Smith David Glenn, McDonough John
Department of Anthropology, University of California-Davis, Davis, California, USA.
Am J Primatol. 2005 Jan;65(1):1-25. doi: 10.1002/ajp.20094.
DNA was extracted from the buffy coats or serum of 212 rhesus macaques (Macaca mulatta) sampled throughout the species' geographic range. An 835 base pair (bp) fragment of mitochondrial DNA (mtDNA) was amplified from each sample, sequenced, aligned, and used to estimate genetic distances from which phylogenetic trees were constructed. A tree that included sequences from rhesus macaques whose exact origins in China are known was used to determine the regional origin of clusters of haplotypes, or haplogroups, defined by the trees. Indian rhesus sequences formed one large homogeneous haplogroup with very low levels of nucleotide diversity and no geographic structure, and a second much smaller haplogroup apparently derived from Burma. The sequences from Burma and eastern and western China were quite divergent from those in the major haplogroup of India. Each of these sequences formed separate clusters of haplotypes that exhibited far greater nucleotide diversity and/or population structure. Correspondingly, sequences from Indian rhesus macaques that are considered to represent different subspecies (based on morphological differences) were intermingled in the tree, while those from China reflected some, but not all, aspects of subspecific taxonomy. Regional variation contributed 72% toward the paired differences between sequences in an analysis of molecular variance (AMOVA), and the average differences between the populations of eastern and western China were also statistically significant. These results suggest that Indian and Chinese rhesus macaques were reproductively isolated during most, if not all, of the Pleistocene, during which time Indian rhesus macaques experienced a severe genetic bottleneck, and that some gene flow westward into India was subsequently reestablished. Samples from breeding centers in three different provinces of China included sequences from rhesus macaques that originated in both eastern (or southern) and western China, confirming anecdotal reports that regional breeding centers in China exchange breeding stock. Genetic differences among rhesus macaques (even those acquired from the same regional breeding center) that originate in different geographic regions and are employed as subjects in biomedical experiments can contribute to phenotypic differences in the traits under study.
从212只恒河猴（猕猴）的血沉棕黄层或血清中提取DNA，这些恒河猴取自该物种地理分布范围内的各个区域。从每个样本中扩增出一段835个碱基对（bp）的线粒体DNA（mtDNA）片段，进行测序、比对，并用于估计遗传距离，进而构建系统发育树。利用一棵包含已知确切中国起源的恒河猴序列的树，来确定由这些树定义的单倍型簇或单倍群的区域起源。印度恒河猴序列形成了一个大型的同质单倍群，核苷酸多样性水平极低且无地理结构，还有一个明显源自缅甸的小得多的单倍群。来自缅甸以及中国东部和西部的序列与印度主要单倍群中的序列差异很大。这些序列中的每一个都形成了单独的单倍型簇，表现出更大的核苷酸多样性和/或种群结构。相应地，基于形态差异被认为代表不同亚种的印度恒河猴序列在树中相互混杂，而来自中国的序列反映了亚种分类学的一些但并非全部方面。在分子方差分析（AMOVA）中，区域变异对序列间配对差异的贡献率为72%，中国东部和西部种群之间的平均差异也具有统计学意义。这些结果表明，印度和中国的恒河猴在更新世的大部分（如果不是全部）时间里是生殖隔离的，在此期间印度恒河猴经历了严重的遗传瓶颈，随后又重新建立了一些向西流入印度的基因流。来自中国三个不同省份繁殖中心的样本包含了起源于中国东部（或南部）和西部的恒河猴序列，证实了有关中国区域繁殖中心交换种畜的传闻报道。起源于不同地理区域并用于生物医学实验的恒河猴（即使是那些从同一区域繁殖中心获得的）之间的遗传差异，可能导致所研究性状的表型差异。
