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14,185 results for “phylogenies”
Taxonomy and Phylogeny of the Family Suberitidae (Porifera: Demospongiae) in California
<div> <div> <div> <p>This study presents a comprehensive taxonomic revision of the family Suberitidae (Porifera: Demospongiae) for California, USA. We include the three species previously known from the region, document two additional species previously known from other regions, and formally describe four new species as <em>Pseudosuberites latke </em>sp. nov., <em>Suberites californiana </em>sp. nov.,<em> </em><em>Suberites kumeyaay </em>sp. nov., and <em>Suberites agaricus </em>sp. nov. Multi-locus DNA sequence data is presented for seven of the nine species, and was combined with all publicly available data to produce the most comprehensive global phylogeny for the family to date. By integrating morphological and genetic data, we show that morphological characters may be sufficient for regional species identification but are likely inadequate for global classification into genera that reflect the evolutionary history of the family. We therefore propose that DNA sequencing is a critical component to support future taxonomic revisions. </p> </div> </div> </div>
FIGURE 4 in Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality
FIGURE 4. Iguanodontian phylogeny presented by Norman (2015). Consensus of three MPTs.
Figure 15 in A phylogeny of Carrerapyrgota Aczél (Diptera, Pyrgotidae)
Figure 15. Optimal cladogram selected to represents the evolutionary relationship among the species of Carrerapyrgota. Black circles represents synapomorphies, white circles represents homoplasies.
Figure 14 in A phylogeny of Carrerapyrgota Aczél (Diptera, Pyrgotidae)
Figure 14. Strict consensus cladogram and Relative Bremer Support of Carrerapyrgota, resultant from analysis with implied weighting from K3.
Figure 13 in A phylogeny of Carrerapyrgota Aczél (Diptera, Pyrgotidae)
Figure 13. Strict consensus cladogram and Absolute Bremer Support of Carrerapyrgota, resulted from analysis with equal weighting of characters.
Figure 16 in A phylogeny of Carrerapyrgota Aczél (Diptera, Pyrgotidae)
Figure 16. Distribution map of Carrerapyrgota species. n. oc.: new occurrences. Modified from Mello et al. (2010).
Data for: Reliable biogeography requires fossils: Insights from a new species-level phylogeny of extinct and living carnivores
<p>A central objective of historical biogeography is to understand where clades originated and how they moved across space and over time. However, given the dynamic history of ecosystem changes in response to climate change and geologic events, the manifold long-distance dispersals over evolutionary timescales, and regional and global extinctions, it remains uncertain how reliable inferences based solely on extant taxa can be achieved. Using a novel species-level phylogeny of all known extant and extinct species of the mammalian order Carnivora and related extinct groups, we show that far more precise and accurate ancestral areas can be estimated by fully integrating extinct species into the analyses, rather than solely relying on extant species or identifying ancestral areas only based on the geography of the oldest fossils. Through a series of simulations, we further show that this conclusion is robust under realistic scenarios in which the unknown extinct taxa represent a biased subset of all extinct species. Our results highlight the importance of integrating fossil taxa into a phylogenetic framework to further improve our understanding of historical biogeography and reveal the dynamic dispersal and diversification history of carnivores.</p>
Data from: Widely acclaimed but poorly named - phylogeny and systematics of the charismatic African daisy genus Dimorphotheca Vaill. ex Moench (Asteraceae, Calenduleae)
<p>Phylogenetic relationships in the South African daisy genus <em>Dimorphotheca </em>have long been uncertain, with the taxonomy of the genus relying on a few morphological traits, most prominently capitulum sexual system (i.e., cypsela type) and ray colour, which may not be evolutionarily conserved. Here we present the first well-sampled molecular phylogeny of <em>Dimorphotheca</em>, based on nuclear ribosomal (ITS and ETS) and plastid <em>trn</em>L<em>-trn</em>F<em> </em>region DNA sequences from multiple accessions per species. Although the relationships suggested by these markers are broadly congruent, we do find some instances of incongruence which we resolve using a combined decomposition and deletion approach. Using our best estimate of phylogenetic relationships, we reconstruct the evolution of capitulum fertility and ray colour to assess the evolutionary conservatism of these traits and their taxonomic utility. We find support for the monophyly of <em>Dimorphotheca</em>, excluding the recently segregated <em>O. polypterum</em>, and our data thus support the modern, enlarged circumscription of the genus incorporating the former genus <em>Castalis </em>and <em>Osteospermum </em>sections <em>Acanthotheca </em>and <em>Blaxium</em>. Major subclades within <em>Dimorphotheca</em> are largely cohesive in terms of geographic distribution and morphological traits such as growth form and cypsela structure. While many species are resolved as monophyletic, the polyphyly of a few species suggests a need for taxonomic re-evaluation. On the basis of both morphological and molecular data, we describe one new species, and elevate one variety to species level. A full taxonomic key to the enlarged genus is presented for the first time. Ancestral reconstructions show that capitulum sexual system and ray lamina colour are not evolutionarily conserved and that neither can therefore be used to delimit major lineages within <em>Dimorphotheca</em>. While our findings resolve some taxonomic problems, they also highlight the need for further species-level taxonomic work on <em>Dimorphotheca</em>.</p>
Phylogenetic and recombination analysis of adenovirus isolates reveals discordance between serotype and phylogeny: Multiple sequence alignments
<p><strong>Background</strong></p> <p>Human adenovirus (HAdV) infections are caused by seven mastadenovirus species (A-G) and are the source for a variety of pathologies including gastrointestinal, respiratory, neurological, and ocular disease. While HAdV-D is the most common cause of adenovirus ocular infections, human adenoviruses B and E have also been isolated from the eye. </p> <p><strong>Results</strong></p> <p>In the course of classifying three new atypical ocular adenovirus samples, taken from the vitreous humor, we found that all three isolates were HAdV-B species, with isolate BP-AdV1 sorting with the B1 clade, and isolates BP-AdV2 and BP-AdV3 grouping into the B2 clade. The three Bascom Palmer HAdV-B genomes were then combined with over 300 HAdV-B genome sequences, including 9 ocular HAdV-B genome sequences. The whole genome phylogenetic analysis showed that 9 of the 11 ocular sequences grouped into the B1 clade, forming two clusters within B1. Attempts to categorize the penton, hexon and fiber serotypes using phylogeny of the three Bascom Palmer samples were inconclusive due to incongruence between serotype and phylogeny in the dataset. Recombination analysis using a subset of HAdV-B strains to generate a hybridization network detected recombination between non-human primate and human derived strains, recombination between one HAdV-B strain and the HAdV-E outgroup and limited recombination between the B1 and B2 clades. </p> <p><strong>Conclusions</strong></p> <p>The discordance between serotype and phylogeny detected in this study suggests that the current penton/hexon/fiber-based classification mechanism does not accurately describe the natural history and phylogenetic relationships amongst adenoviruses. A new adenovirus strain classification strategy may be beneficial to the field.</p>
Supplementary Data for "Phylogeny and evolution of dissimilatory sulfite reduction in Prokaryotes"
<p><span>Supplementary Data for "Phylogeny and evolution of dissimilatory sulfite reduction in Prokaryotes"</span></p> <p><span><span>Supplementary Data 1</span>: The information of the genomes we used in our analyses. The “DsrAB” sheet included the information of DsrAB-containing genomes and denoted whether DsrC, DsrM, DsrK, DsrJ, DsrO, DsrP genes were present. The other sheets included the information of the representative genus-level genomes which comprised DsrAB. These genomes were used to reconstruct genus-level phylogenies to compare tree topologies within phylum. See the “Note” sheet for more details. <span>Supplementary Data 2</span>: The raw data of Ka/Ks values of each gene pair estimated by KaKs_calculator v2.0 with MA method. <span>Supplementary Data 3</span>: the information of the COGs of iron-reducers and SRMs, respectively. <span>Supplementary Data 4</span>: fasta files used for tree reconstruction, including Dsr-related proteins and concatenated sequences for phylogenomic trees. The folder names indicated their analytical purposes. <span>Supplementary Data 5</span>: tree files used in our analyses, including Dsr trees, genetic distance-based trees and dated phylogenetic trees. The folder names indicated their analytical purposes.</span></p>
Viral diversity and co-evolutionary dynamics across the ant phylogeny
<p>This repository contains the alignment file and phylogeny of every viral clade assessed in this study. The viral phylogenies are in Newick format as well as a pdf and contain bootstrap values greater than 50. The alignment files are in PHYLIP format. Additionally, this repository contains nucleotide sequences of every viral sequence identified in this study and it is entitled: "final_viruses_contigs.fasta" in fasta format. </p>
Figure 1 in An update on the phylogeny and biogeographical history of Rhipicephalus sanguineus complex
Figure 1. Map of collecting sites. (The map was generated using QGIS 3.22.2 software.)
Fig. 4b in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 4b. Tillomorphites elachys (Martins & Galileo, 2013) n. comb., Paratype.
Fig. 3c Tillomorphites spinipes n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 3c Tillomorphites spinipes n. sp., Holotype, particular.
Fig. 3b Tillomorphites spinipes n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 3b Tillomorphites spinipes n. sp., Holotype, ventral view.
Fig. 3a Tillomorphites spinipes n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 3a Tillomorphites spinipes n. sp., Holotype, dorsal view.
Fig. 2 d. Tillomorphites otiliae n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 2 d. Tillomorphites otiliae n. sp., Holotype, colour reconstruction.
Fig. 2b. Tillomorphites otiliae n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 2b. Tillomorphites otiliae n. sp., Paratype.
Fig. 2a. Tillomorphites otiliae n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 2a. Tillomorphites otiliae n. sp., Holotype.
Fig. 1a. Tillomorphites robustus Vitali, 2011 in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 1a. Tillomorphites robustus Vitali, 2011, Holotype.
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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.