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• W2000646917 abstract "An important challenge for phylogenetic studies of closely related species is the existence of deep coalescence and gene tree heterogeneity. However, their effects can vary between species and they are often neglected in phylogenetic analyses. In addition, a practical problem in the reconstruction of shallow phylogenies is to determine the most efficient set of DNA markers for a reliable estimation. To address these questions, we conducted a multilocus simulation study using empirical values of nucleotide diversity and substitution rates obtained from a wide range of mammals and evaluated the performance of both gene tree and species tree approaches to recover the known speciation times and topological relationships. We first show that deep coalescence can be a serious problem, more than usually assumed, for the estimation of speciation times in mammals using traditional gene trees. Furthermore, we tested the performance of different sets of DNA markers in the determination of species trees using a coalescent approach. Although the best estimates of speciation times were obtained, as expected, with the use of an increasing number of nuclear loci, our results show that similar estimations can be obtained with a much lower number of genes and the incorporation of a mitochondrial marker, with its high information content. Thus, the use of the combined information of both nuclear and mitochondrial markers in a species tree framework is the most efficient option to estimate recent speciation times and, consequently, the underlying species tree." @default.
• W2000646917 created "2016-06-24" @default.
• W2000646917 creator A5014728174 @default.
• W2000646917 creator A5050373175 @default.
• W2000646917 date "2012-01-19" @default.
• W2000646917 modified "2023-10-09" @default.
• W2000646917 title "Impact of Deep Coalescence on the Reliability of Species Tree Inference from Different Types of DNA Markers in Mammals" @default.
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• W2000646917 doi "https://doi.org/10.1371/journal.pone.0030239" @default.
• W2000646917 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3261886" @default.
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