期刊
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
卷 174, 期 1, 页码 169-184出版社
OXFORD UNIV PRESS
DOI: 10.1111/zoj.12231
关键词
deep coalescences; incomplete lineage sorting; phylogeny; species trees
类别
资金
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET) [PICT 2006506 ANPCYT-FONCYT, ANPCYT-FONCYT 33789]
- Brigham Young University Kennedy Center for International Studies, Department of Biology
- M. L. Bean Life Science Museum
- NSF-PIRE [OISE 0530267]
Lack of resolution in a phylogenetic tree is usually represented as a polytomy, and often adding more data (loci and taxa) resolves the species tree. These are the soft' polytomies, but in other cases additional data fail to resolve relationships; these are the hard' polytomies. This latter case is often interpreted as a simultaneous radiation of lineages in the history of a clade. Although hard polytomies are difficult to address, model-based approaches provide new tools to test these hypotheses. Here, we used a clade of 144 species of the South American lizard clade Eulaemus to estimate phylogenies using a traditional concatenated matrix and three species tree methods: *BEAST, BEST, and minimizing deep coalescences (MDC). The different species tree methods recovered largely discordant results, but all resolved the same polytomy (e.g. very short internodes amongst lineages and low nodal support in Bayesian methods). We simulated data sets under eight explicit evolutionary models (including hard polytomies), tested these against empirical data (a total of 14 loci), and found support for two polytomies as the most plausible hypothesis for diversification of this clade. We discuss the performance of these methods and their limitations under the challenging scenario of hard polytomies.(c) 2015 The Linnean Society of London
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