genomic insights into the relationship between neolithic ... · between neolithic japanese...
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Genomic insights into the relationship between Neolithic Japanese hunter-gatherer, Jomon, and modern East
Eurasians
Hideaki KANZAWA-KIRIYAMADepartment of Anthropology, National
Museum of Nature and Science
Upper Paleolithic Jomon Yayoi
3,00035-40,000 1,70015,000 0 (YBP)
Jomon
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Out of Africa
Scally and Durbin, 2012
• Homo Sapiens emerged in Africa and radiated from there.
• They entered East Asia 40-50k years ago.
Paleoanthropology
Archeology
Genetics
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Ainu, Mainland Japanese, and Ryukyuan
Ainu
MainlandJapanese
Ryukyuan
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Uniqueness of Ainu in East Eurasians
Mainland Japanese
RyukyuanAinu
The Japanese Archipelago Human Population Genetics Consortium, 2012
Southern East Asians
R
Northern East Asians
MA
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Ainu is outgroup of all East Asian farmers
Jeong et al., 2016
• Deep divergence and isolation in Ainu people
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Modern and Ancient populations
40-50 ka
0 ka
?
A B C D E A B C D E
X?
YZ
X? ?
?
??
A’?
Outgroup?
Gene flow?
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Ancient DNA analysis
• Sequencing DNA extracted from ancient teeth/bone
• Direct evidence of ancient genotype
NGS(Next Generation
sequencer)
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Genetic continuity from earliest modern humans in East Asia
40,000-y old human remains from Tianyuan, Beijing (Fu et al., 2013)
Chr. 22
Tree of mtDNA haplogroup B
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• Stone tools from everywhere in Japan from Hokkaido to Okinawa
• Dating to younger than 40,000 years old
From Japanese Palaeolithic Research Association
Upper Paleolithic human bones are quite rare.
Upper Paleolithic Jomon Yayoi3 kya35~40 kya
Historical1.7 kya
First modern humans in Japan16 kya
海部. 2016
Wakabanomori(30,000 YBP)Turanukinoki/
Hinatabayashi B(37,000 YBP?)
Idemaruyama(38,000 YBP)
Ishinomoto(38,000 YBP)
Yamashita-cho No.1(36,500 YBP)
①
③
②
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Neolitic hunter-gathers; Jomon
Upper Paleolithic Jomon Yayoi Historical
3 kya35~40 kya 1.7 kya16 kya
海部. 2016
Oodaiyamamoto No.1(16,500 YBP)
Hunting and Gathering
Q2: Origin of Jomon
Q1: Genetic relationship with modernhumans
Ainu
MainlandJapanese
Ryukyuan
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Investigating Jomon Nuclear Genome
Sanganji Shell Mound(about 3,000 cal. BP)
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Sampling to sequencing
http://www.nhk.or.jp/zero/contents/dsp540.html
GAIIx/HiSeq 2000 (120/100bp paired end)
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Data analysisFastq file
• Adapter trimming, filtering low quality bases (FASTX-Toolkit)• Merging plus and minus strand (fastq-join)
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0.4%~9% of sequence data were from Jomon
Metagenomic analysis for three Sanganji Jomons using BLASTN (parameters were –evalue 3.80e-2, -dbsize 3,200,000,000 )
Primates1.12% 0.43% 8.91%
Kanzawa-Kiriyama et al. 2016
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Data analysisFastq file
• Adapter trimming, filtering low quality bases (FASTX-Toolkit)• Merge plus and minus strand (fastq-join)
• Checking post-mortem changes• Contamination estimates
• Mapping to hg19 (BWA, aln, -l 1000)• Mapping quality >= 30 (SAMtools), length >= 35bp• Remove PCR depulicates (Picking Bases)
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Post-mortem misincorporation and depurination
• Characteristic to ancient DNA
C to T misincorporation
Depurination
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Comparison with worldwide populations
Kanzawa-Kiriyama et al. 2016
• HapMap project (The International HapMap Consortium, 2005)• Human Genome Diversity Project (HGDP) (Li et al., 2008)• 1000 Genomes (1000 Genomes Project Consortium, 2012)• Japanese populations (Japanese Archipelago Human Population Genetics
Consortium, 2012)
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Jomon and 1KG worldwide populations
• Creating homozygous diploid genotypes • HWE p<1e-10, minor allele <0.01, genotype call <0.95 (PLINK)• PCA (EIGENSOFT, smartpca)
Kanzawa-Kiriyama et al. 2016
Sanganji JomonEast Eurasians
Europeans
Africans
• 68,542 SNPs
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Jomon and 1KG East Eurasians
Sanganji Jomon
Mainland Japanese
• 46,158 SNPs
Kanzawa-Kiriyama et al. 2016
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Comparison with Ainu, Mainland Japanese, and Ryukyuan
Kanzawa-Kiriyama et al. 2016
Sanganji Jomon
Ainu
Ryukyuan
Mainland Japanese
Han Chinese• 5,392 SNPs
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D-statistics to detect gene flow
NorthernEast Asians
SouthernEast Asians
Kanzawa-Kiriyama et al. 2016
NativeAmericans
• 7,529 SNPs
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Jomon diverged from ancestor of East Eurasians
African
Ancient W. Siberian (45,000 YBP)
Ancient S.C. Siberian(24,000 YBP)
Europeans
East Eurasians
•ML tree with 3 gene flow events base on 43,310 SNPs using TreeMix
Kanzawa-Kiriyama et al. 2016
Archaic human
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No gene flow with other modern/ancient Eurasians
A) 7,529 SNPs Comparison with
A) Europeans, Native Americans, and
Oceanians
B) Mal’ta MA1 (24,000 YBP Siberians)
C) Ust’-Ishim (45,000 YBP Siberians)
Kanzawa-Kiriyama et al. 2016
A)
B), C) 15,549 SNPs (only Tv)
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Comparison with Archaic humans
DenisovanNeanderthal
Admixture:Neanderthalー Non AfricansDenisovan ー Oceanians
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No additional gene flow with Archaic humans
Kanzawa-Kiriyama et al. 2016
Neanderthal
Denisovan
Africans
Non-Africans
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Conclusion
?
?
?• Deep divergence
• Genetic Isolation from continental populations after the divergence
• Affinity to three Japanese populations
Q2: Origin of Jomon
Q1: Genetic relationship with modernhumans
• No answer…
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Thank you for your listening
2014.08.03Shitsukari-Abe cave