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.
351
datasets available to search
ShareScore release 0.9.0
Dataset results
351 results for “gene tree”
FIGURE 4. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in Laimaphelenchus persicus n. sp. (Nematoda: Aphelenchoididae) from Iran
FIGURE 4. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
FIGURE 1. Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50 in New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda: Triplonchida: Tripylidae). II: Two new, a known species and key to species
FIGURE 1. Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 7. Bayesian phylogenetic tree inferred from SSU rRNA gene sequences. Posterior probabilities greater than 50 in Description of Trischistoma abharensis n. sp. (Nematoda: Trischistomatidae) and first record of Tripylella intermedia (Bütschli, 1873) Brzeski & Winiszewska-Ślipinska, 1993 (Nematoda: Tripylidae) from Iran
FIGURE 7. Bayesian phylogenetic tree inferred from SSU rRNA gene sequences. Posterior probabilities greater than 50% are given on appropriate clades. Nematode species, GenBank accession numbers, and locations are listed for each taxon if known. The accession no. AY284737 was originally deposited in GenBank as Paratripyla sp., but it was used as Tripylella sp. by van Megen et. al. (2009).
FIGURE 4. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in Laimaphelenchus hyrcanus n. sp. (Nematoda: Aphelenchoididae), a new species from northern Iran
FIGURE 4. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank accession numbers are listed for each taxon.
FIGURE 1. Neighbour joining COI gene tree using uncorrected p in Description of two final stadium platystictid larvae from Borneo, including that of Drepanosticta? attala Lieftinck, identified using DNA barcoding (Odonata: Zygoptera: Platystictidae)
FIGURE 1. Neighbour joining COI gene tree using uncorrected p–distance for Drepanosticta attala and D. barbatula adults and larva plus related platystictid taxa with Sinosticta hainanense as outgroup. All voucher specimens except that of D. barbatula have a six digit collection number with an RMNH.INS. prefix; this prefix is omitted in the figure for clarity.
FIGURE 1. Neighbour-joining COI gene tree using uncorrected p in Description of the final stadium larvae of Onychargia atrocyana Selys, 1865 from Sarawak, identified using DNA barcoding (Odonata: Zygoptera: Platycnemididae), with an overview of larval characters in the Platycnemididae
FIGURE 1. Neighbour-joining COI gene tree using uncorrected p-distance for Onychargia atrocyana using Paracnemis alluaudi and Podolestes harrissoni as outgroups. All voucher specimens have a six-digit collection number with an RMNH.INS. prefix; this prefix is omitted in the figure for clarity.
FIGURE 5. 28S gene tree for 33 in Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae)
FIGURE 5. 28S gene tree for 33 specimens of Devadatta and one outgroup taxon, from Bayesian Inference analysis. Posterior probability values are shown (as percentages) if less than 100%. RMNH collection codes are shown for each specimen, with the RMNH.INS. prefix omitted for clarity.
FIGURE 3. 16S gene tree for 33 in Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae)
FIGURE 3. 16S gene tree for 33 specimens of Devadatta and one outgroup taxon, from Bayesian Inference analysis. Posterior probability values are shown (as percentages) if less than 100%. RMNH collection codes are shown for each specimen, with the RMNH.INS. prefix omitted for clarity.
FIGURE 4. ITS gene tree for 33 in Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae)
FIGURE 4. ITS gene tree for 33 specimens of Devadatta and one outgroup taxon, from Bayesian Inference analysis. Posterior probability values are shown (as percentages) if less than 100%. RMNH collection codes are shown for each specimen, with the RMNH.INS. prefix omitted for clarity.
FIGURE 2. COI gene tree for the 33 in Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae)
FIGURE 2. COI gene tree for the 33 specimens of Devadatta also used in the analysis with other markers and one outgroup taxon. Posterior probability values are shown (as percentages) if less than 100%. RMNH collection codes are shown for each specimen, with the RMNH.INS. prefix omitted for clarity.
FIGURE 1. COI gene tree for 73 in Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae)
FIGURE 1. COI gene tree for 73 specimens of Devadatta and one outgroup taxon, from Bayesian Inference analysis. Posterior probability values are shown (as percentages) if less than 100%. RMNH collection codes are shown for each specimen, with the RMNH.INS. prefix omitted for clarity.
Figure 1. Neighbour joining COI gene tree using uncorrected p in Description of larvae of two species of Coeliccia Selys, 1865 from Sarawak, identified using DNA barcoding (Odonata: Platycnemididae)
Figure 1. Neighbour joining COI gene tree using uncorrected p-distance for species of the Coeliccia borneensis-group, including both adults and larvae of C. campioni and C.flavostriata, and their sampling sites (except for Lestes dissimulans all from Sarawak, East Malaysia). Coeliccia didyma and Lestes dissimulans are used as outgroups.
SUPPLEMENTARY FIGURE 2. Tree generated from the nucleotide sequence for the mitochondrial gene region, igr1–cox1 in A taxonomic revision of Anthothela (Octocorallia: Scleraxonia: Anthothelidae) and related genera, with the addition of new taxa, using morphological and molecular data
SUPPLEMENTARY FIGURE 2. Tree generated from the nucleotide sequence for the mitochondrial gene region, igr1–cox1 of Anthothela-like specimens. Bayesian posterior probabilities shown above branch, ML bootstrap values below branch; HKY+G (Bayesian results split freq = 0.0019, 10000000 gen, burnin=25000). (* indicates nodes present only in Bayesian analysis).
FIGURE 6. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in A new species of the genus Tripylina Brzeski, 1963 (Nematoda: Enoplida: Trischistomatidae) from Zhejiang Province, eastern China
FIGURE 6. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
FIGURE 5. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50 in A new species of the genus Tripylina Brzeski, 1963 (Nematoda: Enoplida: Trischistomatidae) from Zhejiang Province, eastern China
FIGURE 5. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
Fig. 6. Single-gene Bayesian trees for 16S and FoxQ2 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 6. Single-gene Bayesian trees for 16S and FoxQ2 markers. Numbers above nodes indicate bootstrap values from Bayesian Interference (BI), black numbers below—posterior probabilities from Maximum Likelihood (ML), only bootstrap values> 60 are shown.
Eukaryotic gene trees with 150 leaves
<p>Gene loss is an important process in gene and genome evolution. If a gene is present at the root of a rooted binary phylogenetic tree and can be lost in one descendant lineage, it can be lost in other descendant lineages as well, and potentially can be lost in all of them, leading to extinction of the gene on the tree. In that case, just before the gene goes extinct in the rooted phylogeny, there will be one lineage that still retains the gene for some period of time, representing a 'last-one-out' distribution. If there are many (hundreds) of leaves in one clade of a phylogenetic tree, yet only one leaf possesses the gene, it will look like the result of a recent gene acquisition, even though the distribution at the tips was generated by loss. Here we derive the probability of observing last-one-out distributions under a Markovian loss model and a given gene loss rate μ. We find that the probability of observing such cases can be calculated mathematically, and can be surprisingly high, depending upon the tree and the rate of gene loss. Examples from real data show that gene loss can readily account for the observed frequency of last-one-out gene distribution patterns that might otherwise be attributed to lateral gene transfer.</p>
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T in Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T and other type strains of the genus Gordonia. Only values above 50% are shown. Asterisks represent clades that were also recovered by the maximum-likelihood and maximum-parsimony methods. Bar, one nucleotide substitution per 100 nucleotides.
Sergestidae shrimp family single- and multi-gene alignments and tree files
<p>Deep-sea shrimp belonging to the family Sergestidae provide a unique system for studying the evolution of bioluminescence. Most species within the family possess autogenic bioluminescent photophores in one of three distinct forms: lensed photophores, non-lensed photophores, or internal organs of Pesta. This morphological diversity across Sergestidae has resulted in recent major taxonomic revisions, dividing the two major genera (<em>Sergia </em>and<em> Sergestes</em>) into 15. Here, we capitalize on molecular data to construct an updated genus-level phylogeny of sergestid shrimp. DNA was successfully extracted from approximately 87 individuals belonging to 13 of the 15 newly proposed genera. We implemented a "genome skimming" approach, allowing us to capture mitochondrial genomic data across 19 Sergestidae species. Additional individuals have been incorporated into the phylogeny through Sanger sequencing of both nuclear (H3, NAK) and mitochondrial (16S and COI) genes. The resulting molecular phylogeny is compared with previous morphological trees with specific attention to genus-level relationships. The -<em>sergestes</em> group was rendered non-monophyletic, and the -<em>sergia</em> group was recovered as monophyletic. Ancestral state reconstructions of light organ type indicate the organs of Pesta is the ancestral state for the family. Non-lensed photophores evolved once across the -<em>sergia</em> group, but were later lost in the deepest living genus, <em>Sergia</em>. Lensed photophores also evolved once within the genera <em>Prehensilosergia</em>, <em>Lucensosersgia</em>, and <em>Challengerosergia</em>. Our findings identify preliminary patterns across light organ type and species' depth distributions, however future research that incorporates finer-scale depth data and more species is needed to confirm our findings. </p>
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
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.