Nelson Ting

Publications of Nelson Ting

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

  Authors: Xiao Ping Wang, Li Yu, Christian Roos, Nelson Ting, Cui Ping Chen, Jing Wang, Ya Ping Zhang

  PloS one. 01/2012; 7(4):e36274.

  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 AsianPhylogenetic 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. 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 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. 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.

• Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation.

  Authors: Li Yu, Xiaoping Wang, Nelson Ting, Yaping Zhang

  Mitochondrion. 01/2011; 11(3):497-503.

  Chinese snub-nosed monkeys belong to the genus Rhinopithecus and are limited in distribution to six isolated mountainous areas in the temperate regions of Central and Southwest China. Compared to theChinese snub-nosed monkeys belong to the genus Rhinopithecus and are limited in distribution to six isolated mountainous areas in the temperate regions of Central and Southwest China. Compared to the other members of the subfamily Colobinae (or leaf-eating monkeys), these endangered primates are unique in being adapted to a high altitude environment and display a remarkable ability to tolerate low temperatures and hypoxia. They thus offer an interesting organismal model of adaptation to extreme environmental stress. Mitochondria generate energy by oxidative phosphorylation (OXPHOS) and play important roles in oxygen usage and energy metabolism. We analyzed the mitochondrial genomes of two Chinese snub-nosed monkey species and eight other colobines in the first attempt to understand the genetic basis of high altitude adaptation in non-human primates. We found significant evidence of positive selection in one Chinese snub-nosed monkey, Rhinopithecus roxellana, which is suggestive of adaptive change related to high altitude and cold weather stress. In addition, our study identified two potentially important adaptive amino acid residues (533 and 3307) in the NADH2 and NADH6 genes, respectively. Surprisingly, no evidence for positive selection was found in Rhinopithecus bieti (the other Chinese snub-nosed monkey analyzed). This finding is intriguing, especially considering that R. bieti inhabits a higher altitudinal distribution than R. roxellana. We hypothesize that a different adaptive genetic basis to high altitude survival exists in R. bieti from those seen in other mammals, and that positive selection and functionally associated mutations in this species may be detected in nuclear genes related to energy and oxygen metabolism. More information on the structure, function, and evolution of mitochondrial and nuclear genomes in Chinese snub-nosed monkeys is required to reveal the molecular mechanisms that underlie adaptations to high altitude survival in non-human primates.

• Adaptive evolution of digestive RNASE1 genes in leaf-eating monkeys revisited: new insights from 10 additional Colobines.

  Authors: Li Yu, Xiao-Yan Wang, Wei Jin, Peng-Tao Luan, Nelson Ting, Ya-Ping Zhang

  Molecular biology and evolution. 09/2009;

  Pancreatic RNase genes implicated in the adaptation of the colobine monkeys to leaf-eating have long intrigued evolutionary biologists since the identification of a duplicated RNASE1 gene withPancreatic RNase genes implicated in the adaptation of the colobine monkeys to leaf-eating have long intrigued evolutionary biologists since the identification of a duplicated RNASE1 gene with enhanced digestive efficiencies in Pygathrix nemaeus. The recent emergence of two contrasting hypotheses, i.e., independent duplication and one duplication event hypotheses, make it into focus again. Current understanding of Colobine RNASE1 gene evolution largely depends on the analyses of few colobine species. The present study with more intensive taxonomic and character sampling not only provides a clearer picture of Colobine RNASE1 gene evolution, but also allows to have a more thorough understanding about the molecular basis underlying the adaptation of Colobinae to the unique leaf-feeding lifestyle. The present broader and detailed phylogenetic analyses yielded two important findings: (1) All trees based on the analyses of coding, noncoding and both regions provided consistent evidence indicating RNASE1 duplication occurred after Asian and African colobines speciation, i.e., independent duplication hypothesis; (2) No obvious evidence of gene conversion in RNASE1 gene was found, favoring independent evolution of Colobine RNASE1 gene duplicates. The conclusion drawn from previous studies that gene conversion has played a significant role in the evolution of Colobine RNASE1 was not supported. Our selective constraint analyses also provided interesting insights, with significant evidence of positive selection detected on ancestor lineages leading to duplicated gene copies. The identification of a handful of new adaptive sites and amino acid changes that have not been characterized previously also provide a necessary foundation for further experimental investigations of RNASE1 functional evolution in Colobinae.

• Mitochondrial relationships and divergence dates of the African colobines: evidence of Miocene origins for the living colobus monkeys.

  Authors: Nelson Ting

  Journal of human evolution. 05/2008;

  The African colobines represent a neglected area of cercopithecid systematics. Resolving the phylogenetic relationships and estimating divergence dates among the living forms will provide insightThe African colobines represent a neglected area of cercopithecid systematics. Resolving the phylogenetic relationships and estimating divergence dates among the living forms will provide insight into the evolution of this group and may shed light upon the evolution of other African primates as well. This is the first molecular assessment of the evolutionary relationships among the modern colobus monkeys, which are comprised of the black-and-white, olive, and red colobus groups. Over 4,000 base pairs of mitochondrial DNA were amplified and sequenced in over 40 colobus monkey individuals incorporating representatives from all commonly recognized species. Gene trees were inferred using maximum likelihood and Bayesian inference, and penalized likelihood was employed to estimate mitochondrial divergence dates among the sampled taxa. The results are congruent with some aspects of previous phylogenetic hypotheses based on morphology and vocalizations, although the relationships among several West and Central African taxa differ to some degree. The divergence date analysis suggests that the black-and-white, olive, and red colobus had diverged from one another by the end of the Miocene, and that by the Plio-Pleistocene many of the species lineages were already present. This demonstrates that the initial extant colobus monkey diversification occurred much earlier than previously thought and was likely part of the same adaptive radiation that produced the diverse colobine taxa seen in the African Plio-Pleistocene fossil record. The lack of early members from the modern lineages in fossiliferous deposits suggests that they resided in part in the forests of Central and West Africa, which also currently harbor the highest levels of colobus monkey diversity. These forests should not be ignored in models of Plio-Pleistocene human and nonhuman primate evolution.

• Phylogenetic incongruence between nuclear and mitochondrial markers in the Asian colobines and the evolution of the langurs and leaf monkeys.

  Authors: Nelson Ting, Anthony J Tosi, Ying Li, Ya-Ping Zhang, Todd R Disotell

  Molecular phylogenetics and evolution. 02/2008; 46(2):466-74.

  Evidence of incongruence between mitochondrial and nuclear gene trees is now becoming documented with increasing frequency. Among the Old World monkeys, this discordance has been well demonstrated inEvidence of incongruence between mitochondrial and nuclear gene trees is now becoming documented with increasing frequency. Among the Old World monkeys, this discordance has been well demonstrated in the Cercopithecinae, but has not yet been investigated in the Colobinae. The mitochondrial relationships between the colobine genera have recently been clarified and cluster Presbytis and Trachypithecus as sister taxa to the exclusion of Semnopithecus. This is incongruent with previous morphological hypotheses that suggest the latter two are sister taxa, and perhaps even congeneric. In addition to analyzing a previously published 10,896 bp mitochondrial dataset, we sequenced and analyzed a 4297 bp fragment of the X-chromosome in order to test the competing mitochondrial and morphological phylogenetic hypotheses. The results from the mitochondrial dataset again support a Presbytis+Trachypithecus group while the X-chromosomal dataset supported a Semnopithecus+Trachypithecus group. A Shimodaira-Hasegawa test performed on both datasets indicates that the mitochondrial and X-chromosomal trees are significantly better at explaining their respective datasets than alternative topologies (p<0.05). We suggest that differential lineage sorting or ancient hybridization may be the cause of this strong discordance between the mitochondrial and X-chromosomal markers in these taxa.

• Molecular phylogenetic affinities of the simakobu monkey (Simias concolor).

  Authors: Danielle J Whittaker, Nelson Ting, Don J Melnick

  Molecular phylogenetics and evolution. 07/2006; 39(3):887-92.