Wu Meng Yue, Low Gabriel Weijie, Forcina Giovanni, van Grouw Hein, Lee Benjamin P Y-H, Oh Rachel Rui Ying, Rheindt Frank E
Department of Biological Sciences National University of Singapore Singapore Singapore.
School of Biological Sciences Monash University Clayton Victoria Australia.
Evol Appl. 2020 Jun 4;13(9):2300-2315. doi: 10.1111/eva.13023. eCollection 2020 Oct.
The red junglefowl is the ancestor of the domestic chicken and arguably the most important bird species on Earth. Continual gene flow between domestic and wild populations has compromised its gene pool, especially since the last century when human encroachment and habitat loss would have led to increased contact opportunities. We present the first combined genomic and morphological admixture assessment of a native population of red junglefowl, sampled from recolonized parts of its former range in Singapore, partly using whole genomes resequenced from dozens of individuals. Crucially, this population was genomically anchored to museum samples from adjacent Peninsular Malaysia collected ~110-150 years ago to infer the magnitude of modern domestic introgression across individuals. We detected a strong feral-wild genomic continuum with varying levels of domestic introgression in different subpopulations across Singapore. Using a trait scoring scheme, we determined morphological thresholds that can be used by conservation managers to successfully identify individuals with low levels of domestic introgression, and selected traits that were particularly useful for predicting domesticity in genomic profiles. Our study underscores the utility of combined genomic and morphological approaches in population management and suggests a way forward to safeguard the allelic integrity of wild red junglefowl in perpetuity.
原鸡是家鸡的祖先，可以说是地球上最重要的鸟类物种。家养和野生种群之间持续的基因流动损害了它的基因库，尤其是自上世纪以来，人类的侵占和栖息地丧失导致了更多的接触机会。我们首次对原鸡的一个本地种群进行了基因组和形态混合评估，样本取自其在新加坡以前分布范围内重新定殖的地区，部分样本使用了数十个个体的全基因组重测序。至关重要的是，这个种群在基因组上与约110 - 150年前从马来西亚半岛相邻地区采集的博物馆样本相关联，以推断现代家养基因渗入个体的程度。我们在新加坡不同亚种群中检测到了一个具有不同家养基因渗入水平的强大的野生 - 家养基因组连续体。通过一种性状评分方案，我们确定了保护管理人员可用于成功识别家养基因渗入水平较低个体的形态阈值，并选择了对预测基因组图谱中的家养性特别有用的性状。我们的研究强调了基因组和形态学相结合的方法在种群管理中的实用性，并提出了一种永久保护野生原鸡等位基因完整性的前进方向。
