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Figure 14 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 14. Detailed segment of strict consensus tree of all MPTs recovered in present study. Part C. Neornithes: nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type).
Figure 6 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 6. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), VI. A, Van Tuinen et al. (2000); B, Van Tuinen et al. (2001).
Figure 5 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 5. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), V. A, Espinosa de los Monteros (2000); B, Johansson et al. (2001).
Figure 4 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 4. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), IV. A, Sibley & Ahlquist (1990: figs 354–356), simplified to orders, wherein parenthetical 'para' indicates paraphyly of sampled members, and 'aug' indicates unconventional content; B, Mindell et al. (1997).
Figure 2 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 2. Morphological phylogenetic trees proposed in previous studies (see Fig. 1 for details), II. A, Mayr & Clarke (2003); B, Bourdon et al. (2005).
Figure 10 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 10. Ordinal-level strict consensus tree for orders of Neornithes based on 2954 morphological characters, indicating delimitations of segments detailed in Figures 12–18.
Figure 1 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 1. Morphological phylogenetic trees proposed in previous studies, I. A, Cracraft (1988); B, Mayr et al. (2003). Some trees were subjected to topologically neutral modifications of taxa to facilitate comparisons (also Figs 2–9). See corresponding papers for analytical methods and topological statistics.
Figure 13 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 13. Detailed segment of strict consensus tree of all MPTs recovered in present study. Part B. Neornithes: Palaeognathae and Galloanserae. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type).
Figure 17 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 17. Detailed segment of strict consensus tree of all MPTs recovered in present study. Part F. Neornithes: Columbiformes, Caprimulgiformes, Apodiformes, Coliiformes, Trogoniformes and Coraciiformes. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type).
Figure 7 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 7. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), VII. A, Paton et al. (2002); B, Sorenson et al. (2003).
Figure 3 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 3. Morphological phylogenetic trees proposed in previous studies (see Fig. 1 for details), III. A, Mayr (2005b); B, Mayr (2005f: fig. 9), excluding fossils Prefica and Paraprefica.
Figure 16 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 16. Detailed segment of strict consensus tree of all MPTs recovered in present study. Part E. Neornithes: Falconiformes, Strigiformes, Cuculiformes and Psittaciformes. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type).
Figure 12 in Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
Figure 12. Detailed segments of strict consensus tree of all MPTs recovered in present study. Part A. Outgroup (non-neornithine) taxa. Nodes are labelled by percentages of bootstrapped replicates in which node was retained (numerator), and below by Bremer support indices (denominator).
Figure 6. Fossil tadornine bones compared with modern Tadorna tadornoides SAM B.39591 in Descriptions and phylogenetic relationships of two new genera and four new species of Oligo-Miocene waterfowl (Aves: Anatidae) from Australia
Figure 6. Fossil tadornine bones compared with modern Tadorna tadornoides SAM B.39591. Tadorna tadornoides: A,C. proximal right carpometacarpus; and H, dorsal view cranial half coracoid. Fossils referred to Australotadorna alecwilsoni: B, D, E, proximal right carpometacarpus; F, distal right tibiotarsus SAM P.36762 in anterior view; G, cranial part right coracoid (SAM P.24531) in dorsal aspect; I, cranial part right coracoid (SAM P.43137) in dorsal aspect. Fossils referred to an undetermined tadornine from Alcoota: J, left radius UCMP 65985 in dorsal aspect; and right carpometacarpus NT P.2913 in K, ventral; L, dorsal; and M, caudal views. Scale bars = 10 mm. See main text for abbreviations.
A unified genealogy of modern and ancient genomes: Unified, inferred tree sequences of 1000 Genomes, Human Genome Diversity, and Simons Genome Diversity Projects with ancient samples
<p>Unified, inferred tree sequences built from the 1000 Genomes phase 3, Human Genome Diversity, and Simons Genome Diversity Projects with high coverage sequenced ancient samples. The ancient samples are the Altai, Chagyrskaya, and Vindija Neanderthals, the Denisovan, and a high-coverage family of four from the Afanasievo Culture.</p> <p>Each tree sequence is the arm of an autosome (the short arm of acrocentric chromosomes are not included). Tree sequences were inferred with <a href="https://tsinfer.readthedocs.io/">tsinfer</a> version 0.2.1 and <a href="https://tsdate.readthedocs.io/en/latest/">tsdate</a> version 0.1.4, as described in <a href="http://www.biorxiv.org/content/10.1101/2021.02.16.431497v2">Wohns et al. (2021)</a>. The files were compressed using <a href="https://tszip.readthedocs.io/en/stable/">tszip</a>. All data is in GRCh38.</p> <p>The full data pipeline used to generate these tree sequences and associated metadata is available on <a href="https://github.com/awohns/unified_genealogy_paper">GitHub</a>. A description can be found in the Supplementary Material of <a href="https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2">Wohns et al. (2021)</a>.</p> <p>Tree sequences can be decompressed as follows:</p> <pre><code>$ tsunzip hgdp_tgp_sgdp_high_cov_ancients_chr1_p.dated.trees.tsz</code></pre> <p>Once decompressed, trees files can be loaded and processed in Python using <a href="https://tskit.readthedocs.io/">tskit</a>. </p> <pre><code>import tskit ts = tskit.load("hgdp_tgp_sgdp_high_cov_ancients_chr1_p.dated.trees") # ts is an instance of tskit.TreeSequence print("The short arm of chromosome 1 contains {} trees".format(ts.num_trees))</code></pre> <p>Accessing variant sites in the tree sequence provides the position and id of variants:</p> <pre><code>import json site = ts.site(1000) site_metadata = json.loads(site.metadata) print("The position of site 1000 is {} and its ID is {}.".format(site.position, site_metadata["ID"]))</code></pre> <p>Metadata associated with individuals and populations was derived from the original sources (<a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130606_sample_info/20130606_g1k.ped">TGP</a>, <a>HGDP</a>, and <a href="https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/SGDP_metadata.279public.21signedLetter.samples.txt">SGDP</a>) and converted to JSON form. For example, to access individual metadata we can use:</p> <pre><code>ind = ts.individual(0) metadata_dict = json.loads(ind.metadata)</code></pre> <p>The metadata_dict variable will now contain all the metadata for the individual with ID 0 as a dictionary. Metadata associated with populations can be found in a similar way. Population IDs are associated with individuals via their constituent nodes. For example,</p> <pre><code>pop_metadata = [json.loads(pop.metadata) for pop in ts.populations()] ind_node = ts.node(ind.nodes[0]) ind_pop_metadata = pop_metadata[ind_node.population]</code></pre> <p>After this, the ind_pop_metadata variable will contain the population level metadata for individual ID 0.</p>
Data from: How long does a brachiopod shell last on a seafloor? Modern mid-bathyal environments as taphonomic analogues of continental shelves prior to the Mesozoic Marine Revolution
<p class="MsoNormal">Carbonate skeletal remains are altered and disintegrate at yearly to decadal scales in present-day shallow-marine environments with intense bioerosion and dissolution. Present-day brachiopod death assemblages are invariably characterized by poor preservation on continental shelves, and abundant articulated shells of brachiopods with well-preserved brachidia are thus not expected to be preserved if not rapidly buried. However, such preservation is paradoxically observed in shallow-water Paleozoic and Mesozoic brachiopod assemblages. Here, we show that a bathyal death assemblage time-averaged to several millennia (Adriatic Sea) consists of sediment-filled articulated shells of <em>Gryphus</em> <em>vitreus</em> with complete brachidia. Postmortem age distributions indicate that disintegration half-lives exceed several centuries (~500-1,700 years). The high frequency of articulated but centuries-old shells (>50%) and the fitting of taphonomic models to postmortem ages indicate that disarticulation half-life is unusually long (~200 years). Rapid sediment filling of shells (1) inhibited disarticulation, loop fragmentation and colonization by coelobites and (2) induced precipitation of ferromanganese oxides at redox fronts within shells. Sediment-filled articulated shells, however, still resided at the sediment-water interface as indicated by encrusters and sponges that infested them after death. Sediment-filled shells disintegrated through bioerosion and wear when residence time in the taphonomically active zone exceeded ~2,000 years. We suggest that the articulation paradox is driven by the Mesozoic Marine Revolution (MMR) that escalated predation, bioturbation and organic matter recycling, all intensifying shell disintegration. A scenario with slow disarticulation in bathyal environments can be an analogue of conditions leading to preservation of articulated shells in shallow-water assemblages prior to the MMR.</p>
Early Modern Danish Postils v0.2.0
<p>This release is an update from the previous release in two major ways:</p> <ol> <li> <p><strong>brochmand_sabbati_sanctificatio_sommer.txt</strong> and <strong>brochmand_sabbati_sanctificatio_vinter.txt</strong> have been revised to exclude header, footer, and marginalia in order to avoid noise and be consistent with the other texts in the corpus.</p> </li> <li> <p><strong>hemmingsen_postilla.txt</strong>, <strong>luther_husspostille.txt</strong>, and <strong>medelby_ungdommens_postil.txt</strong> have all been split up into smaller components, since the books from which the data were derived were originally bound with multiple smaller parts (such as winter, summer, and festal parts). To the extent these could be identified, the smaller separate files have replaced the single large file to enable better comparative studies of individual parts. If author based comparative studies are desired, this can easily be achieved by merging the relevant texts.</p> </li> </ol>
Code and data used for the study: 'BioDeepTime: a database of biodiversity time series for modern and fossil assemblages'
<p>The repository includes code and data to reproduce the results in the manuscript ‘BioDeepTime: a database of biodiversity time series for modern and fossil assemblages' by Smith et al. (<code>analysis_biodeeptime.zip</code>).</p>
Database of the artistic transfer in the building factory in the ancient kingdom of Seville in the transition to the Modern Age [Dataset]
<p>Los datos recopilados se almacenan en una base de datos de Microsoft Access® que se ha diseñado para integrarse físicamente en un sistema SIG y a herramientas para modelos orientado a Grafo, como Gephi®. La estructura de esta base de datos está compuesta por entidades y relaciones que son representadas por tablas de entidades principales (E), tablas de clasificación/valores - entidades secundarias (Ee) y relaciones (RS). Cada una de las tablas está formada por una serie de registros (cada registro corresponde a una entidad o elemento) y por columnas o campos. Existen 5 tablas de entidades principales: “E1 profesionales”, “E2 mecenas”, “E3 edificios”, “E4 parte_edificio” (objetos asociados a arquitectura y estructura); 4 tablas de entidades secundarias: “Ee1 categoria agente”, “Ee2 tipo-clasificacion”, “Ee3 autor-dato” y “Ee4 ref-docu”; y 2 tablas de Relaciones: “RS1 Evento” y “RS2 tiene pariente”. El objetivo es identificar los eventos relacionados con la actividad constructiva durante el fenómeno del Gótico Tardio, mediados del Siglo XV y XVI de los profesionales que han trabajado en el antiguo Reino de Sevilla con el fin de analizar los movimientos, actividades y red de relaciones de los profesionales en el tiempo y espacio.</p>
FIG. 14 in Modern taxonomic approaches to identifying diatrypaceous fungi from marine habitats, with a novel genus Halocryptovalsa Dayarathne & K.D.Hyde, gen. nov.
FIG. 14. — Halocryptovalsa salicorniae Dayarathne & K.D.Hyde, sp. nov. (MFLU 16-0551 – holotype): A, host (Salicornia sp.); B, C, appearance of ascostromata on host; D, horizontal section through ascostroma; E, section through neck region; F, peridium; G, H, asci; I, asci with paraphyses; J-M, ascospores; N, germinating ascospores; O, P, culture on PDA (O-upper, P-lower). Scale bars: B, 500 µm; D-F, 100 μm; G-I, 50 μm; J-N, 5 μm.
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.