Alu evolution in human populations: Using the coalescent to estimate effective population size
There are estimated to be ~1000 members of the Ya5 Alu subfamily of retroposons in humans. This subfamily has a distribution restricted to humans, with a few copies in gorillas and chimpanzees. Fifty-seven Ya5 elements were previously cloned from a HeLa-derived randomly sheared total genomic library, sequenced, and screened for polymorphism in a panel of 120 unrelated humans. Forty-four of the 57 cloned Alu repeats were monomorphic in the sample and 13 Alu repeats were dimorphic for insertion presence/absence. The observed distribution of sample frequencies of the 13 dimorphic elements is consistent with the theoretical expectation for elements ascertained in a single diploid cell line. Coalescence theory is used to compute expected total pedigree branch lengths for monomorphic and dimorphic elements, leading to an estimate of human effective population size of ~18,000 during the last one to two million years.
Publication Source (Journal or Book title)
Sherry, S., Harpending, H., Batzer, M., & Stoneking, M. (1997). Alu evolution in human populations: Using the coalescent to estimate effective population size. Genetics, 147 (4), 1977-1982. Retrieved from https://digitalcommons.lsu.edu/biosci_pubs/292