Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken

Abstract

Background: Domestication of chicken is believed to have occurred in Southeast Asia, especially in Indus valley. However, non-inclusion of Indian red jungle fowl (RJF), Gallus gallus murghi in previous studies has left a big gap in understanding the relationship of this major group of birds. In the present study, we addressed this issue by analyzing 76 Indian birds that included 56 G. g. murghi (RJF), 16 G. g. domesticus (domestic chicken) and 4 G. sonneratii (Grey JF) using both microsatellite markers and mitochondrial D-loop sequences. We also compared the D-loop sequences of Indian birds with those of 779 birds obtained from GenBank.

Results: Microsatellite marker analyses of Indian birds indicated an average FST of 0.126 within G. g. murghi, and 0.154 within G. g. domesticus while it was more than 0.2 between the two groups. The microsatellite-based phylogenetic trees showed a clear separation of G. g. domesticus from G. g. murghi, and G. sonneratii. Mitochondrial DNA based mismatch distribution analyses showed a lower Harpending's raggedness index in both G. g. murghi (0.001515) and in Indian G. g. domesticus (0.0149) birds indicating population expansion. When meta analysis of global populations of 855 birds was carried out using median joining haplotype network, 43 Indian birds of G. g. domesticus (19 haplotypes) were distributed throughout the network sharing haplotypes with the RJFs of different origins.

Conclusion: Our results suggest that the domestication of chicken has occurred independently in different locations of Asia including India. We found evidence for domestication of Indian birds from G. g. spadiceus and G. g. gallus as well as from G. g. murghi, corroborating multiple domestication of Indian and other domestic chicken. In contrast to the commonly held view that RJF and domestic birds hybridize in nature, the present study shows that G. g. murghi is relatively pure. Further, the study also suggested that the chicken populations have undergone population expansion, especially in the Indus valley.

Figure 1

a) A Maximum likelihood phylogenetic tree constructed using microsatellite data of Indian birds. Contml program of Phylip package was used to construct a ML tree. The birds segregate according to the groups as domestic (red hexagonal), RJF (pink square) clades with GJF as an outgroup (grey triangle). Scale indicates the allele frequency. b) A neighbor-joining phylogenetic tree constructed based on genetic distance using microsatellite data of Indian birds. Genetic distance was calculated with GenAlEx program and the distance matrix was used to construct NJ tree in MEGA with K2P parameter. The distinct clades of G. g. murghi and G. g. domesticus is evident with G. sonneratii forming the outgroup. Scale indicates the genetic difference.

Figure 2

Principal component analysis based on genetic distances of Indian chicken. The clear clustering of all domestic chicken to a single quadrate (upper left) indicates absence of hybridization between domestic chicken and RJFs.

Figure 3

Mismatch distribution of G. g. murghi, G. g. domesticus (India) and G. g. gallus. Observed and model frequencies are indicated. A bell shaped curve characteristic of expanding population is seen for G. g. murghi.

Figure 4

A NJ haplotype tree obtained by 50% consensus rule using 117 variable sites within the sequenced portion of the D-loop, with their corresponding haplotypes generated from the 146 haplotypes of 855 birds. Different haplotypes are color-coded based on the group they belong to (See methods section for grouping details) as indicated. Filled structures indicate haplotypes consisting of all birds of the same group (e.g. Indian RJF-pink colored), while open structures indicate the presence of at least one bird of a specified/color-coded group that also contains birds belonging to other groups (e.g. Indian RJF containing domestic birds). Different sub-species of G. gallus form only two clusters, one of G. g. bankiva and others containing all other sub-species. The cluster of G. gallus sub-species, however also contained another species of Gallus, namely G. lafayettei. Identical sequences are shown as dots in comparison with H_11. A specific mutation found in 96% of G. g. murghi is shown in bold and red color and the corresponding nucleotide is underlined in H_11. This position corresponds to the nucleotide number 360 (where there is 'C') in the complete mitochondrial genome sequence of G. gallus (Acc. No. NC_001323). The color-coding used is represented below the figure.

Figure 5

Median-joining haplotype network of 855 birds belonging to 146 haplotypes. Various haplotypes of chicken species/sub-species are represented in different colored circles. The size of the circles is proportional to the haplotype frequency. Some of the important haplotype numbers are indicated. The median vectors that represent hypothetical intermediates or un-sampled haplotypes, are shown in blue circles. The data indicate formation of a star-like phylogeny of G. g. murghi around H_112. Black circle (H_47) indicates C. japonica. Other Gallus species are indicated by their names.

Figure 6

Comparison of (A) single domestication against (B) multiple domestication hypothesis. The present study supports the hypothesis B for origin of domestic chicken. The numbers in parenthesis indicate the nucleotide diversity (p-black), transition-to-transversion ratio (Ts/Tv-blue) and haplotype diversity (Hd-violet), respectively. The number inside the square indicates average number of mutational events of each group from the outgroup, C. japonica. The sharing of the haplotypes (as exemplified by H_number) indicates the multiple origin of the domestic chicken from different jungle fowls. Low mutational distance, low Ts/Tv ratio and high nucleotide diversity indicate the ancient nature of Indian RJF, G. g. murghi. The dashed line separates domestic chicken (below the line) from other birds.

Figure 7

Map of India showing the sampling locations. RJFs were collected from two districts, while domestic birds were from the same district of Haryana state in north-west India. Grey jungle fowls were from south India. Distances between the villages are shown in kilometers. The places from where the samples were collected are shown in colored circles. G. sonneratii was collected from the south Indian states of Karnataka and Tamilnadu.