Phylogeography and population genetics of Taiwanese macaque (Macaca cyclopis)
Date Issued
2004
Date
2004
Author(s)
Chu, Jui-Hua
DOI
en-US
Abstract
Abstract
The dissertation is organized into 5 chapters, which include aspects of inter-specific, intra-specific, and intra-populational genetic studies of Formosan macaques (Macaca cyclopis). Chapter One gives general introductions of 1) phylogenetic relationship of Formosan macaque and its sister species (the fascicularis group); 2) phylogeographic patterns associated with Pleistocene effect; 3) geodynamic history of Taiwan; 4) phylogeographic patterns and possible locations of Pleistocene refugia for species in Taiwan; and 5) the application of low- and non-invasive sampling method in primate genetic studies. These topics illustrate general background associated with the study.
In Chapter Two, evolutionary relationship of the closely related species in the mulatta group (including M. mulatta, M. cyclopis and M. fuscata) was investigated by sequences of mtDNA control region (CR). The hypothetical scenario for evolution and dispersal of M. mulatta suggested by Fooden and Albrecht (1999) was described and tested. The results indicate that the southward retreat and the northward recolonization of M. mulatta populations in the eastern Asia proposed in the scenario were supported by the genetic evidence. However, the age of retreat and recolonization may be dated back to a more ancient past during the middle Pleistocene instead of during the last glacial period. In addition, a more recent age of mtDNA lineage isolation, 0.17 mya, among the 3 species is suggested.
In Chapter Three, phylogeographic pattern of M. cyclopis was studies. Samples from 31 local populations were incorporated in the mtDNA CR analyses. Five distinct phylogenetic clades (North, Northeast, Central, South, and East clades) were found to be clustered mainly according to their geographic regions with a major suture zone located in the eastern side of the central mountain range (CMR). It indicates that the CMR may not be a serious physical barrier for M. cyclopis. Although genetic pattern of isolation by distance is accepted in the species, the deep divergence between phylogenetic clades suggests that different mtDNA lineages might have been isolated in different refugia during glacial times. Inferences of population histories were also derived from results analyzed by mismatch distribution analysis (MDA) and nested clad analysis (NCA).
Chapter Four describes an application of assignment-based approaches to detect population substructure and to identify origins of male migrants in the Shoushan macaque population. Microsatellite genotypes (9 loci) from 126 adult individuals were analyzed. Significant but low to moderate genetic differentiation (FST =0.023-0.098) was found between social troops, which may be associated with female philopatry and non-random mating. An acceptable accuracy of the results (~85%) can be obtained according to the criteria suggested by Cornuet et al. (1999). The accuracy can be improved by increasing number of samples or microsatellite loci. The assignment approaches thus provide a quick alternative to field observation in understanding patterns of male dispersal.
Chapter Five illustrates a pilot study that was conducted to test the applicability of non-invasive sampling approach in the population genetic studies of Taiwanese macaques. Feces were used as DNA sources in the study. Success rate of microsatellite PCR amplification is low (42.4%, n=181) while that of mtDNA PCR amplification is acceptable (66.5%, n=334). The low PCR success rate and poor PCR repeatability of microsatellite alleles (high allelic dropout rate and appearance of false alleles) makes it difficult to obtain a reliable microsatellite data set. However, the difficulties may be overcome by new techniques. The putative benefits and drawbacks of the approach are also discussed in this chapter.
Subjects
親緣地理
無侵略性遺傳研究
族群遺傳
Phylogeography
Macaca cyclopis
Population genetics
Non-invasive genetic sampling
Type
other
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