Phylogenetic Relationships among the Colobine Monkeys Revisited: New Insights from Analyses of Complete mt Genomes and 44 Nuclear Non-Coding Markers

<div><h3>Background</h3><p>Phylogenetic relationships among Asian and African colobine genera have been disputed and are not yet well established. In the present study, we revisit the contentious relationships within the Asian and African Colobinae by analyzing 44 nuclear non-coding genes (>23 kb) and mitochondrial (mt) genome sequences from 14 colobine and 4 non-colobine primates.</p> <h3>Principal Findings</h3><p>The combined nuclear gene and the mt genome as well as the combined nuclear and mt gene analyses yielded different phylogenetic relationships among colobine genera with the exception of a monophyletic ‘odd-nosed’ group consisting of <em>Rhinopithecus</em>, <em>Pygathrix</em> and <em>Nasalis</em>, and a monophyletic African group consisting of <em>Colobus</em> and <em>Piliocolobus</em>. The combined nuclear data analyses supported a sister-grouping between <em>Semnopithecus</em> and <em>Trachypithecus</em>, and between <em>Presbytis</em> and the odd-nosed monkey group, as well as a sister-taxon association of <em>Pygathrix</em> and <em>Rhinopithecus</em> within the odd-nosed monkey group. In contrast, mt genome data analyses revealed that <em>Semnopithecus</em> diverged earliest among the Asian colobines and that the odd-nosed monkey group is sister to a <em>Presbytis</em> and <em>Trachypithecus</em> clade, as well as a close association of <em>Pygathrix</em> with <em>Nasalis</em>. The relationships among these genera inferred from the analyses of combined nuclear and mt genes, however, varied with the tree-building methods used. Another remarkable finding of the present study is that all of our analyses rejected the recently proposed African colobine paraphyly and hybridization hypothesis and supported reciprocal monophyly of the African and Asian groups.</p> <h3>Significance</h3><p>The phylogenetic utility of large-scale new non-coding genes was assessed using the Colobinae as a model, We found that these markers were useful for distinguishing nodes resulting from rapid radiation episodes such as the Asian colobine radiation. None of these markers here have previously been used for colobine phylogenetic reconstruction, increasing the spectrum of molecular markers available to mammalian systematics.</p>