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35 results for “Specimen tree”
Text-fig. 5. Fossil remains of a leafy Lepidodendron ophiurus BRONGN. shoot bearing a Flemingites strobilus produced by a tree similar to that shown in Text-fig. 2a; Middle Coal Measures Formation (Duckmantian – upper Bashkirian), Brymbo, near Wrexham, UK (see Thomas et al. 2020: fig. 16b); National Museum Wales specimen 2013.43G.120. in Naming Of Parts: The Use Of Fossil-Taxa In Palaeobotany
Text-fig. 5. Fossil remains of a leafy Lepidodendron ophiurus BRONGN. shoot bearing a Flemingites strobilus produced by a tree similar to that shown in Text-fig. 2a; Middle Coal Measures Formation (Duckmantian – upper Bashkirian), Brymbo, near Wrexham, UK (see Thomas et al. 2020: fig. 16b); National Museum Wales specimen 2013.43G.120.
Text-fig. 2. The distinction between fossil plants (a) and plant fossils (b). a: Reconstruction of a late Carboniferous arborescent lycopsid, often referred to as the Lepidodendron-tree; artwork by A. Townsend (formerly of National Museum Wales, Cardiff, UK; see Townsend et al. 1998); b: Lepidodendron aculeatum STERNB.; Middle Coal Measures Formation (Duckmantian – upper Bashkirian), Brymbo, near Wrexham, UK (see Thomas et al. 2020: fig. 16b); National Museum Wales specimen 2013.43G.88. in Naming Of Parts: The Use Of Fossil-Taxa In Palaeobotany
Text-fig. 2. The distinction between fossil plants (a) and plant fossils (b). a: Reconstruction of a late Carboniferous arborescent lycopsid, often referred to as the Lepidodendron-tree; artwork by A. Townsend (formerly of National Museum Wales, Cardiff, UK; see Townsend et al. 1998); b: Lepidodendron aculeatum STERNB.; Middle Coal Measures Formation (Duckmantian – upper Bashkirian), Brymbo, near Wrexham, UK (see Thomas et al. 2020: fig. 16b); National Museum Wales specimen 2013.43G.88.
Fig. 1. Species tree reconstruction inferred from ASTRAL-II using 89 specimens and 787 in One in, one out: Generic circumscription within subtribe Manilkarinae (Sapotaceae)
Fig. 1. Species tree reconstruction inferred from ASTRAL-II using 89 specimens and 787 individual gene trees obtained using RAxML. The node labels represent ASTRAL support values. Note that ASTRAL only calculates internal branch length and that tip lines are artificially fixed with the same length for all the specimens. Tip labels include the species names and the collector codes. Branch colors represent the traditional classification: Labramia (dark green), Manilkara (orange), Faucherea (yellow) and Labourdonnaisia (pink). The revised four major genetic clades are highlighted by a colored bar as follows: Labramia (dark green), Manilkara s.str. (orange), Faucherea and Labourdonnaisia (pink), and the Abebaia clade (blue). The main regions are indicated as follows: Afr: Africa; Ame: Americas; Com: Comoros; Ind: Indonesia; Mad: Madagascar; Msc: Mascarenes; Pac: Pacific Asia. RN: Réserves Naturelles; SF: Service Forestier.
Data from: Phenological patterns of tropical mountain forest trees across the neotropics: Evidence from herbarium specimens
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Data from: Species tree estimation using ddRADseq data from historical specimens confirms the monophyly of highly disjunct species of Chloropyron (Orobanchaceae)
Sequence data exist for only about 1/5 of plant species; therefore we are at risk of losing many branches of the tree of life even before they are placed into a molecular evolutionary context. This necessitates methods for phylogeny estimation of understudied, rare, and threatened taxa, which often forces researchers to utilize historical collections. The restriction site-associated DNA sequencing (RADseq) family of reduced representation sequence generation has provided a flexible and efficient method for the rapid generation of hundreds to tens of thousands of loci, and has recently seen adoption for phylogeny estimation. However, these methods have been primarily utilized with freshly collected or well preserved tissue. Here we sample all taxa of a genus of rare flowering plants, Chloropyron (Orobanchaceae), from herbarium sheets dating up to 25 yr and use double digest restriction site-associated DNA sequencing (ddRADseq) to resolve intraspecific relationships. We find all species in Chloropyron to be monophyletic, with the inland taxon C. maritimum ssp. canescens sister to the rest of the coastal C. maritimum (ssp. maritimum + ssp. palustre), and the two distinct subspecies of C. molle to be each other's closest relative with strong support. In addition, we demonstrate the utility of reduced representation libraries to address phylogenomic problems in a group of rare species and address pitfalls of accurately inferring relationships when the amount of missing data is large, as is often the case when using historical specimens and rare taxa.
Data from: Species tree estimation using ddRADseq data from historical specimens confirms the monophyly of highly disjunct species of Chloropyron (Orobanchaceae)
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Data from: Moorean and Tahitian Partula tree snail survival after a mass extinction: new genomic insights using museum specimens
Natural history museum collections provide a biodiversity window into the past and are of particular importance to the study of extinction-impacted clades such as the Pacific Island tree snail family Partulidae. Deliberate introduction of the predatory rosy wolf snail Euglandina rosea in the late 20th century led to the extinction/extirpation of 55/61 Society Island Partulidae species. In this study, we phylogenomically investigated the inter-relationships of the three surviving Society Island valley Partula species: P. taeniata (Moorea), P. clara and P. hyalina (Tahiti). All three formed a distinct clade in earlier mitochondrial phylogenies. Using Next Generation Sequencing (NGS) double digested Restriction Associated DNA sequencing (ddRADseq), we found that 46-year-old lyophilized museum specimens produced similar numbers of reads, sequencing depth, and loci as 10-year old ethanol-preserved collections. Phylogenomic trees indicated that Tahitian P. clara and P. hyalina are the result of a single founding lineage from Moorea, contrasting previous mitochondrial results and clarifying the enigmatic taxonomic status of P. c. incrassa. Our study highlights the utility and viability of NGS techniques for museum specimens and their increased resolution of evolutionary patterns. Sampling will be expanded to include the remaining Society Island partulid taxa to further explore the evolutionary history of this radiation.
FIGURE 1. Neighbor joining tree for 34 in Revision of the Australian Oenochroma vinaria Guenée, 1858 species-complex (Lepidoptera: Geometridae, Oenochrominae): DNA barcoding reveals cryptic diversity and assesses status of type specimen without dissection
FIGURE 1. Neighbor joining tree for 34 Australian specimens in the genus Oenochroma (Kimura 2 Parameter, built with MEGA4; all codon positions unweighted) based on sequences of the mtDNA COI gene (barcoding fragment 5'). Values above branches are bootstrap support values superior to 95%. Terminals are identified by their process ID code on BOLD.
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a in A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadinae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a number of named, primarily Palaearctic taxa included. Species groups that are characterizable morphologically and discussed are indicated in different colours. The tree is rooted using Heterogamus species.
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
Supplementary material 1 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Gazetteer : Authors: Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T. R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jesús E. Maldonado
Supplementary material 3 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Supplementary information figure : Authors: Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T. R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jesús E. Maldonado
Supplementary material 2 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Name and DNA sequences of pairs of primers used for amplification and sequencing of the CYTB gene : Data type: molecular data
FIGURE. Phylogenetic tree derived from Bayesian analysis, based on nrLSU data. Posterior probability (PP> 0.95) values from the Bayesian analysis are added at the nodes. The scale bar represents the number of nucleotide changes per site. (T) indicates the type specimen for this species. The new species are in bold. in Four new species of Entoloma (Entolomataceae, Agaricomycetes) subgenera Cyanula and Claudopus from Vietnam and their phylogenetic position
FIGURE. Phylogenetic tree derived from Bayesian analysis, based on nrLSU data. Posterior probability (PP> 0.95) values from the Bayesian analysis are added at the nodes. The scale bar represents the number of nucleotide changes per site. (T) indicates the type specimen for this species. The new species are in bold.
FIGURE 14. Consensus tree obtained from a 847 in The identity of some specimens previously (mis)identified as Rhinoleucophenga obesa (Loew) (Diptera: Drosophilidae) in Brazil, based on morphological and molecular data, with implications on distribution
FIGURE 14. Consensus tree obtained from a 847-bp alignment of cytochrome c oxidase subunit I (COI) gene sequences of Rhinoleucophenga specimens. Above the branches, support values by Neighbour-joining (10,000 bootstrap replications) and posterior probabilities values using Bayesian inference (1,000,000 generations), respectively.
FIGURES NJ27–NJ30. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ27, Scrobipalpa acuminatella; NJ28, Sophronia gelidella; NJ29, Anthophila fabriciana; NJ30, Phiaris bipunctana. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ27–NJ30. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ27, Scrobipalpa acuminatella; NJ28, Sophronia gelidella; NJ29, Anthophila fabriciana; NJ30, Phiaris bipunctana.
FIGURES NJ17–NJ19, NJ21. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ17, Agonopterix conterminella. NJ18, Depressaria depressana; NJ19, Coleophora atriplicis; NJ21, Coleophora granulatella. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ17–NJ19, NJ21. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ17, Agonopterix conterminella. NJ18, Depressaria depressana; NJ19, Coleophora atriplicis; NJ21, Coleophora granulatella.
FIGURES NJ20, NJ22–NJ26. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ20, Coleophora glitzella; NJ22, Coleophora texanella; NJ23, Coleophora vitisella; NJ24, Scythris sinensis; NJ25, Altenia perspersella; NJ26, Gnorimoschema jalavai. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ20, NJ22–NJ26. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ20, Coleophora glitzella; NJ22, Coleophora texanella; NJ23, Coleophora vitisella; NJ24, Scythris sinensis; NJ25, Altenia perspersella; NJ26, Gnorimoschema jalavai.
FIGURES NJ7–NJ12. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ7, Parornix betulae; NJ8, Phyllonorycter maestingella; NJ9, Paraswammerdamia albicapitella; NJ10, Paraswammerdamia conspersella; NJ11, Plutella hyperboreella; NJ12, Lyonetia pulverulentella. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ7–NJ12. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ7, Parornix betulae; NJ8, Phyllonorycter maestingella; NJ9, Paraswammerdamia albicapitella; NJ10, Paraswammerdamia conspersella; NJ11, Plutella hyperboreella; NJ12, Lyonetia pulverulentella.
FIGURES NJ1–NJ6. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ1, Scardia amurensis; NJ2, Triaxomera parasitella; NJ3, Nemapogon cloacella; NJ4, Elabotia montelliella; NJ5, Tinea svenssoni; NJ6, Caloptilia suberinella. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ1–NJ6. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ1, Scardia amurensis; NJ2, Triaxomera parasitella; NJ3, Nemapogon cloacella; NJ4, Elabotia montelliella; NJ5, Tinea svenssoni; NJ6, Caloptilia suberinella.
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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.