A novel measure of genetic distance for highly polymorphic tandem repeat loci - PubMed

Comparative Study

A novel measure of genetic distance for highly polymorphic tandem repeat loci

M D Shriver et al. Mol Biol Evol. 1995 Sep.

Abstract

Genetic distance measures are indicators of relatedness among populations or species and are useful for reconstructing the historic and phylogenetic relationships among such groups. Classical measures of genetic distance were developed to analyze biochemical and serological polymorphisms, systems which generally show limited variability. However, these traditional measures of genetic distance are inadequate for the analysis of certain classes of variable number tandem repeat (VNTR) loci, which have a larger number of alleles and higher levels of heterozygosity than traditional genetic markers. At the higher levels of heterozygosity observed at these loci, the standard measures of genetic distance are nonlinear and do not account for the mutational mechanisms of hypervariable loci. We have developed a measure of genetic distance, DSW, which is appropriate for the analysis of highly polymorphic DNA loci. Using computer simulations of diverging populations, we show that DSW conforms to linearity and that the variance is similar in magnitude to traditional measures of genetic distance. Comparisons of phylogenetic trees derived from the simulated divergence of human racial groups demonstrate that the branch lengths of trees prepared using DSW are more similar to the model tree than those generated using other measures. Finally, we demonstrate the applicability of DSW to evolutionary analysis by reconstructing the relationships among eight human populations using 14 microsatellite and STR loci. The phylogenetic trees generated using DSW are different from trees constructed with traditional measures and better reflect the well-documented ancient divergence of African and non-African populations.

Similar articles

• Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data.

  Nei M, Tajima F, Tateno Y. Nei M, et al. J Mol Evol. 1983;19(2):153-70. doi: 10.1007/BF02300753. J Mol Evol. 1983. PMID: 6571220

• Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens.

  Penny D, Steel M, Waddell PJ, Hendy MD. Penny D, et al. Mol Biol Evol. 1995 Sep;12(5):863-82. doi: 10.1093/oxfordjournals.molbev.a040263. Mol Biol Evol. 1995. PMID: 7476132

• Estimating divergence time with the use of microsatellite genetic distances: impacts of population growth and gene flow.

  Zhivotovsky LA. Zhivotovsky LA. Mol Biol Evol. 2001 May;18(5):700-9. doi: 10.1093/oxfordjournals.molbev.a003852. Mol Biol Evol. 2001. PMID: 11319254

• Human evolution. A new molecular view of human origins.

  Brookfield JF. Brookfield JF. Curr Biol. 1994 Jul 1;4(7):651-2. doi: 10.1016/s0960-9822(00)00145-7. Curr Biol. 1994. PMID: 7953547 Review.

Cited by

• Deriving evolutionary relationships among populations using microsatellites and (deltamu)(2): all loci are equal, but some are more equal than others..

  Landry PA, Koskinen MT, Primmer CR. Landry PA, et al. Genetics. 2002 Jul;161(3):1339-47. doi: 10.1093/genetics/161.3.1339. Genetics. 2002. PMID: 12136035 Free PMC article.

• Mapping genes of complex psychiatric diseases in Daghestan genetic isolates.

  Bulayeva KB, Leal SM, Pavlova TA, Kurbanov RM, Glatt SJ, Bulayev OA, Tsuang MT. Bulayeva KB, et al. Am J Med Genet B Neuropsychiatr Genet. 2005 Jan 5;132B(1):76-84. doi: 10.1002/ajmg.b.30073. Am J Med Genet B Neuropsychiatr Genet. 2005. PMID: 15389762 Free PMC article.

• Dynamics of microsatellite divergence under stepwise mutation and proportional slippage/point mutation models.

  Calabrese PP, Durrett RT, Aquadro CF. Calabrese PP, et al. Genetics. 2001 Oct;159(2):839-52. doi: 10.1093/genetics/159.2.839. Genetics. 2001. PMID: 11606557 Free PMC article.

• A genetic Study of the Ghanaian Population Using 15 Autosomal STR Loci.

  Kofi AE, Agyemang DA, Ghansah A, Awandare GA, Hakim HM, Khan HO, Nur Haslindawaty AR, Aziz MY, Chambers GK, Edinur HA. Kofi AE, et al. Biochem Genet. 2023 Oct;61(5):1850-1866. doi: 10.1007/s10528-023-10347-3. Epub 2023 Mar 4. Biochem Genet. 2023. PMID: 36869999

• DNA fingerprinting in anthropological genetics: past, present, future.

  Crawford MH, Beaty KG. Crawford MH, et al. Investig Genet. 2013 Nov 18;4(1):23. doi: 10.1186/2041-2223-4-23. Investig Genet. 2013. PMID: 24245746 Free PMC article.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Silverchair Information Systems