The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius

It is postulated that chickens (Gallus gallus domesticus) became domesticated from wild junglefowls in Southeast Asia nearly 10,000 years ago. Based on 19 individual samples covering various chicken breeds, red junglefowl (G. g. gallus), and green junglefowl (G. varius), we address the origin of domestic chickens, the relative roles of ancestral polymorphisms and introgression, and the effects of artificial selection on the domestic chicken genome. DNA sequences from 30 introns at 25 nuclear loci are determined for both diploid chromosomes from a majority of samples. The phylogenetic analysis shows that the DNA sequences of chickens, red and green junglefowls formed reciprocally monophyletic clusters. The Markov chain Monte Carlo simulation further reveals that domestic chickens diverged from red junglefowl 58,000±16,000 years ago, well before the archeological dating of domestication, and that their common ancestor in turn diverged from green junglefowl 3.6 million years ago. Several shared haplotypes nonetheless found between green junglefowl and chickens are attributed to recent unidirectional introgression of chickens into green junglefowl. Shared haplotypes are more frequently found between red junglefowl and chickens, which are attributed to both introgression and ancestral polymorphisms. Within each chicken breed, there is an excess of homozygosity, but there is no significant reduction in the nucleotide diversity. Phenotypic modifications of chicken breeds as a result of artificial selection appear to stem from ancestral polymorphisms at a limited number of genetic loci

マイクロサテライトDNAタケイジョウホウ ニ モトヅク ニホンケイ,トクニ ジトリ,ショウコク オヨビ ソノキンエンヒンシュ ノ イデンテキタヨウセイ ト シュウダンコウゾウ

地鶏や小国およびその近縁品種において,品種内に生じた遺伝的差異に関する研究は少ない。本研究はマイクロサテライトDNA多型情報を用いて地鶏,小国およびその近縁品種の遺伝的多様性および集団構造につき分析を行なった。供試鶏として7品種(会津地鶏,岐阜地鶏,土佐地鶏,小国,尾長鶏,東天紅,唐丸)136羽を用い,マイクロサテライト28座位の分析を行なった。その結果,小国系品種(小国,尾長鶏,東天紅)は地鶏や唐丸と比べて高い遺伝的多様性を示した。また,同じ長鳴鶏でも東天紅の遺伝的多様性は高く,唐丸は低い多様性を示した。地鶏は会津地鶏を除き,小国系品種よりも低い多様性を示した。一方,小国系品種はヘテロ接合体率の観察値と期待値の差が大きく,有意な正のF_IS値が得られた。これは,各品種の採取地間で近親交配による遺伝的差異が生じているためと考えられた。各品種間のペアワイズF_STは有意な値を示した。D_AおよびD_AS系統樹において,小国,尾長鶏,東天紅の3品種は1つのクラスターを形成した。一方,地鶏3品種および唐丸は両系統樹で各品種が明確に分かれる結果となった。Structure解析もD_AS系統樹の樹形を支持するものであり,小国,尾長鶏,東天紅は採取地間で遺伝的差異が生じていることが明らかとなった。The genetic relationships between the Jidori, Shokoku and their related breeds, and their genetic population structure are unclear. In this study, microsatellite DNA polymorphisms were used to analyze the genetic relationships and structure among Jidori, Shokoku, and related breeds. A total of 136 individuals of seven breeds, Aizu-Jidori, Gifu-Jidori, Tosa-Jidori, Shokoku, Onagadori, Totenko, and Tomaru, were used in the analyses of the 28 microsatellite loci. High genetic diversity was observed in Shokoku and related breeds. In contrast, low genetic diversity was observed in the Tomaru and Jidori breeds, except in the Aizu-Jidori. A high and positive F_IS value indicating high inbreeding was also detected in Shokoku-related breeds. Among long-crowing breeds, Totenko showed high genetic diversity, but Tomaru showed low genetic diversity. The pairwise F_ST values estimated among breeds were high and significant. In the phylogenetic tree analysis, Shokoku, Onagadori, and Totenko were located in the same cluster in the D_A and D_AS trees. In contrast, three Jidori breeds and Tomaru were clearly separated in each tree. The structure analysis supports the topology of D_AS tree and reveals genetic differentiation among sampling locations in the Shokoku-related breeds as Shokoku, Onagadori and Totenko

マイクロサテライトDNAタガタジョウホウ ニ モトヅク ニホンケイ,トク ニ シャモ オヨビ ソノ キンエンヒンシュ ノ イデンテキタヨウセイ ト シュウダンコウゾウ

軍鶏は多くの日本鶏品種の作出に広く用いられてきたが,それら軍鶏およびその近縁品種間の遺伝的類縁関係や品種内に生じた遺伝的差異については現在でも不明な点が多い。そこで本研究はマイクロサテライトDNA多型情報を用いて軍鶏およびその近縁品種につき分析を行なった。供試鶏として6品種9集団122羽を用い,マイクロサテライト28座位の分析を行なった。その結果,交雑により作出された品種であっても,選抜や品種を維持する過程で遺伝的多様性が低下したと考えられる品種も認められた。特に声良は12座位で多型が認められず,もっとも低い遺伝的多様性を示した。品種間の遺伝的類縁関係は書誌学的,形態学的研究にもとづく説をおおむね支持するものであった。品種間の遺伝的分化の程度は高かった一方,同一品種の別地域集団は系統樹においてクラスターを形成した。軍鶏,薩摩鶏,矮鶏において,品種内に生じた遺伝的差異の程度は異なるものであった。軍鶏は地域集団間で明確な遺伝的差異が認められた一方,矮鶏は地域集団間や内種間で明確な差異は認められなかった。薩摩鶏は地域集団間で差異が認められ,さらに内種によっても遺伝的差異が生じていた。本研究結果より,軍鶏およびその近縁品種間の遺伝的類縁関係は従来説をおおむね支持する一方,品種内に生じる遺伝的差異は品種の維持形態やそれを取り巻く人側の要因により,程度や分集団の単位が異なることが明らかとなった。Shamo is a breed of Japanese native chicken that has been used to establish various modern Japanese native breeds. However, genetic relationships among the breeds derived from the Shamo and their genetic population structure is unclear. In this study, microsatellite DNA polymorphisms were used to analyze the genetic relationship among Shamo and its related breeds. A total of 122 individuals of six breeds (nine populations), Shamo, Ko-Shamo, Hinai-dori, Koeyoshi, Satsuma-dori, and Chabo, were used for the analyses of the 28 loci recommended by ISAG/FAO. In the results, low genetic diversity was observed even in the breeds established by crossbreeding, because of artificial selection and maintenance of these breeds. In particular, the Koeyoshi, which had 12 monomorphic loci, demonstrated the lowest diversity amongst the six breeds. Genetic relationships of these populations were supported by the established theories of their genetic histories. In the phylogenetic tree analysis, local populations of the same breeds were located in the same cluster. However, the star-like topology of the DA tree showed a high and significant genetic differentiation in each population with the exception of two local populations of the Chabo. The degree of genetic differentiation was estimated from local populations of Shamo, Satsuma-dori, and Chabo. A high and significant genetic differentiation was observed in two local populations of the Shamo. In addition, in the Chabo, no genetic differentiation was observed, not only between local populations but also amongst plumage variations. In the Satsuma-dori, differentiations were observed among local populations and plumage variation. In conclusion, the results of this study showed that the degree of genetic differentiation and the unit of population segmentation were influenced by the manner in which the breeds are managed and human factors

マイクロサテライトDNAタケイジョウホウ ニ モトヅク ニホンケイ,トクニ カンショウヨウヒンシュ ノ イデンテキタヨウセイ ト シュウダンコウゾウ

日本鶏はわが国の貴重な遺伝資源であるにもかかわらず,生産性が低く,その維持を個人愛好家に依存する品種も少なくない。それらの品種の保全においては,遺伝的多様性や集団構造を明らかにすることが必要となる。本研究はマイクロサテライトDNA多型情報から,観賞用品種を中心に解析をおこなった。供試鶏として7品種125羽を用い,マイクロサテライト28座位の分析をおこなった。その結果,愛好家に維持されている観賞用品種であっても,試験研究機関維持集団や銘柄鶏の素材鶏として系統的に維持されている集団と同程度の遺伝的多様性を示すことが明らかとなった。今回分析した7品種すべてに近親交配(正のFIS値)が認められる結果となった。特に蓑曳,蓑曳矮鶏,烏骨鶏は採取地間で遺伝的差異が生じており,DAS系統樹にてサブクラスターが認められた。一方,鶉矮鶏は採取地間の遺伝的差異は認められず,全個体がひとつのクラスターに含まれる結果となった。Japanese native chickens are valuable genetic resource in Japan ; however, their low productivity limits their industrial use and forces dependence on a personal breeder for their maintenance. To conserve these breeds, it is important to clarify their genetic diversity, relationships, and structure. In this study, microsatellite DNA polymorphisms were used to analyze the genetic relationships and structure among ornamental breeds of Japanese native chickens. A total of 125 individuals of seven breeds, Kurokashiwa, Minohiki, Minohiki-Chabo, Uzura-Chabo, Ukokkei, Chahn, and Issun-Chahn were used in analyses of 28 microsatellite loci recommended by ISAG/FAO. The results showed that ornamental breeds maintained by private breeders showed the same level of genetic diversity compared with populations maintained by institutes or breeding stations. Despite high genetic diversity, significant positive FIS values indicating high inbreeding were estimated for all seven breeds analyzed in this study. Furthermore, genetic differentiation among sampling locations was observed in Minohiki, Minohiki-Chabo, and Ukokkei. While sub-clustered structure was observed in the DAS tree for these three breeds, in Uzura-Chabo, genetic differentiation was not observed and all specimens (including those from different sampling locations) were included in the same cluster

マイクロサテライトDNAタケイジョウホウ ニ モトヅク リュウジンジドリ ノ イデンテキタヨウセイ

龍神地鶏は和歌山県の旧龍神村(現在の田辺市)で少数が維持されている集団であり,同地で古くから飼養されているものである。1994年には村内で30数羽が飼養されていたが,近年では個体数が減少し,遺伝的多様性の減少が懸念されている。そこで本研究では1994年および2007年に採血された龍神地鶏(1994年12羽,2007年2集団各18羽,7羽)について,ISAG/FAO推奨の30座位のマイクロサテライトマーカーを用いて遺伝的多様性の経時的な比較と他の日本鶏品種との遺伝的類縁関係を明らかにすることを目的とした。龍神地鶏3集団において30座位中12座位で多型が認められず,5座位で対立遺伝子の消失が認められた。さらに6座位においては遺伝子頻度0.5以上の主要な対立遺伝子が変化していた。その他の座位の対立遺伝子数は2から3の範囲であった。龍神地鶏各集団の平均対立遺伝子数およびヘテロ接合体率は既報の他の日本鶏品種よりも低い値を示した。次に,日本鶏品種内における龍神地鶏の遺伝的な位置を明確にするため,他品種の解析データを加えてD^A遺伝距離にもとづく近隣結合系統樹を作成した。その結果,龍神地鶏は比較に用いたどの品種ともクラスターを形成せず,高いブートストラップ値で他の品種から分かれる結果となった。以上の結果より,龍神地鶏は地域に固有の品種である一方,小集団で長く維持されてきたため近交がすすみ,遺伝的多様性が低くなった集団であると考えられた。今後この品種を維持するためには,現在残されている2つの集団のみならず,県の試験場等を含めて十分な集団サイズを確保し,集団間の系統的維持が必要であると考えられた。Ryujin-Jidori is one of the Japanese native chicken breeds kept in Ryujin village in Wakayama prefecture. Recently, a reduction in population size and in genetic diversity were detected in this breed. In this study, ISAG/FAO recommended 30 microsatellite markers be used to investigate temporal change in genetic diversity and phylogenetic relationships among Ryujin-Jidori and other Japanese native chicken breeds. The Ryujin-Jidori samples were collected in 1994 (n=12) and 2007 (two populations, n=18, 7), respectively. In this analysis, twelve monomorphic loci were observed. Allele loss at five loci and shift of major allele (allele frequency>0.5) at six loci were also observed. In other loci, number of alleles ranged from two to three. Mean number of alleles (MNA) and average expected heterozygosity (H^E) of Ryujin-Jidori populations were lower than previously reported in other Japanese native chicken breeds. No significant difference in MNA was observed between the two Ryujin-Jidori populations. However, a temporal decrease over time in H^E was observed. On the neighbor joining dendrogram based on D^A genetic distance, the Ryujin-Jidori populations were sepa- rated from all other breeds (Gifu-Jidori, Tosa-Jidori, Shokoku and Shamo) with robust bootstrap value. Therefore, it is suggested that Ryujin-Jidori is a unique and valuable genetic resource for Wakayama prefecture. However, to keep Ryujin-Jidori in small population could lead to an affect of genetic drift, intensify inbreeding and decrease genetic diversity

Molecular Phylogeny of Junglefowls, genus Gallus and Monophyletic Origin of Domestic Fowls

　With the aim of elucidating the evolutionary origin of junglefowls and their domestication processes, I conducted molecular evolutionary analyses of mitochondrial DNAs for various kinds of birds belonging to the subfamily Phasianinae. I then found that the real matriarchic origin of all the domestic fowls examined in the present study was an Asian continental population of Gallus gallus gallus. The phylogenetic analysis conducted in this study also suggested that the continental population of Gallus gallus gallus is the monophyletic ancestor of all domestic fowls. These findings resolve the long-time controversy concerning monophyletic versus polyphyletic origin theories of domestic fowls. 　The present thesis is composed of four chapters. In Chapter 1, as an introduction, I described the evolutionary significance of the domestication processes of junglefowls and the overview of taxonomical problems of birds within the subfamily Phasianinae, particularly junglefowls and domestic fowls. 　In Chapter2, attention is focused on the molecular phylogeny of the subfamily Phasianinae. Comparisons of DNA sequences for mitochondrial control regions among 16 avian species belonging to the subfamily Phasianinae, revealed the following: (1) Generalized perdicine birds (quails and partridges) are descended from ancient lineages. Even the closest pair, the common quail of the Japanese subspecies (Coturnix coturnix japonica) and the Chinese bamboo partridge (Bambusicola thoracica), maintained only a 85.7l% identity. (2) The 12 species of phasianine birds previously and presently studied belong to three distinct branches. The first branch is made up exclusively of members of the genus gallus, while the second branch is made up of pheasants of the genera Phasianus, Chrysolophus and Syrmaticus. Gallopheasants of the genus Lophura are distant cousins to these pheasants. The great argus (Argusianus argus) and peafowls of the genus Pavo constitute the third branch. Members of the fourth phasianine branch, such as tragopans and monals, were not included in the present study. (3) The one perdicine species, Bambusicola thoracica, is more closely related to the phasianine genera Gallus and Pavo than to members of other perdicine genera. The above might indicate that Bambusicola belongs to one stem of the perdicine lineage which later split into two sublineages that yielded phasianine birds; one evolving to Gallus, while the other differentiated toward Pavo and related genera. (4) Tandem duplication of the 60-base unit was established as a trait unique to the genus Gallus, which is shared neither by pheasant nor by quail. 　In Chapter 3, I discuss evolutionary relationships between red and green junglefowls. The noncoding control region of the mitochondrial DNA of various gallinaceous birds was studied with regard to its RFLP (restriction fragment length polymorphism) and sequences of the first 400 bases. Unlike its close ally green junglefowl, the red junglefowl Gallus gallus is a genetically very diverse species; a 7.0% sequence divergence was seen between those from Thailand (Gallus gallus gallus and Gallus gallus spadiceus) and that of the Indonesian island of Java(Gallus gallus bankiva). Furthermore, the divergence increased to 27.83% when each transversion was regarded as an equivalent of 10 transitions. On the other hand, a mere 0.5-3.0% difference (all transitions) separated various domestic breeds of chicken from two subspecies of Gallus gallus gallus of Thailand, thus indicating a single domestication event in the area inhabited by this subspecies, with the red junglefowl being the origin of all domestic breeds. Only transitions separated six diverse domesticated breeds. Nevertheless, a 2.75% difference was seen between RFLP type I breeds (white leghorn and nagoya) and a RFLP type VIII breed (ayam pelung). The above data suggest that although the mitochondrion of RFLP type V is the main contributor to domestication, hens of other RFLP types also contributed to this event. 　Finally, in Chapter 4, the evolutionary origin and dispersal patterns of domestic fowls are discussed from various .aspects of molecular evolution and human history. With the aim of elucidating in more detail, the genealogical origin of the present domestic fowls of the world, I determined mitochondrial DNA (mtDNA) sequences of the D-loop regions for a total of 21 birds which belong to the red junglefowl (Gallus gallus) comprising three subspecies (6 Gallus gallus gallus, 3 Gallus gallus spadiceus and 3 Gallus gallus bankiva) and 9 birds representing diverse domestic breeds (Gallus gallus domesticus) . I also sequenced mtDNAs from 4 green junglefowl (Gallus varius), 2 Cingalese junglefowl (Gallus lafayettei) and 1 grey junglefowl (Gallus sonnerati). I then constructed a phylogenetic tree for these birds using nucleotide sequences, choosing the Japanese quail (Coturnix coturnix japonica) as an outgroup. Moreover, I found that a continental population of Gallus gallus gallus was the real matriarchic origin of all the domestic species examined in the present study. It is also of particular interest to note that there were no discernible differences among Gallus gallus subspecies; Gallus gallus bankiva being a notable exception. This was because Gallus gallus spadiceus and a continental population of Gallus gallus gallus formed a single cluster in the phylogenetic tree. One obvious and distinct feature that customarily separates Gallus gallus gallus from Gallus gallus spadiceus is the color of their ear lobes: white for the former and red for the latter. The fact that domestic breeds of the chicken are of two kinds as to color of ear lobes is a clear reflection of the contribution made by Gallus gallus gallus as well as by Gallus gallus spadiceus to their ancestry. Gallus gallus bankiva, on the other hand, is a distinct entity, thus, deserving its subspecies status. This implies that a continental population of Gallus gallus gallus was the monophyletic ancestor of all domestic breeds. I also discuss the possible significance of the initial dispersal pattern of present domestic fowls, utilizing the phylogenetic tree

Musculoskeletal System of Huge Tarsometatarsal Region in the Dong Tao Fowls from North Vietnam

A macroscopic examination of the huge leg of the Dong Tao breed from North Vietnam was conducted. Bone and muscular tendon morphometric data demonstrated that the Dong Tao breed was equipped with the extraordinarily thick and large tarsometatarsal bone and distal parts of the related tibiotarsus regions. Morphological differences between dorsal and plantar sides were clearly observed. First, on the dorsal side, fleshy bundles were extended effectively using the enlarged dorsal surface of tarsometatarsal bone shown as Musuculus extensor digitorum brevis, M. extensor digiti I brevis and M. adductor digiti IV. The strong and fleshy extensor bellies of M. tibialis cranialis and M. extensor digitorum longus were enlarged in the crural region, functioning to dorsally pull the heavy tarsometatarsal region through the ankle joint. Second, on the plantar side, the flexor tendon groups around the ankle joint were wider and thicker than those of other ordinary breeds, possibly to stabilize the tarsometatarsal bone and to flex the phalange as observed in M. flexor perforatus digiti II, M. flexor perforans et perforatus digiti II, M. flexor perforatus digiti III, M. flexor perforans et perforatus digiti III, M. flexor perforatus digiti IV, and M. flexor perforans digitorum profundus. The mass of the huge tarsometatarsal region does not contribute to effective locomotion in the Dong Tao fowl in comparison with that associated with normal breeds. However, we suggest that these morphological changes in the musculoskeletal system may functionally compensate for the physical disadvantages of the large weight of the distal part of the hindlimb in the Dong Tao fowl