Journal
MOLECULAR PHYLOGENETICS AND EVOLUTION
Volume 84, Issue -, Pages 14-26Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2014.11.001
Keywords
Mammalia; Phylogenetic asymmetry; Species-level phylogeny; Supermatrix; Supertree
Funding
- Danish Natural Science Research Council [11-115750]
- European Research Council [310886]
- European Research Council (ERC) [310886] Funding Source: European Research Council (ERC)
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Across large clades, two problems are generally encountered in the estimation of species-level phylogenies: (a) the number of taxa involved is generally so high that computation-intensive approaches cannot readily be utilized and (b) even for clades that have received intense study (e.g., mammals), attention has been centered on relatively few selected species, and most taxa must therefore be positioned on the basis of very limited genetic data. Here, we describe a new heuristic-hierarchical Bayesian approach and use it to construct a species-level phylogeny for all extant and late Quaternary extinct mammals. In this approach, species with large quantities of genetic data are placed nearly freely in the mammalian phylogeny according to these data, whereas the placement of species with lower quantities of data is performed with steadily stricter restrictions for decreasing data quantities. The advantages of the proposed method include (a) an improved ability to incorporate phylogenetic uncertainty in downstream analyses based on the resulting phylogeny, (b) a reduced potential for long-branch attraction or other types of errors that place low-data taxa far from their true position, while maintaining minimal restrictions for better-studied taxa, and (c) likely improved placement of low-data taxa due to the use of closer outgroups. (C) 2014 Elsevier Inc. All rights reserved.
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