Genetic variation

I hadn’t seen these numbers on genetic variation between and among populations before.  From a 2004 paper, Genetic variation, classification and ‘race’:

The average proportion of nucleotide differences between a randomly chosen pair of humans (i.e., average nucleotide diversity, or pi) is consistently estimated to lie between 1 in 1,000 and 1 in 1,500 (refs. 9,10). This proportion is low compared with those of many other species, from fruit flies to chimpanzees11, 12, reflecting the recent origin of our species from a small founding population13. The pi-value for Homo sapiens can be put into perspective by considering that humans differ from chimpanzees at only 1 in 100 nucleotides, on average14, 15. Because there are approximately three billion nucleotide base pairs in the haploid human genome, each pair of humans differs, on average, by two to three million base pairs.

Of the 0.1% of DNA that varies among individuals, what proportion varies among main populations? Consider an apportionment of Old World populations into three continents (Africa, Asia and Europe), a grouping that corresponds to a common view of three of the ‘major races’16, 17. Approximately 85−90% of genetic variation is found within these continental groups, and only an additional 10−15% of variation is found between them18,19, 20 (Table 1). In other words, ~90% of total genetic variation would be found in a collection of individuals from a single continent, and only ~10% more variation would be found if the collection consisted of Europeans, Asians and Africans. The proportion of total genetic variation ascribed to differences between continental populations, called FST, is consistent, regardless of the type of autosomal loci examined (Table 1). FST varies, however, depending on how the human population is divided. If four Old World populations (European, African, East Asian and Indian subcontinent) are examined instead of three, FST(estimated for 100 Alu element insertion polymorphisms) decreases from 14% to 10% (ref.21). These estimates of FST and pi tell us that humans vary only slightly at the DNA level and that only a small proportion of this variation separates continental populations.

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2 thoughts on “Genetic variation”

  1. Do you find that genetic variation still has importance beyond some sort of historical marker? Do people still care about sequencing genomes except as a stepping stone to transcriptomes and proteomes? Back when I studied this for a little bit, I felt that there was a dawning realization that genomes really didn’t explain squat except taxonomy. I heard on the radio there are now efforts to map environmental effects on the genome – can’t remember what they’re calling it. It must be both frustrating and exciting in bioinformatics right now. Frustrating because it seems like every opened door leads to a thousand closed ones but exciting because there are just more data to mine and cool things to learn.

  2. hey Doruk!

    Genetic variation can lead to malformed proteins, and you can find this in the transcripts like you say. But single nucleotide variants in promoter regions can also affect regulation, by changing how well proteins bind. There is lots of research now into non coding RNA like microRNA which have a secondary effect on top of transcription factor regulation. There is definitely frustration that sequencing hasn’t unraveled cancer, but it’s like reading a stream of bits and trying to deduce what’s going on in your computer. it will take some time to reverse engineer models of what is going on.

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