Ranajit Chakraborty and others have long worked on STRs and their variation within populations (note that Shriver was working on this in the 1990s). Here are some relevant papers:
Silva DA, Crouse CA, Chakraborty R, Goes AC, Carvalho EF. Statistical analyses of 14 short tandem repeat loci in Brazilian populations from Rio de Janeiro and Mato Grosso do Sul states for forensic and identity testing purposes. Forensic Sci Int. 2004 Jan 28;139(2-3):173-6.
Budowle B, Chakraborty R. Population variation at the CODIS core short tandem repeat loci in Europeans. Leg Med (Tokyo). 2001 Mar;3(1):29-33.
Sun G, McGarvey ST, Bayoumi R, Mulligan CJ, Barrantes R, Raskin S, Zhong Y, Akey J, Chakraborty R, Deka R. Global genetic variation at nine short tandem repeat loci and implications on forensic genetics. Eur J Hum Genet. 2003 Jan;11(1):39-49.
Budowle B, Chidambaram A, Strickland L, Beheim CW, Taft GM, Chakraborty R. Population studies on three Native Alaska population groups using STR loci. Forensic Sci Int. 2002 Sep 10;129(1):51-7.
Cerda-Flores RM, Budowle B, Jin L, Barton SA, Deka R, Chakraborty R. Maximum likelihood estimates of admixture in Northeastern Mexico using 13 short tandem repeat loci. Am J Human Biol. 2002 Jul-Aug;14(4):429-39.
Ramana GV, Su B, Jin L, Singh L, Wang N, Underhill P, Chakraborty R. Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India. Eur J Hum Genet. 2001 Sep;9(9):695-700.
Budowle B, Shea B, Niezgoda S, Chakraborty R. CODIS STR loci data from 41 sample populations. J Forensic Sci. 2001 May;46(3):453-89.
Chakraborty R, Stivers DN, Su B, Zhong Y, Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis. 1999 Jun;20(8):1682-96.
Desmarais D, Zhong Y, Chakraborty R, Perreault C, Busque L. Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA). J Forensic Sci. 1998 Sep;43(5):1046-9.
Busque L, Desmarais D, Provost S, Schumm JW, Zhong Y, Chakraborty R. Analysis of allele distribution for six short tandem repeat loci in the French Canadian population of Quebec. J Forensic Sci. 1997 Nov;42(6):1147-53.
Chakraborty R, Stivers DN, Zhong Y. Estimation of mutation rates from parentage exclusion data: applications to STR and VNTR loci. Mutat Res. 1996 Jul 5;354(1):41-8.
Chakraborty R, Stivers DN. Paternity exclusion by DNA markers: effects of paternal mutations. J Forensic Sci. 1996 Jul;41(4):671-7.
Budowle B, Monson KL, Chakraborty R. Estimating minimum allele frequencies for DNA profile frequency estimates for PCR-based loci. Int J Legal Med. 1996;108(4):173-6.
Shriver MD, Jin L, Boerwinkle E, Deka R, Ferrell RE, Chakraborty R. A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol Biol Evol. 1995 Sep;12(5):914-20.
Jin L, Chakraborty R. Population structure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics. Heredity. 1995 Mar;74 ( Pt 3):274-85.
Hammond HA, Jin L, Zhong Y, Caskey CT, Chakraborty R. Evaluation of 13 short tandem repeat loci for use in personal identification applications. Am J Hum Genet. 1994 Jul;55(1):175-89.
Shriver MD, Jin L, Chakraborty R, Boerwinkle E. VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics. 1993 Jul;134(3):983-93.
Edwards A, Hammond HA, Jin L, Caskey CT, Chakraborty R. Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics. 1992 Feb;12(2):241-53.
Here is the abstract abstract of one of the above papers which is particularly interesting:
Global genetic variation at nine short tandem repeat loci and implications on forensic genetics.
Sun G, McGarvey ST, Bayoumi R, Mulligan CJ, Barrantes R, Raskin S, Zhong Y, Akey J, Chakraborty R, Deka R.
Center for Genome Information, Department of Environmental Health, University of Cincinnati, Ohio 45267, USA.
We have studied genetic variation at nine autosomal short tandem repeat loci in 20 globally distributed human populations defined by geographic and ethnic origins, viz., African, Caucasian, Asian, Native American and Oceanic. The purpose of this study is to evaluate the utility and applicability of these nine loci in forensic analysis in worldwide populations. The levels of genetic variation measured by number of alleles, allele size variance and heterozygosity are high in all populations irrespective of their effective sizes. Single- as well as multi-locus genotype frequencies are in conformity with the assumptions of Hardy-Weinberg equilibrium. Further, alleles across the entire set of nine loci are mutually independent in all populations. Gene diversity analysis shows that pooling of population data by major geographic groupings does not introduce substructure effects beyond the levels recommended by the National Research Council, validating the establishment of population databases based on major geographic and ethnic groupings. A network tree based on genetic distances further supports this assertion, in which populations of common ancestry cluster together. With respect to the power of discrimination and exclusion probabilities, even the relatively reduced levels of genetic variation at these nine STR loci in smaller and isolated populations provide an exclusionary power over 99%. However, in paternity testing with unknown genotype of the mother, the power of exclusion could fall below 80% in some isolated populations, and in such cases use of additional loci supplementing the battery of the nine loci is recommended.
I have for some time wondered whether a combined STR/SNP approach might well be able to shed more light on population affinity, and whether this has any possible bearing on the development of ABD/DNAWitness 3.0.
