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15 results for “avian phylogeny”
Data from: A new Paleogene fossil and a new dataset for waterfowl (Aves: Anseriformes) clarify phylogeny, ecological evolution, and avian evolution at the K-Pg boundary
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Host phylogeny and elevation predict infection by avian haemosporidians in a diverse New Guinean bird community (R script for analyses, figures, and supplemental figures )
<p>This script performs the glmm analysis of the elevation and infection prevalence data as well as the script required to generate the figures in the article.</p>
The limits of convergence: the roles of phylogeny and dietary ecology in shaping non-avian amniote skulls
Cranial morphology is remarkably varied in living amniotes, ranging from short-faced mammals to the elongate snouts of crocodylians. This diversity of shapes is thought to correspond with feeding ecology, a relationship repeatedly demonstrated at smaller phylogenetic scales, but one that remains untested across amniote phylogeny. Using a combination of 2D geometric and linear morphometrics, we investigate the links between phylogenetic relationships, diet, and skull shape in an expansive dataset of extant amniotes with teeth: mammals, lepidosaurs, and crocodylians. We find that both phylogeny and diet have statistically significant effects on skull shape, although these effects differ depending on the dataset analyzed. The three major clades largely partition morphospace, each plotting in separate regions with limited overlap. Mammals and squamates extensively diversify within their respective regions. Among all three groups, dietary generalists often occupy clade-specific central regions of morphospace. Some parallel changes in skull shape occur in clades with distinct evolutionary histories but similar diets. However, members of a given clade often present distinct skull shape solutions for a given diet, and the vast majority of species retain the unique aspects of their ancestral skull plan, underscoring the limits of morphological convergence due to ecology in amniotes. These data demonstrate that certain skull shapes may provide functional advantages suited to particular diets, but accounting for both phylogenetic history and ecology can provide a more nuanced approach for inferring the ecology and functional morphology of cryptic or extinct amniotes.
Down feather morphology reflects adaptation to habitat and thermal conditions across the avian phylogeny
<p>Down feathers are the first feather types that appear in both the phylogenetic and the ontogenetic history of birds. Although it is widely acknowledged that the primary function of downy elements is insulation, little is known about the interspecific variability in the structural morphology of these feathers, and the environmental factors that have influenced their evolution. Here, we collected samples of down and afterfeathers from 156 bird species and measured key morphological characters that define the insulatory properties of the downy layer. We then tested if habitat and climatic conditions could explain the observed between-species variation in down feather structure. We show that habitat has a very strong and clearly defined effect on down feather morphology. Feather size, barbule length and nodus density all decreased from terrestrial towards aquatic birds, with riparian species exhibiting intermediate characters. Wintering climate, expressed as windchill (a combined measure of the ambient temperature and wind speed) had limited effects on down morphology, colder climate only being associated with higher nodus density in dorsal down feathers. Overall, an aquatic lifestyle selects for a denser plumulaceous layer, while the effect of harsh wintering conditions on downy structures appear limited. These results provide key evidence of adaptations to habitat at the level of the downy layer, both on the scale of macro- and micro-elements of the plumage. Moreover, they reveal characters of convergent evolution in the avian plumage and mammalian fur, that match the varying needs of insulation in terrestrial and aquatic modes of life.</p>
Data from: A multilocus molecular phylogeny for the avian genus Liocichla (Passeriformes: Leiothrichidae: Liocichla)
Background: Historically the babblers have been assigned to the family Timaliidae but several recent studies have attempted to rest the taxonomy of this diverse passerine assemblage on a more firm evolutionary footing. The result has been a major rearrangement of the group. A well-supported and comprehensive phylogeny for this widespread avian group is an important part of testing evolutionary and biogeographic hypotheses, especially in Asia where the babblers are a key component of many forest ecosystems. However, the genus Liocichla is poorly represented in these prior studies of babbler systematics. Methods: We used a multilocus molecular genetic approach to generate a phylogenetic hypothesis for all five currently recognized species in the avian genus Liocichla. Multilocus DNA sequence data was used to construct individual gene trees using maximum likelihood and species trees were estimated from gene trees using Bayesian analyses. Divergence dates were obtained using a molecular clock approach. Results: Molecular data estimate a probable window of time for the origin for the Liocichla from the mid to late Miocene, between 5.55 and 12.87 Ma. Despite plumage similarities between the insular Taiwan endemic, L. steerii, and the continental L. bugunorum and L. omeiensis, molecular data suggest that L. steerii is the sister taxon to all continental Liocichla. The continental Liocichla are comprised of two lineages; a lineage containing L. omeiensis and L. bugunorum and a lineage comprised of L. phoenicea and L. ripponi. The comparatively early divergence of L. steerii within the Liocichla may be illusory due to extinct and therefore unsampled lineages. L. ripponi and L. phoenicea are parapatric with a Pleistocene split (0.07–1.88 Ma) occurring between an Eastern Himalayan L. phoenicea and a Northern Indochina distributed L. ripponi. L. bugunorum and L. omeiensis underwent a similar split between the Eastern Himalaya (L. bugunorum) and Central China (L. omeiensis) divided by the Hengduan Mountains. Conclusions: This study supports an origin of the Liocichla occurring sometime prior to the Miocene–Pliocene boundary, a period of significant climatic upheaval in Asia. The biogeographical patterns within the Liocichla mirror those of other birds in the region and allude to common geological and climatic drivers of avian diversification in Asia.
Figure 1. Calibrated phylogeny for the main avian taxa. Tree topology was obtained from O in Multivariate analysis of neognath skeletal measurements: implications for body mass estimation in Mesozoic birds
Figure 1. Calibrated phylogeny for the main avian taxa. Tree topology was obtained from O'Connor, Chiappe & Bell (2011) and divergence times are based on a 'literal' interpretation of the fossil record from Brockelhurst et al. (2012). Taxa abbreviations: Nth, Neornithes; Orph, Ornithuromorpha; Orn, Ornithothoraces; Orth, Ornithurae; Pyg, Pygostylia.
The effects of foraging ecology and allometry on avian skull shape vary across levels of phylogeny
<p>Avian skull shape diversity is classically thought to result from selection for structures that are well-adapted for distinct ecological functions, but recent work has suggested that allometry is the dominant contributor to avian morphological diversity. If true this hypothesis would overturn much conventional wisdom regarding the importance of form-function relationships in adaptive radiations, but it is possible that these results are biased by the low taxonomic levels of the clades that have been studied. Using 3D morphometric data from the skulls of a relatively old and ecologically diverse order of birds, the Charadriiformes (shorebirds and relatives), we found that foraging ecology explains more than two-thirds of the variation in skull shape across the clade. However, we also found support for the hypothesis that skull allometry evolves, contributing more to shape variation at the level of the family than the order. Allometry may provide an important source of shape variation on which selection can act over short time scales, but its potential to evolve complicates generalizations between clades. Foraging ecology remains a better predictor of avian skull shape over macroevolutionary time scales. </p>
Figure 1 in Molecular phylogeny of major lineages of the avian family Phasianidae inferred from complete mitochondrial genome sequences
Figure 1. Molecular phylogenetic tree derived from complete DNA sequences of the 12 mitochondrial protein-coding genes using Bayesian inference, maximum parsimony and maximum likelihood analysis. The numbers beside the nodes are Bayesian posterior probabilities (≥ 0.95 retained) and bootstrap proportions (≥ 50% retained). Anas platyrhynchos was set as outgroup. ∗demonstrates that MP analysis does not support this branch.
The limits of convergence: the roles of phylogeny and dietary ecology in shaping non-avian amniote skulls
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Data from: A multilocus molecular phylogeny for the avian genus Liocichla (Passeriformes: Leiothrichidae: Liocichla)
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Down feather morphology reflects adaptation to habitat and thermal conditions across the avian phylogeny
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Data from: Most genomic loci misrepresent the phylogeny of an avian radiation because of ancient gene flow
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The effects of foraging ecology and allometry on avian skull shape vary across levels of phylogeny
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PERMANOVA results from Principal component analysis of avian hind limb and foot morphometrics and the relationship between ecology and phylogeny
<p class="MsoNoSpacing">Principal component analysis has been used to test for similarities in ecology and life habit between modern and fossil birds, however, the two main portions of the hindlimb—the foot and the long bone elements—have not been examined separately. We examine the potential links between morphology, ecology, and phylogeny through a synthesis of phylogenetic paleoecological methods and morphospace analysis. Both hindlimb morphologies and species' ecologies exhibit extreme phylogenetic clumping, although these patterns are at least partially explainable by a Brownian motion style of evolution. Some morphologies are strongly correlated with particular ecologies, while some ecologies are occupied by a variety of morphologies. Within the morphospace analyses, the length of the hallux (toe I) is the most defining characteristic of the entire hindlimb. The foot and hindlimb are represented on different axes when all measurements are considered in an analysis, suggesting that these structures undergo morphological change separately from each other. Early birds tend to cluster together, representing an unspecialized basal foot morphotype and a hindlimb reliant on hip-driven, not knee-driven, locomotion. Direct links between morphology, ecology, and phylogeny are unclear and complicated, and may be biased due to sample size (~60 species). This study should be treated as a preliminary analysis that further studies, especially those examining the vast diversity of modern birds, can build upon.</p>
PERMANOVA results from Principal component analysis of avian hind limb and foot morphometrics and the relationship between ecology and phylogeny
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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.