Vlax Roma history: What do coalescent-based methods tell us?

European Journal of Human Genetics

Volumn 12, Issue 4, 2004, Pages 285-292

  Chaix, Raph ^a   Austerlitz, F ^b   Morar, B ^c   Kalaydjieva, L ^c   Heyer, E ^a  

^a MUSÉE DE L HOMME   (France)

^b UNIVERSITÉ PARIS SUD   (France)

^c UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Coalescence; Demography; Genetic diversity; Gypsies; Parameter estimation

Indexed keywords

MITOCHONDRIAL PROTEIN;

AGE DISTRIBUTION; ANALYTIC METHOD; ARTICLE; BULGARIA; CHROMOSOME 8; CONTROLLED STUDY; DEMOGRAPHY; EUROPE; EXTRACHROMOSOMAL INHERITANCE; GENDER; GENETIC MARKER; GENETIC PARAMETERS; GENETIC VARIABILITY; GIPSY; HUMAN; LINGUISTICS; MALE; MICROSATELLITE MARKER; MITOCHONDRIAL GENETICS; POPULATION GENETICS; POPULATION GROWTH; POPULATION MIGRATION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; Y CHROMOSOME;

FEMALE; FOUNDER EFFECT; GENETICS, POPULATION; GENOMIC IMPRINTING; GYPSIES; HUMANS; MALE; TRANSIENTS AND MIGRANTS;

EID: 1942440876     PISSN: 10184813     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.ejhg.5201126     Document Type: Article

References (54)

1. Fraser A: The Gypsies. Oxford: Blackwell Publishers; 1992.
2. Liégeois J-P: Roma, Gypsies, Travellers. Strasbourg: Council of Europe Press; 1994.
3. Gresham D, Morar B, Underhill PA et al: Origins and divergence of the Roma (Gypsies). Am J Hum Genet 2001; 69: 1314-1331.
4. Kalaydjieva L, Hallmayer J, Chandler D et al: Gene mapping in Gypsies identifies a novel demyelinating neuropathy on chromosome 8q24. Nat Genet 1996; 14: 214-217.
5. Kalaydjieva L, Gresham D, Gooding R et al: N-myc downstream-regulated gene 1 is mutated in hereditary motor and sensory neuropathy-Lom. Am J Hum Genet 2000; 67: 47-58.
6. Rogers T, Chandler D, Angelicheva D et al: A novel locus for autosomal recessive peripheral neuropathy in the EGR2 region on 10q23. Am J Hum Genet 2000; 67: 664-671.
7. Hantke J, Rogers T, French L et al: Refined mapping of the HMSNR critical gene region - construction of a high-density integrated genetic and physical map. Neuromusc Disord 2003; 13 (9): 729-736.
8. Angelicheva D, Turnev I, Dye D et al: Congenital cataracts facial dysmorphism neuropathy (CCFDN) syndrome: a novel developmental disorder in Gypsies maps to 18qter. Eur J Hum Genet 1999; 7: 560-566.
9. Merlini L, Gooding R, Lochmueller W et al: Genetic identity of Marinesco-Sjogren/ myoglobinuria and CCFDN syndromes. Neurology 2002; 58: 231-236.
10. Kalaydjieva L, Perez-Lezaun A, Angelicheva D et al: A founder mutation in the GK1 gene is responsible for galactokinase deficiency in Roma (Gypsies). Am J Hum Genet 1999; 65: 1299-1307.
11. Hunter M, Heyer E, Austerlitz F et al: The P28T mutation in the GALK1 gene accounts for galactokinase deficiency in Roma (Gypsy) patients across Europe. Pediatr Res 2002; 51: 602-606.
12. Kalaydjieva L, Calafell F, Jobling MA et al: Patterns of inter- and intra-group genetic diversity in the Vlax Roma as revealed by Y chromosome and mitochondrial DNA lineages. Eur J Hum Genet 2001; 9: 97-104.
13. Hey J, Machado CA: The study of structured populations - new hope for a difficult and divided science. Nat Rev Genet 2003; 4: 535-543.
14. Beerli P, Felsenstein J: Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 1999; 152: 763-773.
15. Beerli P, Felsenstein J: Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci USA 2001; 98: 4563-4568.
16. Kuhner MK, Yamato J, Felsenstein J: Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 1995; 140: 1421-1430.
17. Kuhner MK, Yamato J, Felsenstein J: Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 1998; 149: 429-434.
18. Wilson IJ, Balding DJ: Genealogical inference from microsatellite data. Genetics 1998; 150: 499-510.
19. Wilson IJ, Weale ME, Balding DJ: Inferences from DNA data: population histories, evolutionary processes, and forensic match probabilities. J R Statist Soc A 2003; 166: 1-33.
20. Rolf B, Meyer E, Brinkmann B, de Knijff P: Polymorphism at the tetranucleotide repeat locus DYS389 in 10 populations reveals strong geographic clustering. Eur J Hum Genet 1998; 6: 583-588.
21. Chandler D, Angelicheva D, Heather L et al: Hereditary motor and sensory neuropathy - Lom (HMSNL): refined genetic mapping in Romani (Gypsy) families from several European countries. Neuromusc Disord 2000; 10: 584-591.
22. Schneider S, Roessli D, Excoffier L: Arlequin ver. 2000: a software for population genetics data analysis. Switzerland: Genetics and Biometry Laboratory, University of Geneva; 2000.
23. Excoffier L, Smouse PE, Quattro JM: Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 1992; 131: 479-491.
24. Tajima F: Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989; 123: 585-595.
25. Tajima F: The effect of change in population size on DNA polymorphism. Genetics 1989; 123: 597-601.
26. Watterson GA: The homozygosity test after a change in population size. Genetics 1986; 112: 899-907.
27. Fu YX: Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997; 147: 915-925.
28. Slatkin M, Hudson RR: Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 1991; 129: 555-562.
29. Tremblay M, Vezina H: New estimates of intergenerational time intervals for the calculation of age and origins of mutations. Am J Hum Genet 2000; 66: 651-658.
30. Heyer E, Zietkiewicz E, Rochowski A, Yotova V, Puymirat J, Labuda D: Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees. Am J Hum Genet 2001; 69: 1113-1126.
31. Howell N, Kubacka I, Mackey DA: How rapidly does the human mitochondrial genome evolve? Am J Hum Genet 1996; 59: 501-509.
32. Parsons TJ, Muniec DS, Sullivan K et al: A high observed substitution rate in the human mitochondrial DNA control region. Nat Genet 1997; 15: 363-368.
33. Sigurgardottir S, Helgason A, Gulcher JR, Stefansson K, Donnelly P: The mutation rate in the human mtDNA control region. Am J Hum Genet 2000; 66: 1599-1609.
34. Tamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10: 512-526.
35. Horai S, Hayasaka K, Kondo R, Tsugane K, Takahata N: Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc Natl Acad Sci USA 1995; 92: 532-536.
36. Heyer E, Puymirat J, Dieltjes P, Bakker E, de Knijff P: Estimating Y chromosome specific microsatellite mutation frequencies using deep rooting pedigrees. Hum Mol Genet 1997; 6: 799-803.
37. Kayser M, Roewer L, Hedman M et al: 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 2000; 66: 1580-1588.
38. Kingman: On the genealogy of large populations. J Appl Probab 1982; 19: 27-43.
39. Tajima F: Evolutionary relationship of DNA sequences in finite populations. Genetics 1983; 105: 437-460.
40. Fu YX, Li WH: Coalescing into the 21st century: an overview and prospects of coalescent theory. Theor Popul Biol 1999; 56: 1-10.
41. Harding RM, Fullerton SM, Griffiths RC et al: Archaic African and Asian lineages in the genetic ancestry of modern humans. Am J Hum Genet 1997; 60: 772-789.
42. Thomson R, Pritchard JK, Shen P, Oefner PJ, Feldman MW: Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc Natl Acad Sci USA 2000; 97: 7360-7365.
43. Hurles ME, Nicholson J, Bosch E, Renfrew C, Sykes BC, Jobling MA: Y chromosomal evidence for the origins of oceanic-speaking peoples. Genetics 2002; 160: 289-303.
44. Stephens M, Donnelly P: Inferences in molecular population genetics. J R Statist Soc, Series B 2000; 62: 605-655.
45. Vitalis R, Couvet D: Estimation of effective population size and migration rate from one- and two-locus identity measures. Genetics 2001; 157: 911-925.
46. Hancock I: The Pariah Syndrome. Ann Arbor, Michigan: Karoma Publishers Inc.; 1987.
47. Achim V: Tigani in Istoria Romaniei. Bucuresti: Editura Enciclopedica; 1998.
48. Slatkin M, Bertorelle G: The use of intraallelic variability for testing neutrality and estimating population growth rate. Genetics 2001; 158: 865-874.
49. Austerlitz F, Kalaydjieva L, Heyer E: Detecting population growth, selection and inherited fertility from haplotypic data. (in press).
50. Marushiakova E, Popov V: Gypsies (Roma) in Bulgaria. Studien zur Tsiganologie und Folkloristik. Frankfurt am Main: Editions Peter Lang; 1997.
51. Excoffier L, Yang Z: Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees. Mol Biol Evol 1999; 16: 1357-1368.
52. Watterson GA: On the number of segregating sites in genetical models without recombination. Theor Popul Biol 1975; 7: 256-276.
53. Kimura M, Ohta T: Stepwise mutation model and distribution of allelic frequencies in a finite population. Proc Natl Acad Sci USA 1978; 75: 2868-2872.
54. Abramowitz M, Stegun IA: Handbook of Mathematical Functions, Applied Mathematics Series, Vol. 55, Government Printing Office, Washington DC, 1964.