• Share
  • Email
  • Embed
  • Like
  • Save
  • Private Content
STRs
 

STRs

on

  • 777 views

Powerpoint presentation of the STR results

Powerpoint presentation of the STR results

Statistics

Views

Total Views
777
Views on SlideShare
777
Embed Views
0

Actions

Likes
0
Downloads
1
Comments
0

0 Embeds 0

No embeds

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment
  • 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.

STRs STRs Presentation Transcript

  • 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
  • A comprehensive genome scan on 92 populations - 42 from the Pacific (almost 2,000 individuals).
    • The markers – 687 Short Tandem Repeats ( STRs ) and
    • 203 insertion/deletions (indels)
    • STR s are short DNA sequence blocks (e.g. ATTA) – can mutate by accumulating copies of the block, causing different number of repeated segments.
      • Advantages - they appear not to have an ascertainment bias, and are assumed neutral over long time periods (unlike SNPs).
      • Variable - t he mean number of different blocks per locus = 12.3
      • In our Pacific set, the mean number is lower, = 10.4
      • Diallelic Insertion/Deletions ( Indels ) - another “length variant,” but with only 2 forms (long and short).
    TGCATT --- TAGGC TGCATT CCG TAGGC TGG A TT AA TT AA TT AA TT A GCT TGG A TT AA TT AA TT A---- GCT
  • I. Augmenting the Global Diversity Sample (CEPH)
  • Human Diversity Panel Populations (CEPH)
  • Adding Pacific samples Taiwan Aborigines Micronesia Samoa Maori Melanesia
  • 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
  • “ STRUCTURE” analysis (developed by J. Pritchard and P. Donnelly)
    • The STRUCTURE algorithm compares individual genetic profiles.
      • Assigns individuals, by their similarity, to a pre-specified number of clusters (K = 2, or 3, or 4, etc.)
      • Partial assignment probabilities to different groups are possible.
      • After individual assignments, populations are identified.
    • Avoids a priori population definitions and can detect intermixture or affinities at the individual level.
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • II. Asia/Pacific
  • Pacific Genetic Diversity
    • The Polynesians – Who are their closest relatives? (the Melanesians, or Taiwan Aboriginals/Southeast Asians?)
    • The Melanesians – Just how diverse are they?
    • a) Is there a pattern to the diversity?
    • b) Whom are they related to outside the region?
    • c) Are there “Polynesian” genetic influences there?
  • Taiwan Aborigines Micronesia Samoa Maori Melanesia Pacific Migration Sketch Near Oceania >30,000 The Wallace Line Sunda >60,000 Sahul <3,300 Remote Oceania
  • Contradictions
    • mitochondrial DNA evidence –
      • Polynesians derive almost exclusively from Taiwan/Southeast Asia
      • there is a very strong “Polynesian” trail in Melanesia.
    • Y-chromosome evidence -
      • Polynesians derive mostly from Melanesians.
      • there is a vanishingly small “Polynesian” trail in Melanesia.
    • Some single gene distributions are similar to one or the other of these patterns.
    • All of these are only small part of the total genetic picture.
  • Languages in Melanesia (Austronesian are yellow, others are Papuan)
  • 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
  • The Pacific, Asia, and France: K = 10 by individuals, and by populations.
    • 8 of 19 Austronesian groups in Island Melanesia have a “Polynesian/Asian” footprint (>5%).
    • No Papuan group has it.
    • Samoans and Micronesians have a small “New Ireland” component
    • Maori have ~10% European admixture (Samoans less)
    100% 75% 50% 25% 0% New Guinea New Britain New Ireland Bougainville Micronesia / Polynesia Taiwan Asia Europe
  • Polynesia / Micronesia Taiwan Asia Baining Ata/Mamusi Bougainville New Ireland /Tolai New Guinea STR Fst NJ Tree New Britain
  • 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
  • Extreme Island Melanesian Diversity - STR Clusters by Population
  • 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.
  • Conclusions Asia-Pacific STR/indels
    • 1. Polynesians – are primarily related to Taiwan/ISEA.
      • Proto-Polynesians received little or no Melanesian contribution. (Samoans have a small “New Ireland” component…).
    • 2. Melanesians - a very modest “Asian/Polynesian” signature, almost exclusively in Austronesian groups (never exceeds 20%)
    • 3. Melanesian Diversity , that has been under appreciated, is driven by isolated Papuan group distinctions – and organized by island size . There is also a relationship between Genetics and Language here.
      • Among-group diversity is much greater in Melanesia than in Africa, and exceeded only in the Americas (the importance of genetic drift).
      • Caused by very limited marital migration rates, especially in remote island interiors, and not along shorelines (not discussed here).
  • The End