ADZE: a rarefaction approach for counting alleles private to combinations of populations.
BACKGROUND
Analysis of the distribution of alleles across populations is a useful tool for examining population diversity and relationships. However, sample sizes often differ across populations, sometimes making it difficult to assess allelic distributions across groups.


RESULTS
We introduce a generalized rarefaction approach for counting alleles private to combinations of populations. Our method evaluates the number of alleles found in each of a set of populations but absent in all remaining populations, considering equal-sized subsamples from each population. Applying this method to a worldwide human microsatellite dataset, we observe a high number of alleles private to the combination of African and Oceanian populations. This result supports the possibility of a migration out of Africa into Oceania separate from the migrations responsible for the majority of the ancestry of the modern populations of Asia, and it highlights the utility of our approach to sample size correction in evaluating hypotheses about population history.


BACKGROUND
We have implemented our method in the computer pro-gram ADZE, which is available for download at http://rosenberglab.bioinformatics.med.umich.edu/adze.html.
Szpiech
Zachary A
ZA
Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA. szpiechz@umich.edu
Jakobsson
Mattias
M
Rosenberg
Noah A
NA
D000483:Alleles; D044383:Black People / Q000235:genetics; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D006801:Humans; D018895:Microsatellite Repeats; D044468:Native Hawaiian or Pacific Islander / Q000235:genetics; D012984:Software
Ecology. 1971 Jul;52(4):577-586
28973811
Eur J Hum Genet. 1998 Jan;6(1):38-49
9781013
PLoS Genet. 2008 Jan;4(1):e19
18208337
Proc Natl Acad Sci U S A. 1978 Apr;75(4):1904-8
273918
Science. 2002 Dec 20;298(5602):2381-5
12493913
Ann Hum Genet. 2006 Nov;70(Pt 6):841-7
17044859
Am J Hum Genet. 2003 May;72(5):1171-86
12690579
J Hum Evol. 1999 Jun;36(6):591-612
10330330
Biol Lett. 2007 Apr 22;3(2):218-23
17301009
Nat Genet. 1999 Dec;23(4):437-41
10581031
Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15942-7
16243969
PLoS Genet. 2005 Dec;1(6):e70
16355252