Abstract
BackgroundPhylogenetic 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.Principal FindingsThe 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 Rhinopithecus, Pygathrix and Nasalis, and a monophyletic African group consisting of Colobus and Piliocolobus. The combined nuclear data analyses supported a sister-grouping between Semnopithecus and Trachypithecus, and between Presbytis and the odd-nosed monkey group, as well as a sister-taxon association of Pygathrix and Rhinopithecus within the odd-nosed monkey group. In contrast, mt genome data analyses revealed that Semnopithecus diverged earliest among the Asian colobines and that the odd-nosed monkey group is sister to a Presbytis and Trachypithecus clade, as well as a close association of Pygathrix with Nasalis. 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.SignificanceThe 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.
Highlights
The Old World monkeys are comprised of two living subfamilies – the cheek-pouch monkeys (Cercopithecinae) and the leaf-eating monkeys (Colobinae)
The 44 nuclear noncoding genes of 18 species varied in length from 337 bp to 862 bp (ENC15) aligned positions
Length differences were largely due to the variation in copy number of tandem repeat sequences in the conserved sequence block (CSB) domains of the mt control region
Summary
The Old World monkeys are comprised of two living subfamilies – the cheek-pouch monkeys (Cercopithecinae) and the leaf-eating monkeys (Colobinae). Close to the initial appearance of colobines in the fossil record, most the extant colobine genera diversify from one another within a four million year window [12,13,14]. For this reason, attempts to clarify relationships among these colobine genera have encountered challenges. Attempts to clarify relationships among these colobine genera have encountered challenges Given that they share with apes a close relatedness, historically similar distribution in the Old World, and similar timing of diversification events, elucidating colobine evolutionary history can shed light upon the evolution and dispersal of apes (and other mammals) across the Old World, including our own ancestors. 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 noncolobine primates
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