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635 results for “comparative phylogenetics”
Figure 33 in Comparative osteology and phylogenetic systematics of fossil and living bony-tongue fishes (Actinopterygii, Teleostei, Osteoglossomorpha)
Figure 33. Some elements of the left branchial arches of A, Heterotis niloticus (UMA F10653, 75 mm SL) and B, Pantodon buchholzi (FMNH 63752, 74 mm SL) in dorsal and medial views showing position of the accessory cartilages associated with the fourth and fifth branchial arches. Gill rakers omitted. Cartilage shown in black. Anterior facing right.
Data from: Ppgm: an R package for integrating neontological, palaeontological, and climate data in a phylogenetic comparative framework
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The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships
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A Bayesian extension of phylogenetic generalized least squares (PGLS): incorporating uncertainty in the comparative study of trait relationships and evolutionary rates
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Empirical data for: Extending phylogenetic regression models for comparing within-species patterns across the Tree of Life
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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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Supplementary material: How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature
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Data from: Pollinator shifts, contingent evolution, and evolutionary constraint drive floral disparity in Salvia (Lamiaceae): evidence from morphometrics and phylogenetic comparative methods
Switches in pollinators have been argued to be key drivers of floral evolution in angiosperms. However, few studies have tested the relationship between floral shape evolution and switches in pollination in large clades. In concert with a dated phylogeny, we present a morphometric analysis of corolla, anther connective, and style shape across 44% of nearly 1,000 species of Salvia (Lamiaceae) and test four hypotheses of floral evolution. We demonstrate that floral morphospace of New World (NW) Salvia is largely distinct from that of Old World (OW) Salvia and that these differences are pollinator driven; that shifts in floral morphology sometimes mirror shifts in pollinators; that anther connectives (key constituents of the Salvia staminal lever) and styles co-evolved from curved to linear shapes following shifts from bee to bird pollination; and that morphological differences between NW and OW bee flowers are partly the legacy of constraints imposed by an earlier shift to bird pollination in the NW. The distinctive staminal lever in Salvia is a morphologically diverse structure that has evolved in concert with both the corolla and style, under different pollinator pressures, and in contingent fashion.
Data from: Phylogenetic comparative methods on phylogenetic networks with reticulations
The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.
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.
Supplementary material - Comparative genitalic morphology in ten genera of thread-legged bugs of the tribe Metapterini, and its phylogenetic importance (Hemiptera: Heteroptera: Reduviidae)
<p><strong>Supplementary information of the paper entitled: Comparative genitalic morphology in ten genera of thread-legged bugs of the tribe Metapterini, and its phylogenetic importance (Hemiptera: Heteroptera: Reduviidae), original images and data matrix in nexus format.</strong></p>
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>
Data from: Remarkably conserved plastid genomes of Quercus Group Cerris in China: comparative and phylogenetic analyses
Quercus is one of the most important genera for considering its economic and ecological values, with approximately 500 species worldwide. Quercus group Cerris is endemic to Eurasia (including 11 species), and three species (Quercus acutissima, Quercus chenii and Quercus variabilis) are widely distributed in China. Here, we sequenced the complete plastid genomes of Q. acutissima and Q. chenii by Illumina pair-end sequencing, and obtained an additional plastome of Q. variabilis from GenBank. Although geographically distant sampling, the three plastomes in group Cerris were remarkably conserved with regard to genome size, gene organization, GC content, and IR/SC boundary regions. The phylogenetic analysis showed that group Cerris nested in group Ilex, forming a Cerris-Ilex clade. The current study provided plastid genomic-scale data for the less intensively studied group Cerris, which would be useful for studying speciation processes, geographical structure and phylogeny within the group Cerris in the future.
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.
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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.