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927 results for “genetic study”
Evaluating the genetic variation of the COI gene of Insecta: Implications for DNA barcoding, metabarcoding and species delimitation studies
<p>The genetic variation of the COI gene has a great effect on the final results of the species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for comprehensively appraising the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis based on different thresholds were compared among 4,288 genera (35,068 species). Besides, we also compared the match ratios obtained from two species delimitation methods: the clustering analysis (distance-based method) and the bPTP analysis (tree-based method). Furthermore, the effectiveness of two different results of the bPTP analysis: bPTP_h and bPTP_ml was also tested. Approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (> 3%), and a conservative estimate of this value is 12.05-22.58%. The application of empirical thresholds (e.g., 2% and 3%) in the clustering analysis may result in the overestimation of species diversity. In metabarcoding studies, a threshold of 3% can only be used to estimate the insect diversity roughly. As for the clustering analysis, the "threshOpt" or "localMinima" algorithms can provide a priori value for the researcher. Nevertheless, if the minimum interspecific genetic distance of congeneric species was greater than or equal to 2%, it is possible to avoid overestimating the species diversity based on the empirical thresholds. Besides, the match ratios of the bPTP_ml results were higher than those of the bPTP_h results. As for the bPTP analysis, the bPTP_ml results were recommended. If a proper threshold was selected, the clustering analysis may outperform the bPTP analysis.</p>
FIGURE 23 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 23. Habitat of Ahaetulla travancorica sp. nov. in the upper reaches of Podhigai hills, a part of the Agasthyamalai Ranges, Southern Western Ghats (in Tirunelveli district, Tamil Nadu State, India) showing montane shola grasslands.
FIGURE 22 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 22. Images of Ahaetulla travancorica sp. nov. Images of BNHS 3592 (CESS075). (a) Head lateral, (b) Head dorsal, (c) Ventral section, (d) Whole specimen Live uncollected individual from Kalakkadu Mundunthurai, (e) Head Dorso-lateral, (f) Head lateral, (g) Threat display (Photos: Vivek Philip Cyrac) (Images a & b to scale, other images not to scale).
FIGURE 25 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 25. Habitat of Ahaetulla perroteti, Mukurthi Hills, in the upper Nilgiris (in the Nilgiri district, Tamil Nadu State, India) showing montane shola grasslands.
FIGURE 19 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 19. Images of Ahaetulla borealis sp. nov. Images of holotype BNHS 3590 (CESS421). (a) Head lateral, (b) Head dorsal, (c) Ventral section, (d–e) Everted hemipenis, (f) Whole specimen. Live uncollected individual from Siddapur (Jog Falls), (g) Threat display of CESS104 from Matheran and (h) Head lateral of CESS103 from Matheran (Images a & b; d & e to scale, other images not to scale).
FIGURE 21 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 21. Images of Ahaetulla dispar. Live uncollected individual from High Wavy Mts.(a) Head lateral, (b) Head Dorsolateral, (c) Full body image (live) from High Wavy, (d) Threat display of CESS188 from Anamudi Hills, (e) Habitat of A. dispar, Eravikulam.
FIGURE 20 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 20. Habitat of Ahaetulla borealis sp. nov. Khandala, Northern Western Ghats (in Pune district, Maharashtra State, India) showing moist deciduous and semi-evergreen forest vegetation type.
FIGURE 18 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 18. Habitat of Ahaetulla farnsworthi sp. nov. in Agumbe, Central Western Ghats (in Shimoga district, Karnataka State, India) showing tropical rainforest vegetation type.
FIGURE 15 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 15. Images of Ahaetulla malabarica sp. nov. Images of Holotype BNHS 3586 (CESS090). (a) Head lateral, (b) Head dorsal, (c) Ventral section, (d–f) Everted Hemipenis. Whole specimen (CESS090). Head lateral images of different colour morphs (live), (g) CESS090 from Brahmagiri, (h) CESS144 from Siruvani, (i) CESS143 from Poochipara, (j) CESS090 from Brahmagiri. Image of a live, uncollected individual, (k) Whole animal from Brahmagiri Hills (Images a & b; d & e to scale, other images not to scale).
FIGURE 17 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 17. Images of Ahaetulla farnsworthi sp. nov.. Images of Holotype BNHS 3588 (CESS288). (a) Head lateral, (b) Head dorsal, (c) Ventral section, (d–f) Dissected hemipenis, (g) Whole specimen. Head lateral images of different individuals (live), (h) CESS158 from Kudremukh, (i) CESS157 from Kudremukh, (j) Body section showing interscalar colouration (CESS158), (k) Image of a live, uncollected individual from Agumbe (Photo: Shreeram M.V.) (Images a & b; d, e & f to scale, other images not to scale).
FIGURE 6 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 6. Ahaetulla lineages in Peninsular India and Sri Lanka showing side-by-side comparison of their superficial head morphology and maxillary dentition. (From the top) (a) Ahaetulla farnsworthi sp. nov. (b) A. isabellina comb. nov. (c) A. malabarica sp. nov. (d) A. borealis sp. nov. (e) A. nasuta (f) A. oxyrhyncha comb. nov. (g) A. sahyadrensis nom. nov. (h) A. travancorica sp. nov. (i) A. dispar & A. travancorica sp. nov. (j) A. perroteti (1) Ahaetulla farnsworthi sp. nov. (2) A. isabellina comb. nov. (3) A. malabarica sp. nov. (4) A. borealis sp. nov. (5) A. nasuta (6) A. oxyrhyncha comb. nov. (7) A. pulverulenta (8) A. sahyadrensis nom. nov. (9) A. dispar (10) A. travancorica sp. nov. (11) A. perroteti.
FIGURE 14 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 14. Habitat of Ahaetulla isabellina comb. nov., near Valparai, Anamalai Hills, Southern Western Ghats (Tirupur district, Tamil Nadu State, India) showing evergreen and semi-evergreen forest vegetation types.
FIGURE 10 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 10. Images of Ahaetulla oxyrhyncha comb. nov. Head lateral images of (a) CESS211, (b) CESS244, (d) CESS506, & (c) dorso-lateral of a live specimen (from the CESS244 population). Images of a live, uncollected individual from Coimbatore. Tamil Nadu (e) showing threat display, (f) Full animal, (g) Habitat (images not to scale).
FIGURE 3 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 3. PCA plot shows quantitative morphological space shared by Western Ghats Ahaetulla spp.. In the figure, members of the Ahaetulla nasuta species complex with lineages L3—A. borealis sp. nov. (dark blue crosses), L4—A. farnsworthi sp. nov. (green filled squares), L5—A. isabellina comb. nov. (brown cross) and L6—A. malabarica sp. nov. (black squares) from the Western Ghats are clustered together and share morphological space. The PCA plots correspond to the scores and loadings presented in Appendix IV (D, E & F).
FIGURE 5 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 5. Phylogenetic reconstruction of Ahaetulla species revealing the cladistic relationships and lineage diversity. Gray bar depicts species-level entities, some of which are numbered and depicted adjacent to their cluster.
FIGURE 4 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 4. Maps showing the distribution of lineages in the Western Ghats (in Peninsular India) and Sri Lanka. (A) Map showing our study's point locations of Ahaetulla farnsworthi sp. nov., A. isabellina comb. nov., A. malabarica sp. nov., A. borealis sp. nov., A. nasuta & A. oxyrhyncha comb. nov.. (B) Map showing our study's point locations of Ahaetulla perroteti, A. dispar & A. travancorica sp. nov..
FIGURE 13 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 13. Images of Ahaetulla isabellina comb. nov. Images of holotype BNHS 3584 (CESS183). (a) Head lateral, (b) Head Dorsal, (c) Ventral section, (d–f) Dissected hemipenis, (g) Whole specimen. Images of live individuals, (h) BNHS 3584 (CESS183) head lateral, (i) head lateral of CESS182, (j) body section of CESS182. Image of a live, uncollected individual from Valparai, (k) showing threat display (Images a & b; d, e & f to scale, other images not to scale).
FIGURE 1. Maximum likelihood tree generated from three mitochondrial genes shows a in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 1. Maximum likelihood tree generated from three mitochondrial genes shows a number of new lineages (L1–L13) identified in our study. The lineages are marked with grey bars which represent the criteria used to delimit species boundaries, where three gene bPTP (P3), genetic p-distance (GD), morphological separation (M) and geographic isolation (G) are used to predict the number of putative lineages. The nodes below 70% parametric bootstrap support are indicated with asterisk (*). "+" indicates that the status of A. nasuta cf. isabellina needs further work (see Deepak et al. 2019).
FIGURE 16 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 16. Habitat of Ahaetulla malabarica sp. nov. in Brahmagiri Hills, Central Western Ghats (borders Kodagu district, Karnataka State and Waynad district, Kerala State, India) showing semi-evergreen and evergreen forest vegetation types.
FIGURE 9 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 9. Reproductions of colour plates of (a) Coluber nasutus (La Nasique) from Lacepede (1789: 302, pl. 4); (b) Dryinus oxyrhynchus (Passeriki Pam) from Russell (1796: pl. 12); (c) Dryinus russellianus (Botla Passeriki) from Russell (1796: pl. 13); (d) Photo of the preserved skin of BMNH 1904.7.27.25 Dryophis passeriki Photo: Gernot Vogel.
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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.