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116 results for “phylogenetic signal”
Radiation with reproductive isolation in the near-absence of phylogenetic signal
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Phylogenetic signal and evolutionary correlates of urban tolerance in a widespread neotropical lizard clade
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Data from: Wood anatomical and hydraulic traits of Tamarix species across a large Eurasian gradient show a stronger climatic than phylogenetic signal
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Detecting phylogenetic signal and adaptation in papionin cranial shape by decomposing variation at different spatial scales
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Supplementary material 1 from: Antoł A, Kozłowski J (2020) Scaling of organ masses in mammals and birds: phylogenetic signal and implications for metabolic rate scaling. ZooKeys 982: 149-159. https://doi.org/10.3897/zookeys.982.55639
Figures S1–S5. Additional graphs with result analysis and phylogenetical trees used in data analysis
Data from: Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks
Across different taxa, networks of mutualistic or antagonistic interactions show consistent architecture. Most networks are modular, with modules being distinct species subsets connected mainly with each other and having few connections to other modules. We investigate the phylogenetic relatedness of species within modules and whether a phylogenetic signal is detectable in the within- and among module connectivity of species using 27 mammal-flea networks from the Palaearctic. In the 24 networks that were modular, closely-related hosts co-occurred in the same module more often than expected by chance; in contrast, this was rarely the case for parasites. The within- and among-module connectivity of the same host or parasite species varied geographically. However, among-module but not within-module connectivity of host and parasites was somewhat phylogenetically constrained. These findings suggest that the establishment of host-parasite networks results from the interplay between phylogenetic influences acting mostly on hosts and local factors acting on parasites, to create an asymmetrically constrained pattern of geographic variation in modular structure. Modularity in host-parasite networks seems to result from the shared evolutionary history of hosts and by trait convergence among unrelated parasites. This suggests profound differences between hosts and parasites in the establishment and functioning of bipartite antagonistic networks.
Data from: Phylogenetic signal in diatom ecology: perspectives for aquatic ecosystems biomonitoring
Diatoms include a great diversity of taxa and are recognized as powerful bioindicators in rivers. However using diatoms for monitoring programs is costly and time consuming because most of the methodologies necessitate species-level identification. This raises the question of the optimal tradeoff between taxonomic resolution and bioassessment quality. Phylogenetic tools may form the bases of new more efficient approaches for biomonitoring if relationships between ecology and phylogeny can be demonstrated. We estimated the ecological optima of 127 diatom species for 19 environmental parameters using count data from 2119 diatom communities sampled during 8 years in eastern France. Using uni- and multivariate analyses, we explored the relationships between freshwater diatom phylogeny and ecology (i.e. the phylogenetic signal). We found a significant phylogenetic signal for many of the ecological optima that were tested, but the strength of the signal varied significantly from one trait to another. Multivariate analysis also showed that the multidimensional ecological niche of diatoms can be strongly related to phylogeny. The presence of clades containing species that exhibit homogeneous ecology suggests that phylogenetic information can be useful for aquatic biomonitoring. This study highlights the presence of significant patterns of ecological optima for freshwater diatoms in relation to their phylogeny. These results suggest the presence of a signal above the species level, which is encouraging for the development of simplified methods for biomonitoring survey.
Data from: Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution
Background. Anchors are one of the important attachment appendages for monogenean parasites. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies. When combined with morphological and molecular data, analysis of anchor morphometry can potentially answer a wide range of biological questions. Materials and Methods. We used data from anchor morphometry, body size and morphology of 13 Ligophorus (Monogenea: Ancyrocephalidae) species infecting two marine mugilid (Teleostei: Mugilidae) fish hosts: Moolgarda buchanani (Bleeker) and Liza subviridis (Valenciennes) from Malaysia. Anchor shape and size data (n = 530) were generated using methods of geometric morphometrics. We used 28S rRNA, 18S rRNA, and ITS1 sequence data to infer a maximum likelihood phylogeny. We discriminated species using principal component and cluster analysis of shape data. Adams's Kmult was used to detect phylogenetic signal in anchor shape. Phylogeny-correlated size and shape changes were investigated using continuous character mapping and directional statistics, respectively. We assessed morphological constraints in anchor morphometry using phylogenetic regression of anchor shape against body size and anchor size. Anchor morphological integration was studied using partial least squares method. The association between copulatory organ morphology and anchor shape and size in phylomorphospace was used to test the Rohde-Hobbs hypothesis. We created monogeneaGM, a new R package that integrates analyses of monogenean anchor geometric morphometric data with morphological and phylogenetic data. Results. We discriminated 12 of the 13 Ligophorus species using anchor shape data. Significant phylogenetic signal was detected in anchor shape. Thus, we discovered new morphological characters based on anchor shaft shape, the length between the inner root point and the outer root point, and the length between the inner root point and the dent point. The species on M. buchanani evolved larger, more robust anchors; those on L. subviridis evolved smaller, more delicate anchors. Anchor shape and size were significantly correlated, suggesting constraints in anchor evolution. Tight integration between the root and the point compartments within anchors confirms the anchor as a single, fully integrated module. The correlation between male copulatory organ morphology and size with anchor shape was consistent with predictions from the Rohde-Hobbs hypothesis. Conclusions. Monogenean anchors are tightly integrated structures, and their shape variation correlates strongly with phylogeny, thus underscoring their value for systematic and evolutionary biology studies. Our MonogeneaGM R package provides tools for researchers to mine biological insights from geometric morphometric data of speciose monogenean genera.
Data from: Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods
Determining which biological traits affect taxonomic durations is critical for explaining macroevolutionary patterns. Two approaches are commonly used to investigate the associations between traits and durations and/or extinction and origination rates: analyses of taxonomic occurrence patterns in the fossil record and comparative phylogenetic analyses, predominantly of extant taxa. By capitalizing upon the empirical record of past extinctions, paleontological data avoid some of the limitations of existing methods for inferring extinction and origination rates from molecular phylogenies. However, most paleontological studies of extinction selectivity have ignored phylogenetic relationships because there is a dearth of phylogenetic hypotheses for diverse non-vertebrate higher taxa in the fossil record. This omission inflates the degrees of freedom in statistical analyses and leaves open the possibility that observed associations are indirect, reflecting shared evolutionary history rather than the direct influence of particular traits on durations. Here we investigate global patterns of extinction selectivity in Devonian terebratulide brachiopods and compare the results of taxonomic vs. phylogenetic approaches. Regression models that assume independence among taxa provide support for a positive association between geographic range size and genus duration but do not indicate an association between body size and genus duration. Brownian motion models of trait evolution identify significant similarities in body size, range size, and duration among closely related terebratulide genera. We use phylogenetic regression to account for shared evolutionary history and find support for a significant positive association between range size and duration among terebratulides that is also phylogenetically structured. The estimated range size–duration relationship is moderately weaker in the phylogenetic analysis due to the down-weighting of closely related genera that were both broadly distributed and long lived; however, this change in slope is not statistically significant. These results provide evidence for the phylogenetic conservatism of organismal and emergent traits, yet also the general phylogenetic independence of the relationship between range size and duration.
Data and Code for: Oh, the places you will grow: intraspecific latitudinal clines in butterfly size suggest a phylogenetic signal
<p>This publication contains the R-Scripts and other supplementary files necessary to reproduce the analyses and figures of Merwin A, Hilliard J, Larsen<span> </span>A, Lasken A, Johnson I (2022) Oh, the places you will grow: intraspecific latitudinal clines in butterfly size suggest a phylogenetic signal. Ecology and Evolution</p> <p>All files are compressed into a single ZIP folder. All directories contain README files that explain their contents.</p>
Data from: Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae
Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira–Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia + the Asian clade, Baisseeae + milkweeds, and Periplocoideae + the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the basis for study of convergent floral morphologies and their adaptive value.
Data from: Clock gene evolution: seasonal timing, phylogenetic signal, or functional constraint?
Genetic determinants of seasonal reproduction are not fully understood, but may be important predictors of organism responses to climate change. We used a comparative approach to study the evolution of seasonal timing within a fish community in a natural common garden setting. We tested the hypothesis that allelic length variation in the PolyQ domain of a circadian rhythm gene, Clock1a, corresponded to interspecific differences in seasonal reproductive timing across five native and one introduced cyprinid fishes (n = 425 individuals) that co-occur in the Rio Grande, New Mexico, USA. Most common allele lengths were longer in native species that initiated reproduction earlier (Spearman's r = -0.70, p = 0.23). Clock1a allele length exhibited strong phylogenetic signal and earlier spawners were evolutionarily derived. Aside from length variation in Clock1a, all other amino acids were identical across native species, suggesting functional constraint over evolutionary time. Interestingly, the endangered Rio Grande silvery minnow (Hybognathus amarus) exhibited less allelic variation in Clock1a and observed heterozygosity was 2- to 6-fold lower than the five other (non-imperiled) species. Reduced genetic variation in this functionally important gene may impede this species' capacity to respond to ongoing environmental change.
Figure 3. A, B in Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns
Figure 3. A, B, musculature of Milnesium cf. tardigradum (A, dorso-lateral view; B, ventro-lateral view). C, D, musculature of Acutuncus antarcticus (C, lateral view; D, ventro-lateral 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–D, CSLM, maximum projection. B, C, colour coded by depth. Scale bars: A–D = 50 μm.
Figure 4. A in Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns
Figure 4. A, musculature of Paramacrobiotus richtersi (ventro-lateral view). B, C, musculature of Bertolanius volubilis (A, dorsal view; B, ventro-lateral view; colour coded by depth). 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. C, colour coded by depth. Scale bars: A–C = 50 μm.
Figure 9. Ventral musculature associated with the A in Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns
Figure 9. Ventral musculature associated with the A node; the A-LIc muscle fibre crosses the corresponding fibre of the opposite leg (arrow). A, Paramacrobiotus richtersi; B, Milnesium cf. tardigradum; C, Echiniscus testudo. A–C, CSLM, maximum projection. Letters and numbers identify the muscle attachment points (see text). Ph, pharynx. Scale bars: 10 μm.
Figure 12 in Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns
Figure 12. Schematic representations of hypothetical ancestral serial homologies of the different muscle groups in tardigrades. A, dorsal muscle group in eutardigrades; B, dorsal muscle group in heterotardigrade echiniscids; C, lateral muscle group in tardigrades; D, ventral muscle group in tardigrades.
Figure 7 in Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns
Figure 7. Schematic representations of musculature. A, Paramacrobiotus richtersi; B, Bertolanius volubilis. Muscles of the ventral group are in red, their nodes are marked by hexagons; muscles of the lateral group are in blue, their attachment points and nodes are marked by squares; muscles of the dorsal group are in green, their attachment points and nodes are marked by circles. Letters and numbers identify the muscle attachment points (see text). Ph, pharynx.
Figure 11 in Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns
Figure 11. Phylogenetic tree obtained with Bayesian analyses based on molecular data (18S rRNA + 28S rRNA). The posterior probability values are indicated next to each node.
Figure 2. A, B in Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns
Figure 2. A, B, the eutardigrade Milnesium cf. tardigradum in active state (A, ventral view; B, lateral view). C, D, the eutardigrade Paramacrobiotus richtersi in active state (C; dorsal view) and in dry anhydrobiotic state (D; tun shape). Asterisk indicates front. Letters and numbers identify the muscle attachment points (see text). A–D, SEM. Scale bars: A–C = 50 μm; D = 20 μm.
Figure 1. A in Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns
Figure 1. A, muscle fibres (white arrows) and ventral ganglion (black arrow) of the nervous system in the eutardigrade Paramacrobiotus richtersi. B, C, dorsal view of the heterotardigrade Echiniscus testudo in active state (B) and anhydrobiotic state (C; tun shape). Asterisk indicates the front. Letters identify muscle attachment points (see text). A–C, SEM. Scale bars: A = 20 μm, B–C = 50 μm.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.