This document summarizes a genome study of over 1,900 individuals from 92 Pacific populations. The study used 687 short tandem repeats and 203 insertion/deletions to analyze genetic diversity and relationships between Pacific groups. Key findings include: 1) Polynesians are primarily genetically related to Taiwanese and Southeast Asian groups with little Melanesian ancestry; 2) Melanesians show modest genetic signatures from Asia and Polynesia restricted to Austronesian-speaking groups; 3) Melanesian genetic diversity, often underappreciated, is high due to isolation of island populations.
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STRs
1. Peopling of the Pacific: Resolving the Controversy J. Friedlaender, F. Friedlaender, J. Hodgson, L. Scheinfeldt, K. Kidd, J. Kidd, M., G. Chambers, R. Lea, George Koki, F. Reed, A. Merriwether, and J. Weber Supported by The N.S.F. and N.I.H. of the USA; The Taiwan NSF; The Wenner-Gren Foundation and The National Geographic Exploration Fund; Temple, Michigan, and Binghamton Universities. STR/indel analysis was performed at the Marshfield Clinic. Acknowledgement: Thanks to the many cooperating populations in the Pacific, and to Sarah Tishkoff
6. Africa America Europe Asia Melanesia / Polynesia / Taiwan CEPH panel Melanesia Polynesia/Micronesia Taiwan Aborigines STR heterozygosity in the Global CEPH Diversity Panel, plus our Pacific set (CEPH Panel analysis after Rosenberg et al. 2002) Declining Variability Out of Africa - a series of subsets
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8. 22 chromosomes (687 STRs and 203 indels)– 20000/10000 (burnin/MCMC) K=2 New Britain New Ireland Bougainville Micronesia / Polynesia Taiwan Europe / Middle East Africa America Asia New Guinea Asia Pakistan Global samples (CEPH Diversity Panel), plus our Pacific set “ Structure” analysis of STRs on 1,984 individuals, 92 populations K=6 K=5 K=4 K=3
9. Americas Africa Baining Ata/Mamusi Bougainville Europe/MiddleEast Asia-Pakistan Asia Polynesia/ Micronesia Taiwan Pairwise Fst NJ Tree (using GDA) Comparing “Structure” and a PopulationTree
10. Americas Africa Baining Ata/Mamusi Bougainville Europe/MiddleEast Asia-Pakistan Taiwan Polynesia/ Micronesia Asia Pairwise Fst NJ Tree (using GDA) Comparing “Structure” and a PopulationTree
11. Americas Baining Ata/Mamusi Bougainville Europe/MiddleEast Asia-Pakistan Taiwan Africa Asia Polynesia/ Micronesia Pairwise Fst NJ Tree (using GDA) Comparing “Structure” and a PopulationTree
12. Americas Baining Ata/Mamusi Bougainville Europe/MiddleEast Asia-Pakistan Taiwan Polynesia/ Micronesia Asia Africa Pairwise Fst NJ Tree (using GDA) Comparing “Structure” and a PopulationTree
13. Americas Baining Ata/Mamusi Bougainville Europe/MiddleEast Asia-Pakistan Taiwan Polynesia/ Micronesia Asia Africa Pairwise Fst NJ Tree (using GDA) Comparing “Structure” and a PopulationTree
19. 22 chromosomes (687 STRs and 203 indels)– 20000/10000 (burnin/MCMC) Our Pacific dataset, plus Asians and French from the Diversity Panel K=3 K=4 K=5 K=6 K=7 K=8 K=9 K=10 K=2 New Guinea New Britain New Ireland Bougainville Micronesia / Polynesia Taiwan Asia Europe
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21. Polynesia / Micronesia Taiwan Asia Baining Ata/Mamusi Bougainville New Ireland /Tolai New Guinea STR Fst NJ Tree New Britain
22. Polynesia / Micronesia Taiwan Asia Baining Ata/Mamusi Bougainville New Ireland /Tolai New Guinea > 95% bootstrap values > 75% bootstrap values New Britain STR Fst NJ Tree 100 trees, majority rule
24. Geography - the among-island and (especially) within-island distinctions are significant. Language - The Papuan vs. Oceanic distinction is only significant at 0.05 level; Variation among Papuans is almost twice that among Oceanic groups.
This is very much a collaboration among many individuals
This paper deals with a large number of Short Tandem Repeat polymorphisms and Insertion/deletions scattered across the 22 autosomes.
Part 1 of 2 parts of the talk – putting the Pacific samples in a Global context
Here is the distribution of the previously analyzed Human Diversity Panel – the Pacific is grossly underrepresented
Here’s the distribution of our samples, with the 2 CEPH ones in red.
Out of Africa, there is a succession of major “founder” events – the analogy of moving into a series of empty rooms.
When 2 clusters are specified (K-2), our Pacific dataset, centered on New Britain (Baining) is contrasted with the rest of the world. At K=3, East Asia comes out, with intergradations not only through Eurasia, but into the Pacific. At K=4, a Native American cluster is identified; K=5, at K=6, a Melanesian distinction between Bougainville and central New Britain occurs, and K=7, Africa appears. NOTE THE CONSISTENT “ASIAN’ SIGNAL IN CERTAIN MELANESIAN POPULATIONS; THE AMBIGUOUS POSTIOION OF POLYNESIANS AND MICRONESIANS, AND THE TAIWAN ABORIGINALS CLEARLY IN THE EAST ASIAN CLUSTER
COMPARING “STRUCTURE’ WITH A STANDARD NEIGHBOR-JOINING TREE, USING THE SAME STR/INDEL DATA. K= 2 COLORS ARE SUPERIMPOSED ON THE TREE
K=3 – ASIA/AMERICAS
AMERICAN GROUP
K=5 – BOUGAINVILLE/NEW BRITAIN DISTINCTION
K=6 – AFRICA APPEARS (THIS IS ALL TO DO WITH AMONG GROUP VARIATION, NOT WITHIN GROUP, WHICH A PREVIOUS SLIDE SHOWED AFRICAN POPULATIONS WERE MUCH MORE INTERNALLY DIVERSE)
SECOND PART OF THE TALK – FOCUSSING ON THE PACIFIC
Here is a simplified sketch of what we know from the archaeological record of ancient Pacific settlement. The first settlers of Sahul plus the neighboring islands of Near Oceania took place at approximately 40,000 – 50,000 years ago (Bougainville/Buka at 29,000). This was followed by a long pause, and then people with advanced sailing technologies entered Near Oceania (specifically the region around New Britain) somewhere between 5,000 and 3,500 years ago from somewhere to the west (Taiwan or Island Southeast Asia – some contention there). By 3,300 years ago, there was a clear expansion of people from this region to the formerly uninhabited (and smaller) islands to the east (Remote Oceania). And later expansions into the even more remote islands of the Pacific occurred over the following 1,500 years.
Northern Island Melanesia, which we intensively sampled, is central in Pacific prehistory, because it was settled so early, and then 30,000 years later was the launching pad for the colonization of Remote Oceania. Note the pervasive yellow, Austronesian, languages in the islands, with inland brown Papuan ones (almost all the languages of New Guinea are other Papuan language families).
In this set of Structure runs, Francoise anchored our dataset with the CEPH East Asians and added one European group (the French), to account for possible admixture. K=2, 3, and 4 all echo the global run at higher K’s, with distinctins amon central New Britain, Bougainville, and New Guinea, and with the “Asian” signature. At K= 5, a second (yellow) New Britain cluster appears. K = 6, the Maori form a Polynesian cluster, with some affinities for Taiwan Aborigines. The “Asian” signature in Melanesia turns predominantly Polynesian. K= 7, yet another New Britain cluster appears; K=8, a New Ireland (green) cluster appears, centered on the Papuan-speaking Kuot; K=9, another New Britain gray cluster appears (Papuan Kol), and at K=10, the French cluster appears.
Here is K=10 enlarged, and underneath are the same results, averaged by population. The vermillion arrows indicate those Austronesian-speaking populations that have an “Asian/Polynesian” signature of assignment probabilities – 8 of 19 have between 5 and 20% signature, and the dotted arrows show those Austronesian-speaking groups that don’t. No Papuan-speaking groups have it. The Maori have about a 10% European admixture rate, as they apparently reported.
The STR Neighbor-joining tree follows the Structure pattern, minus the indications of admixture, of course.
Generating bootstrap values from 100 trees (from allele frequencies) shows how comparatively differentiated the Melanesians are from the East Asians, and how extraordinary New Britain diversity is (the colors are the same as those in the Structure run).
The clusters of Structure on the different Melanesian Islands shows just how diverse New Britain is, and that New Ireland is comparatively homogeneous (the Tolai on east New Britain are known to have migrated 1,000 years ago from southern New Ireland). The ISLAND SIZE/COMPLEXITY is critical in maintaining among-group variation, here and elsewhere.
Continental - Validation of the trees - Americas are aberrant, but drifted; Melanesians are more heterogeneous than Africans. Melanesia – within island variation is 3 times the among island variation (mostly because of New Britain) Language distinction is marginally significant, but variation among Papuan groups is almost twice as great as among Austronesian groups, even among islands.
Summary
While we should remember how diverse people look on these Near Oceanic Islands, we cannot see is the small Austronesian component unevenly distributed among these groups.
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