Genetic affinities between the Yami tribe people of Orchid Island and the Philippine Islanders of the Batanes archipelago

<p>Abstract</p> <p>Background</p> <p>Yami and Ivatan islanders are Austronesian speakers from Orchid Island and the Batanes archipelago that are located between Taiwan and the Philippines. The paternal genealogies of the Yami tribe from 1962 monograph of Wei and Liu were compared with our dataset of non-recombining Y (NRY) chromosomes from the corresponding families. Then mitochondrial DNA polymorphism was also analyzed to determine the matrilineal relationships between Yami, Ivatan, and other East Asian populations.</p> <p>Results</p> <p>The family relationships inferred from the NRY Phylogeny suggested a low number of paternal founders and agreed with the genealogy of Wei and Liu (P < 0.01). Except for one Y short tandem repeat lineage (Y-STR), seen in two unrelated Yami families, no other Y-STR lineages were shared between villages, whereas mtDNA haplotypes were indiscriminately distributed throughout Orchid Island.</p> <p>The genetic affinity seen between Yami and Taiwanese aborigines or between Ivatan and the Philippine people was closer than that between Yami and Ivatan, suggesting that the Orchid islanders were colonized separately by their nearest neighbors and bred in isolation. However a northward gene flow to Orchid Island from the Philippines was suspected as Yami and Ivatan peoples both speak Western Malayo-Polynesian languages which are not spoken in Taiwan. Actually, only very little gene flow was observed between Yami and Ivatan or between Yami and the Philippines as indicated by the sharing of mtDNA haplogroup B4a1a4 and one O1a1* Y-STR lineage.</p> <p>Conclusions</p> <p>The NRY and mtDNA genetic information among Yami tribe peoples fitted well the patrilocal society model proposed by Wei and Liu. In this proposal, there were likely few genetic exchanges among Yami and the Philippine people. Trading activities may have contributed to the diffusion of Malayo-Polynesian languages among them.</p> <p>Finally, artifacts dating 4,000 YBP, found on Orchid Island and indicating association with the Out of Taiwan hypothesis might be related to a pioneering stage of settlement, as most dating estimates inferred from DNA variation in our data set ranged between 100-3,000 YBP.</p

The Genetic Structure of Pacific Islanders

Human genetic diversity in the Pacific has not been adequately sampled, particularly in Melanesia. As a result, population relationships there have been open to debate. A genome scan of autosomal markers (687 microsatellites and 203 insertions/deletions) on 952 individuals from 41 Pacific populations now provides the basis for understanding the remarkable nature of Melanesian variation, and for a more accurate comparison of these Pacific populations with previously studied groups from other regions. It also shows how textured human population variation can be in particular circumstances. Genetic diversity within individual Pacific populations is shown to be very low, while differentiation among Melanesian groups is high. Melanesian differentiation varies not only between islands, but also by island size and topographical complexity. The greatest distinctions are among the isolated groups in large island interiors, which are also the most internally homogeneous. The pattern loosely tracks language distinctions. Papuan-speaking groups are the most differentiated, and Austronesian or Oceanic-speaking groups, which tend to live along the coastlines, are more intermixed. A small “Austronesian” genetic signature (always <20%) was detected in less than half the Melanesian groups that speak Austronesian languages, and is entirely lacking in Papuan-speaking groups. Although the Polynesians are also distinctive, they tend to cluster with Micronesians, Taiwan Aborigines, and East Asians, and not Melanesians. These findings contribute to a resolution to the debates over Polynesian origins and their past interactions with Melanesians. With regard to genetics, the earlier studies had heavily relied on the evidence from single locus mitochondrial DNA or Y chromosome variation. Neither of these provided an unequivocal signal of phylogenetic relations or population intermixture proportions in the Pacific. Our analysis indicates the ancestors of Polynesians moved through Melanesia relatively rapidly and only intermixed to a very modest degree with the indigenous populations there

Association of HLA class I with severe acute respiratory syndrome coronavirus infection

BACKGROUND: The human leukocyte antigen (HLA) system is widely used as a strategy in the search for the etiology of infectious diseases and autoimmune disorders. During the Taiwan epidemic of severe acute respiratory syndrome (SARS), many health care workers were infected. In an effort to establish a screening program for high risk personal, the distribution of HLA class I and II alleles in case and control groups was examined for the presence of an association to a genetic susceptibly or resistance to SARS coronavirus infection. METHODS: HLA-class I and II allele typing by PCR-SSOP was performed on 37 cases of probable SARS, 28 fever patients excluded later as probable SARS, and 101 non-infected health care workers who were exposed or possibly exposed to SARS coronavirus. An additional control set of 190 normal healthy unrelated Taiwanese was also used in the analysis. RESULTS: Woolf and Haldane Odds ratio (OR) and corrected P-value (Pc) obtained from two tails Fisher exact test were used to show susceptibility of HLA class I or class II alleles with coronavirus infection. At first, when analyzing infected SARS patients and high risk health care workers groups, HLA-B*4601 (OR = 2.08, P = 0.04, Pc = n.s.) and HLA-B*5401 (OR = 5.44, P = 0.02, Pc = n.s.) appeared as the most probable elements that may be favoring SARS coronavirus infection. After selecting only a "severe cases" patient group from the infected "probable SARS" patient group and comparing them with the high risk health care workers group, the severity of SARS was shown to be significantly associated with HLA-B*4601 (P = 0.0008 or Pc = 0.0279). CONCLUSIONS: Densely populated regions with genetically related southern Asian populations appear to be more affected by the spreading of SARS infection. Up until recently, no probable SARS patients were reported among Taiwan indigenous peoples who are genetically distinct from the Taiwanese general population, have no HLA-B* 4601 and have high frequency of HLA-B* 1301. While increase of HLA-B* 4601 allele frequency was observed in the "Probable SARS infected" patient group, a further significant increase of the allele was seen in the "Severe cases" patient group. These results appeared to indicate association of HLA-B* 4601 with the severity of SARS infection in Asian populations. Independent studies are needed to test these results

Traces of Archaic Mitochondrial Lineages Persist in Austronesian-Speaking Formosan Populations

Genetic affinities between aboriginal Taiwanese and populations from Oceania and Southeast Asia have previously been explored through analyses of mitochondrial DNA (mtDNA), Y chromosomal DNA, and human leukocyte antigen loci. Recent genetic studies have supported the “slow boat” and “entangled bank” models according to which the Polynesian migration can be seen as an expansion from Melanesia without any major direct genetic thread leading back to its initiation from Taiwan. We assessed mtDNA variation in 640 individuals from nine tribes of the central mountain ranges and east coast regions of Taiwan. In contrast to the Han populations, the tribes showed a low frequency of haplogroups D4 and G, and an absence of haplogroups A, C, Z, M9, and M10. Also, more than 85% of the maternal lineages were nested within haplogroups B4, B5a, F1a, F3b, E, and M7. Although indicating a common origin of the populations of insular Southeast Asia and Oceania, most mtDNA lineages in Taiwanese aboriginal populations are grouped separately from those found in China and the Taiwan general (Han) population, suggesting a prevalence in the Taiwanese aboriginal gene pool of its initial late Pleistocene settlers. Interestingly, from complete mtDNA sequencing information, most B4a lineages were associated with three coding region substitutions, defining a new subclade, B4a1a, that endorses the origin of Polynesian migration from Taiwan. Coalescence times of B4a1a were 13.2 ± 3.8 thousand years (or 9.3 ± 2.5 thousand years in Papuans and Polynesians). Considering the lack of a common specific Y chromosomal element shared by the Taiwanese aboriginals and Polynesians, the mtDNA evidence provided here is also consistent with the suggestion that the proto-Oceanic societies would have been mainly matrilocal

Systemic Lupus Erythematosus in the Elderly

SummaryBackgroundSystemic lupus erythematosus (SLE) is a multisystem inflammatory disease predominantly occurring in females of childbearing age. Late onset SLE patients are uncommon and have different clinical and laboratory characteristics compared with younger patients.MethodsFor further investigation of this subgroup, we retrospectively reviewed and analyzed 19 SLE patients with disease onset at age 60 years or older (Group A) collected from 1998 to 2008 in the computerized database of outpatients and inpatients of our hospital. For comparison, 50 SLE patients with disease onset between 15 and 40 years (Group B) were also selected using a simple random sampling method during the same period from the same database.ResultsWhen compared with Group B, Group A had: (1) a decreased ratio of female to male; (2) a longer lag time from disease onset to diagnosis; (3) higher rates of renal insufficiency and mortality; and (4) lower immunologic disorder rates, including anti-double-stranded DNA antibody, anti-ribonucleoprotein antibody and hypocomplementemia. The main cause of death in both groups was septic shock.ConclusionThe clinical and laboratory features were found to be different between Groups A and B. Late onset SLE patients had a more insidious onset, a longer lag time from disease onset to diagnosis and, therefore, a higher mortality rate. Thus, this particular subgroup of SLE patients should be afforded greater attention to avoid delays in diagnosis or misdiagnosis

Mitochondrial DNA Diversity of the Nangan Islanders Living in the Mazu Archipelago of the Taiwan Strait

This study investigates the genetic relationship of the Mazu peoples on the east coast of China in the Taiwan Strait. Using partial and complete mitochondrial DNA (mtDNA) sequences, we compare Mazu with surrounding East Asia populations. Mazu shows no exclusive affinities with either Southeast or Northeast Asia. High genetic diversity and a very high number of exclusive haplogroups of various Asian origins suggest that Mazu resulted from a process of continuous resettlement that started when it first became an archipelago at the end of the last glacial maximum and that continued till the last century. As a result, genetic drift did not contribute to an exclusive Mazu profile. The structure of haplogroups that show signatures of the Neolithic era (N9a10a), or influx from Island Southeast Asia (F1a4a) suggest recent gene flows and Mazu relationship with it's pre-Neolithic era (presence of pre-E1a or R9/pre-F from Liangdao man) was not seen.</jats:p

Mitochondrial DNA Polymorphisms of the Saisiyat Indigenous Group of Taiwan, Search for a Negrito Signature

The genetic profile of Negritos of the Philippines differs from the non-Negrito groups with mitochondrial DNA haplogroups B4b1a2, B5, D6a, M, M52a, and N11b. Although Negritos are not seen in Taiwan, the strong genetic affinity between the Philippines and Taiwan Mountain Tribe Aborigines (TwMtA), and Folks tales of TwMtA, Saisiyat and Atayal recounting past contacts with Negritos, warrant the search for a Negrito signature in Taiwan. Material and Method: Discriminant Analysis of Principal Component (DAPC) was used to determine the genetic relationship between TwMtA, Filipino and non-TwMtA groups. Results: The deep coalescence of B4b1a2 in the Philippine Negritos, Saisiyat, Atayal, Island Southeast Asia, and SEA (Southeast Asia) suggested a deeply rooted common ancestry, but could not support a past Negrito presence in Taiwan. Conversely, the sharing of cultural components and mtDNA (mitochondrial DNA) haplogroup D6a2 in Saisiyat, Atayal and Philippine Negritos may characterize a Negrito signature in Taiwan. Although the molecular variation of D6a2 determines its presence in Taiwan back to middle Neolithic, other markers, Y-SNP haplogroups C-M146 and K-M9, warrant further analysis. Conclusion: Most likely, the physical characteristics, languages, and the genetic makeup of the Negritos in Taiwan have been diluted as the result of heavy migration from the mainland in the last 400 years.</jats:p

Correction to: Genetic diversity of the Thao people of Taiwan using Y-chromosome, mitochondrial DNA and HLA gene systems

Following publication of the original article [1], we have been notified that Additional file 3 was published with track changes.</jats:p