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Genetics. Sep 2002; 162(1): 473–484.
PMCID: PMC1462258

Is a multivariate consensus representation of genetic relationships among populations always meaningful?

Abstract

To determine the relationships among closely related populations or species, two methods are commonly used in the literature: phylogenetic reconstruction or multivariate analysis. The aim of this article is to assess the reliability of multivariate analysis. We describe a method that is based on principal component analysis and Mantel correlations, using a two-step process: The first step consists of a single-marker analysis and the second step tests if each marker reveals the same typology concerning population differentiation. We conclude that if single markers are not congruent, the compromise structure is not meaningful. Our model is not based on any particular mutation process and it can be applied to most of the commonly used genetic markers. This method is also useful to determine the contribution of each marker to the typology of populations. We test whether our method is efficient with two real data sets based on microsatellite markers. Our analysis suggests that for closely related populations, it is not always possible to accept the hypothesis that an increase in the number of markers will increase the reliability of the typology analysis.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics. 1999 Dec;153(4):1989–2000. [PMC free article] [PubMed]
  • Felsenstein J. How can we infer geography and history from gene frequencies? J Theor Biol. 1982 May 7;96(1):9–20. [PubMed]
  • Goldstein DB, Roemer GW, Smith DA, Reich DE, Bergman A, Wayne RK. The use of microsatellite variation to infer population structure and demographic history in a natural model system. Genetics. 1999 Feb;151(2):797–801. [PMC free article] [PubMed]
  • Ayala FJ, Escalante A, O'Huigin C, Klein J. Molecular genetics of speciation and human origins. Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):6787–6794. [PMC free article] [PubMed]
  • Hanslik S, Harr B, Brem G, Schlötterer C. Microsatellite analysis reveals substantial genetic differentiation between contemporary New World and Old World Holstein Friesian populations. Anim Genet. 2000 Feb;31(1):31–38. [PubMed]
  • Barker JS, Moore SS, Hetzel DJ, Evans D, Tan SG, Byrne K. Genetic diversity of Asian water buffalo (Bubalus bubalis): microsatellite variation and a comparison with protein-coding loci. Anim Genet. 1997 Apr;28(2):103–115. [PubMed]
  • Bjørnstad G, Røed KH. Breed demarcation and potential for breed allocation of horses assessed by microsatellite markers. Anim Genet. 2001 Apr;32(2):59–65. [PubMed]
  • Jorde LB, Rogers AR, Bamshad M, Watkins WS, Krakowiak P, Sung S, Kere J, Harpending HC. Microsatellite diversity and the demographic history of modern humans. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):3100–3103. [PMC free article] [PubMed]
  • Blott SC, Williams JL, Haley CS. Genetic relationships among European cattle breeds. Anim Genet. 1998 Aug;29(4):273–282. [PubMed]
  • Koskinen MT, Bredbacka P. Assessment of the population structure of five Finnish dog breeds with microsatellites. Anim Genet. 2000 Oct;31(5):310–317. [PubMed]
  • Bosch E, Calafell F, Pérez-Lezaun A, Comas D, Mateu E, Bertranpetit J. Population history of north Africa: evidence from classical genetic markers. Hum Biol. 1997 Jun;69(3):295–311. [PubMed]
  • Laval G, Iannuccelli N, Legault C, Milan D, Groenen MA, Giuffra E, Andersson L, Nissen PH, Jørgensen CB, Beeckmann P, et al. Genetic diversity of eleven European pig breeds. Genet Sel Evol. 2000 Mar-Apr;32(2):187–203. [PMC free article] [PubMed]
  • Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL. High resolution of human evolutionary trees with polymorphic microsatellites. Nature. 1994 Mar 31;368(6470):455–457. [PubMed]
  • Cañon J, Checa ML, Carleos C, Vega-Pla JL, Vallejo M, Dunner S. The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Anim Genet. 2000 Feb;31(1):39–48. [PubMed]
  • MacHugh DE, Shriver MD, Loftus RT, Cunningham P, Bradley DG. Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics. 1997 Jul;146(3):1071–1086. [PMC free article] [PubMed]
  • Cañn J, Alexandrino P, Bessa I, Carleos C, Carretero Y, Dunner S, Ferran N, Garcia D, Jordana J, Laloë D, et al. Genetic diversity measures of local European beef cattle breeds for conservation purposes. Genet Sel Evol. 2001 May-Jun;33(3):311–332. [PMC free article] [PubMed]
  • Cavalli-Sforza LL. Genes, peoples, and languages. Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7719–7724. [PMC free article] [PubMed]
  • Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967 Feb;27(2):209–220. [PubMed]
  • Cavalli-Sforza LL, Piazza A. Human genomic diversity in Europe: a summary of recent research and prospects for the future. Eur J Hum Genet. 1993;1(1):3–18. [PubMed]
  • Moazami-Goudarzi K, Laloë D, Furet JP, Grosclaude F. Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites. Anim Genet. 1997 Oct;28(5):338–345. [PubMed]
  • Chen KH, Cann H, Chen TC, Van West B, Cavalli-Sforza L. Genetic markers of an aboriginal Taiwanese population. Am J Phys Anthropol. 1985 Mar;66(3):327–337. [PubMed]
  • Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics. 1999 Dec;153(4):1989–2000. [PMC free article] [PubMed]
  • Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000 Jun;155(2):945–959. [PMC free article] [PubMed]
  • Saha N, Tay JS. Origin of the Koreans: a population genetic study. Am J Phys Anthropol. 1992 May;88(1):27–36. [PubMed]
  • Cymbron T, Loftus RT, Malheiro MI, Bradley DG. Mitochondrial sequence variation suggests an African influence in Portuguese cattle. Proc Biol Sci. 1999 Mar 22;266(1419):597–603. [PMC free article] [PubMed]
  • Saha N, Mak JW, Tay JS, Liu Y, Tan JA, Low PS, Singh M. Population genetic study among the Orange Asli (Semai Senoi) of Malaysia: Malayan aborigines. Hum Biol. 1995 Feb;67(1):37–57. [PubMed]
  • Saitbekova N, Gaillard C, Obexer-Ruff G, Dolf G. Genetic diversity in Swiss goat breeds based on microsatellite analysis. Anim Genet. 1999 Feb;30(1):36–41. [PubMed]
  • Wimmers K, Ponsuksili S, Hardge T, Valle-Zarate A, Mathur PK, Horst P. Genetic distinctness of African, Asian and South American local chickens. Anim Genet. 2000 Jun;31(3):159–165. [PubMed]
  • Takezaki N, Nei M. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics. 1996 Sep;144(1):389–399. [PMC free article] [PubMed]
  • Yang L, Zhao SH, Li K, Peng ZZ, Montgomery GW. Determination of genetic relationships among five indigenous Chinese goat breeds with six microsatellite markers. Anim Genet. 1999 Dec;30(6):452–455. [PubMed]
  • Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonné-Tamir B, Bertranpetit J, Francalacci P, et al. Y chromosome sequence variation and the history of human populations. Nat Genet. 2000 Nov;26(3):358–361. [PubMed]

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