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Supplemental_Data_S1 for "Kmer Manifold Approximation and Projection for visualizing DNA sequences"
<p>This dataset includes the results generated by KMAP software applied to the htselexdata dataset. Each folder within the dataset contains outputs from multiple dimensionality reduction techniques, including KMAP, UMAP, t-SNE, and MDS. Additionally, motifs and logos have been derived using both KMAP and MEME methods. This data provides insights into motif patterns and structures, which can be beneficial for further bioinformatics and computational biology analyses.</p>
Fig. 8 in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 8. Thyropygus sutchariti sp. nov., from Kaeng Krachan, holotype (CUMZ-D00090), ♂, gonopods. A. Anterior view, left telopodite removed. B. Posterior view, left telopodite removed. C. Left telopodite, posterior-mesal view. D. Left telopodite, anterior-lateral view.
Fig. 11. A in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 11. A. Thyropygus navychula sp. nov., specimen from Surin Islands, living ♂ (paratype, CUMZ-D00089-1). B. Thyropygus forceps sp. nov., specimen from Namwang Srithammasokrach, living ♂ (paratype, CUMZ-D00073-1).
Fig. 5 in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 5. Thyropygus mesocristatus sp. nov., from Srikasorn, holotype (CUMZ-D00094), ♂, gonopods. A. Anterior view, left telopodite removed. B. Posterior view, left telopodite removed. C. Lateral view. D. Left telopodite, posterior-mesal view. E. Left telopodite, anterior-lateral view.
Fig. 2 in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 2. Thyropygus cimi sp. nov., from Namwang Srithammasokrach, holotype (CUMZ-D00086), ♂, gonopods. A. Anterior view, left telopodite removed. B. Posterior view, left telopodite removed. C. Lateral view. D. Left telopodite, posterior-mesal view. E. Left telopodite, anterior-lateral view.
Fig. 1 in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 1. Phylogenetic relationships of Thyropygus species based on maximum likelihood analysis (ML) and Bayesian Inference (BI) of 1147 bp of concatenated gene fragments of COI (660 bp) and 16S rRNA (487 bp). Numbers at nodes indicate branch support based on bootstrapping (ML) / posterior probability (BI). Scale bar = 0.06 substitutions/site. # indicates branches which received <50% ML bootstrap support, - indicates non-supported branches by posterior probability. Clade memberships and designations are shown as vertical bars; 1A1 = T. allevatus, 1A2 = cuisinieri subgroup, 1A3 = opinatus subgroup and 1A4 = induratus subgroup. The coloured area marks the T. opinatus subgroup. Abbreviations after species names refer to locality names as shown in Table 1.
Fig. 7 in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 7. Thyropygus planispina sp. nov., from Tham Sua temple, holotype (CUMZ-D00088), ♂, gonopods. A. Anterior view, left telopodite removed. B. Posterior view, left telopodite removed. C. Lateral view. D. Left telopodite, posterior-mesal view. E. Left telopodite, anterior-lateral view.
Fig. 6 in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 6. Thyropygus navychula sp. nov., from Surin Islands, holotype (CUMZ-D00095), ♂, gonopods. A. Anterior view, left telopodite removed. B. Posterior view, left telopodite removed. C. Left telopodite, posterior-mesal view. D. Left telopodite, anterior-lateral view.
Fig. 4 in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 4. Thyropygus forceps sp. nov., gonopods. – A, C–E. Holotype (CUMZ-D00092), ♂, from Namwang Srithammasokrach. A. Anterior view, left telopodite removed. C. Posterior view, left telopodite removed. D. Left telopodite, posterior-mesal view. E. Left telopodite, anterior-lateral view. – B. Specimen from Tham Pha Deang temple (CUMZ-D00093), ♂. Anterior view, left telopodite removed.
Fig. 10 in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 10. Thyropygus ursus sp. nov., from Lanta Islands, holotype (NMHW-Inv.7855), ♂, gonopods. A. Anterior view, left telopodite removed. B. Posterior view, left telopodite removed. C. Left telopodite, posterior-mesal view. D. Left telopodite, anterior-lateral view.
Fig. 9 in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 9. Thyropygus undulatus sp. nov., from Khao Phanom Bencha, holotype (CUMZ-D00087), ♂, gonopods. A. Anterior view, left telopodite removed. B. Posterior view, left telopodite removed. C. Lateral view. D. Left telopodite, posterior-mesal view. E. Left telopodite, anterior-lateral view.
Fig. 3 in A revision of the Thyropygus allevatus group. Part V: Nine new species of the extended opinatus subgroup, based on morphological and DNA sequence data (Diplopoda: Spirostreptida: Harpagophoridae)
Fig. 3. Thyropygus culter sp. nov., from Rorn waterfall, holotype (CUMZ-D00091), ♂, gonopods. A. Anterior view, left telopodite removed. B. Posterior view, left telopodite removed. C. Left telopodite, posterior-mesal view. D. Left telopodite, anterior-lateral view.
Figure 1 in Evaluation of the taxonomy of Helix cincta (Muller, 1774) and Helix nucula (Mousson, 1854); insights using mitochondrial DNA sequence data
Figure 1. Map showing the localities of samples used in the present study representing the morphologically defined species and the distribution of Helix cincta (dash line, light grey) and Helix nucula (continuous line, dark grey).
Fig. 3 in Relationships Of The Heteronchocleidids (Heteronchocleidus, Eutrianchoratus And Trianchoratus) As Inferred From Ribosomal Dna Nucleotide Sequence Data
Fig. 3. Bayesian consensus tree for the anabantoids, channids and catfishes (silurids, bagrids, clariids) obtained using partial Cytochrome b sequences with cyprinids as outgroup. The heteronchocleidids genera present on the anabantoids and channids are shown with their geographical areas. Values shown at each node refer to Bayesian posterior probabilities. (*refer to Table 3 for names used in GenBank).
Fig. 2. Bayesian consensus tree generated from partial 28S in Relationships Of The Heteronchocleidids (Heteronchocleidus, Eutrianchoratus And Trianchoratus) As Inferred From Ribosomal Dna Nucleotide Sequence Data
Fig. 2. Bayesian consensus tree generated from partial 28S rDNA sequences (D1 domain) with Diplectanum spp. and Gyrodactylus spp. as outgroups. Values shown at each node refer to Bayesian (BI) posterior probabilities/maximum likelihood (ML) percentages of the bootstrap values with 100 replicates. Bootstrap values lower than 50 are given as dashes (-).
Fig. 1 in Relationships Of The Heteronchocleidids (Heteronchocleidus, Eutrianchoratus And Trianchoratus) As Inferred From Ribosomal Dna Nucleotide Sequence Data
Fig. 1. Neighbour joining (NJ) tree constructed by PAUP* using partial 28S rDNA sequences (D1 domain) with Diplectanum spp. and Gyrodactylus spp. as outgroups. Percentages of the bootstrap values for neighbour joining (NJ)/maximum parsimony (MP) (NJ & MP=1,000 replicates) are shown along the branches. Bootstrap values lower than 50 are given as dashes (-).
Data from: A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus), and Panthera species, using targeted bisulfite sequencing and machine learning models
<p><span>Knowledge of individual age can help both in-situ and ex-situ conservation programs to design more efficient and suitable management plans for targeted wildlife species. DNA methylation is one of the epigenetic aging markers that has emerged as a promising tool that can estimate age with high accuracy using only a tiny amount of biological material, which can be collected in a minimally invasive way. Here, we sequenced five targeted genetic regions and used </span><span>8–23</span><span> selected CpG sites to build age estimation models with machine learning methods </span><span>with about only $3–7 per sample</span><span>, using blood samples of seven Felidae species—ranging from small to big, and domestic to endangered species: domestic cats (<em>Felis catus</em>, 139 samples), Tsushima leopard cats (<em>Prionailurus bengalensis euptilurus</em>, 84 samples), and five<em> Panthera </em>species (96 samples). </span><span>The models built achieved satisfactory accuracy—the mean absolute error of the best models was 1.966, 1.348, and 1.552 years in domestic cats, Tsushima leopard cats, and <em>Panthera</em> spp., respectively.</span><span> Our models in domestic cats and Tsushima leopard cats were applicable to individuals regardless of health conditions, indicating the high applicability of our models to samples collected from diverse situations, e.g., rescued individuals in the context of conservation. We also showed the possibility of developing universal age estimation models for the five<em> Panthera</em> spp. using two of the five genetic regions, suggesting an even lower cost to use our models for future applications.</span></p>
Data from: Restriction site-associated DNA sequencing reveals local adaptation despite high levels of gene flow in Sardinella lemuru (Bleeker, 1853) along the northern coast of Mindanao, Philippines
<p>Stock identification and delineation are important in the management and conservation of marine resources. These were highlighted as priority research areas for Bali sardinella (<em>Sardinella lemuru</em>) which is among the most commercially important fishery resources in the Philippines. Previous studies have already assessed the stocks of <em>S. lemuru</em> between Northern Mindanao Region (NMR) and Northern Zamboanga Peninsula (NZP), yielding conflicting results. Phenotypic variation suggests distinct stocks between the two regions, while mitochondrial DNA did not detect evidence of genetic differentiation for this high gene flow species. This paper tested the hypothesis of regional structuring using genome-wide single nucleotide polymorphisms (SNPs) acquired through restriction-site associated DNA sequencing (RADseq). We examined patterns of population genomic structure using a full panel of 3,573 loci, which was then partitioned into a neutral panel of 3,348 loci and an outlier panel of 31 loci. Similar inferences were obtained from the full and neutral panels, which were contrary to the inferences from the outlier panel. While the full and neutral panels suggested a panmictic population (global F<sub>ST</sub> ~ 0, p > 0.05), the outlier panel revealed genetic differentiation between the two regions (global F<sub>ST</sub> = 0.161, p = 0.001; F<sub>CT</sub> = 0.263, p < 0.05). This indicated that while gene flow is apparent, selective forces due to environmental heterogeneity between the two regions play a role in maintaining adaptive variation. Annotation of the outlier loci returned five genes that were mostly involved in organismal development. Meanwhile, three unannotated loci had allele frequencies that correlated with sea surface temperature. Overall, our results provided support for local adaptation despite high levels of gene flow in <em>S. lemuru</em>. Management therefore should not only focus on demographic parameters (e.g., stock size, catch volume), but also consider the preservation of adaptive variation.</p>
Morphological and DNA sequence data generated by Sanger sequencing and target capture methods for moss plants in the genus Fissidens from herbarium specimens
<p><span>Morphological evolution in mosses has long been hypothesized to accompany shifts in microhabitats and can be tested using comparative phylogenetics. These lines of inquiry have developed substantially, in part, by target capture sequencing allowing for phylogenomic scale data generated from herbarium specimens. In the present study, we test the relationship between taxonomically important morphological characters in the moss genus <em>Fissidens</em>, using both a 400-locus dataset generated using a target-capture approach as well as a three-locus phylogeny generated using sanger sequencing. Phylogenetic trees were generated using ASTRAL and Bayesian Inference and used to test the monophyly of subgenera/sections and provided the basis for ancestral character reconstruction and phylogenetic correlation analyses among five morphological characters as well as habitat moisture scored from literature. The characters <em>axillary hyaline nodules</em>, <em>limbidium</em>, <em>costa</em>, and <em>peristome morphology</em> as well as <em>sexual system</em>, <em>minimum habitat moisture</em>, <em>average habitat moisture</em>, <em>maximum habitat moisture</em>, and <em>habitat moisture niche breadth</em> each exhibit statistically significant phylogenetic signal. Significant correlations were found between the limbidium (phyllid/leaf border) and habitat moisture niche breadth, which could be interpreted as a more extensive <em>limbidium</em> enabling species to survive across a wider variety of habitats. Correlations were also found between <em>costa anatomy</em> and the <em>limbidum</em> of the gametophyte and sporophyte <em>peristome</em> <em>morphology</em>, as well as <em>average habitat moisture</em> and <em>sexual system</em>. Continued exploration of the relationships between morphological evolution, life history, and habitat will enable us to expand our understanding of functional morphology in mosses.</span></p>
Figure 2. A in Mitochondrial Dna Sequence Data Indicate Evidence For Multiple Species Within Peromyscus Maniculatus
Figure 2. A) Phylogenetic tree generated using Bayesian (MrBayes; Huelsenbeck and Ronquist 2001), maximum likelihood (RAxML; Version 8.1.17, Stamatakis 2006), and parsimony methods (PAUP* v. 4.0a165, Swofford 2002) and DNA sequence data from the mitochondrial cytochrome-b gene. The topology depicted is from the Bayesian analysis. Clade probability values (≥ 0.95) for the Bayesian analysis are indicated by an asterisk (*) and are to the left of the first slash, bootstrap values for the maximum likelihood analysis are shown between the two slashes, and bootstrap values obtained from the parsimony analysis are to the right of the last slash. Line at bottom of figure depicts the nucleotide substitution rate per site per million years. B) Same phylogenetic tree as depicted in Figure 2A except unsupported nodes (C, G, and H) were collapsed.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.