Chicken domestication: an updated perspective based on mitochondrial genomes

Abstract

Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A-I and W-Z. Common haplogroups A-G were shared by domestic chickens and red junglefowl. Rare haplogroups H-I and W-Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.

Genetic structure in Red Junglefowl (Gallus gallus) populations: Strong spatial patterns in the wild ancestors of domestic chickens in a core distribution range

“…In the current work, we compared our population‐level results with other studies (e.g., Akaboot et al., 2012; Berthouly et al., 2010; Granevitze et al., 2007; Liu et al., 2006; Miao et al., 2013; Nishibori et al., 2005; Okumura et al., 2006; Peterson & Brisbin, 1998) that also addressed genetic exchange between feral or free‐ranging domestic chickens and so‐called wild Red Junglefowl. Advantageously, these studies used Red Junglefowl also obtained from South and Southeast Asia.…”

“…Most, if not all, recent genetic studies involving junglefowl, however, sample birds from captive colonies (e.g., Berthouly et al., 2009; Eriksson et al., 2008; Fumihito et al., 1994; Gering, Johnsson, Willis, Getty, & Wright, 2015; Mekchay et al., 2014; Moiseyeva, Romanov, Nikiforov, Sevastyanova, & Semyenova, 2003; Romanov & Weigend, 2001; Rubin et al., 2010; Tadano et al., 2008; Worley et al., 2010) or from vaguely described geographic localities (e.g., Akaboot, Duangjinda, Phasuk, Kaenchan, & Chinchiyanond, 2012; Granevitze et al., 2007; Liu et al., 2006; Miao et al., 2013; Nishibori et al., 2005; Okumura et al., 2006; Ulfah et al., 2016). Even the female Red Junglefowl individual used for the Gallus gallus reference sequence (International Chicken Genome Sequencing Consortium, 2004) is traceable to the San Diego Zoo, itself believed to be introgressed with White Leghorn alleles (M. E. Delany, University of California, Davis, CA, personal communication).…”

The role of mitochondrial DNA to determine the origin of domestic chicken

“…Recently, the analysis of the entire mtDNA genome has demonstrated that domestic chickens and wild Junglefowl may have substantial gene flow and genetic admixture following the domestication. In other case, some domestic chickens might have become feral with their descendants living as wild fowl (Miao et al, 2013). The various investigative techniques described above, do not substitute each other, but rather come together as different tools that complement each other in their specific specialisations to unravel the riddle of the history of domestication.…”

“…Possible interactions may be reconstructed by mapping the presence of chickens in archaeological assemblages (Storey et al, 2008) using historical evidence (Peters, 1913;Crawford, 1984) also thought the mtDNA application (Liu et al, 2006, Miao et al, 2013.…”

“…It is widely accepted that within and between populations genetic diversity is essential for effective management practices and to develop sustainable conservation strategies. Most studies of chicken mtDNA rely on sequences of partial control region (Muchadeyi et al, 2008;Razafindraibe et al, 2008) but recent researches used the complete mtDNA genome to reconstruct the history of animal domestication, such as in cattle (Achilli et al, 2008;Bonfiglio et al, 2010), pigs (Wu et al, 2007), chicken (Miao et al, 2013) and sheep . As already alluded two different hypotheses are discernible about the origin of domestic chickens.…”