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Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)
<p>Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial Control Region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (FST=0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and pre-existing microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (FST=0.08, p<0.001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (FST=0.103, p<0.001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p<0.001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life-history, particularly in light of the natal-homing paradigm.</p>
FIGURE 7 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
FIGURE 7. Scatter plot of Multivariate Principal Component Analysis (PCA) for male individuals using 13 morphometric characters marked as * Supplementary file Table 1 transformed to their ratio to SVL for Minervarya species A (M. species A) and Minervarya species B (M. species B)
FIGURE 3 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
FIGURE 3. Morphological characters of Minervarya species A and Minervarya species B. Minervarya species A (A) and Minervarya species B (B) in life. Note the longitudinal skin folds on dorsal side of Minervarya species A and granular blotches on Minervarya species B. Difference in the webbing pattern on the foot of Minervarya species A (C) and Minervarya species B (D).
FIGURE 10 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
FIGURE 10. Morphological variation in Minervarya syhadrensis frogs from different localities in the Western Ghats. (A and B) Coorg, (C) Goa, (D) Koyna, (E) Silvasa and (F) Calicut.
FIGURE 9 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
FIGURE 9. Dorsal view of M. syhadrensis (Minervarya species A collected for the present study, ZSI/WRC/A/2255) and M. caperata (type specimen BNHS4657). Note the presence of longitudinal skin folds on dorsal side. Scale bar = 1cm.
FIGURE 5 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
FIGURE 5. Advertisement call of Minervarya species B. Microtemporal structure (A) and spectrogram (B) of a call group. (C) Microtemporal structure of a call depicting its pulsatile nature.
FIGURE 2 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
FIGURE 2. Type specimen of Minervarya syhadrensis (ZSI 19764). Note the presence of longitudinal skin folds on dorsal side. Scale bar = 1cm.
FIGURE 1 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
FIGURE 1. Map showing type localities of Minervarya syhadrensis (▲), M. caperata (■) and collection localities (●) in the present study.
FIGURE 4 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
FIGURE 4. Advertisement call of Minervarya species A. Microtemporal structure (A) and spectrogram (B) of a call group. (C) Microtemporal structure of a single call. Note the pulsed nature of call.
FIGURE 6 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
FIGURE 6. Comparison of five call properties between Minervarya species A and Minervarya species B. Bar graphs represent mean±SE (P ˂ 0.05). CD = call duration, PRR = pulse repetition rate, FF = fundamental frequency, and DF = dominant frequency.
FIGURE 8 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
FIGURE 8. Maximum Likelihood tree based on 574 bp of mitochondrial (16S) gene for Minervarya clade having predominant distribution in Sri Lanka, India, Bangladesh and Nepal (Fig 2, Phuge et al. 2019). Locations marked as blue represents the localities from where samples were collected for the present study.
Fig. 2 in Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator
Fig. 2. Last-instar caterpillars of 10 species in the A. fulgerator complex from the ACG. Interim names reflect the primary larval food plant and, in some cases, a color character of the adult.
Fig. 3 in Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator
Fig. 3. NJ tree based on Kimura-2-Parameter distances for COI DNA sequences from 466 individuals of the A. fulgerator complex from the ACG. Numbers in parentheses indicate the total sample size for each interim taxon, rectangles caricature caterpillar color patterns, and black backgrounds indicate groups of 10 conspecifics with identical sequences.
Fig. 1. Newly eclosed female A in Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator
Fig. 1. Newly eclosed female A. fulgerator (species LOHAMP, voucher code 02-SRNP-9770) from the ACG.
SUPPLEMENTARY TABLE 3 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
SUPPLEMENTARY TABLE 3. Call properties measurements of Minervarya species A and Minervarya species B in the present study.
SUPPLEMENTARY TABLE 2 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
SUPPLEMENTARY TABLE 2. Morphometric data (in mm) of type specimens of Minervarya caperata deposited at BNHS and described by Kuramoto et al. (2007).
SUPPLEMENTARY TABLE 1 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
SUPPLEMENTARY TABLE 1. Morphometric data (in mm) of Minervarya species A (M. syhadrensis) and Minervarya species B (M. agricola / M. granosa) from Pune
Figure 8. A–C in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 8. A–C. Holotype of Capulus (Hyalorisia) galea Dall, 1889, USNM 508724, off Barbados. D–F. Holotype of Capulus (Hyalorisia) tosaensis Otuka, 1939, Seto Marine Biological Laboratory, collected from Bay of Tosa, Japan. G–I. Syntype of Capulus fragilis E. A. Smith, 1904, NHMUK 1904.6.15.136, Laccadive Sea. J. Original figure of Capulus fallax S. V. Wood, 1842 (Wood, 1842: pl. 17, fig. 4a, b), Lower Pliocene of England. K–N. Holotype of Capulus (Hyalorisia) nettlesi J. E. Robinson, 1983, PRI 30058, Upper Eocene of Mississippi. Scale bars: A–E, G–I, K–N = 10 mm; F = 5 mm. Photo credits: A–C, USNM; D–F, Kyoto University (taken by Ryutaro Goto); G–I, NHMUK (taken by Harry Taylor); K–N, Paleontological Research Institution, Ithaca, NY.
Figure 10. A–K in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 10. A–K. Distribution of Hyalorisia species (based on our data) and of the Propeamussium host species from GBIF records (L). A. Hyalorisia galea. B. Hyalorisia kely n. sp. C. Hyalorisia lehibe n. sp. D. Hyalorisia madagascarensis n. sp. E. Hyalorisia tosaensis. F. Hyalorisia profunda n. sp. G. Hyalorisia nanhaiensis n. sp. H. Hyalorisia solomonensis n. sp. I. Hyalorisia melanesica n. sp. J. Hyalorisia neocaledonica n. sp. K. Hyalorisia nupta n. sp. L. Distribution of Propeamussium host species based on GBIF records. Ranges are given in different colours as follows: blue, P. dalli; red, P. caducum; yellow, P. watsoni; orange, P. sibogai; green, P. investigatoris; violet, P. jeffreysii. In maps A–K, Hyalorisia records are shown in the same colour as the host species to which they were attached at the time of collection (as in L), or are shown in grey, indicating that samples were not collected directly from a host.
Figure 6 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 6. Shells of Hyalorisia (A–C) and detail of the lamella (D, E). A. Hyalorisia profunda, holotype, MNHN-IM-2013-59695, South China Sea (L = 7 mm). B. Hyalorisia madagascarensis n. sp., holotype, MNHN-IM-2007-39090, off Mahajanga, Madagascar (L = 6.5 mm). C. Hyalorisia solomonensis n. sp., holotype, MNHN-IM-2007-34203, SE of Santa Isabel, Solomon Islands (L = 8 mm). D. Wide lamella of Hyalorisia neocaledonica n. sp., MNHN-IM-2013-65645, Lord Howe Rise, New Caledonia. E. Narrow lamella of Hyalorisia tosaensis, MNHN-IM-2013-58352, New Ireland, Papua New Guinea. Scale bars = 2 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)
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DANDI Archive for NWB datasets
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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.