Analysis of mtDNA sequences shows Japanese native chickens have multiple origins

Oka, Takahiro; Ino, Yasuko; Nomura, Kazutaka; Kawashima, Shinichi; Kuwayama, Takehito; Hanada, Hirofumi; Amano, Takashi; Takada, Moriatsu; Takahata, Naoyuki; Hayashi, Yoshihiro; Akishinonomiya, Fumihito

doi:10.1111/j.1365-2052.2007.01604.x

Cited by 106 publications

(174 citation statements)

References 13 publications

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“…The median-joining (MJ) network analysis of the mtDNA D-loop haplotypes observed in Tanzanian local chickens, together with most frequently observed haplotypes from Liu et al (2006) and Oka et al (2007) as a skeletal frame reference, is shown in Figure 4. Twenty-three haplotypes were observed in Tanzanian chickens and were found to cluster with haplogroups D and E identified by Liu et al (2006 …”

Section: Resultsmentioning

confidence: 99%

“…Besides the sequences of the Tanzanian chicken populations, the network analysis included the most frequent haplotypes of nine clades from Liu's network and of three clades from Oka's, which were used as a reference frame in haplotype analysis (Liu et al, 2006;Oka et al, 2007). The list of haplotypes and their GenBank accession numbers are given in Table 2.…”

Section: Methodsmentioning

confidence: 99%

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Assessing the genetic diversity of five Tanzanian chicken ecotypes using molecular tools

Lyimo¹,

Weigend²,

Janssen-Tapken³

et al. 2014

SA J. An. Sci.

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The study aimed to evaluate the genetic diversity of Tanzanian chicken populations through phylogenetic relationship, and to trace the history of Tanzanian indigenous chickens. Five ecotypes of Tanzanian local chickens (Ching'wekwe, Kuchi, Morogoro-medium, Pemba and Unguja) from eight regions were studied. Diversity was assessed based on morphological measurements and 29 microsatellite markers recommended by ISAG/FAO advisory group on animal genetic diversity. A principal component analysis (PCA) of morphological measures distinguished individuals most by body sizes and body weight. Morogoro Medium, Pemba and Unguja were grouped together, while Ching'wekwe stood out because of their disproportionate short shanks and ulna bones. Kuchi formed an independent group owing to their comparably long body sizes. Microsatellite analysis revealed three clusters of Tanzanian chicken populations. These clusters encompassed i) Morogoro-medium and Ching'wekwe from Eastern and Central Zones ii) Unguja and Pemba from Zanzibar Islands and iii) Kuchi from Lake Zone regions, which formed an independent cluster. Sequence polymorphism of D-loop region was analysed to disclose the likely maternal origin of Tanzanian chickens. According to reference mtDNA haplotypes, the Tanzanian chickens that were sampled encompass two haplogroups of different genealogical origin. From haplotype network analysis, Tanzanian chickens probably originated on the Indian subcontinent and in Southeast Asia. The majority of Kuchi chickens clustered in a single haplogroup, which was previously found in Shamo game birds sampled from Shikoku Island of Japan in the Kōchi Prefecture. Analysis of phenotypic and molecular data, as well as the linguistic similarity of the breed names, suggests a recent introduction of the Kuchi breed to Tanzania.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Assessing the genetic diversity of five Tanzanian chicken ecotypes using molecular tools

Lyimo¹,

Weigend²,

Janssen-Tapken³

et al. 2014

SA J. An. Sci.

View full text Add to dashboard Cite

show abstract

“…([9]; Japanese domestic chickens); Kanginakudru et al . ([11]; Indian domestic chickens and G. gallus murghi ) and Silva et al .…”

Section: Methodsmentioning

confidence: 99%

“…Therefore two assumptions can be made from these data: (1) the wild population carrying haplogroup E has not been sampled yet, and sampling effort within the natural distribution range of G. g. murghi is needed; (2) this haplogroup belongs to an ancestral population from the Indian subcontinent that is now extinct. Furthermore, Haplogroup C has mainly been found in Japanese breeds that originate from commercial exchanges with Korea, Taiwan or the eastern provinces of China [9]. This haplogroup is also frequently present in breeds from the Chinese Guangdong province (Figure 4; Huxu breed: 100% and Qinyuan breed: 67%).…”

Section: Methodsmentioning

confidence: 99%

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Vietnamese chickens: a gate towards Asian genetic diversity

Berthouly‐Salazar

Rognon

Van³

et al. 2010

BMC Genet

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BackgroundChickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process.ResultsA total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69).The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used.ConclusionsIn contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation.

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Polynesian chickens in the New World: a detailed application of a commensal approach

Storey¹,

Quiroz

Beavan

et al. 2013

Archaeology in Oceania

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In 2007, based on direct radiocarbon dates, we presented evidence that chickens were introduced to Chile before Europeans first made contact with the New World. The pre‐Columbian age of the chicken bones and their mtDNA affinities with one of two prehistoric Pacific chicken haplogroups (E) led us to conclude that Polynesia was the most likely origin for these pre‐Columbian chickens. Subsequently, the mtDNA and radiocarbon evidence provided has been applied to a range of studies and occasionally reinterpreted. This has revealed issues related to the brevity of the initial report in 2007. Here, we provide a full discussion of the evidence, including the relevant archaeological, historical and biological information necessary to provide the context for interpreting genetic analyses and understanding their implications for addressing archaeological questions. We include a comprehensive analysis of the isotope data within a geographical and temporally relevant dataset to verify the pre‐Columbian age of the El Arenal chickens. In addition, we provide longer DNA sequences obtained from some of the ancient Chilean chicken remains to address objections raised by critics and to demonstrate that longer sequences do not change the observed affinities of the mtDNA sequences, nor their interpretation. In this analysis, historical information is used to critically evaluate the results of phylogenetic analyses. This comprehensive approach demonstrates that the examination of modern chicken DNA sequences does not contribute to our understanding of the origins of Chile's earliest chickens. Interpretations based on poorly sourced and documented modern chicken populations, divorced from the archaeological and historical evidence, do not withstand scrutiny. Instead, this expanded account will confirm the pre‐Columbian age of the El Arenal remains and lend support to our original hypothesis that their appearance in South America is most likely due to Polynesian contact with the Americas in prehistory.

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Analysis of mtDNA sequences shows Japanese native chickens have multiple origins

Cited by 106 publications

References 13 publications

Assessing the genetic diversity of five Tanzanian chicken ecotypes using molecular tools

Assessing the genetic diversity of five Tanzanian chicken ecotypes using molecular tools

Vietnamese chickens: a gate towards Asian genetic diversity

Polynesian chickens in the New World: a detailed application of a commensal approach

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