Detailed East Asian Calculator Update (K=19)

For obvious reasons, my machine is now taking longer to run higher Ks. Because of this, I have enlisted the help of a friend who works at a local university which has really fast machines. I removed the 23andme participants that I do not own and used the university machine to run the higher Ks. Same purpose of breaking down and finding the E & N Asian subdivisions. Again, once I find the optimum K, I will rerun the set with the 23andme participants on my machine.

I’ll try a jump in K value. Maybe I’ll try 50 just to see.

So far, the last interesting run is K=19.

To save time (since I'm doing this on a part time basis) I will likely not detail the non- E/N Asian populations. I'll assign them as African, W Asian, S Asian, & European.

The S Asian - Indian can also be S Asian as a whole including populations in Pakistan.

Detailed East Asian Calculator Update (K=16)

Just completed up to K=21 but K=16 has the lowest cross validation error, so I’ll present K=16 results here.

As expected, basically has 4 large clusters:

1. Africans
2. Papuans
3. Europeans/Middle Easterners/S, SW Asians
4. N & E Asians, Native Americans

In general, the Papuans & Native Americans remains as is (no further breakdown).

NORTH & EAST ASIANS

The E Asians further subdivided into 3 groups. The Nihonjin (Japanese) is the first ethnicity that is appearing; they are however still part of the larger E Asian population. The SE Asians in this run are not only from SE Asia (both Mainland and Island SE Asia) but also comprised of non-Han people from South China (from Guangdong to Yunnan provinces). I expect the SE Asians will be very diverse, hence, will breakdown into further subgroups.

The Eskimo-Aleuts are also forming as a subgroup of N Asians. Just to note, the Eskimo-Aleuts include populations from North America; it’s basically people in and around the Bering Strait. For the mean time I will call them “North Asians – Eskimo-Aleut”.

One thing that would be great to have are participants from Malagasy people of Madagascar. They are migrants from both mainland Africa and SE Asia (more specifically Borneo). Here’s the genetic and linguistic evidence of the SE Asian source.

One of the Hawaiian participants have large SE Asian component. This is expected because the Polynesian origins are of SE Asia (linguistic evidence of the SE Asian source). One distinction though is the larger Papuan component. One theory (Bellwood), that I agree with, shows that as they migrated out of Island SE Asia, they came and admixed with the local Papuan population. As they explored further to populate Oceania, they brought with them the Papuan genes.

Here’s more info on the Papuan and Negrito populations of SE Asia.

AFRICANS

I stand corrected. The Hadza people seems to be diverging away from most of the African populations. No wonder the language is considered an isolate. We now have the Khoisans, E & W Africans.

I noticed the “African Caribbean in Barbados” (ACB) and “African Ancestry in SW USA” (ASW) data from 1000Genomes cluster with the West Africans. I know this could be a touchy subject but I would like to say objectively that the ACB & ASW population may have been descendants of West Africans (mainly Niger-Congo speakers) or at least descendants from those people similar to West Africans.

EUROPEANS, MIDDLE EASTERNERS, & S/SW ASIANS

The S Asians include the Dravidans. It’s worth noting the SW Asians and N Europeans are clustered together and the same for the Middle Easterners and S Europeans; not sure why but it could be some clues to migration patterns. What I called SW Asians include Caucasus people. The Middle Easterners are basically Semitic speaking people (Arabic mostly). I was checking these results to 23andme and Gedmatch tools and some minor details are not aligning well but overall is pretty representative. But again, the focus of this project is the E & N Asians. If you’re interested in learning more of the S Asian and the Indian Subcontinent, Zack Jamal of Harappa project has a lot of information. For the Europeans/Middle Easterners, Dienekes Pontikos is a great source.

NOTES

• I initially wanted to run supervised but I misunderstood the model. For every supervised K run, the algorithm needs the same amount of pre-identified K (not just African or any other groupings). This defeats the purpose of the project. So no supervised runs at the moment. I will keep running unsupervised until I see further subgrouping of the N & E Asians. Perhaps once I find the optimum K, I will re-run supervised to reduce the African and European subgroups.
• Still no luck resurrecting the Singapore Malays but I haven’t given up yet.
• I’m looking at creating a pseudo Negrito population; a hybrid. The plan is to extract all the Negrito markers from PASNP and use someone else’s markers and replace those markers with the Negrito. Not sure what the result will looks like but we’ll see. OpenSNP has a lot of open DNA raw data. I will pick from those.
• OpenSNP may have some N & E Asian folks. I’ll run it with PASNP to see which ones and maybe include it in the project.
• Current run includes 27 of the 38 donors. Out of 38, only 27 were unrelated.
• I included one sample, SL00010 (who agreed to allow me to post it on this blog). The large SE Asian chunk needs to be subdivided further which should happen in larger K runs.
• My European, South Asian, Middle Eastern and African assignments may not be accurate but it’s the best the list has been giving me. I’m mainly focusing on the E & N Asian components which we’ll probably see in higher K runs.
• The CV error at K=16 is 0.52234
• Based from the Admixture paper, the minimum amount of markers we must have is inversely proportional to the target Fst. For this project, the smallest Fst so far is 0.015 which means I need to have at least 66,667 markers. I have about 200,000 markers for this project which is more than enough for accuracy. This means the min Fst I can go would be 0.005; we’ll see how far K will take us :-)

Detailed East Asian Calculator Update

Since my project announcement on 23andme, I have received 30 raw data so far. 19 of which I merged with the following database:

1. HGDP
2. HapMap
3. Rasmussen et al
4. Metspalu et al
5. Fedorova et al
6. Chaubey et al
7. Behar et al
8. Yunusbayev et al
9. Schlebusch et al
10. Henn (2011) et al
11. Haber et al

 
I was not able to include the few new 23andme donors are I already started with the cross validation runs. Once I complete the runs I will merge the rest of the unrelated 23andme samples and start with the calculator.

I ran a script that was supposed to run it up to K=16. The other day, my machine finished up to 9 so far so I stopped it. I dug through the K=9 output to perform check which I can supervise. I have not run supervised runs so I do not know exactly how the algorithm will behave but I assume it will basically not further find sub-populations for the ones I really am not interested at the moment (mainly non-East Asians). For example if I assign all Africans as supervised Africans, it will not further look into African subpopulations (i.e. N Africans, S Africans, Khoisan, etc.). The supervise run will help me with computing time so Admixture will extract populations for mainly East Asians.

While deciding the supervise runs, I restarted running again with the new used desktop. Today it finished up to K=11. I want to present these two data K=9 and K=11.

Fst table above is for K=9. I sorted the first column as what is closest to E Asians.

Dendrogram above is for K=9

Fst table above is for K=11. I sorted the first column as what is closest to E Asians.

Dendrogram above is for K=11

 
The dendrograms are as expected for E Asians and other populations.

The S Asians further subdivided into two populations: S Asians & Dravidan speakers. Dravidans are from South India; they speak Telugu, Malayalam, Kannada, Tamil etc. I have a a few co-workers which I also consider friends that speak the language. Once Dravidan was separated from the rest of the S Asian population, the S Asians became much closer to the Europeans.

The Africans further subdivided into the Khoisan and Niger-Congo. The Hadza peoples language are considered an isolate but would not be surprised if linguists starts linking them to the Niger-Congo due to close genetic distance.

This further subdivision of non E/N Asians also shows why I need supervised runs. I really want to focus on E/N Asian subgroups.

Luson, Bisaya & Mindanao

For this blog, I’m basically looking at the peopling of the Philippines; where did the Filipinos come from and who are the modern day Filipinos? Additionally, in order to explore the topic, we need to look at Southeast Asia as a whole.

The Ice Age

Before we embark on our journey, the basic understanding of a great event that peaked at least twice during the migration of our ancestors should first be understood. Theories surrounding the causes of ice ages are still up for debate. The Earth’s wobble and the amount of greenhouse gases are the main theories linked with the occurrence of the ice ages. Ice ages are marked by two periods, the glacial and interglacial. Glacial periods are the period of colder temperatures while Interglacial are the relatively warmer periods.

A glacial maxima happens during a glacial period when the temperatures are at its lowest point; in essence it is the peak of an ice age. Interglacial is basically the period between glacial maximas. As the temperatures decrease, the Earth’s water accumulates as glaciers in the northern and southern hemispheres; it is at these times when the polar ice caps get closest to the equator. The source of water that form these glaciers are mainly from the ocean, hence at a glacial maxima, the sea level is at its lowest point which gives rise to shallow seabed and becomes what scientists calls “land bridges”. The increase in ice in the European and Asian continents and the emergence of land bridges especially in between continents, as scientists know today, played a major role in the peopling of the world.

The last two glacial maxima had been estimated to be between 25,000 to 15,000 BP and 175,000 to 125,000 BP (Kaplan et al. 2005).

Timeframe

Another important vocabulary we need to have a basic understanding of is about the two epochs. Geological epochs are geologic stratifications/timescales involving different rock layers that form the Earth’s crust; the significance of which is the present and last epochs provided many fossil finds that helps in the understanding of the peopling of the world. The Pleistocene epoch spans approximately 1.6 million BP to 10,000 BP. The next epoch is the Holocene and spans up to the present time. The last two glacial maxima that happened in the late Pleistocene and early Holocene may have played a significant role in the peopling of the world.

Models of Migration in Southeast Asia

As scientists have explained, there are at least two great migrations to the Philippines; the Itas and the Malay speakers. Gaillard and Mallari compiled the various theories behind the peopling of the Philippines and of course it touched on the surrounding areas within Southeast Asia. From what I observed, the PASNP may support Manuel’s and Bellwood’s theories where the origins of the Malay speakers may have been from mainland South China; more specifically, I believe we are from Southwest China.

Ita ang Unang Tao sa Luson, Bisaya, at Mindanao

Itas are the first people to settle Luson, Bisaya, & Mindanao

The Itas (Negritos) were the first to settle Island Southeast Asia (ISEA). The famous Tabon Man was discovered by Dr. Robert B. Fox in 1962 in the Tabon Caves of Palawan island is one proof; it was dated at 22.5K BP. Although Scott states in his book that the Tabon Man is not Ita I believe the opposite is true. My reasoning is simply by process of elimination; all of the archeological findings that links to the Austronesian speaking people (Nusantao) in ISEA have never been more than 5.5K years old (Bellwood). If not the Itas nor the Nusantao, who else can the Tabon Man be? Aside from the Tabon Man, a new discovery by Dr. Armand Salvador B. Mijares of what may be the oldest human fossil find in Southeast Asia called the Callao Man; the Callao Man has been dated 67K BP and scientists describes part of the bones found to be similar to modern Itas. There are also other sites from other islands as shown in Table 1; this table shows the various archaeological finds in Southeast Asia linked to the Itas.

BTW: I call the Negritos, Tasmanians, Orang Asli (Negritos), Australoids, Australo-Melanesian, & Melanesoid as Ita including all other group of people with the phenotype pigmented skin, frizzy/curly hair and typically shorter in stature than the average East Asian population. Ita is a term that my parent and my parents parents thought us who these people were/are (at least in the Philippines at the time). This is what what the Northern Itas call themselves also; the spelling may have evolved over time. I have Ita blood myself and Itas are part of the fabric that makes a Malay.

Since there are no known land bridges that can connect Palawan to mainland Luson (see satellite image from Google), we can infer that, at least for the Itas in the Philippines (except Palawan), they have reached the islands by means of a raft or some sort.

Figure 1: Snapshot of Philippines with the visible but submerged land bridges connecting Palawan to the Sunda shelf (from Google maps). The added highlights shows where humans would need a raft of some sort to cross to the next island and reach Luson.

Table 1: List of Archaeological Finds Linked to the Itas

Number	Date (BP in thousand)	Item	Site	Island	Country	Reference	Remarks
1	65.7	human third metatarsal bone	Callao Cave	Luson	Philippines	Mijares et al. 2010	"Negrito"
2	40	deep skull	Niah Cave	Kalamintan	Malaysia	Kennedy 1977	"Tasmanians"
3	37	human tibia	Tabon Cave	Palawan	Philippines	Détroit et al. 2004, Fox 1970	"Melanesoid"
4	25.5	flaked artefacts and charcoal	Callao Cave	Luson	Philippines	Mijares 2007, 2008
5	22	charcoal	Tabon Cave	Palawan	Philippines	Fox 1970
6	14.5	frontal bone	Tabon Cave	Palawan	Philippines	Dizon et al. 2002, Fox 1970
7	13.9	small flake assemblage	Ille Cave	Palawan	Philippines	Lewis et al. 2008
8	10.7	projectile points made of bone and stingray spine	Niah Cave	Kalamintan	Malaysia	Barton et al. 2009
9	10	twenty-seven burial remains	Gua Cha	Peninsular	Malaysia	Sieveking 1954, Adi 1985	"Melanesian"
10	10	male skeleton	Gua Gunung Runtuh	Peninsular	Malaysia	Zuraina 1994	"Australo-Melanesian"
11	7.5	twelve disturbed skeletons	Sukajadi Pasar	Sumatra	Indonesia	Budhisampurno 1985	"Australo-Melanesian"
12	6.5	burials	Moh Khiew Cave	Peninsular	Malaysia		"Australo-Melanesian"
13	6.5	red painted bones, two skulls	Wajak	Java	Indonesia	Dubois 1890	"Australo-Melanesian" ?

There are many surprising results regarding the Itas from a previous blog which I will expand here. First, there seems to be at least four unique Ita populations in Southeast Asia.

1.     Orang Asli (Malaysian Itas: Kensui and Jehai)

2.     Ati Ita (Philippine Itas: Ayta, Ati, Agta, & Iraya, North Ita)

3.     Mamanwa Ita (Philippine Ita, South Ita)

4.     Papuan

Table 2: Ita Populations Relative Fst

Figure 2: PC1 vs PC2 Plot (Zoomed)

These separations are demonstrated through the genetic distance produced by Admixture, the correlation analysis, principal component analysis and dendrogram. These large Ita separation is likely a very long period of separation from each other. It is odd though that the obvious phenotypes did not change much (pigmented skin and curly/frizzy hair – another topic for another blog J ). Initially, the Itas populated Southeast Asia including ISEA through land bridges that appeared as an effect of ice ages. These land bridges lasted for a very long time since population movements are not as quick as it is today; we’re talking about thousands of years. Then later, the sea level rose and the land bridges disappeared to where they are today. Since the Itas and most people in the world did not have the technology to travel long distance by sea; the genetic separation began and since the genetic distances are large, it must have been thousands of years (long period).
I have updated the dendrogram from the previous blog using “complete” method. The “ward” method gave results inconsistent with the Fst table. I have also added some cluster box equal to 9, representing the 9 cluster populations.

Figure 3: PASNP Dendrogram (K=19)

The same can be said with the separation for the two groups of Itas in the Philippines, the Mamanwa and North Itas. We can probably deduce from this that the separation of the two Philippine Ita populations was due to at least two major island groups that formed the Philippines during those ice ages. If we look carefully at the Philippine map including the seabed, you can almost make out at least two island groups. The Luzon – North Bisaya island and the South Bisaya - Mindanao island. Again, these long period of physical separation probably also caused the large genetic distance.

It’s interesting that the Papuans and Atis are close to each other; I would have expected the Atis and Mamanwas would be closer due to proximity. Perhaps the Mamanwas had a “bottle neck” founder populations similar to the Mlabri, meaning, the founders of the Mamanwa before the separation came from a small group of the bigger Ita group (bottle neck).

Figure 4: Ita Admixture

The Mamanwa and the Ati Itas have significant admixture with each other (Figure 5). Mamanwa also have admixture with the 2nd group of migrants, the Malay speakers; it shows an admixture range from 1.2% to 1.5% for the Ilokano, Bisaya, & Tagalog samples while the Manobo (Mindanao Nusantao) clearly admixed with Mamanwa at a higher percentage, 6.6%. The Ati Itas & Mamanwa gene is present (albeit small amount) with all the countries in Southeast Asia (Indonesia, Malaysia, Thailand, South China, Indian) in the PASNP data. This gene presence is probably proof that they have once lived among the mainland East Asians – Mon-Khmer, Nusantao, Tai-Kadai, & Sino-Tibetan, at the least and South Asians (Indians). Note that there is a paper out there shows the South Indians (Dravada speakers) to be another Ita group. (Vedoid) but the 4 Ita groups in Southeast Asia are definitely distinct from the ancient Dravada speakers.

Figure 5: Mamanwa Gene Percentage

Figure 6: Mamanwa Gene Prevalence

Figure 7: Ati Gene Percentage

Figure 8: Ati Gene Prevalence

Figure 9 & Figure 10 bring in some inferences. The Ati & Mamanwa groups have only recently admixed with the Malay speakers (Nusantao). This is likely since the archaeological evidence of Malay settlements to ISEA are less than 5.5K BP. The significant Papuan presence in the Ati samples is a surprise. As mentioned, the four Ita groups have large separation. If it is true then the Papuan content is of recent admixture. Were the Papuans and/or Atis able to develop maritime technology (sea worthy ships)? The other possibility is that the Ati’s were the founder source for the Papuans (and perhaps the Mamanwas); given the relatively greater Ati diversity. Note the Mamanwas has 1.1% Papuan content. The Papuans, on the other hand, has 99.2% Papuan, 0.5% Ati, & 0.3% Mamanwa. Whatever the possibilities are, the Papuans, Mamanwas & Atis have significant interactions in Luson, Bisaya, & Mindanao.

Note: Although percentage less than 0.25% maybe be a margin of error in admixture analysis, I would not completely dismiss these results since we are only comparing 55,000 SNPs compared to the millions unidentified. For the moment, I will most likely not explore percentage less than 0.25%.

Figure 9: Mamanwa Admixture

Figure 10: Ati Admixture

Figure 11: Papuan Gene Percentage

Figure 12: Papuan Gene Prevalence

Figure 13: Malaysia Ita Gene Prevalence

Figure 14: Malaysian Ita Admixture

  

References

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2.     D.H. Alexander, J. Novembre, and K. Lange. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655–1664, 2009

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