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129 results for “phylogenetic comparative analysis”
Fig. 17 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 17. Medial view of left adductor mandibulae and attached lower jaw of Microcambeva ribeirae (Sarcoglanidinae), MZUSP 65764 (41.8 mm SL).
Fig. 20 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 20. Left lateral view of head of Tridentopsis pearsoni (Tridentinae), MZUSP 38671 (18.3 mm SL).
Fig. 24 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 24. Posterior view of left adductor mandibulae and attached lower jaw of Haemomaster venezuelae (Stegophilinae), LIRP 7438 (36.9 mm SL).
Supplementary datasets, data analysis code, and R tutorials for: Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs
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Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating
<pre class="js_message_plain ng-binding"><em>Sanguisorba</em> is a small genus, which consists of about 15 species widely distributed in North America and Eurasia. Previous studies on <em>Sanguisorba</em> are useful for understanding of phylogeny and chloroplast (cp) genome evolution of <em>Sanguisorba</em>. However, the cp genome resources of <em>Sanguisorba</em> are still limited, and the phylogeny and molecular dating for <em>Sanguisorba</em> and its relatives still need further explored. Here, we reported four cp genomes of <em>Sanguisorba</em> and conducted comparative analysis of the four <em>Sanguisorba</em> cp genomes plus five previously published ones. The nine cp genomes of <em>Sanguisorba</em> have typical tetrad quadripartite structure, with a total length of 154 282 to 155 730 bp, and their gene content, gene structure, and gene order are relatively conservative. The analysis of single copy (SC)/inverted repeat (IR) boundaries shows very slight boundary differences in <em>Sanguisorba</em> cp genomes. Eight variation hotspots were screened as excellent candidate markers of <em>Sanguisorba</em>. Phylogenetic analysis indicated <em>Sanguisorba</em> was monophyletic and was a member of tribe Agrimonieae subtribe Sanguisorbinae. Within <em>Sanguisorba</em>, <em>S. filiformis</em> is a sister group of six other taxa in the present sampling. Estimation of the divergence times indicated that subtribes Agrimoniinae and Sanguisorbinae diverged at the transition between the Oligocene and the Miocene, and divergent times of Agrimonieae genera ranged from the late Miocene to the Middle Pleistocene. This study enriches the available cp genome resources of <em>Sanguisorba</em>, and it is of great significance to further study the phylogeny and evolution of <em>Sanguisorba</em> and its relatives.</pre>
Data from: Trophic guilds differ in blood glucose concentrations: A phylogenetic comparative analysis in birds
<p>Glucose is a central metabolic compound used as a source of energy across all animal taxa. There is high interspecific variation in glucose concentration between taxa, the origin and the consequence of which remain largely unknown. Nutrition may affect glucose concentrations because carbohydrate content of different food sources may determine the importance of metabolic pathways in the organism. Birds sustain high glucose concentrations that may entail the risks of oxidative damage. We collected glucose concentration and life history data from 202 bird species from 171 scientific publications; classified them into seven trophic guilds and analysed the data with a phylogenetically controlled model. We show that glucose concentration is negatively associated with body weight and is significantly associated with trophic guilds with a moderate phylogenetic signal. After controlling for allometry, glucose concentrations were highest in carnivorous birds, which rely on high rates of gluconeogenesis to maintain their glycemia and lowest in frugivorous/nectarivorous species, which intake carbohydrates directly. However, trophic guilds with different glucose concentrations did not differ in lifespan. These results link nutritional ecology to physiology and suggest that at the macroevolutionary scale, species requiring constantly elevated glucose concentrations may have additional adaptations to avoid the risks associated with high glycemia.</p>
Assemblies and phylogenetic analyses for the comparative analysis of Chara tomentosa and Chara baltica
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Fig. 3 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 3. Relative synonymous codon usage of Protein-coding genes in Oxyurichthys ophthalmonema.
Fig. 2 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 2. Gene map of Oxyurichthys microlepis mitogenome.
Fig. 1 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 1. Gene map of Oxyurichthys ophthalmonema mitogenome.
Fig. 4 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 4. Relative synonymous codon usage of Protein-coding genes in Oxyurichthys microlepis.
Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 34 primate species
<p>Dorsal view of the reconstructed cerebral hemispheres of 34 different primate species.</p> <p>This figure is from our open access paper:</p> <p>Heuer, K., Gulban, O. F., Bazin, P.-L., Osoianu, A., Valabregue, R., Santin, M., Herbin, M., & Toro, R. (2018). Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 33 primate species. bioRxiv. <a href="https://doi.org/10.1101/379750">https://doi.org/10.1101/379750</a>. </p> <p>Abstract</p> <p>We present a comparative analysis of cerebral size and neocortical folding. Magnetic resonance imaging data was collected from 66 individuals belonging to 34 different primate species. We measured several neocortical folding parameters and studied their evolution using phylogenetic comparative methods. Our results suggest that the most likely model is one where phenotypical differences vary randomly through evolution (the Brownian Motion model). We present estimations of the ancestral primate phenotypes as well as estimations of the rates of phenotypic change.</p> <p> </p>
Complex ecological phenotypes on phylogenetic trees: a Markov process model for comparative analysis of multivariate count data
The evolutionary dynamics of complex ecological traits – including multistate representations of diet, habitat, and behavior – remain poorly understood. Reconstructing the tempo, mode, and historical sequence of transitions involving such traits poses many challenges for comparative biologists, owing to their multidimensional nature. Continuous-time Markov chains (CTMC) are commonly used to model ecological niche evolution on phylogenetic trees but are limited by the assumption that taxa are monomorphic and that states are univariate categorical variables. A necessary first step in the analysis of many complex traits is therefore to categorize species into a pre-determined number of univariate ecological states, but this procedure can lead to distortion and loss of information. This approach also confounds interpretation of state assignments with effects of sampling variation because it does not directly incorporate empirical observations for individual species into the statistical inference model. In this study, we develop a Dirichlet-multinomial framework to model resource use evolution on phylogenetic trees. Our approach is expressly designed to model ecological traits that are multidimensional and to account for uncertainty in state assignments of terminal taxa arising from effects of sampling variation. The method uses multivariate count data for individual species to simultaneously infer the number of ecological states, the proportional utilization of different resources by different states, and the phylogenetic distribution of ecological states among living species and their ancestors. The method is general and may be applied to any data expressible as a set of observational counts from different categories.
FIGURE 10 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 10. Hypothetical scapular transition series in Notoungulata. Not drawn to scale.
FIGURE 6 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 6. Mandible of Elmerriggsia fieldia (FMNH P 13501) in occlusal (A) and lateral (B) views.
Fig. 27 in Dorsolateral head muscles of the catfish families Nematogenyidae and Trichomycteridae (Siluriformes: Loricarioidei): comparative anatomy and phylogenetic analysis
Fig. 27. Dorsal view of head of Pareiodon microps (Stegophilinae), LIRP 7422 (112.9 mm SL).
Data from: Trophic guilds differ in blood glucose concentrations: A phylogenetic comparative analysis in birds
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Comparative chloroplast genome and phylogenetic analysis of Central Asian Tulips
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Environmental predictability in phylogenetic comparative analysis: how to measure it and does it matter?
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Complex ecological phenotypes on phylogenetic trees: a Markov process model for comparative analysis of multivariate count data
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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.