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

Abstract

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.

Figure 1

Distribution of haplogroups of FE groups. This figure shows the haplogroups that are present in ≥10 individuals across the entire FE group data set and those of major interest (haplogroups M52'58 and M52a). The figure legend on the lower left section of the figure shows the list of haplogroups whose color code correspond to those on the pie charts. Haplogroups represented by <10 individuals across the entire FE group data set are pooled into the dark gray pie chart sections and labeled as ‘Others' in the figure legend. Numbers in each pie chart section indicate the number of individuals that possess the haplogroup and total to each FE groups' sample size (Table 2).

Figure 2

Multivariate analyses of Filipino mtDNA data. (a) MDS plot of Φ_ST genetic distances based on complete mtDNA data of FE groups. (b) CA plot of haplogroup counts in FE groups. (c) MDS plot of Φ_ST genetic distances based on HVS-1 sequence data of FE groups and RC groups (Luzon, Visayas, Mindanao, undefined) from Tabbada et al.. (d) CA plot of haplogroup counts in FE and RC groups. FE group names are indicated and are adjacent to shapes. Shapes indicate northern (triangles), central (circles) and southern (squares) geographical locations of FE groups. Open shapes indicate FEnN groups, while filled shapes indicate FEN groups. Plus signs (+) indicate RC groups from Tabbada et al.. In CA plots (b, d), haplogroup names are in narrow italicized font. Other relevant details are in Supplementary Text.

Figure 3

MDS plot of FE groups and the reference data set. MDS plot of Φ_ST genetic distances based on complete mtDNA data of FE groups and the reference data set. Shown here is the biplot of dimensions 1 and 2. The biplots of dimensions 2 to 5 are shown in Supplementary Figure 6. Stress value is 0.12. FE group names are indicated and are adjacent to shapes. These shapes indicate northern (triangles), central (circles) and southern (squares) geographical locations. Open shapes indicate FEnN groups, while filled shapes indicate FEN groups. Asian and Pacific groups of the reference data set are represented by the following symbols: filled diamonds (South Asia: 28 Indian groups, including Andaman Islanders); asterisks (Southeast Asia: Vietnam, the Besemah and Semende groups of Sumatra, Indonesia and the Bidayuh, Jehai, Seletar and Temuan groups of Malaysia); open diamonds (North East Asia: Han Chinese, Japan and Taiwan); plus signs (Australia, Near Oceania and Remote Oceania). Other relevant details are in Supplementary Text and Supplementary Table 3.

Figure 4

CA plot of haplogroup counts in FE groups and reference data set. The CA result here involved five reference data set groups (Supplementary Table 8) and is the last of a series of CA that started with 18 reference data set groups (Supplementary Table 7; Supplementary Figure 7). FE group and reference data set group names are indicated in bold print. Haplogroup names are in narrow italicized font. Other relevant details are in Supplementary Text and Supplementary Table 3.