Godinez Cyrill John P, Dadios Peter June D, Espina Dinah M, Matsunaga Megumi, Nishibori Masahide
Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan.
Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines.
Front Genet. 2021 Jul 22;12:698401. doi: 10.3389/fgene.2021.698401. eCollection 2021.
The Philippines is considered one of the biodiversity hotspots for animal genetic resources. In spite of this, population genetic structure, genetic diversity, and past population history of Philippine chickens are not well studied. In this study, phylogeny reconstruction and estimation of population genetic structure were based on 107 newly generated mitochondrial DNA (mtDNA) complete D-loop sequences and 37 previously published sequences of Philippine chickens, consisting of 34 haplotypes. Philippine chickens showed high haplotypic diversity ( = 0.915 ± 0.011) across Southeast Asia and Oceania. The phylogenetic analysis and median-joining (MJ) network revealed predominant maternal lineage haplogroup D classified throughout the population, while support for Philippine-Pacific subclade was evident, suggesting a Philippine origin of Pacific chickens. Here, we observed Philippine red junglefowls (RJFs) at the basal position of the tree within haplogroup D indicating an earlier introduction into the Philippines potentially via mainland Southeast Asia (MSEA). Another observation was the significantly low genetic differentiation and high rate of gene flow of Philippine chickens into Pacific chicken population. The negative Tajima's and Fu's neutrality tests revealed that Philippine chickens exhibited an expansion signal. The analyses of mismatch distribution and neutrality tests were consistent with the presence of weak phylogeographic structuring and evident population growth of Philippine chickens (haplogroup D) in the islands of Southeast Asia (ISEA). Furthermore, the Bayesian skyline plot (BSP) analysis showed an increase in the effective population size of Philippine chickens, relating with human settlement, and expansion events. The high level of genetic variability of Philippine chickens demonstrates conservation significance, thus, must be explored in the future.
菲律宾被认为是动物遗传资源的生物多样性热点地区之一。尽管如此，菲律宾鸡的种群遗传结构、遗传多样性和过去的种群历史尚未得到充分研究。在本研究中，系统发育重建和种群遗传结构估计基于107条新生成的线粒体DNA（mtDNA）完整D环序列和37条先前发表的菲律宾鸡序列，共包含34个单倍型。菲律宾鸡在东南亚和大洋洲表现出较高的单倍型多样性（ = 0.915 ± 0.011）。系统发育分析和中介网络（MJ）显示，整个种群中主要的母系谱系单倍群D占主导地位，同时菲律宾 - 太平洋亚分支的支持明显，表明太平洋鸡起源于菲律宾。在这里，我们观察到菲律宾红原鸡（RJF）处于单倍群D内树的基部位置，这表明它们可能较早通过东南亚大陆（MSEA）引入菲律宾。另一个观察结果是，菲律宾鸡与太平洋鸡种群之间的遗传分化显著较低，基因流动率较高。负的 Tajima's 和 Fu's 中性检验表明，菲律宾鸡呈现出扩张信号。错配分布分析和中性检验与菲律宾鸡（单倍群D）在东南亚岛屿（ISEA）中存在微弱的系统地理结构和明显的种群增长一致。此外，贝叶斯天际线图（BSP）分析显示菲律宾鸡的有效种群大小增加，这与人类定居和扩张事件有关。菲律宾鸡的高遗传变异性具有保护意义，因此，未来必须对其进行探索。
