Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys.

BACKGROUND: Colobine monkeys constitute a diverse group of primates with major radiations in Africa and Asia. However, phylogenetic relationships among genera are under debate, and recent molecular studies with incomplete taxon-sampling revealed discordant gene trees. To solve the evolutionary history of colobine genera and to determine causes for possible gene tree incongruences, we combined presence/absence analysis of mobile elements with autosomal, X chromosomal, Y chromosomal and mitochondrial sequence data from all recognized colobine genera. RESULTS: Gene tree topologies and divergence age estimates derived from different markers were similar, but differed in placing Piliocolobus/Procolobus and langur genera among colobines. Although insufficient data, homoplasy and incomplete lineage sorting might all have contributed to the discordance among gene trees, hybridization is favored as the main cause of the observed discordance. We propose that African colobines are paraphyletic, but might later have experienced female introgression from Piliocolobus/Procolobus into Colobus. In the late Miocene, colobines invaded Eurasia and diversified into several lineages. Among Asian colobines, Semnopithecus diverged first, indicating langur paraphyly. However, unidirectional gene flow from Semnopithecus into Trachypithecus via male introgression followed by nuclear swamping might have occurred until the earliest Pleistocene. CONCLUSIONS: Overall, our study provides the most comprehensive view on colobine evolution to date and emphasizes that analyses of various molecular markers, such as mobile elements and sequence data from multiple loci, are crucial to better understand evolutionary relationships and to trace hybridization events. Our results also suggest that sex-specific dispersal patterns, promoted by a respective social organization of the species involved, can result in different hybridization scenarios.

Retropositional events consolidate the branching order among New World monkey genera.

Due to contradicting relationships obtained from various morphological and genetic studies, phylogenetic relationships among New World monkey genera are highly disputed. In the present study, we analyzed the presence/absence pattern of 128 SINE integrations in all New World monkey genera. Among them, 70 were specific for only a single genus, whereas another 18 were present in all New World monkey genera. The 40 remaining insertions were informative to elucidate phylogenetic relationships among genera. Several of them confirmed the monophyly of the three families Cebidae, Atelidae and Pitheciidae as well as of the subfamily Callithrichinae. Further markers provided evidence for a sister grouping of Cebidae and Atelidae to the exclusion of Pitheciidae as well as for relationships among genera belonging to Callithrichinae and Atelidae. Although a close affiliation of Saimiri, Aotus and Cebus to Callithrichinae was shown, the relationships among the three genera remained unresolved due to three contradicting insertions.

A PCR-based marker to simply identify Saimiri sciureus and S. boliviensis boliviensis.

Squirrel monkeys, mainly Saimiri sciureus and S. boliviensis, are common in zoos and widely used in biomedical research. However, an exact species identification based on morphological characteristics is difficult. Hence, several molecular methods were proposed, but all of them are expensive and require extensive laboratory work. In contrast, we describe an Alu integration, which is present in S. boliviensis boliviensis and absent in S. sciureus. Among analyzed S. b. peruviensis specimens various presence/absence patterns of the integration were detected indicating that this study population might have originated from a natural hybrid zone. Based on the size of the Alu element ( approximately 300 bp), the presence/absence pattern of the integration can easily be traced by PCR and followed by agarose gel electrophoresis.

Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and genus affiliations of their species groups.

BACKGROUND: The evolutionary history of the Asian colobines is less understood. Although monophyly of the odd-nosed monkeys was recently confirmed, the relationships among the langur genera Presbytis, Semnopithecus and Trachypithecus and their position among Asian colobines remained unclear. Moreover, in Trachypithecus various species groups are recognized, but their affiliations are still disputed. To address these issues, mitochondrial and Y chromosomal sequence data were phylogenetically related and combined with presence/absence analyses of retroposon integrations. RESULTS: The analysed 5 kb fragment of the mitochondrial genome allows no resolution of the phylogenetic relationships among langur genera, but five retroposon integrations were detected which link Trachypithecus and Semnopithecus. According to Y chromosomal data and a 573 bp fragment of the mitochondrial cytochrome b gene, a common origin of the species groups T. [cristatus], T. [obscurus] and T. [francoisi] and their reciprocal monophyly is supported, which is also underpinned by an orthologous retroposon insertion. T. [vetulus] clusters within Semnopithecus, which is confirmed by two retroposon integrations. Moreover, this species group is paraphyletic, with T. vetulus forming a clade with the Sri Lankan, and T. johnii with the South Indian form of S. entellus. Incongruence between gene trees was detected for T. [pileatus], in that Y chromosomal data link it with T. [cristatus], T. [obscurus] and T. [francoisi], whereas mitochondrial data affiliates it with the Semnopithecus clade. CONCLUSION: Neither relationships among the three langur genera nor their position within Asian colobines can be settled with 5 kb mitochondrial sequence data, but retroposon integrations confirm at least a common origin of Semnopithecus and Trachypithecus. According to Y chromosomal and 573 bp mitochondrial sequence data, T. [cristatus], T. [obscurus] and T. [francoisi] represent true members of the genus Trachypithecus, whereas T. [vetulus] clusters within Semnopithecus. Due to paraphyly of T. [vetulus] and polyphyly of Semnopithecus, a split of the genus into three species groups (S. entellus - North India, S. entellus - South India + T. johnii, S. entellus - Sri Lanka + T. vetulus) seems to be appropriate. T. [pileatus] posses an intermediate position between both genera, indicating that the species group might be the result of ancestral hybridization.