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View Full Version : Ancient genomic DNA analysis of Jomon people (Kanzawa-Kiriyama 2013)



Passa
06-17-2015, 04:21 PM
http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=5&ved=0CDYQFjAE&url=http%3A%2F%2Fir.soken.ac.jp%2F%3Faction%3Drepo sitory_uri%26item_id%3D4960%26file_id%3D19%26file_ no%3D2&ei=CIO9VLeFO4OYyASv7oCgAw&usg=AFQjCNE9l1_7Z3jO3v28v_UJztOt2YVYTw&sig2=B6gIGkRtkOeHfNNSOazbPA

Some interesting pics from the study:
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Passa
06-17-2015, 04:24 PM
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Passa
06-17-2015, 04:25 PM
.....

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Passa
06-26-2015, 10:01 PM
Looking at the D-stats of the Jomon study (page 180), the ancient Jomons are:

- More Neanderthal-related than Japanese, French, Han Chinese, Bedouins, Cambodians, Balochis, but less than Melanesians, Dai from South China and Papuans; they are however as Neanderthal-related as Karitiana from South America
- More Denisovan-related than Bedouins, Cambodians, French, Balochis and Japanese, but less than Melanesians, Papuans, Dai, Han Chinese and Karitiana
- Less Khoisan-related than French, Balochis, Bedouins and Han Chinese, but more than Karitiana, Cambodians, Dai, Papuans, Melanesians and Japanese
- More French-related than Cambodians, Dai, Han Chinese, Japanese, Papuans and Melanesians, but less than Balochis, Bedouins and Karitiana
- More Bedouin-related than Melanesians, Papuans and Dai, but less than Balochis, Cambodians, Karitiana, Japanese and Han Chinese
- More Balochi-related than Cambodians, Dai, Melanesians and Papuans, but less than Han Chinese, Japanese and Karitiana
- More Papuan related than Karitiana, but less than Cambodians, Dai, Han Chinese, Japanese and Melanesians

The final picture can be summarized as follows: Jomons were clearly Eurasian, but their position in the Eurasian landscape is peculiar. They are more European-shifted than all modern East Eurasians, but less than South and West Eurasians. This is not to be undervalued and explained as mere affinity to South Asians, because Han Chinese and Japanese are more Balochi-like than Jomons, yet Jomons are closer to Europeans (French in this case) than Han Chinese and Japanese. Therefore we see here not a simple West Eurasian input, but specifically a European-like affinity of ancient Jomons, considering also that Jomons are less Bedouin-like than most East Eurasians. To accompany this European affinity there is a higher African (Khoisan in this case) affinity with respect to all East Eurasians except Han Chinese. Regarding archaic admixtures, Jomon are only slightly Denisovan-admixed, while their Neanderthal admixture is present at good levels. To conclude, Papuan affinity of Jomons is lower than most East Eurasian groups.

J Man
06-27-2015, 01:18 AM
Indeed the Jomons are quite an interesting ancient group.

nuadha
06-27-2015, 07:00 PM
Looking at the D-stats of the Jomon study (page 180), the ancient Jomons are:

- More Neanderthal-related than Japanese, French, Han Chinese, Bedouins, Cambodians, Balochis, but less than Melanesians, Dai from South China and Papuans; they are however as Neanderthal-related as Karitiana from South America
- More Denisovan-related than Bedouins, Cambodians, French, Balochis and Japanese, but less than Melanesians, Papuans, Dai, Han Chinese and Karitiana
- Less Khoisan-related than French, Balochis, Bedouins and Han Chinese, but more than Karitiana, Cambodians, Dai, Papuans, Melanesians and Japanese
- More French-related than Cambodians, Dai, Han Chinese, Japanese, Papuans and Melanesians, but less than Balochis, Bedouins and Karitiana
- More Bedouin-related than Melanesians, Papuans and Dai, but less than Balochis, Cambodians, Karitiana, Japanese and Han Chinese
- More Balochi-related than Cambodians, Dai, Melanesians and Papuans, but less than Han Chinese, Japanese and Karitiana
- More Papuan related than Karitiana, but less than Cambodians, Dai, Han Chinese, Japanese and Melanesians

The final picture can be summarized as follows: Jomons were clearly Eurasian, but their position in the Eurasian landscape is peculiar. They are more European-shifted than all modern East Eurasians, but less than South and West Eurasians. This is not to be undervalued and explained as mere affinity to South Asians, because Han Chinese and Japanese are more Balochi-like than Jomons, yet Jomons are closer to Europeans (French in this case) than Han Chinese and Japanese. Therefore we see here not a simple West Eurasian input, but specifically a European-like affinity of ancient Jomons, considering also that Jomons are less Bedouin-like than most East Eurasians. To accompany this European affinity there is a higher African (Khoisan in this case) affinity with respect to all East Eurasians except Han Chinese. Regarding archaic admixtures, Jomon are only slightly Denisovan-admixed, while their Neanderthal admixture is present at good levels. To conclude, Papuan affinity of Jomons is lower than most East Eurasian groups.

Thanks for the observations.

Im having some trouble putting this all into context; after all I'm trying to put it in the context of other adna which is most relevant for west eurasia. Compared to their neighbors the Jomon are more (not literally) french but less balochi and bedouin. This seems like some aversion to ASI. The jomon are more balochi than southeast asians which suggests some ANE affinity? Jomon have less archaic than pacific islands and have a greater ratio of neandertal/denisovan than their neighbors. Does this suggest a migration that didn't go through southeast asia or at least did not in time to mix with denisovans in southeast asia.

Either way, it seems like the jomon are less the product of the "southern route" (southern india to southeast asia followed by pacific islands) than one would guess by modern uniparental dna.

tamilgangster
06-28-2015, 09:35 AM
Looking at the D-stats of the Jomon study (page 180), the ancient Jomons are:

- More Neanderthal-related than Japanese, French, Han Chinese, Bedouins, Cambodians, Balochis, but less than Melanesians, Dai from South China and Papuans; they are however as Neanderthal-related as Karitiana from South America
- More Denisovan-related than Bedouins, Cambodians, French, Balochis and Japanese, but less than Melanesians, Papuans, Dai, Han Chinese and Karitiana
- Less Khoisan-related than French, Balochis, Bedouins and Han Chinese, but more than Karitiana, Cambodians, Dai, Papuans, Melanesians and Japanese
- More French-related than Cambodians, Dai, Han Chinese, Japanese, Papuans and Melanesians, but less than Balochis, Bedouins and Karitiana
- More Bedouin-related than Melanesians, Papuans and Dai, but less than Balochis, Cambodians, Karitiana, Japanese and Han Chinese
- More Balochi-related than Cambodians, Dai, Melanesians and Papuans, but less than Han Chinese, Japanese and Karitiana
- More Papuan related than Karitiana, but less than Cambodians, Dai, Han Chinese, Japanese and Melanesians

The final picture can be summarized as follows: Jomons were clearly Eurasian, but their position in the Eurasian landscape is peculiar. They are more European-shifted than all modern East Eurasians, but less than South and West Eurasians. This is not to be undervalued and explained as mere affinity to South Asians, because Han Chinese and Japanese are more Balochi-like than Jomons, yet Jomons are closer to Europeans (French in this case) than Han Chinese and Japanese. Therefore we see here not a simple West Eurasian input, but specifically a European-like affinity of ancient Jomons, considering also that Jomons are less Bedouin-like than most East Eurasians. To accompany this European affinity there is a higher African (Khoisan in this case) affinity with respect to all East Eurasians except Han Chinese. Regarding archaic admixtures, Jomon are only slightly Denisovan-admixed, while their Neanderthal admixture is present at good levels. To conclude, Papuan affinity of Jomons is lower than most East Eurasian groups.

It likely that jomons have ANE admixture and/or admixture from a ust ishim related population. There are these wierd claims that Jomon/ainu are australoid related, which is bullshit. But its likely that the jomon are more related to SE asians than yaiyoi japanese. The ainu people were consided sundodont mongoloids. From these charts though it appears, that jomon are a diverged proto east eurasian group though.

paulgill
07-05-2015, 08:41 PM
Online Ancient Genome Repository

https://www.oagr.org.au/

http://www.sciencedaily.com/releases...0617091631.htm

Rafe
03-14-2019, 04:39 AM
Jomon DNA files, are they publicly available for download?

talljimmy0
03-14-2019, 11:24 AM
They are probably representative of a pre-ANE population with pacific aborigine mixture. Meaning, all ANE has some ancestral Jomon component (maternal side most likely).

Psynome
03-14-2019, 12:07 PM
They are probably representative of a pre-ANE population with pacific aborigine mixture. Meaning, all ANE has some ancestral Jomon component (maternal side most likely).

It could be the other way around as well, couldn't it? ANE > Jomon?

talljimmy0
03-14-2019, 03:06 PM
It could be the other way around as well, couldn't it? ANE > Jomon?

Jomon group with East Eurasians and they donít show any particular affinity to Native Americans beyond what other Siberians/East Asians share. Yet there is a distant link to northwestern populations. To me this shows that ANE didnít come into Japanese Jomon more than they did to other Eastern populations, but the ancestors of Jomon once lived where ANE would spread and there mixing occurred. This ancestral Jomon population contributed slightly to ANE and predominantly, along with Eastern contribution, to the Jomon found in Japan.

Rafe
03-14-2019, 07:24 PM
On The Apricity, they're saying Gedmatch kit M592785 belongs to a Jomon sample.

pmokeefe
03-15-2019, 08:52 PM
Jomon genome sheds light on East Asian population history (https://www.biorxiv.org/content/10.1101/579177v1) (Posted March 15, 2019)
Abstract

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

From the Discussion section of the paper:

These results fit the hypothesis that the Ainu and the Jomon share the common ancestor:
the present-day mainland Japanese are the hybrid between the Jomon and migrants from the East
Eurasian continent, and the Hokkaido Ainu have less influence of genetic contribution of the
migrants.

rozenfeld
03-15-2019, 10:24 PM
Jomon genome sheds light on East Asian population history (https://www.biorxiv.org/content/10.1101/579177v1) (Posted March 15, 2019)
Abstract

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

From the Discussion section of the paper:

These results fit the hypothesis that the Ainu and the Jomon share the common ancestor:
the present-day mainland Japanese are the hybrid between the Jomon and migrants from the East
Eurasian continent, and the Hokkaido Ainu have less influence of genetic contribution of the
migrants.

Note: this sample, IK002 was published previously, together with ancient South-East Asian genomes: http://science.sciencemag.org/content/361/6397/88

johen
03-16-2019, 06:37 AM
Jomon genome sheds light on East Asian population history (https://www.biorxiv.org/content/10.1101/579177v1) (Posted March 15, 2019)
Abstract

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

From the Discussion section of the paper:

These results fit the hypothesis that the Ainu and the Jomon share the common ancestor:
the present-day mainland Japanese are the hybrid between the Jomon and migrants from the East
Eurasian continent, and the Hokkaido Ainu have less influence of genetic contribution of the
migrants.

Why cannot the scholars have an access to Yayoi samples?

palamede
03-16-2019, 12:18 PM
it seems the old japonese Y-lineages C1a1 and D2 could be considered Jomon. In Japan C1a1 is about 5% and D2 is between 30 and 35% with an important cline of growing D from South-West to North. On the west coast D would be > 50% from Kanto (Tokyo plain), west coast were more Yayoi .

Altogether anthropologists give a little Jomon part in the genetic pool of the Japonese population.

Here they said for this IK002 Jomon 2500BPCentre Japon (mt N9b1) :"Assuming K=10 ancestral clusters, an ancestral component unique to IK002 appears which is the most prevalent in the Hokkaido Ainu (average 79.3%) . This component is also shared with present-day mainland Japonese as well as Ulchi (9.8% and 6.0% respectively).

I don't know how much can you make confidence in this calculation method and if it shows the ancestry part really.
This means The Jomon would be 10% ancestry of the Mainland Japonese while the Jomon Y-lineages sums to 35-40% of the population. I have difficulties to understand the scenario.
Japon is mysterious often !