SNPSTRs: Empirically Derived, Rapidly Typed, Autosomal Haplotypes for Inference of Population History and Mutational Processes

Abstract

Each independently evolving segment of the genomes of a sexually reproducing organism has a separate history reflecting part of the evolutionary history of that organism. Uniparentally or clonally inherited DNA segments such as the mitochondrial and chloroplast genomes and the nonrecombining portion of the Y chromosome have provided, to date, most of the known data regarding compound haplotypic variation within and among populations. These comparatively small segments include numerous polymorphic sites and undergo little or no recombination. Recombining autosomes, however, comprise the major repository of genetic variation. Technical challenges and recombination have limited large-scale application of autosomal haplotypes. We have overcome this barrier through development of a general approach to the assessment of short autosomal DNA segments. Each such segment includes one or more single nucleotide polymorphisms (SNPs) and exactly one short tandem repeat (STR) locus. With dramatically different mutation rates, these two types of genetic markers provide complementary evolutionary information. We call the combination of a SNP and a STR polymorphism a SNPSTR, and have developed a simple, rapid method for empirically determining gametic phase for double and triple heterozygotes. Here, we illustrate the approach with two SNPSTR systems. Although even one system provides insight into population history, the power of the approach lies in combining results from multiple SNPSTR systems.

Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages

“…This discrepancy might be the result of different sexual migration patterns in Central Asia, as noted above. Additional data from autosomal markers, such as SNP or SNPSTR haplotypes, 57 need to be gathered in order to clarify the genetic role of Central Asia in the settlement of modern humans in Europe and Siberia.…”

Re-creation of the genetic composition of a founder population

“…Datasets are often available using other genetic marker systems, raising the possibility for this same type of analysis on SNPs or microsatellites. In fact, forays have already been made into analyzing admixed populations with a variety of genetic systems (Bertorelle and Excoffier 1998;Mountain et al 2002;Choisy et al 2004;Pfaff et al 2004;Price et al 2007). It appears that the HLA system may one end of the spectrum of population haplotype divergence in humans.…”

Les microsatellites des génomes eucaryotes

“…Ainsi, les variations de taux de mutations n'affectent en rien une recherche de paternité. En revanche, le caractère cyclique des processus de mutation pourrait bien rendre complexe la calibration de certains paramètres d'estimation en génétique des populations (coalescence) et invalider l'utilisation de certains systèmes type SNPSTR (single nucleotid polymorphisms short tandem repeats) (voir la discussion du concept dans [37]). Continuer à clamer la parfaite neutralité de ces séquences, du moins sur l'ensemble de leur cycle vital, apparaît peu raisonnable.…”