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.2015 Feb 14;16(1):70.
doi: 10.1186/s12864-014-1201-x.

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

Affiliations

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

Sibylle M Gomes et al. BMC Genomics..

Abstract

Background: Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice.

Results: In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya.

Conclusions: The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated "later" events of (South) East Asian origin pinpoints a highly dynamic migratory phase.

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Figures

Figure 1
Figure 1
The geographic location of East Timor and the populations included in this study. 1 - East Timor, 2 - Nusa Tenggara, 3 - Bali, 4 - Java, 5 - Sumatra, 6 - Mentawai, 7 - Nias, 8 - Peninsular Malaysia, 9 - Borneo, 10 - Sulawesi, 11 - Moluccas, 12 - Philippines, 13 - Vietnam, 14 - Laos, 15 - Thailand, 16 - South Korea, 17 - Taiwan, 18 - Hainan, 19 - Mixed Han (China), 20 - WNG, 21 - PNG, 22 - Admiralty Islands, 23 - Solomon Islands, 24 – Polynesia/Fiji, 25 - Australia, 26 - Cambodia, 27 - Myanmar, 28 - New Britain and New Ireland (Bismarck Archipelago), 29 - Bougainville, 30 - Vanuatu, 31 - New Caledonia, 32 - Micronesia, 33 - New Zealand Maori (not on map). Populations 2–7, 9–11, and 20 are in Indonesia; 22, 28 and 29 in PNG. The population codes were retained throughout this study. For references see Additional file 11 where subpopulations are indicated with suffixes.
Figure 2
Figure 2
Schematic phylogenetic tree of all haplogroups observed in the 324 East Timor samples. Their phylogenetic relation and postulated geographic origin are indicated. The sizes of the circles correspond to haplogroup frequencies. Stem lengths are of no information content. The tree is rooted in the MRCA. All information available was used. Haplogroups are according to [49], build 16.
Figure 3
Figure 3
The refined phylogeny of haplogroup P1. The 12 novel completely sequenced haplogroup P1 mitogenomes from East Timor are shown together with the eight previously published. All differences are indicated (disregarding cytosine insertions after nps 309 and 16193) relative to the rCRS [50]. Haplogroups are according to [49], build 16. “P1e” is a novel suggestion. Bases are indicated according to the IUBMB nucleotide code. The prefix @ indicates the reversion of a mutation occurring earlier in the phylogeny. Underlined mutations are recurrent in the tree. For details and references, see Additional file 5.
Figure 4
Figure 4
MDS plot displaying the genetic distances between East Timor and 24 surrounding populations. Based on pairwiseFST values in HVS-I (nps 16080–16180, 16195–16354). For population codes, see Figure 1. For details and references, see Table 3, Additional file 10.
Figure 5
Figure 5
Distribution of haplogroup P mtDNAs in East Timor and surrounding populations. (A) P1 and P1d1. These categories discernible with HVS-I data enabled equal treatment of all populations included. All other, including unassigned, P clades are combined into “PxP1”;(B) P1-P10. All available information was considered (reading frames varied). The total of haplogroup P has been set to 100% for every population to better depict (small) proportions. Inconclusive P samples were denoted as “P*”. Frequencies are indicated by colored circle segments. See legends for color codes. Population reference numbers located within a circle indicate that the analyzed haplogroup(s) were not found in this population. Populations: 1 - East Timor, 2 - Nusa Tenggara (2A - West Timor, 2B - Lembata, 2C - Sumba, 2D - Lombok, 2E - Flores, 2F - Solor, 2G - Adonara, 2H - Pantar, 2K - Alor), 3 - Bali, 4 - Java, 5 - Sumatra, 6 - Mentawai, 7 - Nias, 8 - Peninsular Malaysia, 9 - Borneo, 10 - Sulawesi, 11 - Moluccas (11A - Ternate, 11B – Ambon), 12 - Philippines, 13 - Vietnam, 14 - Laos, 15 - Thailand, 16 - South Korea, 17 - Taiwan, 18 - Hainan, 19 - Mixed Han (China), 20 - WNG (20A - highlands, 20B - lowlands, 20C - Southwest and Lowland Riverine), 21 – PNG (21A - pooled, 21B - Wewak, 21C - Bundi, 21D - Gidra, 21E - East Sepik, 21F- Kula Ring), 22 - Admiralty Islands, 23 - Solomon Islands, 24 - Polynesia/Fiji, 25 - Australia (25A - Northwest, Northern Territory, Far North Queensland, 25B - New South Wales, Paakintji, Ngiyambaa), 26 - Cambodia, 27 - Myanmar, 28 - New Britain and New Ireland, 29 - Bougainville, 30 - Vanuatu, 31 - New Caledonia, 32 - Micronesia, 33 - New Zealand Maori. For more information, see Additional file 11.
Figure 6
Figure 6
Bayesian Skyline Plot of mtDNA haplogroup P1. The hypothetical effective female population size is based on the complete P1 mitogenomes (Additional files 4 and 5) assuming a generation time of 25 years.
Figure 7
Figure 7
Distribution of mtDNA haplogroups Q and N21 in East Timor and surrounding populations. (A) Haplogroups Q1-Q3. Unassigned/inconclusive Q samples were denoted as “Q*”;(B) Haplogroup N21. All available information was considered (reading frames varied). Frequencies in populations are indicated by colored circle segments. See legends for color codes. Population reference numbers located within a circle indicate that the analyzed haplogroup(s) were not found in this population. For the populations included, see Figure 5. For details and references, see Additional file 11.
Figure 8
Figure 8
Migration routes and their contribution to the East Timor mtDNA pool. The major postulated migration events into ISEA and our novel findings are depicted. The asterisk highlights East Timor. The darker grey areas indicate the predicted late Pleistocene coastline.(A) The initial human settlement carrying haplogroups P, Q, N21 and others that arrived (1) between 60–40 kya. Our results indicate (2) a colonization of Australia (southern Sahul) before 37 kya and (3) an incubation period in northern Sahul (NG) followed by westward expansions after 28 kya;(B) The Holocene (1) southward out of Taiwan movement marked by haplogroups M7c1, D5, F1a3, F1a4 between 8–4 kya followed a (2) western or (3) eastern route (that we favour for East Timor), and (4) a local arisal, possibly connected to (1), of the “Polynesian motif” ~6 kya followed by west- and eastward migrations;(C) the postglacial expansion of haplogroup E (and others) (1) originating in eastern Sunda and a dispersal 30–5 kya that (2) reached eastern Indonesia ~10 kya. The inlay pie chart in(A) depicts the proportions of haplogroups associated with(A),(B) and(C) within the extant East Timor population. The dashed line separates the proportion of the “Polynesian motif”, as it has also been described to derive from a separate event. See text for details.
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References

    1. National Statistics Directorate (NSD) [Timor-Leste], Ministry of Finance [Timor-Leste], and ICF Macro . Timor-Leste Demographic and Health Survey 2009–10. Díli: NSD and ICF Macro; 2010.
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