October 08, 2010

ADMIXTURE on HapMap 3 populations

Here is the result of running ADMIXTURE on about ~50K markers from the HapMap 3 populations. I'll annotate the final K=9 run; the rest are given at the end:

I list the distinctive colors for the populations, Left-to-Right. The minor components are easy enough to pick up and as expected:

ASW (A): African ancestry in Southwest USA [Sub-Saharan blue]

CEU (C): Utah residents with Northern and Western European ancestry from the CEPH collection [European yellow]

CHB (H): Han Chinese in Beijing, China [East Asian orange]
CHD (D): Chinese in Metropolitan Denver, Colorado [East Asian orange]

GIH (G): Gujarati Indians in Houston, Texas [South Asian purple]

JPT (J): Japanese in Tokyo, Japan [East Asian light green]

LWK (L): Luhya in Webuye, Kenya [East African bright green]

MEX (M): Mexican ancestry in Los Angeles, California [Amerindian pink]

MKK (K): Maasai in Kinyawa, Kenya [East African light blue]

TSI (T): Tuscan in Italy [European yellow]

YRI (Y): Yoruban in Ibadan, Nigeria (West Africa) [Sub-Saharan blue]

The rest of the runs for K=3 to K=8 are below:

K=3: Notice: Asian red+Caucasoid blue on Gujarati Indians and Mexicans. At this level of resolution, these two populations look similar. Notice presence of blue in East Africans but not Yorubans (green at the end).
K=4: East Africans get their own (yellow) cluster. Notice the diminution of the Sub-Saharan (purple) element, relative to the previous figure. This is due to the fact that the East African element is intermediate between Caucasoids and Sub-Saharans and "eats up" the other two elements, although residual Caucasoid red and Sub-Saharan purple remains. The tripartite origin of Mexicans is especially visible in this plot, with components being in order of European, East Eurasian, Sub-Saharan.
K=5: Gujarati Indians now get their own (purple) cluster. Here the difference between Luhya (mostly Sub-Saharan blue + East African yellow) and Maasai (the reverse) is quite striking. The former are Bantu speakers and thus not indigenous to east Africa.
K=6: Mexicans get their own cluster (blue) reflecting their Amerindian, rather than East Asian ancestry which could not be resolved in the previous figures.
K=7: the Luhya get their own cluster, splitting off from the Maasai. There are now 3 components in Africa centered on Yorubans (light blue), Luhya (very light green) and Maasai (red).
K=8: A low-frequency element appears in Maasai that is hard to interpret; it is preserved in the next and final K=9 run (shown at the beginning of the post), in which the Japanese and Chinese are split off.


Cuah123 said...

Curious how does the map data fair up against the finding of "Genetic admixture, relatedness, and structure patterns among Mexican populations revealed by the Y-chromosome"-Rangel Villalobes H et al 2008

Mexico has a large stratification of people with a European contingency in the West, perhaps reflecting population migrations from east to west (conquest and colonization).

I would be curious to see a study between Los Angeles "Mexicans" versus Santa Monica "Mexicans." I would be willing to bet there is a huge difference, with a larger cluster of European mixed mexicans in Santa Monica due to migrations from Western Mexico.

Marnie said...

Mexicans: A proportion of the K=5 Caucasian (green) element and almost all of the Asian (red) is absorbed into the Amerindian (blue) element at K=6.

Maasai: Cool. At K=8, they appear to have two dominant components and several minor ones.

Luhya: At K = 8, they share the dark blue component with the Maasai, but not the light blue. They have their own green component (Yoruban). What is the origin of the dark blue component? Some other Bantu, West African, non-Yoruban component?

At K=8, it's interesting that there are three major components at play between the Yorubans, the Maasai and the Luhya.

What is that trace magenta component in the Maasai?

Something else that you can pick up from these plots is the degree to which admixture has distributed itself throughout a population. For instance, at K=8, the Lubya dark blue/green admixture is evenly distributed across the population. Not so for Mexican and Maasai admixture. There's quit a lot of "chatter" in those distributions.

onur said...

It is good that you didn't use Sardinians and Basques this time.

Neither Gujaratis nor Mexicans represent South Asianness and Amerindianness respectively, as both of them have high Caucasoid admixture. So both of their own clusters have Caucasoid element and thus the small presence of the Gujarati and Mexican clusters in the Caucasoid populations (i.e., CEU and TSI) certainly doesn't mean that all of them are from Dravidoids (the South Asian race) and Amerindians respectively but means that at least some part of them are from the shared Caucasoid element between Caucasoids, Gujaratis and Mexicans. If you used completely or almost pure Dravidoids and Amerindians like the low caste/tribal South Indians and the Totonac used in Xing et al. 2010 instead of Gujaratis and Mexicans, the Caucasoid populations would show up purer (maybe completely pure Caucasoid) at all Ks.

Fanty said...

"Something else that you can pick up from these plots is the degree to which admixture has distributed itself throughout a population. For instance, at K=8, the Lubya dark blue/green admixture is evenly distributed across the population. Not so for Mexican and Maasai admixture. There's quit a lot of "chatter" in those distributions."

In this case one needs to know if the admixtured profiles are all in one region or not.

I would think, so more ancient an admixture is, so more evenly spread it should be amoung the population.

Huge difference in the profiles of one population would either indicate that the profiles are from different places (north and south or east and west, of a country) or more "recent" admixture.

Peoples DNA must become more and more homogenous so longer they are isolated and only intermix inside a closed group.

Just my guess.

empanada said...

Cuah123, I think the difference is more like northern vs southern Mexicans rather west vs east. This is because the north is mainly deserts that had a lower concentration of Amerindian populations in the first place before the conquerors came. I'm not quite sure why you think western Mexicans (do you mean from Baja California, Sonora, Jalisco, etc?) ended up in Santa Monica vs LA. IME there are a lot of lighter-complexioned northern-looking Mexicans in East LA and SGV, while there are a lot of very Amerindian-looking Mexicans living in South LA, Mid-City neighborhoods and Santa Monica. Santa Monica for one thing is known for its Oaxacan community which is mostly Zapotec and Mixtec.

Cuah123 said...

The Oaxacan community in Santa Monica and Venice are recent arrivals. The Mexicans that arrived a little over 100 years ago to Santa Monica (my family are from Jalisco). Their ancestors are mostly western europeans or r1b u106 l48. There's a movie out there about the different "old" families. There is also a contingency of families from Zacatecas with med. Greek/Italian mix.

The conquista went from east to west, recent studies of haplogroups reflect this movement.

Santa Monica, Malibu, Venice, were lands of the Chumash indians not Mixtec or Zapotec.