Abstract

Pakistan is one of a few sites, associated with the earliest known independent domestication event in the evolutionary history of chicken, which is socio-economically and historically the most important poultry bird in the country. However, the divergence, past population dynamics, and demographic history of Pakistani chickens have not been addressed so far. Therefore, we herein investigated the indigenous Pakistani chickens using mitogenomic markers. We first prepared individual DNA samples from the chicken feathers, and generated nucleotide sequence data, which was then subjected to various population genetics analyses. In molecular phylogenetic analysis, the Pakistani chickens were clustered under nine different clades. Among the wild fowls, the Indian red jungle fowl (IRJF) shared very close affinities to Pakistani chickens. The Bayesian skyline plot showed an increase in the effective population size of Pakistani chickens during the last 50 years. Finally, a time-calibrated phylogeny inferred molecular divergence of the Pakistani chickens. A molecular rate of 3.6 × 10⁻⁶ mutations/site/year (95% HPD interval: 2.28 × 10⁻⁸ to 9.32 × 10⁻⁶) was estimated for the data set. In a rooted tree with root-age of 12058 years (95% HPD interval: 1161–38411), the Pakistani chicken haplotypes showed divergence from IRJF haplotypes around 6987 years (95% HPD interval: 1132–20746) ago, and they shared their most recent common ancestor with Gallus gallus spadiceus, and G. g. jabouillei at the root of the tree. Overall, these results suggest that Pakistani chicken haplotypes share their ancestral gene pool with the IRJF as compared to other red jungle fowl subspecies.

摘要

巴基斯坦是为数不多的地点之一，与鸡的进化史上已知最早的独立驯化事件有关，这在社会经济和历史上是该国最重要的家禽。但是，到目前为止，巴基斯坦鸡的分歧，过去的人口动态和人口历史尚未得到解决。因此，我们在本文中使用线粒体基因组标记物调查了巴基斯坦土鸡。我们首先从鸡毛中制备了单个DNA样本，并生成了核苷酸序列数据，然后将其进行了各种种群遗传学分析。在分子系统发育分析中，巴基斯坦鸡聚集在九个不同进化枝下。在野生禽类中，印度红丛林禽（IRJF）与巴基斯坦鸡有着非常相似的亲缘关系。贝叶斯天际线图显示了过去50年中巴基斯坦鸡的有效种群数量增加。最后，经过时间校准的系统发育推断巴基斯坦鸡的分子差异。分子速率为3.6×10为数据集估计了^-6个突变/位点/年（95％HPD间隔：2.28×10 ^-8至9.32×10 ^-6）。在根龄为12058年（95％HPD区间：1163-138411）的有根树中，巴基斯坦鸡的单倍型在6987年左右（95％HPD区间：1132-20746）与IRJF单倍型存在差异，并且他们共享最近的共同祖先与鸡胆spa和G. g。。jabouillei在树的根部。总体而言，这些结果表明，与其他红色丛林禽亚种相比，巴基斯坦鸡肉单倍型与IRJF共享其祖先基因库。