Corpus ID: 204878872

Software for Systematics and Evolution

@inproceedings{Daniel2016SoftwareFS,
  title={Software for Systematics and Evolution},
  author={Daniel and Ľ. and Ayres and Michael and P. and Cummings and Guy Baele and Aaron and E. and Darling and Paul and {\'O}. and Lewis and David and Swofford and John and Huelsenbeck and Philippe Lemey and Andrew Rambaut and Marc and A. and Suchard},
  year={2016}
}
—Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful… Expand

Figures and Tables from this paper

References

SHOWING 1-10 OF 238 REFERENCES
A framework for delineating biogeographical regions based on species distributions
TLDR
A methodological roadmap for species-level biogeographical regionalizations at the global scale is developed and illustrated and it is proposed that this sort of new, quantitative delineation and relationship assessment across taxonomic and geographical grains is likely to offer opportunities for more rigorous inference in historical and ecological biogeography and conservation. Expand
A network approach for identifying and delimiting biogeographical regions
TLDR
This work applies a community detection approach from network theory that incorporates complex, higher order presence-absence patterns to tackle the challenges posed by transition zones and succeeds in retrieving a larger number of commonly recognised biogeographical regions. Expand
SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution
TLDR
The use of SpeciesGeoCoder, an open‐source software package written in Python and R that allows for easy coding of species into user‐defined operational units, is exemplified by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed theIsthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years. Expand
An Update of Wallace’s Zoogeographic Regions of the World
TLDR
A global map of zoogeographic regions is generated by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals, and it is shown that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. Expand
Estimating species diversity and distribution in the era of Big Data: to what extent can we trust public databases?
TLDR
Open databases and integrative bioinformatic tools allow a rapid approximation of large‐scale patterns of biodiversity across space and altitudinal ranges, and it is found that geographic inaccuracy affects diversity patterns more than taxonomic uncertainties. Expand
Multidimensional biases, gaps and uncertainties in global plant occurrence information.
TLDR
This study provides an empirical baseline for evaluating and improving global floristic knowledge, along with a conceptual framework that can be applied to study other hyperdiverse clades. Expand
Terrestrial Ecoregions of the World: A New Map of Life on Earth
TLDR
This article has developed a detailed map of the terrestrial ecoregions of the world that is better suited to identify areas of outstanding biodiversity and representative communities and addresses the disparity in resolution between maps currently available for global conservation planning and the reality of the Earth’s intricate patterns of life. Expand
Bayesian analysis of biogeography when the number of areas is large.
TLDR
A Bayesian approach for inferring biogeographic history that extends the application of biogeographical models to the analysis of more realistic problems that involve a large number of areas, and develops this approach in a Bayesian framework, marginalizing over all possible biogeography histories using Markov chain Monte Carlo. Expand
Biogeographical regionalisation of the Neotropical region.
TLDR
A biogeographic regionalisation of the Neotropical region is proposed as a hierarchical classification of sub-regions, dominions, provinces and districts that seeks to provide universality, objectivity and stability, such that it can be applied when describing distributional areas of particular taxa or comparing different biogeographical analyses. Expand
Model selection in historical biogeography reveals that founder-event speciation is a crucial process in Island Clades.
  • N. Matzke
  • Biology, Medicine
  • Systematic biology
  • 2014
TLDR
The re-implementing of the Dispersal-Extinction-Cladogenesis model of LAGRANGE is modified to create a new model, DEC + J, which adds founder-event speciation, the importance of which is governed by a new free parameter, and the results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods. Expand
...
1
2
3
4
5
...