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14,185 results for “phylogenies”
Phlorest phylogeny derived from Bouckaert et al. 2018 'The origin and expansion of Pama–Nyungan languages across Australia'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Bouckaert RR, Bowern C & Atkinson QD. 2018. The origin and expansion of Pama–Nyungan languages across Australia. Nature Ecology and Evolution. 2: 741–749</p> </blockquote>
Phlorest phylogeny derived from Honkola et al. 2013 'Cultural and climatic changes shape the evolutionary history of the Uralic languages'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Honkola T, Vesakoski O, Korhonen K, Lehtinen J, Syrjänen K & Wahlberg N. 2013. Cultural and climatic changes shape the evolutionary history of the Uralic languages. Journal of Evolutionary Biology, 26(6):1244–1253.</p> </blockquote>
Phlorest phylogeny derived from Dunn et al. 2011 'Evolved structure of language shows lineage-specific trends in word-order universals'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Dunn M, Greenhill SJ, Levinson SC & Gray RD. 2011. Evolved structure of language shows lineage-specific trends in word-order universals. Nature, 473(7345), 79-82.</p> </blockquote>
Phlorest phylogeny derived from Kitchen et al. 2009 'Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Kitchen A, Ehret C, Assefa S & Mulligan CJ. 2009. Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East. Proceedings of the Royal Society B: Biological Sciences, 270(1668), 2703-2710.</p> </blockquote>
Phlorest phylogeny derived from De Filippo et al. 2012 'Bringing together linguistic and genetic evidence to test the Bantu expansion'
<p>Cite the source of the dataset as:</p> <blockquote> <p>De Filippo, C., Bostoen, K., Stoneking, M., & Pakendorf, B. (2012). Bringing together linguistic and genetic evidence to test the Bantu expansion. Proceedings of the Royal Society B: Biological Sciences, 279(1741), 3256–3263. doi:10.1098/rspb.2012.0318</p> </blockquote>
Phlorest phylogeny derived from Greenhill 2015 'TransNewGuinea.org: An Online Database of New Guinea Languages'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Greenhill, S. J. (2015). TransNewGuinea.org: An Online Database of New Guinea Languages. PLOS ONE, 10(10), e0141563. doi:10.1371/journal.pone.0141563</p> </blockquote>
Phlorest phylogeny derived from Lee & Hasegawa 2011 'Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Lee S, Hasegawa T (2011) Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages. Proceedings of the Royal Society B: Biological Sciences, 278(1725):3662–9.</p> </blockquote>
The phylogeny of ceutorhynchine weevils (Ceutorhynchinae, Curculionidae): mitogenome data improve the resolution of tribal relationships.
Open the record for dataset details and reuse information.
Training data for 'Preparing genomic data for phylogeny reconstruction' (Galaxy Training Material)
<p>This data is used for Galaxy Training Network training 'Preparing genomic data for phylogeny reconstruction'. There are four nucleotide sequences from chromosome 5 of four strains of S. cerevisiae. The GenBank annotated sequenced were produced using 'funannotate predict annotation' (Galaxy Version 1.8.9+galaxy2) on the nucleotide sequences sequences. References: DOI: 10.1126/science.274.5287.546; DOI: 10.1126/science.1189015; DOI: 10.1016/j.cell.2016.08.020</p>
Taxonomy, occurrences, phylogeny, traits and uses of the entire plant genus Scleria (Cyperaceae)
<p>This resource includes several datasets:</p> <p>(1) Taxonomy (261 species): Updated taxonomy of the genus Scleria at the species level based on Bauters et al. 2016 and 2019.</p> <p>(2) Occurrences (latitude/longitude): data was compiled using observations from the Global Biodiversity Information Facility, Red List, research grade identifications from iNaturalist (accessed 13/08/2023) and records for collections from BR, K, GENT, L, MO, NY, P, US and WAG which were georeferenced using Google Earth. The dataset includes 22,759 observations from 248 species. Methodology follows Larridon et al. (2021).</p> <p>(3) Phylogeny of the genus based on three markers (ITS, ndhF, rps16) from Larridon et al. (2021) (136 species).</p> <p>(4) Traits. (i) We measured maximum height, maximum blade length, maximum blade width, stem width, nutlet length and nutlet width from 1,254 specimens of 209 species housed at Royal Botanic Gardens, Kew and the Muséum National d'Histoire Naturelle in Paris. (ii) We also compiled another dataset of 16 continuous and categorical traits for all 261 Scleria species derived from protologues and descriptions from regional floras. (iii) We measured nutlet weight for 141 species.</p> <p>(5) Uses & ecology: ethnobotany (mostly medicinal uses) and references to its ecology in several ecosystems (e.g., pollination, dispersal, ecological role). This data was gathered from several bibliographical sources, also provided.</p> <p>(6) Pictures of nutlets from 141 species.</p>
A new spiralian phylogeny places the enigmatic arrow worms in gnathiferans
<p>This study attempts to elucidate the position of chaetognaths, an enigmatic marine group using multigene phylogeny derived from transcriptome sequencing. Its main conclusion is that they group in Gnathifera together with rotifers. Our trees also suggest alternative relationships within spiralians with a new clade uniting annelid, platyhelminthes and nemerteans ('vermizoa'). This dataset contains alignments and raw output files from phylogenetic reconstruction generated in this study. </p> <ul> <li>'alis.tgz' contains the raw individual alignments for each gene family.</li> <li>'alis_filtered.tgz' contains the alignments after filtering with HMMClean and BMGE that were used in concatenation.</li> <li>'cat-gtr-dh6.tgz' contains the bayesian sample (tree files and trace files with parameters) for the analysis conduced on the Dayhoff6 recoded dataset.</li> <li>'cat-gtr.tgz' contains the bayesian sample for the analysis conduced on the non-recoded reduced dataset. </li> <li>'Concat-alis.tgz' contains the alignments used for phylogenetic analyses. </li> <li>'IQTree-C20.tgz' contains the run files for the IQTREE analyses of reduced dataset using C20 model. </li> <li>'IQTree-LG4X.tgz' contains the run files for the IQTREE analyses if the whole matrix using LG4X model. </li> <li>'Results_phylogenetic_analyses.pdf' contains all the consensus generated for this study</li> </ul>
Supporting Data: Phylogeny of Arbacia Gray, 1835 (Echinoidea) reveals diversification patterns in the Atlantic and Pacific Oceans.
<p>This dataset contains:</p> <ol> <li>Appendix S1, metadata asociated with the specimens (collection localities, specimen numbers)</li> <li>The aligned sequence files for each marker: COI_fasta, 16S_fasta, CR_fasta</li> <li>The concatenated sequence file COI + 16S + CRA + 28S Arbacia_supermatrix_fasta and the partition file partitions_concat</li> <li>The Bayesian trees for COI, 16S, CRA, and the supermatrix: BI_tree_16S, BI_tree_COI, BI_tree_CR, BI_tree_Arbacia_supermatrix</li> <li>The ML tree of the supermatrix: ML_tree_Arbacia_supermatrix</li> <li>Appendix S2, which includes various information on the primers used, PCR cycles, etc.</li> <li>Appendix S3, which includes the index calculations for each marker.</li> </ol>
Phlorest phylogeny derived from Michael et al. 2015 'A Bayesian Phylogenetic Classification of Tupi-Guarani'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Michael L, Chousou-Polydouri N, Bartolomei K, Donnelly E, Wauters V, Meira S & O'Hagan Z. 2015. A Bayesian Phylogenetic Classification of Tupi-Guarani. LIAMES 15(2):1–36.</p> </blockquote>
The World Asellidae database and phylogeny: a collaborative backbone resource for comparative studies of subterranean life evolution
<p>Supplementary material for the article "The World Asellidae database and phylogeny: a collaborative backbone resource for comparative studies of subterranean life evolution"</p> <p>- SI Figure 5: The World Asellidae phylogeny with credibility Intervals for the age of the nodes. Node labels of the phylogeny indicate the 95% credibility intervals of the estimated dates.</p> <p>- SI Table 1: Metadata for the 2093 COI sequences used in the study.</p> <p>- SI Table 4: Alignment of the 2093 COI sequences used for the delimitation of MOTUs.</p> <p>- SI Table 5: Alignment of the 424 COI sequences used for the four-gene dated phylogeny.</p> <p>- SI Table 6: Alignment of the 424 16S sequences used for the four-gene dated phylogeny.</p> <p>- SI Table 7: Alignment of the 424 FASTKD4 sequences used for the four-gene dated phylogeny.</p> <p>- SI Table 8: Alignment of the 424 28S sequences used for the four-gene dated phylogeny.</p> <p>- SI Table 9: Metadata for the DNA sequences used for the 4-gene dated phylogeny.</p> <p>- SI Table 11: Data on body size, sexual body size dimorphism, habitat specialization and habitat size used in comparative analyses.</p> <p>- SI Table 12: Metadata for the DNA sequences deposited in NCBI as part of this study.</p>
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
Open the record for dataset details and reuse information.
Appendix 1 in Contribution to chromosome numbers and phylogeny of Turkish Vincetoxicum Wolf (Apocynaceae, Asclepiadoideae)
Appendix 1. Locality information, voucher specimens and accession numbers for sequences in GenBank (NCBI) of the examined specimens used for molecular (Mol.) and cytological (Cyt.) studies. Sequences previously published are indicated in brackets (A=Liede-Schumann et al. 2016, B=Liede- Schumann et al. 2012, C=Liede et al. 2002, D=Liede 2001, E=Berner & Carter Unpublished, F=Lahaye et al. 2005, G=Liede & Täuber 2002, H=Goyder et al. 2007, PS=present study).
Fig. 3 in Systematics, Morphology and Biogeography Phylogeny of the Augochlora clade with the description of four new species (Hymenoptera, Apoidea)
Fig. 3. Paratypemaleof Augochlorellakelliae sp. nov.(A) Dorsalview; (B) frontalview of head; (C) ventral view of genitalia. Scale bar: Aand Bat 0.5 mm, Cat 0.25 mm.
FIG. 8 in A review of fossil Bursidae and their use for phylogeny calibration
FIG. 8. — Stratigraphic range of the extinct and extant Bursidae. Black arrows indicate total stratigraphic range; grey arrows indicate regional stratigraphic range. Abbreviations: P, Peru; WI, Western Indian Ocean; AB, Aquitaine Basin; CWA, Caribbean, Western Atlantic Ocean; PT, Paratethys, CWT: Central Western Tethys; EA, Eastern Atlantic; CWM, Central Western Mediterranean; WP, Western Pacific Ocean; J, Java, Indo-Pacific; S, Sumatra, Indo-Pacific; EP, Eastern Pacific Ocean. Grey squares regroup accepted genera and putative genera within Bursa.
FIG. 5 in A review of fossil Bursidae and their use for phylogeny calibration
FIG. 5. — Extinct Bursidae species: A, B, Marsupina judensis Beu, 2010; NMB H 18308, holotype, late Miocene, Punta Judas, Pacific Costa Rica, reproduced from Beu (2010); C, D, "Bursa" landaui Harzhauser, 2009, NHMW 2007z0181/0029 (C) holotype and NHMW 2007z0181/0030 (D), both from the Aquitanian of Ras Tipuli, Lindi Bay, Tanzania, reproduced from Harzhauser (2009); E, Lampadopsis sangirana (Beu, 2005), RGM 456 230, holotype, late Pliocene of Kalibeng layers, Sangiran, central Java, reproduced from Beu (2005); F, G, Aquitanobursa chipolana (Schmelz, 1997) n. comb., USNM 647108, paratype, specimen illustrated by Vokes (1973: text-figs 2a, b), coral reef facies of Chipola Formation (late Early Miocene), loc. TU547, reproduced from Beu (2010); H, I, Marsupina freya (Olsson, 1932), PRI 2312, holotype, "Zorritos Miocene," divide between Quebrada Conchudo Bravo and Quebrada Seca,Mancora, Peru; J, K, Olssonia chira (Olsson, 1930) n. comb., PRI 24257, holotype, Late Eocene/Oligocene of Chira Formation, Quercotilla, Peru; L-O, Olssonia yasila (Olsson, 1930) n. comb., PRI 24254 (L, M) and PRI 24255 (N, O), Middle Eocene Talara Formation, Yasila, Peru; P-S, Aquitanobursa morrisi (d'Archiac & Haime, 1853) n. comb., original representation of one of the syntypes by d'Archiac & Haime (1853) (P, R) and (NHMUK PI TG 27045) lectotype,from "Calcaire grossier jaune de la chaîne d'Hala" (Aquitanian?) Pakistan; T, Aquitanobursa amphitrites (Maury, 1917) n. comb., PRI 28763, holotype, Cercado Fm (Late Miocene), Maury's bluff 3, Cercado de Mao, Dominican Republic, reproduced from Beu (2010). Scale bar: 2 cm.
FIG. 1 in A review of fossil Bursidae and their use for phylogeny calibration
FIG. 1. — Taxa excluded from Bursidae: A, B, Hanaibursa aquilana (Parona, 1909) UMUT MM15655, Hiraiga Formation (Aptian of Japan), reproduced from Kase (1984: pl. 28, fig. 16a); A, dorsal view; B, ventral view; C, D, Bursa saundersi Adegoke, 1977, UIMG 394, holotype, Ewekoro Formation (Selandian of Nigeria), reproduced from Adegoke (1977: pl. 31, figs 27, 28); C, ventral view; D, dorsal view. Scale bar: 2 cm.
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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)
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.