Molecular evidence for hybridization of species in the genus<i>Gallus</i>except for<i>Gallus varius</i>

Nishibori, Masahide; Shimogiri, Takeshi; Hayashi, Takeshi; Yasue, Hiroshi

doi:10.1111/j.1365-2052.2005.01318.x

Cited by 149 publications

(133 citation statements)

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“…The previous reference sequence NC_001323 (Desjardins and Morais, 1990) likely had sequencing errors, including excessive indels, and it was abandoned (Figure 2). Variants in the mtDNA sequences were scored relative to the new reference sequence NC_007235 (Nishibori et al, 2005). The classification of the variants of each chicken mtDNA genome was performed with mtDNAGeneSyn v.1.0 (Pereira et al, 2009).…”

Section: Sequence Analysismentioning

confidence: 99%

Chicken domestication: an updated perspective based on mitochondrial genomes

et al. 2012

Heredity

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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.

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Section: Sequence Analysismentioning

confidence: 99%

Chicken domestication: an updated perspective based on mitochondrial genomes

et al. 2012

Heredity

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“…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.…”

Section: Discussionmentioning

confidence: 99%

“…Red Junglefowl still commonly exist in their native habitats (Brickle et al., 2008; Brisbin, 1995) and are clearly distinguishable from domestic chickens (Johnsgard, 1999). Although genetic contributions from multiple Junglefowl species may have played a role in the domestication process (Eriksson et al., 2008; Nishibori, Shimogiri, Hayashi, & Yasue, 2005), archeological and genetic evidence (Fumihito et al., 1994, 1996; Gongora et al., 2008; Storey et al., 2012; Thomson et al., 2014) indicate that Red Junglefowl from Southeast Asia was the primary progenitor of all domestic breeds of modern chickens. In a previous study, we identified substantial haplotype variation in the major histocompatibility complex (MHC) B‐locus of wild Red Junglefowl (Fulton et al., 2016; Nguyen‐Phuc, Fulton, & Berres, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

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

Nguyen-Phuc

Berres

2018

Ecology and Evolution

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Red Junglefowl (Gallus gallus) are among the few remaining ancestors of an extant domesticated livestock species, the domestic chicken, that still occur in the wild. Little is known about genetic diversity, population structure, and demography of wild Red Junglefowl in their natural habitats. Extinction threats from habitat loss or genetic alteration from domestic introgression exacerbate further the conservation status of this progenitor species. In a previous study, we reported extraordinary adaptive genetic variation in the MHC B‐locus in wild Red Junglefowl and no evidence of allelic introgression between wild and domestic chickens was observed. In this study, we characterized spatial genetic variation and population structure in naturally occurring populations of Red Junglefowl in their core distribution range in South Central Vietnam. A sample of 212 Red Junglefowl was obtained from geographically and ecologically diverse habitats across an area of 250 × 350 km. We used amplified fragment‐length polymorphism markers obtained from 431 loci to determine whether genetic diversity and population structure varies. We found that Red Junglefowl are widely distributed but form small and isolated populations. Strong spatial genetic patterns occur at both local and regional scales. At local scale, population stratification can be identified to approximately 5 km. At regional scale, we identified distinct populations of Red Junglefowl in the southern lowlands, northern highlands, and eastern coastal portions of the study area. Both local and long‐distance genetic patterns observed in wild Red Junglefowl may reflect the species’ ground‐dwelling and territorial characteristics, including dispersal barriers imposed by the Annamite Mountain Range. Spatially explicit analyses with neutral genetic markers can be highly informative and here elevates the conservation profile of the wild ancestors of domesticated chickens.

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“…Archaeological research has identified centres of chicken domestication in India and China; both within the natural range of wild Junglefowl (Crawford, 1990). Chickens were likely domesticated from wild Red Junglefowl, though some have suggested possible genetic contributions from other Junglefowl species (Eriksson et al, 2008;Nishibori et al, 2005). Darwin (1896) was the first to propose that all domestic fowls descended directly from one common ancestor; the Gallus Bankiva, or wild Junglefowl breed that originated in Eastern and Southern Asia.…”

Section: Introductionmentioning

confidence: 99%

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

Lorenzo

Ceccobelli

Panella

et al. 2015

World's Poultry Science Journal

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Mitochondrial DNA (mtDNA) is has recently lost relevance especially when utilised to study species that are characterised with a history of several migrations. Nonetheless, mtDNA can still represents a useful additional tool in the study of molecular genetic diversity. The reason for the adoption of mtDNA is that it is easy to amplify because it appears in multiple copies in the cells and the mitochondrial gene content is strongly conserved across generations. Thousands of published studies have reached conclusions about population history, patterns of gene flow, genetic structure, and species limits, on the basis of mtDNA sequence variation. MtDNA has been used to study phylo-geographic structure of avian species, and to identify the number of maternal lineages and their geographic origins. Most studies of chicken mtDNA rely on sequences of partial control region but recent researches used the complete mtDNA genome to reconstruct the history of animal domestication. The first genetic study on mtDNA suggests that the Indochinese Red Junglefowl subspecies Gallus gallus gallus is the primary ancestor of the domestic chicken (Gallus gallus domesticus). Other studies showed that at least three subspecies of Gallus gallus were enrolled in the origin of domestic chicken breeds, and that there may be at least two domestication centres: one in Southeast Asia and one in the Indian subcontinent. The authors suggested nine highly divergent clades (named clade A-I) related to geographical distribution in a wide range of domestic chickens and Red Junglefowls across Eurasian regions. Understanding when chickens were transported out of domestication centres and the directions in which they were moved provides information about prehistoric human migration, trade routes and cultural diffusion. MtDNA has been used to infer regions of domestication and to identify the number of maternal lineages and their geographic origins in macroevolution studies. IntroductionThe chicken has a long history of anthropomorphic usage in Southeast and East Asia, where it has been bred for entertainment and show (Macdonald and Blench, 2000). The origin and domestication of chickens has been of interest to people since at least Roman times (Storey et al., 2012). Based on archaeological and historical evidence the domestication of the fowl is thought to have occurred in multiple, independent centres. Archaeological research has identified centres of chicken domestication in India and China; both within the natural range of wild Junglefowl (Crawford, 1990). Chickens were likely domesticated from wild Red Junglefowl, though some have suggested possible genetic contributions from other Junglefowl species (Eriksson et al., 2008;Nishibori et al., 2005). Darwin (1896) was the first to propose that all domestic fowls descended directly from one common ancestor; the Gallus Bankiva, or wild Junglefowl breed that originated in Eastern and Southern Asia. He came to this conclusion based on comparisons of morphology and progeny produced from crosses between vari...

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Molecular evidence for hybridization of species in the genusGallusexcept forGallus varius

Cited by 149 publications

References 16 publications

Chicken domestication: an updated perspective based on mitochondrial genomes

Chicken domestication: an updated perspective based on mitochondrial genomes

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

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

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