Kristina A. Tabbada

Mapping Human Genetic Diversity in Asia

Patterns of Early Migration In order to gain insight into various migrations that must have happened during movement of early humans into Asia and the subsequent populating of the largest continent on Earth, the HUGO Pan-Asian SNP Consortium (p. 1541) analyzed genetic variation in almost 2000 individuals representing 73 Asian and two non-Asian populations. The results suggest that there may have been a single major migration of people into Asia and a subsequent south-to-north migration across the continent. While most populations from the same linguistic group tend to cluster together in terms of relatedness, several do not, clustering instead with their geographic neighbors, suggesting either substantial recent mixing among the populations or language replacement. Furthermore, data from indigenous Taiwanese populations appear to be inconsistent with the idea of a Taiwan homeland for Austronesian populations. Genetic analyses of Asian peoples suggest that the continent was populated through a single migration event. Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

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.

Complete mtDNA genomes of Filipino ethnolinguistic groups: A melting pot of recent and ancient lineages in the Asia-Pacific region

The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups. The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent. Although some mtDNA haplogroups can be associated with the Austronesian expansion, there are others that associate with South Asia, Near Oceania and Australia that are consistent with a southern migration route for ethnolinguistic group ancestors into the Asia-Pacific, with a timeline that overlaps with the initial colonization of the Asia-Pacific region, the initial colonization of the Philippines and a possible separate post-colonization migration into the Philippine archipelago.

Evaluating DNA tests of motherless cases using a Philippine genetic database

BACKGROUND: In 5 percent of paternity determination cases, only DNA samples from the alleged father and child pairs are tested. The absence of the mothers DNA increases the probability of false paternity inclusions, which affects laboratories that use a limited number of DNA markers. The effect of coincidental matches between unrelated individuals on DNA tests of motherless cases was determined using the Philippine population genetic database of the National Capital Region (NCR).

Allele frequencies of eight short tandem repeat loci in three Visayas regional populations of the Philippines.

The Philippine Archipelago, composed of 7,100 islands and more than 70 ethno-linguistic groups, is divided into 15 regions on the basis of geographical, cultural, and political variations. Each region is classified under three major island groups: Luzon, Visayas, and Mindanao. The National Capital Region (NCR) is situated south of Luzon, and its population genetic database has been reported (1). However, because the NCR is geographically separated by sea from the rest of the island groups, and because each island group has its own distinct cultural identity, there is a need to study and compare the genetic composition of other regional populations to that of NCR. The present study reports population data at eight short tandem repeat (STR) loci, namely HUMvWA, HUMCSF1PO, HUMTH01, HUMTPOX, HUMF13A01, HUMFES/ FPS, HUMFOLP23, and D8S306 for the Visayas. Visayas refers to the central group of islands in the Philippine Archipelago, where the major language spoken is the Visaya or Bisaya, instead of the more common Filipino (Tagalog) language. It is composed of three political regions, namely, Region VI, VII, and VIII. Blood samples were collected in Region VI (Aklan, Iloilo, n = 114), Region VII (Cebu, n = 140), and Region VIII (Leyte, n = 92) and blotted on FITZCO FTA™ cards. Genomic DNA was purified according to manufacturers instructions (Flinders Technology, Massachusetts). PCR amplification was performed as described previously (1). Amplified products were detected with the ALFExpress sequencer and using ALFwin and Allelelinks software (Pharmacia Biotech) using automated flourescence technology. Hardy-Weinberg equilibrium (HWE) and linkage equilibrium (LE) were checked by the Exact Test using the DNA View software (2). Homogeneity tests were performed using Popgene ver 1.32 (3).

Population Data of 10 Y-chromosomal STR Loci in Cebu Province, Central Visayas (Philippines)

Population:  103 unrelated male individuals from Cebu province, Central Visayas region of the Philippines.