ミトコンドリアDNA D-loopリョウイキ カラ アキラカニ サレタ フィリピン オヨビ ソノ シュウヘン ショコク スイギュウ シュウダン ノ イデンテキ ブンカ ト ケイトウ イデンガク テキ カンケイ

沼沢スイギュウ（Bubalus bubalis）は，小規模な稲作農家の役畜として大変重要であり，乳，肉および皮も活用されている。これまでにフィリピンとその他周辺諸国スイギュウの遺伝的分化や系統遺伝学的関係は明確にされていない。本研究は，フィリピンで飼養されているスイギュウ集団と中国を含むインドシナ半島集団間の遺伝的分化と系統遺伝学的関係を明らかにすることを目的とした。367頭のミトコンドリアDNA D-loop領域の塩基配列を用い解析を行った。その結果，遺伝的分化の程度を示す指数からフィリピンのVisayasおよびMindanao集団は，台湾集団と近いことが推定された。また，系統樹からもフィリピンおよび台湾集団は近い関係を示し，ミャンマーおよび中国集団と同一のクラスターを形成した。これまでに報告された仮説と一致していることから，中国から台湾，フィリピンへスイギュウが伝わってきたことが推察された。本研究は，頭数が減少しつつある東南アジアのスイギュウの多様な遺伝子をフィリピンスイギュウが保有していることから，国内で利活用しながら貴重な遺伝資源として保全・維持する必要があることを示した。The swamp buffalo (Bubalus bubalis) provides a major source of draft power in cultivating rice farms and has great potential for meat, milk, and hide sources, particularly to smallhold farmers. To date, there is limited published information on mtDNA D-loop sequence variation, genetic divergence, and genetic relationship between the Philippine carabao and other swamp buffalo populations in Asia. Thus, the objective of the study is to determine the phylogenetic relationship among the swamp buffalo populations with Asiatic origins. Dataset construction and data analyses were performed from 307-bp of 367 mtDNA D-loop sequences of swamp buffaloes from the Philippines and Asian countries which were retrieved from NCBI GenBank. The research findings highlighted the genetic relationship among the modern Asian swamp buffalo populations and could be explained in two points : First, the Philippine carabao (native swamp buffalo), particularly the Visayas and Mindanao populations, had the closest affinity to Taiwan swamp buffalo population based on the low pair-wise distance (FST), and, second, the Chinese swamp buffalo could be the ancestral population of the modern population of the swamp buffaloes in Asia, as inferred by mtDNA haplotype phylogenetic tree. The results of this research agreed with the hypothesis of Lau et al. 1998 that after the domestication in the China region, the domesticated swamp buffalo spread with rice farming into Taiwan to the Philippines and the eastern islands of Borneo and Sulawesi. This study revealed that native buffaloes in the Philippines have various genes of buffaloes of which numbers are declining in Southeast Asian countries and showed that it is necessary to conserve and maintain them as valuable genetic resources while utilizing them in the Philippines

Identification of Close Relatives in the HUGO Pan-Asian SNP Database

The HUGO Pan-Asian SNP Consortium has recently released a genome-wide dataset, which consists of 1,719 DNA samples collected from 71 Asian populations. For studies of human population genetics such as genetic structure and migration history, this provided the most comprehensive large-scale survey of genetic variation to date in East and Southeast Asia. However, although considered in the analysis, close relatives were not clearly reported in the original paper. Here we performed a systematic analysis of genetic relationships among individuals from the Pan-Asian SNP (PASNP) database and identified 3 pairs of monozygotic twins or duplicate samples, 100 pairs of first-degree and 161 second-degree of relationships. Three standardized subsets with different levels of unrelated individuals were suggested here for future applications of the samples in most types of population-genetics studies (denoted by PASNP1716, PASNP1640 and PASNP1583 respectively) based on the relationships inferred in this study. In addition, we provided gender information for PASNP samples, which were not included in the original dataset, based on analysis of X chromosome data

Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups

Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia

Overview of forensic services by the UP-NSRI DNA Laboratory: A 4-year report

This paper reports the use of DNA analysis in 342 cases that were handled by the DNA Analysis Laboratory of the Natural Sciences Research Institute, University of the Philippines, Diliman during the period from January 2005 to August 2008. Different DNA markers namely Short Tandem Repeats on autosomal and Y-chromosome as well as mitochondrial DNA sequences were used depending on the type and availability of samples that were submitted. The utility of the technology for human identification for diverse purposes was shown. The work presented here puts forward the importance of developing DNA laboratories to make this type of service available in the Philippines

The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups

The Philippines exhibits a rich diversity of people, languages, and culture, including so-called ‘Negrito' groups that have for long fascinated anthropologists, yet little is known about their genetic diversity. We report here, a survey of Y-chromosome variation in 390 individuals from 16 Filipino ethnolinguistic groups, including six Negrito groups, from across the archipelago. We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito. Filipino non-recombining region of the human Y chromosome lineages reflect a chronology that extends from after the initial colonization of the Asia-Pacific region, to the time frame of the Austronesian expansion. Filipino groups appear to have diverse genetic affinities with different populations in the Asia-Pacific region. In particular, some Negrito groups are associated with indigenous Australians, with a potential time for the association ranging from the initial colonization of the region to more recent (after colonization) times. Overall, our results indicate extensive heterogeneity contributing to a complex genetic history for Filipino groups, with varying roles for migrations from outside the Philippines, genetic drift, and admixture among neighboring groups

Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion

Although the Austronesian expansion had a major impact on the languages of Island Southeast Asia, controversy still exists over the genetic impact of this expansion. The coexistence of both Asian and Papuan genetic ancestry in Eastern Indonesia provides a unique opportunity to address this issue. Here, we estimate recombination breakpoints in admixed genomes based on genome-wide SNP data and date the genetic admixture between populations of Asian vs. Papuan ancestry in Eastern Indonesia. Analyses of two genome-wide datasets indicate an eastward progression of the Asian admixture signal in Eastern Indonesia beginning about 4,000-3,000 y ago, which is in excellent agreement with inferences based on Austronesian languages. The average rate of spread of Asian genes in Eastern Indonesia was about 0.9 km/y. Our results indicate that the Austronesian expansion had a strong genetic as well as linguistic impact on Island Southeast Asia, and they significantly advance our understanding of the biological origins of human populations in the Asia-Pacific regionclose222