Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Visca, Baybay City, Leyte, 6521, Philippines.
Sci Rep. 2022 Aug 26;12(1):14609. doi: 10.1038/s41598-022-18904-3.
The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985-4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467-2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.
鸡的驯化的复杂地理和时间起源引起了分子系统发育学和系统地理学研究的广泛关注，因为这些问题至今仍存在争议。特别是，东南亚（SEA）和太平洋地区鸡的种群动态和谱系特异性分歧时间估计还没有得到很好的研究。在这里，我们分析了 519 条完整的线粒体 DNA 控制区序列，确定了 133 个单倍型，其中有 70 个可变位点。我们记录了 82.7%的地理上独特的单倍型分布在主要单倍型群中，除了单倍型群 C 之外，这表明研究个体之间存在高度多态性。大陆东南亚（MSEA）鸡的总体遗传多样性高于岛屿东南亚（ISEA）鸡。系统发育树和中位数连接网络显示了一个新的分化母系（即单倍型群 V）作为单倍型群 C 的姐妹分支的证据。最大分支可信度树估计了大陆鸡祖先 D 谱系（即亚单倍型 D2）的更早的合并年龄（3.7 kya；95%HPD 1985-4835 年），而岛屿种群在 2.1 kya 时分化（95%HPD 1467-2815 年）。单倍型群 D 祖先母系更早合并年龄的证据表明了向 ISEA 的扩散模式，此后，该岛屿分支作为一个独特的群体多样化。
