population expansion

Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM, Broad GO & Seattle GO, on behalf of the NHLBI Exome Sequencing Project 2012 Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337:64-69.

  • nucleotide diversity (π) varied considerably among genes, ranging from ~0 to 1.319% per bp (mean = 0.042%; Fig. 1B)
  • mean π in AAs (0.047%) was significantly higher (P < 10−15, paired t test) than π in EAs (0.035%)
  • we revisited the demographic model from Gravel et al. (23), allowing for a reduced initial European expansion that is compensated for by accelerated growth starting after the split of European and Asian populations
  • we introduced a phase of exponential growth in the African population starting at the same time
  • the EA population growth, previously estimated at 0.38% per generation, is now modeled at the first step as 0.307% (SD of ±0.003%), followed by explosive growth of 1.95% (SD ±0.03%) over the past 5115 years
  • the growth in the AA sample during this same period is estimated to be 1.66% (SD ±0.03%)
  • the final population sizes in this model are lower than current census sizes
  • larger sample sizes will be necessary to fully capture the signature recent growth-rate expansion imparted on patterns of DNA sequence variation
  • supplementary materials
  • demographic inference
  • demographic inference based on the site frequency spectrum was performed using the package dadi version 1.5.2 (46), using a demographic model similar to a previously described three-population model (46,47), but with three added parameters to allow for a recent growth
  • we expect the extra information provided by the current data to be particularly informative of recent migration
  • we fixed the parameters of ancient demographic events to those obtained in (47), allowing only the recent European and African demography to change
  • the current data does not include individuals of reported Asian ancestry
  • we did not simulate the Asian population in this model after the split from the European population