Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Computational Performance and Statistical Accuracy of *BEAST and
  Comparisons with Other Methods   Under the multispecies coalescent model of molecular evolution, gene trees
have independent evolutionary histories within a shared species tree. In
comparison, supermatrix concatenation methods assume that gene trees share a
single common genealogical history, thereby equating gene coalescence with
species divergence. The multispecies coalescent is supported by previous
studies which found that its predicted distributions fit empirical data, and
that concatenation is not a consistent estimator of the species tree. *BEAST, a
fully Bayesian implementation of the multispecies coalescent, is popular but
computationally intensive, so the increasing size of phylogenetic data sets is
both a computational challenge and an opportunity for better systematics. Using
simulation studies, we characterize the scaling behaviour of *BEAST, and enable
quantitative prediction of the impact increasing the number of loci has on both
computational performance and statistical accuracy. Follow up simulations over
a wide range of parameters show that the statistical performance of *BEAST
relative to concatenation improves both as branch length is reduced and as the
number of loci is increased. Finally, using simulations based on estimated
parameters from two phylogenomic data sets, we compare the performance of a
range of species tree and concatenation methods to show that using *BEAST with
tens of loci can be preferable to using concatenation with thousands of loci.
Our results provide insight into the practicalities of Bayesian species tree
estimation, the number of loci required to obtain a given level of accuracy and
the situations in which supermatrix or summary methods will be outperformed by
the fully Bayesian multispecies coalescent.

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The categories of this paper are: nucl-th
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The categories of this paper are: eess
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The categories of this paper are: funct-an
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The categories of this paper are: chao-dyn
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The categories of this paper are: hep-th
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The categories of this paper are: hep-ph
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The categories of this paper are: cs
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The categories of this paper are: alg-geom
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The categories of this paper are: dg-ga
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The categories of this paper are: math
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The categories of this paper are: cmp-lg
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The categories of this paper are: adap-org
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The categories of this paper are: gr-qc
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The categories of this paper are: hep-ex
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The categories of this paper are: mtrl-th
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The categories of this paper are: stat