Tag: Human Genetic Variation

"Asian" in all the right places

By Razib Khan | January 29, 2011 3:14 pm

mtDNA haplogroup G1a2

The pith: In this post I examine the most recent results from 23andMe for my family in the context of familial and regional (Bengal) history. I also use these results to offer up a framework for the ethnognesis of the eastern Bengali people within the last 1,000 years, and their relationship to other South Asian and Southeast Asian populations.

Since I received my 23andMe results last May I’ve been blogging about it a fair amount. In a recent post I inferred that perhaps I had a recent ancestor who was an ethnic Burman or some related group. My reasoning was that this explained a pattern of elevated matches on chromosomal segments with populations from southwest China in the HGDP data set. But now we have more than my genome to go on. This week I got the first V3 chip results from a sibling. And finally, yesterday the results from my parents came in. One thing that I immediately found interesting was my father’s mtDNA haplogroup assignment, G1a2. This came from his maternal grandmother, and as you can see it has a distribution which is mostly outside of South Asia. In case you care, I asked my father her background, and like my patrilineage she was a “Khan,” though an unrelated one (“Khan” is just an honorific). I received these results before the total genome assessment, and so initially assumed this confirmed my hunch that my father had some unknown recent ancestry of “eastern” provenance. But it turns out my hunch is probably wrong. In fact, my parents have about the same “eastern” proportion, with my mother slightly more! My expectation was that perhaps my mother would be around 25-30% “Asian,” and my father above 50%. The reality turns out that my father is 38%, and my mother 40%.

Image credit: f_mafra

Below are the “Ancestry Paintings” generated by 23andMe for my family (so far). What you see are the 22 non-sex chromosomes, which have two copies each, and assignments to “Asian,” “European,” and “African,” ancestry groups. The reference populations to generate these assignments come from the HapMap, the northern European sample of white Americans from Utah, Chinese from Beijing, Japanese from Tokyo, and ethnic Yoruba from Nigeria. What the assignment to one of these classes denotes is that that region of the genome is closest to that category in identity. It does not imply that your recent ancestry is European or Asian (African is probably a different matter, but there are many complaints about the results for African Americans and East Africans in the 23andMe forums). This caveat is especially important for South Asians, because we generally find that we’re ~75% European and ~25% Asian. All that means is that though most of our genetic affinity is with Europeans, a smaller fraction seems to resemble Asians more. Via “gene sharing” on 23andMe I can see that the Asian fraction varies from ~35% in South India and Sri Lanka, to ~10% in Pakistan and Punjab. This is not because South Indians have more East Asian ancestry than Punjabis. Rather, to a great extent the South Asian genome can be decomposed into two ancestral elements, one with a distant, but closer, affinity to populations of eastern Eurasia, and one with a close affinity to populations of western Eurasia. What some have termed “Ancient South Indians” (ASI) and “Ancient North Indians” (ANI). ASI ancestry, which is probably just a touch under 50% in South Asians overall, seems to shake out then as somewhat more Asian than European.* The fraction of ASI increases as one moves south and east in South Asia (and as one moves down the caste status ladder).

Read More

More on recombination & natural selection

By Razib Khan | March 28, 2010 1:31 pm

A follow up to the post below, see John Hawks, Selection’s genome-wide effect on population differentiation and p-ter’s Natural selection and recombination. As I said, it’s a dense paper, and I didn’t touch on many issues.

CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics, Science

Natural selection & recombination in the human genome

By Razib Khan | March 26, 2010 11:28 am

If you are like me, and if you are reading this weblog there is a significant probability you are like me, you read L. L. Cavalli-Sforza‘s History and Geography of Human Genes in the 1990s, and in the early aughts Spencer Wells’ A Journey of Man. Science has come very far in the last in the last 10-15 years, even Cavalli-Sforza’s magnum opus pales in comparison to the literal tsunami of data and analysis which the “post-genomic era” has ushered in. Instead of a gene here and there, or even the mtDNA and Y chromosome, researchers are now looking at hundreds of thousands of genetic variants, SNPs, across genomes. We’re rapidly approaching the era of whole genome sequencing, even if we’re not quite there yet.

But what’s the purpose of advances in technique and computation? Though the long-term project is to understand human variation and genetic function so as to have biomedical utility, in the short-term there is an enormous wealth of more abstract population genetic insight which can be extracted. Because of the biomedical focus of contemporary genomics we take a somewhat anthropocentric view, which is fine by me as I am an unregenerate speciest. The fish, fowl and crawling things of the earth can come later. And in any case, the beauty of the human focus of modern evolutionary genomics is that there are whole disciplines such as paleoanthropology which can serve as partners in interdisciplinary projects.

Humans are like any other organism, buffeted by conventional evolutionary genetic dynamics, drift, migration, natural selection, as well as processes which are more biophysically rooted such as recombination and mutation. Each of these processes leave their tell-tale marks on the genome. Mutation replenishes variation which drift and selection often eliminate, the former by chance and the latter in the form of negative selection. Migration serves to homogenize across populations through gene flow, while diversifying within populations by introducing novel variants. Finally, recombination breaks up linear associations of genetic variants along a DNA sequence, and has been used to explain sex.

Read More

CATEGORIZED UNDER: Genetics, Genomics, Science

Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

See More


RSS Razib’s Pinboard

Edifying books

Collapse bottom bar