasing number of phenotypic characters and the usefulness of assessing their phylogenetic information-content and differences between sexes in among-taxa trait variation. Overall, our study highlights the importance of integrating multiple sources of information to test competing phylogenetic hypotheses and elucidate the evolutionary history of species complexes representing early-stages of divergence where conflicting inferences are more prone to appear.
Data from: Delimiting species of marine gastropods (Turridae, Conoidea) using RAD-sequencing in an integrative taxonomy framework
Species delimitation in poorly-known and diverse taxa is usually performed based on monolocus, DNA barcoding-like approaches, while multilocus data are often used to test alternative species hypotheses in well-studied groups. We combined both approaches to delimit species in the Xenuroturris / Iotyrris complex, a group of venomous marine gastropods from the Indo-Pacific. First, COI sequences were analyzed using three methods of species delimitation, ABGD, PTP and GMYC to propose primary species hypotheses (PSH). Second, RAD-seq data were also obtained and an IQ-tree phylogenetic tree produced. We tested the impact of the level of missing data on the robustness of the phylogenetic tree obtained with the RAD-seq data. Alternative species partitions revealed with the COI dataset were also tested using the RAD-seq data and the BFD method. The congruence between the species hypotheses proposed with the mitochondrial gene and the clades in the RAD-seq tree, together with the morphological variability of the shell and the radula and the distribution pattern, was used to turn the PSH into secondary species hypotheses (SSH). Allopatric PSH defined with the COI gene were interpreted to correspond to intraspecific structure. Most of the species are found sympatrically in the Philippines, and only one is confidently identified as a new species and described as Iotyrris conotaxis n. sp. The results obtained demonstrate the efficiency of the combined monolocus/multilocus approach to delimit species.
Figure 8. The species delimitation model retrieved a in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 8. The species delimitation model retrieved a maximum of eight species.
Figure 5 from: Condamine F, Soldati L, Kergoat G, Clamens A, Jourdan H, Jabbour-Zahab R (2014) Integrative taxonomy of New Caledonian beetles: species delimitation and definition of the Uloma isoceroides species group (Coleoptera, Tenebrionidae, Ulomini), with the description of four new species. ZooKeys 415: 133-167. https://doi.org/10.3897/zookeys.415.6623
Figure 5 - Uloma condaminei: A habitus (dorsal view) B habitus (lateral view) C habitus (ventral view) D anterior tibia (upper face) E head (dorsal view). Scale bar: 5 mm.
Figure 1 from: Condamine F, Soldati L, Kergoat G, Clamens A, Jourdan H, Jabbour-Zahab R (2014) Integrative taxonomy of New Caledonian beetles: species delimitation and definition of the Uloma isoceroides species group (Coleoptera, Tenebrionidae, Ulomini), with the description of four new species. ZooKeys 415: 133-167. https://doi.org/10.3897/zookeys.415.6623
Figure 1 - Maximum likelihood tree resulting from the analysis of the combined dataset. Support of major nodes is provided by BV (only BV ≥ 50% are figured). For the group of interest we used coloured frames to highlight the seven sampled morphospecies (Uloma caledonica, Uloma clamensae, Uloma condaminei, Uloma isoceroides, Uloma jourdani, Uloma kergoati and Uloma opacipennis). On the right, corresponding male habitus are also included for illustrative purpose. Results of the PTP analysis are provided using coloured branches. Putative molecular species are indicated using transitions between blue-coloured branches to red-coloured branches. For the two cases (for Uloma isoceroides and Uloma jourdani) in which two distinct putative species clusters are inferred we added numbers into brackets to indicate the assignation of specimens to a specific species cluster.
Figure 8 from: Condamine F, Soldati L, Kergoat G, Clamens A, Jourdan H, Jabbour-Zahab R (2014) Integrative taxonomy of New Caledonian beetles: species delimitation and definition of the Uloma isoceroides species group (Coleoptera, Tenebrionidae, Ulomini), with the description of four new species. ZooKeys 415: 133-167. https://doi.org/10.3897/zookeys.415.6623
Figure 8 - Uloma kergoati: A habitus (dorsal view) B habitus (lateral view) C habitus (ventral view) D anterior tibia (upper face) E head (dorsal view). Scale bar: 5 mm.
Figure 7 from: Condamine F, Soldati L, Kergoat G, Clamens A, Jourdan H, Jabbour-Zahab R (2014) Integrative taxonomy of New Caledonian beetles: species delimitation and definition of the Uloma isoceroides species group (Coleoptera, Tenebrionidae, Ulomini), with the description of four new species. ZooKeys 415: 133-167. https://doi.org/10.3897/zookeys.415.6623
Figure 7 - Uloma jourdani: A habitus (dorsal view) B habitus (lateral view) C habitus (ventral view) D anterior tibia (upper face) E head (dorsal view). Scale bar: 5 mm.
Figure 6 from: Condamine F, Soldati L, Kergoat G, Clamens A, Jourdan H, Jabbour-Zahab R (2014) Integrative taxonomy of New Caledonian beetles: species delimitation and definition of the Uloma isoceroides species group (Coleoptera, Tenebrionidae, Ulomini), with the description of four new species. ZooKeys 415: 133-167. https://doi.org/10.3897/zookeys.415.6623
Figure 6 - Uloma condaminei: F forebody (lateral view) G forebody (ventral view). The arrows show the apical hair tufts on the mentum.
Figure 3 from: Condamine F, Soldati L, Kergoat G, Clamens A, Jourdan H, Jabbour-Zahab R (2014) Integrative taxonomy of New Caledonian beetles: species delimitation and definition of the Uloma isoceroides species group (Coleoptera, Tenebrionidae, Ulomini), with the description of four new species. ZooKeys 415: 133-167. https://doi.org/10.3897/zookeys.415.6623
Figure 3 - Aedeagus (tergal face and lateral view): A–B Uloma caledonica C–D Uloma clamensae E–F Uloma condaminei G–H Uloma isoceroides I–J Uloma jourdani K–L Uloma kergoati M–N Uloma monteithi O–P Uloma opacipennis Q–R Uloma robusta.
Figure 4 from: Condamine F, Soldati L, Kergoat G, Clamens A, Jourdan H, Jabbour-Zahab R (2014) Integrative taxonomy of New Caledonian beetles: species delimitation and definition of the Uloma isoceroides species group (Coleoptera, Tenebrionidae, Ulomini), with the description of four new species. ZooKeys 415: 133-167. https://doi.org/10.3897/zookeys.415.6623
Figure 4 - Uloma clamensae: A habitus (dorsal view) B habitus (lateral view) C habitus (ventral view) D anterior tibia (upper face) E head (dorsal view). Scale bar: 5 mm.
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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.