Characterization of population structure from the mitochondrial DNA vis‐à‐vis language and geography in Papua New Guinea

Abstract

Situated along a corridor linking the Asian continent with the outer islands of the Pacific, Papua New Guinea has long played a key role in understanding the initial peopling of Oceania. The vast diversity in languages and unique geographical environments in the region have been central to the debates on human migration and the degree of interaction between the Pleistocene settlers and newer migrants. To better understand the role of Papua New Guinea in shaping the region's prehistory, we sequenced the mitochondrial DNA (mtDNA) control region of three populations, a total of 94 individuals, located in the East Sepik Province of Papua New Guinea. We analyzed these samples with a large data set of Oceania populations to examine the role of geography and language in shaping population structure within New Guinea and between the region and Island Melanesia. Our results from median-joining networks, star-cluster age estimates, and population genetic analyses show that while highland New Guinea populations seem to be the oldest settlers, there has been significant gene flow within New Guinea with little influence from geography or language. The highest genetic division is between Papuan speakers of New Guinea versus East Papuan speakers located outside of mainland New Guinea. Our study supports the weak language barriers to genetic structuring among populations in close contact and highlights the complexity of understanding the genetic histories of Papua New Guinea in association with language and geography.

Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity

“…The coalescent ages of the autochthonous Southwest Pacific haplogroup P fit intriguingly well with the archaeological dating of the first settlements in this area (~48-40 kya): it was estimated to 51.7-65.4 ky based on CR [5,34,64,71] and 54.8 ky using complete mitogenomes. The latter calculations yielded 41.3-53.0 ky for P2’10, P3, P4 and P6; estimates for the remaining clades were not made due to paucity of data [72].…”

“…A single Q sample was reported from Australia, a Q2 – again from the North [34] (Figure 7, Additional file 11). Haplogroup Q has been dated to 32.0-44.5 (even 74.6) ky using partial [5,34,44,64] and 37.5 ky using complete mitogenomes [72]. The age estimates for Q1, Q2, and Q3 from the latter study were 18.1, 28.7 and 31.0 ky, respectively, and widely ranged (2.9-48.0 ky) when partial mitogenomic data were employed [3,5,34,44,48,64,71].…”

“…Haplogroup Q has been dated to 32.0-44.5 (even 74.6) ky using partial [5,34,44,64] and 37.5 ky using complete mitogenomes [72]. The age estimates for Q1, Q2, and Q3 from the latter study were 18.1, 28.7 and 31.0 ky, respectively, and widely ranged (2.9-48.0 ky) when partial mitogenomic data were employed [3,5,34,44,48,64,71].

Figure 7 Distribution of mtDNA haplogroups Q and N21 in East Timor and surrounding populations.

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“…reduced by the mean of MPD observed within the two populations compared), performed an analysis of molecular variance (AMOVA) using ARLEQUIN v.3.5.1.2 [126] and generated an F ST distance matrix for Multidimensional Scaling (MDS) analysis with the R software package [127] function cmdscale(). All sequences were trimmed to a greatest common range: ( i ) eleven populations (3,276 samples) from (S)EA and Melanesia [28,34,45,57-64] were included based on HVS-I and -II data (nps 16080–16193, 16194–16365, 73–300); (ii) another analysis covered 25 populations (9,634 individuals) from (S)EA, Melanesia, Polynesia, and Australia [3,5,17,24,28,29,34,40,41,45,57-69] in an HVS-I range (nps 16080–16180, 16195–16354). See Figure 1, Tables 2 and 3 for details.…”

Diversity of Mycobacterium tuberculosis in the Middle Fly District of Western Province, Papua New Guinea: microbead-based spoligotyping using DNA from Ziehl-Neelsen-stained microscopy preparations

“…L1 Lineage) would be found in the low density populations of the Highlands, as opposed to modern lineages of Mtb (L2 and L4 Lineages) that would be found in the high density populations of the coastal regions 9 . However, a recent human genetic study determined that the genetic differentiation between populations from highland and lowland PNG does not seem to be as significant as previously thought 26 , and no statistically significant difference in the prevalence of L1 Lineage could be found in Goroka, Eastern Highlands, compared to coastal regions 9 . In the end, the pattern of dominance of modern lineages over ancient L1 Lineage seems consistent across PNG, with the 2% of L1 Lineage found in the Balimo/Bamu region not dissimilar to the 0.6% (1/173) to 8% (3/38) observed in the North Coast (East Sepik, Madang), Goroka or Alotau 8,9 .…”