Data from: Genetic analysis of river, swamp and hybrid buffaloes of north-east India throw new light on phylogeography of water buffalo (Bubalus bubalis)

This study analysed buffaloes from north-east India and compared their
nuclear and mitochondrial DNA variations with buffaloes of mainland India,
China, Mediterranean and South-East Asia. Microsatellite genotypes of 338
buffaloes including 210 from six north-east Indian buffalo populations and
three mainland Indian breeds were analysed to evaluate their genetic
structure and evolutionary relationships. Phylogenetic analysis and
multidimensional scaling plot of pairwise FST revealed the clustering of
all swamp-type buffaloes of north-east India with Lower Assamese
(significantly hybrid type) buffaloes in one plane and all the mainland
river buffaloes in another plane while the upper Assamese buffaloes being
distinct from both these clusters. Analysis of mtDNA D-loop region of
530-bp length was performed on 345 sequences belonging to 23 buffalo
populations from various geographical regions to establish the
phylogeography of Indian water buffalo. The swamp buffaloes of north-east
India clustered with both the lineages of Chinese swamp buffalo.
Multidimensional scaling display of pairwise FST derived from
mitochondrial DNA data showed clustering of upper Assamese, Chilika and
Mediterranean buffaloes distinctly from all the other Indian buffalo
populations. Median-joining network analysis further confirmed the
distinctness and ancestral nature of these buffaloes. The study revealed
north-east region of India forming part of the wider hybrid zone of water
buffalo that may probably extend from north-east India to South-East Asia.

本研究针对印度东北部地区的水牛开展分析，并将其核基因组与线粒体DNA的变异特征，与印度本土、中国、地中海及东南亚地区的水牛进行比对。本研究共分析了338份水牛的微卫星基因型（microsatellite genotypes）数据，其中包含来自印度东北部6个水牛种群的210份样本，以及3个印度本土水牛品种样本，旨在评估其遗传结构与演化亲缘关系。系统发育分析（phylogenetic analysis）与基于成对FST（pairwise FST）的多维尺度分析结果显示，印度东北部所有沼泽型水牛与下阿萨姆（显著杂交型）水牛聚为同一类群，印度本土河流型水牛则单独聚为另一类群，而上阿萨姆水牛则与这两个类群均存在显著分化。本研究针对长度为530bp的线粒体DNA D-loop（mtDNA D-loop）区域展开分析，共使用来自全球23个地理区域水牛种群的345条序列，以明确印度水牛的系统地理学特征。印度东北部的沼泽型水牛与中国沼泽型水牛的两个谱系均聚为一类。基于线粒体DNA数据得到的成对FST多维尺度分析结果显示，上阿萨姆水牛、奇利卡水牛与地中海水牛与其余所有印度水牛种群均呈现显著分化。中介连接网络分析（median-joining network analysis）进一步证实了这些水牛的独特性与祖先起源特征。本研究表明，印度东北部地区是全球水牛杂交带的组成部分，该杂交带大概率可从印度东北部延伸至东南亚地区。