863 genomes reveal the origin and domestication of chicken

Abstract

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.

Fig. 1. Sample distribution and phylogeny of Gallus taxa.

a Map showing the geographic distribution of the sampling localities of all domestic chickens and wild jungle fowls across South Asia, Southeast Asia, and East Asia covered by our study. Map in the left bottom depicts the natural ranges of all jungle fowls (see details in Supplementary information, Fig. S1). b Maximum-likelihood tree depicting the evolutionary relationships among RJF subspecies and other three jungle fowl species. The numbers at the major branches are bootstrap values.

Fig. 2. Domestic chickens were most likely derived from G. g. spadiceus.

a Maximum-likelihood phylogenetic tree showing that domestic chickens form a monophyletic clade, with G. g. spadiceus being the closest wild progenitor. Black dots at nodes indicate ≥ 99% bootstrap support. Domestic chicken and RJF clades are collapsed and colored according to their geographic ranges and subspecies classifications. b PCA showing a closer genetic affinity between domestic chickens and G. g. spadiceus. G. g. bankiva was removed in this analysis because of its high divergence from other four RJF subspecies. RJF subspecies are denoted within rings.

Fig. 3. The admixture and splitting of domestic chickens with RJF subspecies.

a Outgroup-f3 statistics in the form of f3(G. varius; domestic chicken, RJF) show that all domestic chickens carry more genetic ancestry from G. g. spadiceus (GGS, higher f3 values) than from other four RJF subspecies. The estimated f3 value ± 3 standard errors are plotted. b MSMC plots show the divergence time between chicken and each of RJF subspecies. c MSMC plots show the splitting time between chicken and G. g. spadiceus. For clarity, we only present one result of MSMC for each population pair; more pairs were analyzed and shown in Supplementary information, Figs. S30, S31 and S48a. GGB G. g. bankiva, GGG G. g. gallus, GGM G. g. murghi, GGJ G. g. jabouillei.

Fig. 4. Signatures of selection in domestic chickens.

a Genomic landscape of selection signal in domestic chicken. From inner to outer, circle indicates signature of selection from each statistics: π-ratio (I), LSBL_j(chicken; G. g. spadiceus, G. g. jabouillei) (II), LSBL_m(chicken; G. g. spadiceus, G. g. murghi) (III), and chromosome scheme (IV), respectively. b Signals of positive selection on FRGR1. FRGR1-located region in chicken genome showed a lower diversity (π-ratio), lower heterozygosity (Hp) and higher differentiation (LSBL) compared with RJFs. Red dashed line indicates Z-transformed score of 3.3 for each statistic, and pink shadow depicts the location of FGFR1 on the chr22.