Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,110
datasets available to search
ShareScore release 0.9.0
Dataset results
3,110 results for “cryptic species”
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)
<p>GENERAL INFORMATION</p> <p>1. Title of Dataset: Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)</p> <p>2. Author Information<br> A. Principal Investigator Contact Information<br> Name: Scott Burgess<br> Institution: Florida State University<br> Address: 319 Stadium Drive, Tallahassee, FL, USA 32306<br> Email: sburgess@bio.fsu.edu</p> <p><br> 3. Date of data collection (single date, range, approximate date): 2019-08</p> <p>4. Geographic location of data collection: Moorea, French Polynesia</p> <p>5. Information about funding sources that supported the collection of the data: National Science Foundation (NSF; OCE-1829867)</p> <p> </p> <p><br> DATA & FILE OVERVIEW</p> <p>1. File List:<br> Figure 2 Make.R<br> Figure 4 Make.R<br> Figure 5b Make.R<br> Figure 6 Make.R</p> <p>Figure 1 SNAPP species tree.xml<br> Figure 2.txt<br> Figure 2.vcf<br> Figure 3b - Pocillopora mt genomes.nex<br> Figure 4 and 6 data.csv<br> Figure 4 colors.csv<br> Figure 5a - Cladocopium_psbA.nex<br> Figure 5b - Clad clades.csv<br> Figure 5b_Cladocopium.nex<br> Figure 5b_Pocillopora.nex<br> Figure 5b.csv</p> <p><br> 2. Relationship between files:<br> Figure 2 Make.R uses Figure 2.txt and Figure 2.vcf<br> Figure 4 Make.R uses Figure 4 and 6 data.csv and Figure 4 colors.csv<br> Figure 5b Make.R uses Figure 5b - Clad clades.csv, Figure 5b_Cladocopium.nex, Figure 5b_Pocillopora.nex, and Figure 5b.csv<br> Figure 6 Make.R Figure 4 and 6 data.csv</p> <p> </p> <p>3. Metadata</p> <p>Figure 2 Make.R:<br> R code to produce Figure 2, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 2.txt', 'Figure 2.vcf'</p> <p><br> Figure 4 Make.R:<br> R code to produce Figure 4, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 4 and 4 data.csv', 'Figure 4 colors'</p> <p><br> Figure 5b Make.R:<br> R code to produce Figure 5b, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 5b - Clad clades.csv', 'Figure 5b_Cladocopium.nex', 'Figure 5b_Pocillopora.nex', 'Figure 5b.csv'</p> <p><br> Figure 6 Make.R:<br> R code to produce Figure 6, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 4 and 6 data.csv'</p> <p><br> Figure 1 SNAPP species tree.xml:<br> Data for species tree used in Figure 1</p> <p>Figure 2.txt:<br> Metadata<br> Sample_ID: Sample ID<br> Hap_Spp: Pocillopora species or haplotype</p> <p>Figure 2.vcf:<br> Linked dataset of 7,887 SNPs</p> <p>Figure 3b - Pocillopora mt genomes.nex:<br> Nexus tree of Pocillopora mitochondrial genomes used in Figure 3b</p> <p><br> Figure 4 and 6 data.csv:<br> Metadata<br> Species.haplotype: Pocillopora species or haplotype<br> Depth.m: Sampling depth in meters<br> Site: Sampling site, label corresponds to the site used in the Moorea Coral Reef Long-Term Ecological Research (MCR-LTER) program.<br> Coral.ID: Coral colony identifier<br> Type_profile: ITS2 type profile generated by SymPortal<br> Type_profile_Prop: Proportion of that given ITS2 type profile in colony sampled<br> Remaining columns: Proportion of ITS2 sequences in colony sampled</p> <p>Figure 4 colors.csv:<br> Metadata<br> my_colors: Custom colors for each ITS2 sequence<br> Symbio.clade: ITS2 sequences</p> <p>Figure 5a - Cladocopium_psbA.nex:<br> Nexus tree of Cladocopium taxa in figure 5a</p> <p>Figure 5b - Clad clades.csv:<br> Metadata<br> UCI_links: Sample ID that contains Pocillopora species or haplotype, sample ID, and ITS2 type profile<br> Clad_clades: Clade assignment from figure 5a</p> <p>Figure 5b_Cladocopium.nex:<br> Nexus tree of Cladocopium taxa in Figure 5b</p> <p>Figure 5b_Pocillopora.nex:<br> Nexus tree of Pocillopora taxa used in PACo analysis, Figure 5b</p> <p>Figure 5b.csv:<br> Matrix of Pocillopora host and Cladocopium symbiont links</p>
Supplemental material for the manuscript "Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species".
<p><strong>Supplementary material for the manuscript “Extreme genome scrambling in marine planktonic <em>Oikopleura dioica</em> cryptic species”.<br></strong></p> <p><strong><em>BreakpointsData.tar.xz contains:</em></strong></p> <ul> <li>Pairwise genome alignment files for <em>Oikopleura</em>, <em>Ciona</em>, <em>Caenorhabditis</em>, insects and muntjaks in GFF format in `inst/extdata/`.</li> <li>dN / dS computation results in `inst/extdata/dNdS/`.</li> <li>Annotations of gene models and repeat elements in GFF format in `inst/extdata/Annotations/`.</li> <li>OrthoGroups in `inst/extdata/OrthoFinder/`, where N19 represents the _O. dioica_ clade,</li> <li>N3 the tunicates and N20 the _Ciona_ clade.</li> <li>`BreakpointsData_3.11.0.tar.gz`, a R package installing the above files in the R environments where we ran our computations.</li> <li>The files needed to build the `BreakpointsData` package.</li> </ul> <p><em><strong>Oidioi_pairwise_v3.tar.gz contains:</strong></em></p> <ul> <li>The pairwise alignment files between genomes, in MAF format.</li> <li>A copy of the Nextflow pipeline used to generate them.</li> </ul> <p><em><strong>oist-assembler.tar.gz contains:</strong></em></p> <ul> <li>A Singularity image and its definition file for flye version 2.8.3-b1763` Flye-flye.2.8.3-b1763.sif` and `Flye-flye.def`.</li> <li>A copy of the Nextflow pipeline used to assemble the Bar2_p4 genome in `oist-assembler-Bar2_p4`.</li> <li>A copy of the Nextflow pipeline used to assemble the other genome in `oist-assembler-other_genomes`.</li> </ul> <p><em>Please note that these files are provided for reproducibility only and probably can not be used easily for other purposes.</em></p> <p><em><strong>Oidioi_genomes.tar.gz contains:</strong></em></p> <ul> <li>For each genome, one file (`<genome>.fa`) containing the whole genome sequence and one directory (`<genome>`) containing each chromosome, scaffold or contig of the genome as a separate file.</li> <li>For each genome, one R package, its source directory, and the vignette to create it, providing the genome information as a `BSgenome` object.</li> </ul> <p><em><strong>OrthoFinderRun.tar.xz contains:</strong></em></p> <ul> <li>A full copy of the OrthoFinder2 run that we used to compute hierarchical orthogroups.</li> </ul> <p><em><strong>Supplemental_Code.tar.gz contains:</strong></em></p> <ul> <li>A copy of <https://github.com/oist/LuscombeU_OikScrambling>, where the `.git` and `doc` directories were removed to save space.</li> </ul> <p><em><strong>AugustusAnnotation.tar.gz (added July 26th 2024) contains:</strong></em></p> <ul> <li>AUGUSTUS runs to produce the annotations that were input to OrthoFinder2. We provide them for reproducibility, with no guarantee that they are suitable for other purposes. The annotations used in the manuscript are AOM-5-5f.sm.OSKA-CDS, Bar2_p4_Flye.sm, Bsty_SCLE01.1.sm.abi.cionamodel, Fbor_SDII01.1.sm.abi, KUM-M3-7f.sm.OKI-CDS, Mery_SCLF01.1.sm.abi.cionamodel, Oalb_SCLG01.1.sm.abi.cionamodel, OKI2018_I69_annotv2.sm, Olon_SCLD01.1.sm.abi, OSKA2016v1.9.sm and Ovan_SCLH01.1.sm.abi.cionamodel.</li> </ul>
Fig. 1 in Resolving the Ophioderma longicauda (Echinodermata: Ophiuroidea) cryptic species complex: five sisters, three of them new
Fig. 1. Phylogenetic relationships and distribution of species of Ophioderma Müller & Troschel, 1840 in the Northeast and Tropical Atlantic Ocean and the Mediterranean Sea. A. Simplified phylogenetic relationships among species of Ophioderma described in this study, modified from Weber et al. (2019). Summary of reproductive strategy: S = broadcast spawner; B = brooder. Correspondence between species names, nuclear genetic clusters and COI mitochondrial lineages is summarized from Boissin et al. (2011) and Weber et al. (2019). C6 is tentatively assigned to O. zibrowii sp. nov. because it occurs far from the type locality and brooding species are expected to have low dispersal rates, leading to low gene flow between populations. B. Distribution of species of Ophioderma in the Northeast and Tropical Atlantic Ocean. C. Distribution of species of Ophioderma in the Mediterranean Sea.
Figure 2. D in Neotypification of Drawida hattamimizu Hatai, 1930 (Annelida, Oligochaeta, Megadrili, Moniligastridae) as a model linking mtDNA (COI) sequences to an earthworm type, with a response to the 'Can of Worms' theory of cryptic species
Figure 2. D. hattamimizu unscaled habitus (from Watanabe, 2005, fig. 1 after Hatai's 1931 original).
Appendix. List of the 28S and 16S rRNA sequences recovered from GenBank. 28S = 28S rRNA GenBank accession number; 16S = 16S rRNA GenBank accession number. in Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae)
Appendix. List of the 28S and 16S rRNA sequences recovered from GenBank. 28S = 28S rRNA GenBank accession number; 16S = 16S rRNA GenBank accession number.
Fig. 5 in Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae)
Fig. 5. Macrobrachium ustulatus (Nobili, 1899). – A–B, E. MNHN-IU-2013-13202. A. Cephalothorax. B. Epistome. E. Major second pereiopod finger. – C, G. MNHN-IU-2013-13201. C. Fourth thoracic sternite. G. Minor second pereiopod finger. – D, F. MNHN-IU-2013-13203. D. Major second pereiopod. F. Minor second pereiopod. Scale bars: A, E, G = 2 mm; B–C = 1 mm; D, F = 4 mm.
Fig. 3 in Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae)
Fig. 3. Macrobrachium australe (Guérin-Méneville, 1838 in Guérin-Méneville 1829–1838), MNHN- IU-2013-13198. A. Cephalothorax. B. Epistome. C. Fourth thoracic sternite. D. Major second pereiopod. E. Major second pereiopod finger. F. Minor second pereiopod. G. Minor second pereiopod finger. Scale bars: A, E, G = 2 mm; B–C = 1 mm; D, F = 4 mm.
Fig. 1 in Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae)
Fig. 1. Map of the Indo-Pacific showing localities where Macrobrachium australe (Guérin-Méneville, 1838 in Guérin-Méneville 1829–1838) (black area) and M. ustulatum (Nobili, 1899) (red area) were collected and/or recorded. Capitalized locality names correspond to the 7 localities sampled for this study. Non-capitalized locality names correspond to the localities reported from the literature. Stars shows the type localities of the synonyms of M. australe (black stars) and M. ustulatum (red star).
Fig. 4. A in Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae)
Fig. 4. A. Live coloration of Macrobrachium australe (Guérin-Méneville, 1838 in Guérin-Méneville 1829–1838) (photo: E. Vigneux). B. Live coloration of M. ustulatum (Nobili, 1899) (photo: P. Keith).
Fig. 8 in Allopatric cryptic diversity in the alpine species complex Phtheochroa frigidana s. lat. (Lepidoptera: Tortricidae)
Fig. 8. Female genitalia of Phtheochroa spp. A. P. schawerdae (Rebel, 1908) comb. nov., Bulgaria, Rila Mts. – B. P. alpinana sp. nov., France, Alpes Maritimes, paratype. Arrow: ventral diverticulum of ductus bursae. Scale bar = 250 µm.
Fig. 5 in Allopatric cryptic diversity in the alpine species complex Phtheochroa frigidana s. lat. (Lepidoptera: Tortricidae)
Fig. 5. Phalli with vesica everted, Phtheochroa schawerdae (Rebel, 1908) comb. nov. A–B. Bulgaria, Rila Mts. – C–D. Republic of Macedonia, Korab Mts. A, C: left. B, D: dorsal. Abbreviations: gs = gonopore sclerotization; ld = left diverticulum; rd = right diverticulum; svd = small ventral diverticulum; vpp = ventral phallic process. Scale bar = 250 µm.
Fig. 10 in Allopatric cryptic diversity in the alpine species complex Phtheochroa frigidana s. lat. (Lepidoptera: Tortricidae)
Fig. 10. Distribution of the Phtheochroa frigidana s. lat. species complex based on examined material.
Fig. 1 in Allopatric cryptic diversity in the alpine species complex Phtheochroa frigidana s. lat. (Lepidoptera: Tortricidae)
Fig. 1. Adults of Phtheochroa spp. A–D. P. schawerdae (Rebel, 1908) comb. nov. A. ♂, Bulgaria, Pirin Mts. B. ♂, Bulgaria, Rila Mts. C. ♀, Bulgaria, Rila Mts. D. ♂, Republic of Macedonia, Korab Mts. – E–F. P. alpinana sp. nov., France, Alpes Maritimes. E. Holotype, ♂. F. Paratype, ♀. – G. P. apenninana sp. nov., holotype, ♂, Italy, Gran Sasso National Park. – H. P. frigidana (Guenée, 1845) stat. rev., ♂, neotype of Eupoecilia frigidana, Andorra, Pyrenees. – I–J. P. cantabriana sp. nov., Spain, Picos de Europa National Park. I. Holotype, ♂. J. Paratype, ♂. Scale bar = 5 mm, all to scale.
Fig. 9 in Allopatric cryptic diversity in the alpine species complex Phtheochroa frigidana s. lat. (Lepidoptera: Tortricidae)
Fig. 9. Maximum likelihood tree (built with MEGA6) of cytochrome c oxidase subunit I (COI) barcode fragments. Values at the nodes are bootstrap support values based on 500 replicates.
Fig. 4 in Allopatric cryptic diversity in the alpine species complex Phtheochroa frigidana s. lat. (Lepidoptera: Tortricidae)
Fig. 4. Ventral phallic process of Phtheochroa spp., ventral view. A–C. P. schawerdae (Rebel, 1908) comb. nov. A–B. Bulgaria, Rila Mts. C. Republic of Macedonia, Korab Mts. – D–E. P. alpinana sp. nov., France, Alpes Maritimes. D. Holotype. E. Paratype. – F–G. P. apenninana sp. nov., Italy, Gran Sasso National Park. F. Paratype. G. Holotype. – H. P. frigidana (Guenée, 1845) stat. rev., Andorra, Pyrenees, neotype of Eupoecilia frigidana. – I–J. P. cantabriana sp. nov., Spain, Picos de Europa National Park. I. Holotype. J. Paratype. Scale bar = 100 µm, all to scale.
Fig. 6 in Allopatric cryptic diversity in the alpine species complex Phtheochroa frigidana s. lat. (Lepidoptera: Tortricidae)
Fig. 6. Phalli with vesica everted of Phtheochroa spp. A–B. P. alpinana sp. nov., France, Alpes Maritimes, holotype. – C–D. P. apenninana sp. nov., Italy, Gran Sasso National Park, holotype. A, C: left. B, D: dorsal. Abbreviations: dd = dorsal diverticulum; vd = ventral diverticulum; other abbreviations as in Fig. 5. Scale bar = 250 µm.
Fig. 7 in Allopatric cryptic diversity in the alpine species complex Phtheochroa frigidana s. lat. (Lepidoptera: Tortricidae)
Fig. 7. Phalli with vesica everted of Phtheochroa spp. A–B. P. frigidana (Guenée, 1845) stat. rev., Andorra, Pyrenees, neotype of Eupoecilia frigidana. – C–D. P. cantabriana sp. nov., Spain, Picos de Europa National Park, holotype. A, C: left. B, D: dorsal. Abbreviations as in Figs 5–6. Scale bar = 250 µm.
Fig. 2 in Allopatric cryptic diversity in the alpine species complex Phtheochroa frigidana s. lat. (Lepidoptera: Tortricidae)
Fig. 2. Male genitalia (without phalli) of Phtheochroa spp. A–B. P. schawerdae (Rebel, 1908) comb. nov. A. Bulgaria, Rila Mts. B. Republic of Macedonia, Korab Mts. – C. P. alpinana sp. nov., France, Alpes Maritimes, holotype. – D. P. apenninana sp. nov., Italy, Gran Sasso National Park, holotype. – E. P. frigidana (Guenée, 1845) stat. rev., Andorra, Pyrenees, neotype of Eupoecilia frigidana. – F. P. cantabriana sp. nov., Spain, Picos de Europa National Park, holotype. Scale bar = 250 µm, all to scale.
Fig. 3 in Allopatric cryptic diversity in the alpine species complex Phtheochroa frigidana s. lat. (Lepidoptera: Tortricidae)
Fig. 3. Transtilla of Phtheochroa spp. A–B. P. schawerdae (Rebel, 1908) comb. nov., Bulgaria, Rila Mts. – C. P. alpinana sp. nov., France, Alpes Maritimes, holotype. – D. P. apenninana sp. nov., Italy, Gran Sasso National Park, holotype. – E. P. frigidana (Guenée, 1845) stat. rev., Andorra, Pyrenees, neotype of Eupoecilia frigidana. – F. P. cantabriana sp. nov., Spain, Picos de Europa National Park, paratype. Scale bar = 250 µm, all to scale.
Fig. 5 in Reassessment of the taxonomic status of Pseudopaludicola parnaiba (Anura, Leptodactylidae, Leiuperinae), with the description of a new cryptic species from the Brazilian Cerrado
Fig. 5. Holotype and five paratypes of Pseudopaludicola coracoralinae sp. nov. in life. A. ZUEC 24704 (holotype, adult ♂ and call voucher), SVL = 13.1 mm. B. ZUEC 24703 (adult ♂ and call voucher), SVL = 13.2 mm. C. ZUEC 24707 (adult ♂), SVL = 12.5 mm. D. ZUEC 24712 (adult ♀), SVL = 16.0 mm. E. ZUEC 24705 (adult ♀), SVL = 16.8 mm. F. ZUEC 24706 (adult ♀), SVL = 17.0 mm.
ScienceDex guides
Understand access before you commit
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.