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2,185 results for “integrated taxonomy”
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.
Data from: Integrative taxonomy of root-knot nematodes reveals multiple independent origins of mitotic parthenogenesis
During sampling of several Coffea arabica plantations in Tanzania severe root galling, caused by a root-knot nematode was observed. From pure cultures, morphology and morphometrics of juveniles and females matched perfectly with Meloidogyne africana, whereas morphology of the males matched identically with those of Meloidogyne decalineata. Based on their Cox1 sequence, however, the recovered juveniles, females and males were confirmed to belong to the same species, creating a taxonomic conundrum. Adding further to this puzzle, re-examination of M. oteifae type material showed insufficient morphological evidence to maintain its status as a separate species. Consequently, M. decalineata and M. oteifae are synonymized with M. africana, which is herewith redescribed based on results of light and scanning electron microscopy, ribosomal and mitochondrial DNA sequences, isozyme electrophoresis, along with bionomic and cytogenetic features. Multi-gene phylogenetic analysis placed M. africana outside of the three major clades, together with M. coffeicola, M. ichinohei and M. camelliae. This phylogenetic position was confirmed by several morphological features, including cellular structure of the spermatheca, egg mass position, perineal pattern and head shape. Moreover, M. africana was found to be a polyphagous species, demonstrating that "early-branching" Meloidogyne spp. are not as oligophagous as had previously been assumed. Cytogenetic information indicates M. africana (2n = 21) and M. ardenensis (2n = 51–54) to be a triploid mitotic parthenogenetic species, revealing at least four independent origins of mitotic parthenogenesis within the genus Meloidogyne. Furthermore, M. mali (n = 12) was found to reproduce by amphimixis, indicating that amphimictic species with a limited number of chromosomes are widespread in the genus, potentially reflecting the ancestral state of the genus. The wide variation in chromosome numbers and associated changes in reproduction modes indicate that cytogenetic evolution played a crucial role in the speciation of root-knot nematodes and plant-parasitic nematodes in general.
Figure 5 from: Orlov NL, Ermakov OA, Nguyen TT, Ananjeva NB (2021) A new record of odd-scaled snake (Serpentes, Xenodermidae) from Vietnam: expanded description of Parafimbrios vietnamensis based on integrative taxonomy. ZooKeys 1048: 79-89. https://doi.org/10.3897/zookeys.1048.66477
Figure 5 ML phylogenetic tree (HKY+G+I model) based on the mitochondrial COI gene. Numbers near the branches denote percentage bootstrap resampling support from 1000 replications (ML/ME/NJ). Bootstrap support is only shown for values exceeding 80%. Asterisks represent 100% values. Scale bar shows substitutions/site.
Figure 4 from: Orlov NL, Ermakov OA, Nguyen TT, Ananjeva NB (2021) A new record of odd-scaled snake (Serpentes, Xenodermidae) from Vietnam: expanded description of Parafimbrios vietnamensis based on integrative taxonomy. ZooKeys 1048: 79-89. https://doi.org/10.3897/zookeys.1048.66477
Figure 4 Habitat of P. vietnamensis in the primary polydominant forest in Yen Bai Province, Vietnam.
Figure 3 from: Orlov NL, Ermakov OA, Nguyen TT, Ananjeva NB (2021) A new record of odd-scaled snake (Serpentes, Xenodermidae) from Vietnam: expanded description of Parafimbrios vietnamensis based on integrative taxonomy. ZooKeys 1048: 79-89. https://doi.org/10.3897/zookeys.1048.66477
Figure 3 Parafimbrios vietnamensisZISP 31426 in life A dorsal view of head B ventral view of head C dorsolateral view of midbody D ventrolateral view of midbody.
Figure 2 from: Orlov NL, Ermakov OA, Nguyen TT, Ananjeva NB (2021) A new record of odd-scaled snake (Serpentes, Xenodermidae) from Vietnam: expanded description of Parafimbrios vietnamensis based on integrative taxonomy. ZooKeys 1048: 79-89. https://doi.org/10.3897/zookeys.1048.66477
Figure 2 Parafimbrios vietnamensisZISP 31426 A dorsal view in life B ventrolateral view in life C dorsal view in life D ventral view of the preserved specimen.
Figure 1 from: Orlov NL, Ermakov OA, Nguyen TT, Ananjeva NB (2021) A new record of odd-scaled snake (Serpentes, Xenodermidae) from Vietnam: expanded description of Parafimbrios vietnamensis based on integrative taxonomy. ZooKeys 1048: 79-89. https://doi.org/10.3897/zookeys.1048.66477
Figure 1 Map of Indochina showing the known localities of Parafimbrios lao (red dots) and P. vietnamensis (green dots) (after Teynié et al. 2015; Nguyen et al. 2015; Teynié and Hauser. 2017; Ziegler et al. 2018; Bo et al. 2020) 1 Pua district, Nan Province, Thailand 2 Ngoi District, Luangphrabang Province, Laos (type locality of P. lao) 3 Vieng Xai District, Houaphan Province, Laos 4 Thuan Chau District, Son La Province, Vietnam 5 Jiangcheng County, Yunnan Province, Southwestern China; P. vietnamensis6 Hoang Ho Village, Phang So Lin Commune, Sin Ho District, Lai Chau Province, Vietnam, 22.4167°N, 103.3681°E (type locality of P. vietnamensis) 7ZISP 31426, Che Tao Village, The Mu Cang Chai Species and Habitat Conservation Area (SHCA), Yen Bai Province, Vietnam, 21.5435°N, 104.0364°E (new record of P. vietnamensis).
Figure 17 in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 17. Holotype (ZMB 29089) of Acanthocercus minutus, from Dscheffedenza, Ethiopia.
Figure 15 in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 15. Holotype (ZMB 23906) of Acanthocercus kiwuensis, from Kissenji, Rwanda.
Figure 11 in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 11. Holotype (ZFMK 88682) of Acanthocercus branchi, from Chipata, Zambia.
Figure 12 in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 12. Neotype (ZFMK 88492, designated herein) of Agama cyanocephala, from Ikelenge, Zambia.
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 18 in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 18. Holotype (ZMB 11904) of Acanthocercus ugandaensis, from 'Uganda'.
Figure 2 in Lifting the blue-headed veil - integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae)
Figure 2. Overview of the 13 homologous landmarks used for the analysis.
Figure 2 from: Zeng X-G, Wang J, Yang J, Li W-C (2021) Integrative taxonomy reveals a new species of the genus Burmoniscus (Isopoda, Philosciidae) from the Xuefeng Mountains, China. ZooKeys 1055: 123-134. https://doi.org/10.3897/zookeys.1055.66879
Figure 2 Burmoniscus chuanyanensis Li, sp. nov., paratype, male A habitus in dorsal view; blue circles showing insertion of noduli lateralesB pleon in dorsal view C pleon in ventral view D pleopod 1 exopodite E pleopod 1 endopodite.
Figure 3 from: Zeng X-G, Wang J, Yang J, Li W-C (2021) Integrative taxonomy reveals a new species of the genus Burmoniscus (Isopoda, Philosciidae) from the Xuefeng Mountains, China. ZooKeys 1055: 123-134. https://doi.org/10.3897/zookeys.1055.66879
Figure 3 Burmoniscus chuanyanensis Li, sp. nov., holotype A antennule B antenna C left mandible D right mandible E maxillule F maxilla G maxilliped H pereopod 1 I pereopod 7 J pleopod 1 exopodite K pleopod 1 endopodite L pleopod 2 exopodite M pleopod 2 endopodite.
Figure 1 from: Zeng X-G, Wang J, Yang J, Li W-C (2021) Integrative taxonomy reveals a new species of the genus Burmoniscus (Isopoda, Philosciidae) from the Xuefeng Mountains, China. ZooKeys 1055: 123-134. https://doi.org/10.3897/zookeys.1055.66879
Figure 1 Maximum likelihood (ML) tree of the COI dataset with best ModelFinder model applied. Values below the nodes represent bootstrap support (BS) values from 1000 replicates, and values above the nodes represent the posterior probability (PP) of the Bayesian analysis of the same dataset.
Figure 5 from: Zeng X-G, Wang J, Yang J, Li W-C (2021) Integrative taxonomy reveals a new species of the genus Burmoniscus (Isopoda, Philosciidae) from the Xuefeng Mountains, China. ZooKeys 1055: 123-134. https://doi.org/10.3897/zookeys.1055.66879
Figure 5 Burmoniscus kathmandius (Schmalfuss, 1983), male A habitus in dorsal view B telson in dorsal view C pleon in ventral view D pleopod 1 exopodite E pleopod 1 endopodite.
Figure 4 from: Zeng X-G, Wang J, Yang J, Li W-C (2021) Integrative taxonomy reveals a new species of the genus Burmoniscus (Isopoda, Philosciidae) from the Xuefeng Mountains, China. ZooKeys 1055: 123-134. https://doi.org/10.3897/zookeys.1055.66879
Figure 4 Burmoniscus mauritiensis (Taiti & Ferrara, 1983), male A habitus in dorsal view B telson in dorsal view C pleon in lateral view D pleopod 1 exopodite E pleopod 1 endopodite.
Figure 4 in Integrative taxonomy uncovers high levels of cryptic species diversity in Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) and the description of a new species from Peninsular Malaysia
Figure 4. Distribution of the species of the harterti group. Polygons represent type localities.
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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)
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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.