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14,185 results for “phylogenies”
Fig. 14 in Morphology Of The Late Cretaceous Crocodylomorph Shamosuchus Djadochtaensis And A Discussion Of Neosuchian Phylogeny As Related To The Origin Of Eusuchia
Fig. 14. Detail of Shamosuchus djadochtaensis autapomorphic characteristic of a prominent depressed
Fig. 10 in Morphology Of The Late Cretaceous Crocodylomorph Shamosuchus Djadochtaensis And A Discussion Of Neosuchian Phylogeny As Related To The Origin Of Eusuchia
Fig. 10. Referred specimen of Shamosuchus djadochtaensis IGM 100/1195 in lateral view. See appendix
Fig. 9 in Morphology Of The Late Cretaceous Crocodylomorph Shamosuchus Djadochtaensis And A Discussion Of Neosuchian Phylogeny As Related To The Origin Of Eusuchia
Fig. 9. Referred specimen of Shamosuchus djadochtaensis IGM 100/1195 in ventral view. See appendix
Fig. 37 in Morphology Of The Late Cretaceous Crocodylomorph Shamosuchus Djadochtaensis And A Discussion Of Neosuchian Phylogeny As Related To The Origin Of Eusuchia
Fig. 37. Strict consensus of 18 most parsimonious trees obtained in the phylogenetic analysis.
Fig. 1 in Morphology Of The Late Cretaceous Crocodylomorph Shamosuchus Djadochtaensis And A Discussion Of Neosuchian Phylogeny As Related To The Origin Of Eusuchia
Fig. 1. Holotype of Shamosuchus djadochtaensis AMNH FR 6412.
Fig. 8 in The Os Navicular of Humans, Great Apes, OH 8, Hadar, and Oreopithecus: Function, Phylogeny, and Multivariate Analyses
Fig. 8. Total cuneiform facet crosssectional area (mm2) vs. total navicular facet crosssectional
Figure 8 in Description of a new species of Mesochaetopterus (Annelida, Polychaeta, Chaetopteridae), with redescription of Mesochaetopterus xerecus and an approach to the phylogeny of the family
Figure 8. Mesochaetopterus xerecus, scheme of a mature sperm.
Figure 1 in A new species of crown-antlered deer Stephanocemas (Artiodactyla, Cervidae) from the middle Miocene of Qaidam Basin, northern Tibetan Plateau, China, and a preliminary evaluation of its phylogeny
Figure 1. Map of Qaidam Basin showing surrounding mountains and major vertebrate fossil localities.
Figure 26 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figure 26. Neighbor-joining tree based on the concatenated DNA sequences.
Figure 29 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figure 29. Bayesian tree based on the concatenated DNA sequences.
Figure 28 in Taxonomy and molecular phylogeny of the Phortica hani species complex (Diptera: Drosophilidae)
Figure 28. Maximum likelihood tree based on the concatenated DNA sequences (-lnL = 7386.85).
Phlorest phylogeny derived from Sicoli & Holton 2014 'Linguistic phylogenies support back-migration from Beringia to Asia'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Sicoli MA & Holton G (2014) Linguistic phylogenies support back-migration from Beringia to Asia. PLoS One 9(3):e91722.</p> </blockquote>
Phlorest phylogeny derived from Robinson and Holton 2012 'Internal Classification of the Alor-Pantar Language Family Using Computational Methods Applied to the Lexicon'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Robinson, L. C., & Holton, G. (2012). Internal Classification of the Alor-Pantar Language Family Using Computational Methods Applied to the Lexicon. Language Dynamics and Change, 2(2), 123-149. doi:10.1163/22105832-20120201</p> </blockquote>
Phlorest phylogeny derived from Atkinson 2006 'From Species to Languages: a phylogenetic approach to human prehistory'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Atkinson, Quentin D. 2006. From Species to Languages: a phylogenetic approach to human prehistory. PhD Thesis, University of Auckland, New Zealand.</p> </blockquote>
Sign Languages Phylogeny
<p>Code for the replication of the results from the article "Computational phylogenetics reveal the history of sign languages", and to apply the same analysis to different datasets. This is a replicate from the GitHub repository GClarte/SignLanguagesPhylogeny, additional details can be found in the README.</p>
Data from: Bayesian total-evidence dating revisits sloth phylogeny and biogeography: a cautionary tale on morphological clock analyses
<p>Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth <em>Bradypus</em> is consistently recovered as a megatherioid, and <em>Choloepus</em> as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae", whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an <em>a posteriori</em> removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models, and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.</p>
A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade
<p><strong>Background.</strong> Arvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group. </p> <p><strong>Methods.</strong> Here we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data. </p> <p><strong>Results.</strong> Our results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (<em>Lemmus</em> and <em>Myopus</em>) and bog lemmings (<em>Synaptomys</em>), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ~6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary.</p>
Plant size, latitude, and phylogeny explain within-population variability in herbivory
<p>Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.</p>
Molecular phylogeny and morphological perianth evolution in Corymbia (Myrtaceae), and the implications for generic delimitation: data and tree files
<p><strong>Premise:</strong> Eucalypts (Myrtaceae tribe Eucalypteae) are currently placed in seven genera. Traditionally,<em> Eucalyptus</em> was defined by its operculum but when phylogenies placed <em>Angophora</em>, with free sepals and petals, as sister to the operculate bloodwood eucalypts, the latter were segregated into a new genus, <em>Corymbia</em>. Yet generic delimitation in the tribe Eucalypteae remains uncertain. Here we address these problems using phylogenetic analysis with the largest molecular dataset to date.</p> <p><strong>Methods: </strong>We captured 101 low-copy nuclear exons from 392 samples representing 266 species. Our phylogenetic analysis used maximum likelihood (IQtree) and multi-species coalescent (Astral). At two nodes critical to generic delimitation, we tested alternative relationships among <em>Arillastrum</em>, <em>Angophora</em>, <em>Eucalyptus</em> and <em>Corymbia</em> using Shimodaira's AU test. Phylogenetic mapping was used to explore the evolution of perianth traits.</p> <p><strong>Results: </strong>Monophyly of <em>Corymbia</em> relative to <em>Angophora</em> was decisively rejected. All alternative relationships among the seven currently recognised Eucalypteae genera imply homoplasy in evolutionary origins of the operculum. Inferred evolutionary transitions in perianth traits are congruent with divergences between major clades except that expression of separate sepals and petals in <em>Angophora</em>, which is nested within the operculate genus <em>Corymbia</em>, appears to be a reversal to the plesiomorphic perianth structure.</p> <p><strong>Conclusions:</strong> Here we formally raise <em>Corymbia</em> subg. <em>Blakella</em> to genus rank and make the relevant new combinations. We also define and name three sections within <em>Blakella</em> (<em>B.</em> sect. <em>Blakella</em>, <em>B.</em> sect. <em>Naviculares</em> and <em>B.</em> sect. <em>Maculatae</em>), and two series within <em>Blakella</em> sect. <em>Maculatae</em> (<em>B.</em> ser. <em>Maculatae</em> and <em>B.</em> ser. <em>Torellianae</em>). <em>Corymbia</em> is reduced to the red bloodwoods.</p>
Data sets for phylogenomic analyses in: Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data
<p>Ants are the most ubiquitous and ecologically dominant arthropods on Earth, and understanding their phylogeny is crucial for deciphering their character evolution, species diversification, and biogeography. Although recent genomic data have shown promise in clarifying intrafamilial relationships across the tree of ants, inconsistencies between molecular datasets have also emerged. Here I re-examine the most comprehensive published Sanger-sequencing and genome-scale datasets of ants using model comparison methods that model among-site compositional heterogeneity to understand the sources of conflict in phylogenetic studies. My results under the best-fitting model, selected on the basis of Bayesian cross-validation and posterior predictive model checking, identify contentious nodes in ant phylogeny whose resolution is <a>modelling-dependent. </a>I show that the Bayesian infinite mixture CAT model outperforms empirical finite mixture models (C20, C40 and C60) and that, under the best-fitting CAT-GTR+G4 model, the enigmatic <a><em>Martialis</em> </a><em>heureka</em> is sister to all ants except Leptanillinae, rejecting the more popular hypothesis supported under worse-fitting models, that place it as sister to Leptanillinae. These analyses resolve a lasting controversy in ant phylogeny and highlight the significance of model comparison and adequate modelling of among-site compositional heterogeneity in reconstructing the deep phylogeny of insects.</p>
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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.