A study of Y-chromosome microsatellite variation in sub-Saharan Africa: A comparison between FST and RST genetic distances

Human Biology

Volumn 75, Issue 3, 2003, Pages 313-330

  Caglià, Alessandra ^a,b   Tofanelli, Sergio ^c   Coia, Valentina ^a,b   Boschi, Ilaria ^b   Pescarmona, Marina ^b   Spedini, Gabriella ^a   Pascali, Vincenzo ^b   Paoli, Giorgio ^c   Destro Bisol, Giovanni ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b CATHOLIC UNIVERSITY   (Italy)

^c UNIVERSITY OF PISA   (Italy)

Author keywords

Bamileke; Ewondo; Haplotypes; Hutu; Microsatellite; Y Chromosome

Indexed keywords

AFRICA; ANTHROPOLOGY; ARTICLE; CHROMOSOME SATELLITE; FST GENETIC DISTANCE; GENE LOCUS; GENETIC DISTANCE; GENETIC DRIFT; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HAPLOTYPE; HUMAN; MAJOR CLINICAL STUDY; POPULATION GENETICS; RST GENETIC DISTANCE; Y CHROMOSOME;

EID: 0141540857     PISSN: 00187143     EISSN: None     Source Type: Journal    
DOI: 10.1353/hub.2003.0041     Document Type: Article

References (51)

1. Alexandre, P. 1981. Les Africains. Paris, France: Lidis.
2. Atlas National du Cameroun. 1984. Paris, France: Jeune Afrique.
3. Bosch, E., F. Calafell, F.R. Santos et al. 1999. Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome. Am. J. Hum. Genet. 65:1623-1638.
4. Bosch, E., F. Calafell, D. Comas et al. 2001. High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between northwestern Africa and the Iberian Peninsula. Am. J. Hum. Genet. 68:1019-1029.
5. Cavalli-Sforza, L.L., ed. 1986. African Pygmies. Orlando, Florida: Academic Press.
6. Chakraborty, R. 1992. Sample size requirements for addressing the population genetic issues of forensic use of DNA typing. Hum. Biol. 64:141-159.
7. Cruciani, F., P. Santolamazza, P. Shen et al. 2002. An Asia to Sub-Saharan Africa back-migration is supported by high-resolution analysis of human Y Chromosomes. Am. J. Hum. Genet. 70:1197-1214.
8. de Knijff, P., M. Kayser, A. Caglia et al. 1997. Chromosome Y microsatellites: Population genetic and evolutionary aspects. Int. J. Legal Med. 110:134-149.
9. de Knijff, P. 2000. Y chromosomes shared by descent or by state. In Archaeogenetics: DNA and the Population Prehistory of Europe, C. Renfrew and K. Boyle, eds. The McDonald Institute, Cambridge, 301-304.
10. Deka, R., L. Jin, M.D. Shriver et al. 1996. Dispersion of human Y chromosome haplotypes based on five microsatellites in global populations. Genome Res. 6:1177-1184.
11. Destro-Bisol, G., V. Pascali, and G. Spedini. 2000a. Application of different genetic distance methods to microsatellite data. Hum. Genet. 106:130-132.
12. Destro-Bisol, G., I. Boschi, A. Caglia, et al. 2000b. Microsatellite variation in Central Africa: An analysis of intrapopulafional and interpopulafional genetic diversity. Am. J. Phys. Anthropol. 112:319-337.
13. Felsenstein, J. 1989. Phylip-Phylogeny inference package (version 3.2). Cladistics 5:164-166.
14. Forster, P., A. Rohl, P. Lunnemann et al. 2000. A short tandem repeat-based phylogeny for the human Y chromosome. Am. J. Hum. Genet. 67:182-196.
15. Greenberg, J. 1980. Classification des langues d'Afrique. In Histoire générale de l'Afrique, J. Ki Zerbo, ed. Paris: UNESCO/Jeune Afrique, 321-346.
16. Hammer, M.F., T.M. Karafet, A.J. Redd et al. 2001. Hierarchical patterns of global human Y-chromosome diversity. Mol. Biol. Evol. 18:1189-1203.
17. Heyer, E., J. Puymirat, P. Dieltjes et al. 1997. Estimating Y-chromosome-specific microsatellite mutation frequencies using deep rooting pedigrees. Hum. Mol. Genet. 6:799-803.
18. Higuchi, R., C.H. von Beroldingen, G.F. Sesanbaugh et al. 1988. DNA typing from single hairs. Nature 332:543-546.
19. Hitzeroth, H.W. 1986. On the genetic interrelationships of South African Negroes. Am. J. Phys. Anthropol. 69:389-401.
20. Jenkins, T., A. Zoutendyk, A.G. Steinberg. 1970. Gammaglobulin groups (Gm and Inv) of various Southern African populations. Am. J. Phys. Anthropol. 32:197-218.
21. Kayser, M., A. Caglià, D. Corach et al. 1997. Evaluation of Y-chromosomal STRs: A multicenter study. Int. J. Legal Med. 110:125-133.
22. Kayser, M., M. Krawczak, L. Excoffier et al. 2001. An extensive analysis of Y-chromosomal microsatellite haplotypes in globally dispersed human populations. Am. J. Hum. Genet. 68:990-1018.
23. Kayser, M., L. Roewer, M. Hedman et al. 2000. Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. Am. J. Hum. Genet. 66:1580-1588.
24. Kruskal, J.B. 1964. Multidimensional scaling by optimizing a goodness of fit test to a nonmetric hypothesis. Psychometrika 19:1-27.
25. McIntosh, S.K., and R.J. McIntosh. 1982. West African Prehistory. Am. Scientist 69:603-613.
26. Michalakis, Y., and L. Excoffier. 1996. A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics 142:1061-1064.
27. Moscetti, A., I. Boschi, M. Dobosz et al. 1995. Fluorescence-based classification of microsatellites using a single-wavelength semiautomatic sequencer: Genotype assignment and identity tests by analysis of comigrating peak profiles. Electrophoresis 16:1875-1880.
28. Nauta, M.J., and F.J. Weissing. 1996. Constraints on allele size at microsatellite loci: Implications for genetic differentiation. Genetics 143:1021-1032.
29. Nei, M. 1987. Molecular Evolutionary Genetics. New York, NY: Columbia University Press, 176-184.
30. Osier, M.V., K.H. Cheung, J.R. Kidd et al. 2002. ALFRED: An allele frequency database for anthropology. Am. J. Phys. Anthropol. 119:77-83.
31. Parra, E., M.D. Shriver, A. Soemantri et al. 1999. Analysis of five Y-specific microsatellite loci in Asian and Pacific populations. Am. J. Phys. Anthropol. 110:1-16.
32. Pérez-Lezaun, A., F. Calafell, E. Mateu et al. 1997a. Microsatellite variation and the differentiation of modern humans. Hum. Genet. 99:1-7.
33. Pérez-Lezaun, A., F. Calafell, E. Mateu et al. 1997b. Allele frequencies for 20 microsatellites in a worldwide population survey. Hum. Hered. 47:189-196.
34. Pritchard, J.K., M.T. Seielstad, A. Pérez-Lezaun et al. 1999. Population growth of human Y chromosomes: A study of Y chromosome microsatellites. Mol. Biol. Evol. 16:1791-1798.
35. Reynolds, J., B.S. Weir, and C.C. Cockerham. 1983. Estimation of the coancestry coefficient: Basis for a short-term genetic distance. Genetics 105:767-779.
36. Roewer, L., M. Krawczak, S. Willuweit et al. 2001. Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes. Forensic Sci. Int. 118:106-113.
37. Rolf, B., E. Meyer, B. Brinkmann et al. 1998. Polymorphism at the tetranucleotide repeat locus DYS389 in 10 populations reveals strong geographic clustering. Eur. J. Hum. Genet. 6:583-588.
38. Saitou, N., and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
39. Schneider, S., J.M. Kueffer, D. Roessli et al. 1997. Arlequin ver1.1: A software for population genetic data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
40. Seielstad, M., E. Bekele, M. Ibrahim et al. 1999. A view of modern human origins from Y-chromosome microsatellite variation. Genome Res. 9:558-567.
41. Slatkin, M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457-462.
42. Spedini, G., and C. Bailly. 1989. Etude anthropobiologique au Cameroun. Les Bamilèké du plateau occidental. Riv. Antropol. 65:193-212.
43. Spedini, G., G. Destro-Bisol, S. Mondovi et al. 1999. The peopling of sub-Saharan Africa: The case study of Cameroon. Am. J. Phys. Anthropol. 110:143-162.
44. Stringer, C.B., and P. Andrews. 1988. Genetic and fossil evidence for the origin of modern humans. Science 239:1263-1268.
45. Takezaki, N., and M. Nei. 1996. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144:389-399.
46. The World Factbook 2001. http://www.cia.gov/cia/publications/factbook/
47. Thomas, M.G., T. Parfitt, D.A. Weiss et al. 2000. Y chromosomes traveling south: The Cohen modal haplotype and the origins of the Lemba, the "Black Jews of Southern Africa." Am. J. Hum. Genet. 66:674-686.
48. Tofanelli, S., I. Boschi, S. Bertoneri et al. 2003. Variation at 16 STR loci (the CODIS core set plus HumCD4, HumFES, HumF13A1) in the Hutu population from Rwanda. Int. J. Leg. Med. 117:121-126.
49. Trovoada, M.J., C. Alves, L. Gusmao et al. 2001. Evidence for population sub-structuring in São Tomé e Principe as inferred from Y-chromosome STR analysis. Ann. Hum. Genet. 65:271-283.
50. Vansina, J. 1984. Western Bantu expansion. J. Afr. Hist. 25:129-145.
51. Weir, B.S., and C.C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.