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116 results for “phylogenetic signal”
Figure 5. A, B in Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns
Figure 5. A, B, musculature of Echiniscus testudo (A, dorsal view; B, lateral view). C, musculature of Batillipes bullacaudatus (ventral view). Ph, pharynx. Letters and numbers identify the muscle attachment points (see text). Nodes of ventral muscle groups are marked by hexagons; attachment points and nodes of lateral muscle group are marked by squares; attachment points and nodes of dorsal muscle group are marked by circles. A–C, CLSM, maximum projection. Scale bars: A, B = 50 μm; C = 25 μm.
Figure 10. A in Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns
Figure 10. A, unrooted phylogenetic tree based on the musculature dataset. The posterior probability values for MrBayes analysis (top), bootstrap supports for TNT analysis (middle) and PAUP analysis (bottom) are indicated next to each node. B, unrooted phylogenetic tree based on the total evidence approach (morphological data + 18S rRNA + 28S rRNA). The posterior probability values for MrBayes analysis are indicated next to each node.
Figure 1 in Evaluating evolutionary pressures and phylogenetic signal in earthworms: a case study - the number of typhlosole lamellae in Hormogastridae (Annelida, Oligochaeta)
Figure 1. An example of the variability in body size and number of lamellae in Hormogastridae: (A) Hormogaster castillana Qiu & Bouche, 1998 (21 lamellae); (B) Hormogaster pretiosa Michaelsen, 1889 from Segariu (13 lamellae); (C) Hormogaster joseantonioi Marchan et al., 2014 (nine lamellae); (D) Hormogaster redii Rosa, 1887 (seven lamellae); (E) Hormogaster elisae Alvarez, 1977 (five lamellae); (F) Ailoscolex lacteospumosus Bouche, 1969 (three lamellae). To the right the diagrams show how the typhlosole is located in the digestive tract, with different degrees of convolution shown.
Figure 2 in Evaluating evolutionary pressures and phylogenetic signal in earthworms: a case study - the number of typhlosole lamellae in Hormogastridae (Annelida, Oligochaeta)
Figure 2. Ultrametric tree used as the phylogenetic input for the phylogenetic generalized least squares (PGLS) analysis. Number of typhlosole lamellae and average weight are shown as red and green bars for taxa with available information. The colour code for the branches show the main Hormogastridae clades (for details, see Appendix S4).
Figure 10. Reference topology with mapped dermal sculpture characters showing a phylogenetic signal, continued. A, character 10. B, character 11. C, character 12. For character 12 in Sculpture and vascularization of dermal bones, and the implications for the physiology of basal tetrapods
Figure 10. Reference topology with mapped dermal sculpture characters showing a phylogenetic signal, continued. A, character 10. B, character 11. C, character 12. For character 12, the coloration is similar to that in Figure 9, whereas for character 10 (four character states) and 11 (three character states), the lightest shading refers to character state 1, and the increasingly darker shadings refer to the ascending character states. For definition of characters, see Appendix 2.
Phylogenetic signal and bias in paleontology
<p>An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant<span> taxa with a high proportion of missing </span><span>morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation. </span></p>
Local phylogenetic signal in Dutch habitats and other data from Prinzing et al New Phytologist 2021
<p>The functioning of present ecosystems reflects deep evolutionary history of locally co-occurring species if their functional traits show high phylogenetic signal (PS). However, we do not understand what drives local PS. We hypothesize that local PS is high in undisturbed and stressful habitats – either due to ongoing local assembly of species that maintained ancestral traits, or past evolutionary maintenance of ancestral traits within habitat species-pools, or both.</p> <p>We quantified PS and diversity of 10 traits within 6704 local plant communities across 38 Dutch habitat types differing in disturbance or stress.</p> <p>Mean local PS varied 50-fold among habitat types, often independently of phylogenetic or trait diversity. Mean local PS decreased with disturbance but showed no consistent relationship to stress. Mean local PS exceeded species-pool PS, reflecting non-random subsampling from the pool. Disturbance or stress related more strongly to mean local than to species-pool PS.</p> <p>Disturbed habitats harbour species with evolutionary divergent trait values, likely driven by ongoing, local assembly of species: environmental fluctuations might maintain different trait values within lineages through an evolutionary storage effect. If functional traits do not reflect phylogeny, ecosystem functioning might not be contingent on the presence of particular lineages, and lineages might establish evolutionarily novel interactions.</p>
Phylogenetic signal of sub-arctic beetle communities
<p>Post-glacial dispersal and colonization processes have shaped community patterns in sub-Arctic regions such as Churchill, Manitoba, Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub-Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family-level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend towards stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub-Arctic.</p>
FIGURE 2 in Mitochondrial genome of Poecilimon cretensis (Orthoptera: Tettigoniidae: Phaneropterinae): Strong phylogenetic signals in gene overlapping regions
FIGURE 2. Phylogenetic tree inferred by maximum likelihood using W-IQ-Tree from 13 Phaneropterinae mitogenomes representing different tribes (number along the nodes indicate bootstrap support).
Data from: Phylogenetic signal in diatom ecology: perspectives for aquatic ecosystems biomonitoring
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Data from: Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks
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Testing for phylogenetic signal in claws suggests great influence of ecology on Caribbean intertidal arthropods (Acari, Oribatida)
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Data from: Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution
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Data from: Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods
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Phylogenetic signal of sub-arctic beetle communities
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Local phylogenetic signal in Dutch habitats and other data from Prinzing et al New Phytologist 2021
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Data from: Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae
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Data from: Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa
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Phylogenetic signals in pest abundance and distribution range of spider mites
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Data from: Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal
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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.