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33 results for “multispecies modeling”
Figure 1 in Bayesian Poisson tree processes and multispecies coalescent models shed new light on the diversification of Nawab butterflies in the Solomon Islands (Nymphalidae, Charaxinae, Polyura)
Figure 1. Map of the geographic range of Polyura epigenes in the Solomon Islands. Male habitus of the different subspecies are shown above the name of the taxon. The distribution of each taxa is indicated by a coloured dashed line. The colour of the line refers to the pastille on the side of the taxon name. All pictures were taken by Bernard Turlin. The map is from National Geographic's MapMaker Interactive.
Figure 5 in Bayesian Poisson tree processes and multispecies coalescent models shed new light on the diversification of Nawab butterflies in the Solomon Islands (Nymphalidae, Charaxinae, Polyura)
Figure 5. Divergence time estimates derived from the *BEAST analysis. Chronogram derived from the posterior trees of dating analysis conducted in BEAST. The 95% credibility intervals are shown at each node of the phylogeny. A map of the Solomon Islands with bathymetry is shown at the top of the figure. The island of Malaita is highlighted in violet. A picture of a female Polyura epigenes bicolor f. cinereus (orange morph) is presented. Picture taken by Bernard Turlin. T in time bar stands for Tarantian.
Bayesian models' outputs for: A new method to explicitly estimate the shift of optimum along gradients in multispecies studies
<p>This repository contains data to reproduce analysis presented in the paper:</p> <p>B. Mourguiart, B. Liquet, K. Mengersen, T. Couturier, J. Mansons, Y. Braud, A. Besnard . A new method to explicitly estimate the shift of optimum along gradients in multispecies studies. <em>Journal of Biogeography</em>, (in press).</p> <p>The paper introduces a new formulation of a Bayesian hierarchical linear model that explicitly estimates optimum shifts for multiple species having symmetrical response curves. This new formulation, called Explicit Hierarchical Model of Optimum Shifts (EHMOS), is compared to a mean comparison method and a Bayesian generalized linear mixed model (GLMM) using simulated and real datasets. Fitting the models to the simulated data took several days. Here we provide the models' outputs needed to reproduce the results presented in the paper without re-running the models. </p>
Bayesian models' outputs for: A new method to explicitly estimate the shift of optimum along gradients in multispecies studies
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Data from: Integrating over uncertainty in spatial scale of response within multispecies occupancy models yields more accurate assessments of community composition
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Data from: Impact of model violations on the inference of species boundaries under the multispecies coalescent
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Data from: A multispecies occupancy model for two or more interacting species
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Data from: Probabilistic species tree distances: implementing the multispecies coalescent to compare species trees within the same model-based framework used to estimate them
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Data from: A multispecies coalescent model for quantitative traits
We present a multispecies coalescent model for quantitative traits that allows for evolutionary inferences at micro- and macroevolutionary scales. A major advantage of this model is its ability to incorporate genealogical discordance underlying a quantitative trait. We show that discordance causes a decrease in the expected trait covariance between more closely related species relative to more distantly related species. If unaccounted for, this outcome can lead to an overestimation of a trait's evolutionary rate, to a decrease in its phylogenetic signal, and to errors when examining shifts in mean trait values. The number of loci controlling a quantitative trait appears to be irrelevant to all trends reported, and discordance also affected discrete, threshold traits. Our model and analyses point to the conditions under which different methods should fare better or worse, in addition to indicating current and future approaches that can mitigate the effects of discordance.
Data from: Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
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Data from: A multispecies coalescent model for quantitative traits
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Data from: Assessing the impacts of imperfect detection on estimates of diversity and community structure through multispecies occupancy modeling
Detecting all species in a given survey is challenging, regardless of sampling effort. This issue, more commonly known as imperfect detection, can have negative impacts on data quality and interpretation, most notably leading to false absences for rare or difficult‐to‐detect species. It is important that this issue be addressed, as estimates of species richness are critical to many areas of ecological research and management. In this study, we set out to determine the impacts of imperfect detection, and decisions about thresholds for inclusion in occupancy, on estimates of species richness and community structure. We collected data from a stream fish assemblage in Algonquin Provincial Park to be used as a representation of ecological communities. We then used multispecies occupancy modeling to estimate species‐specific occurrence probabilities while accounting for imperfect detection, thus creating a more informed dataset. This dataset was then compared to the original to see where differences occurred. In our analyses, we demonstrated that imperfect detection can lead to large changes in estimates of species richness at the site level and summarized differences in the community structure and sampling locations, represented through correspondence analyses.
Data from: Assessing the impacts of imperfect detection on estimates of diversity and community structure through multispecies occupancy modeling
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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.