Understanding the cryptic introgression and mixed ancestry of Red Junglefowl in India.

Mukesh Thakur,Jianlin Han,Merwyn Fernandes,Ya-Ping Zhang,Ramesh Kumar Vijh,Sujeet K. Singh,Sambandam Sathyakumar,Dong-Dong Wu,Gyaneshwer Chaubey

doi:10.1371/journal.pone.0204351

Abstract

Red Junglefowls (RJFs), the wild progenitor of modern day chickens (DCs), are believed to be in genetic endangerment due to introgression of domestic genes through opportunistic matings with domestic or feral chickens. Previous studies from India reported rare hybridization of RJFs in the wild. However, RJF population genetic structure, pattern of gene flow and their admixture with DC populations are poorly understood at the landscape level. We conducted this study with a large sample size, covering the predicted natural distribution range of RJFs in India. We documented strong evidence of directional gene flow from DCs to free-ranging wild RJFs, with the Northeastern RJF population exhibiting the most genetic variants in their nuclear and mitochondrial genomes, indicating it to be the ancestral population from which early radiation may have occurred. The results provide evidence that landscape features do not act as a barrier to gene flow and the distribution pattern could not be explored due to physical sharing or exchange of wild birds in the past when forests were continuous across RJF range in India.

Highlights

The polyphyletic origins of Domestic Chickens (DCs, Gallus gallus domesticus) is a reason to speculate that gene flow between Red Junglefowls (RJFs) (Gallus gallus murghi) and day chickens (DCs) is widespread and more frequent than supposed by previous studies [1,2,3] while domestication may have occurred at multiple locations in South and South-East Asia [4,5,6,7]
Allendorf et al [17] stated that 5% or less proportion of hybridization in RJFs is an effect of admixture or natural selection whereas another study, based largely on birds reared in captivity and released into the wild, reported rare hybridization between RJFs and DCs in the wild in India [5]
Several loci were deviated individually from Hardy–Weinberg equilibrium (HWE) in different populations e.g. four loci in Cent-Southeast and 22 loci in North RJF populations due to heterozygote deficit following possible inbreeding at regional level

Summary

Introduction

The polyphyletic origins of Domestic Chickens (DCs, Gallus gallus domesticus) is a reason to speculate that gene flow between RJFs (Gallus gallus murghi) and DCs is widespread and more frequent than supposed by previous studies [1,2,3] while domestication may have occurred at multiple locations in South and South-East Asia [4,5,6,7]. Several studies have suggested physical mixing and gene flow between RJF in the wild and DC populations [4,8,9, 10,11]. Genetic introgression of wild Red Junglefowl the issue of 'domestication in reverse'. Hybridization in the absence of reproductive isolation is an inevitable phenomenon and cannot be avoided in cases where domestic and wild congenerics are sympatric [13,14,15,16]. Et al [6] postulated that their observation of low genetic exchange might be due to sampling bias and reported a fair gene flow from RJF to local Vietnamese chicken populations

Methods

Results

Conclusion