The probability and chromosomal extent of trans-specific polymorphism

Genetics

Volumn 168, Issue 4, 2004, Pages 2363-2372

  Wiuf, Carsten ^a,c   Zhao, Keyan ^b   Innan, Hideki ^b,d   Nordborg, Magnus ^b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^c AARHUS UNIVERSITY   (Denmark)

^d UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CHROMOSOME ANALYSIS; DNA POLYMORPHISM; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC LINKAGE; GENETIC RECOMBINATION; GENETIC SELECTION; HUMAN; NONHUMAN; PRIORITY JOURNAL;

CHROMOSOMES; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; MODELS, GENETIC; POLYMORPHISM, GENETIC; TRANS-ACTIVATORS;

EID: 11244317152     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.029488     Document Type: Article

References (32)

1. ANDOLFATTO, P., and M. NORDBORG, 1998 The effect of gene conversion on intralocus associations. Genetics 148: 1397-1399.
2. BOISSINOT, S., Y. TAN, S.-K. SHYUE, H. SCHNEIDER, I. SAMPAIO et al., 1998 Origins and antiquity of X-linked triallelic color vision systems in New World monkeys. Proc. Nad. Acad. Sci. USA 95: 13749-13754.
3. CHEN, F.-C., and W.-H. Li, 2001 Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68: 444-456.
4. FIGUEROA, F., E. GÜNTER and J. KLEIN, 1988 MHC polymorphism pre-dating speciation. Nature 335: 265-267.
5. HEY, J., 1994 Bridging phylogenetics and population genetics with gene tree models, pp. 435-449 in Molecular Ecology and Evolution: Approaches and Applications, edited by B. SCHIERWATER, B. STREIT, G. P. WAGNER and R. DESALLE. Birkhäuser Verlag, Basel, Switzerland.
6. HUDSON, R. R., 1990 Gene genealogies and the coalescent process, pp. 1-43 in Oxford Surveys in Evolutionary Biology, Vol. 7, edited by D. FUTUYMA and J. ANTONOVICS.. Oxford University Press, Oxford.
7. HUDSON, R. R., and J. A. COYNE, 2002 Mathematical consequences of the genealogical species concept. Evolution 56: 1557-1565.
8. HUDSON, R. R., and N. L. KAPLAN, 1988 The coalescent process in models with selection and recombination. Genetics 120: 831-840.
9. INNAN, H., B. PADHUKASAHASRAM and M. NORDBORG, 2003 The pattern of polymorphism on human chromosome 21. Genome Res. 13: 1158-1168.
10. IOERGER, T. R., A. G. CLARK and T.-H. KAO, 1990 Polymorphism at the self-incompatibility locus in Solanaceae predates speciation. Proc. Natl. Acad. Sci. USA 87: 9732-9735.
11. JUKES, T. H., and C. R. CANTOR, 1969 Evolution of protein molecules, pp. 21-123 in Mammalian Protein Metabolism, edited by H. N. MUNRO. Academic Press, New York.
12. KLEIN, J., 1980 Generation of diversity at MHC loci: implications for T-cell receptor repertoires, pp. 239-253 in Immunology 80, edited by M. FOUGEREAU and J. DAUSSET. Academic Press, London.
13. NORDBORG, M., 2000 Linkage disequilibrium, gene trees, and selfing: an ancestral recombination graph with partial self-fertilization. Genetics 154: 923-929.
14. NORDBORG, M., 2001 On detecting ancient admixture, pp. 123-136 in Genes, Fossils, and Behaviour: An Integrated Approach to Human Evolution, edited by P. DONNELLY and R. A. FOLEY. NATO Science Series, 1OS Press, Amsterdam.
15. NORDBORG, M., and H. INNAN, 2003 The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population. Genetics 163: 1201-1213.
16. O'HUIGIN, C., Y. SATTA, N. TAKAHATA and J. KLEIN, 2002 Contribution of homoplasy and of ancestral polymorphism to the evolution of genes in anthropoid primates. Mol. Biol. Evol. 19: 1501-1513.
17. PAMILO, P., and M. NEI, 1988 Relationships between gene trees and species trees. Mol. Biol. Evol. 5: 568-583.
18. PRITCHARD, J. K., and M. PRZEWORSKI, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
19. PRZEWORSKI, M., R. R. HUDSON and A. DI RIENZO, 2000 Adjusting the focus on human variation. Trends Genet. 16: 296-302.
20. ROSENBERG, N. A., 2002 The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol. 61: 225-247.
21. SAITOU, N., and F.-I. YAMAMOTO, 1997 Evolution of primate ABO blood group genes and their homologous genes. Mol. Biol. Evol. 14: 399-411.
22. SAUNDERS, I. W., S. TAVARÉ and G. A. WATTERSON, 1984 On the genealogy of nested subsamples from a haploid population. Adv. Appl. Probab. 16: 471-491.
23. SCHIERUP, M. H., and J. HEIN, 2000 Consequences of recombination on traditional phylogenetic analysis. Genetics 156: 879-891.
24. SHYUE, S.-K., D. HEWETT-EMMETT, H. G. SPERLING, D. M. HUNT, J. K. BOWMAKER et al., 1995 Adaptive evolution of color vision genes in higher primates. Science 269: 1265-1267.
25. SHYUE, S.-K., S. BOISSINOT, H. SCHNEIDER, I. SAMPAIO, M. P. SCHNEIDER et al., 1998 Molecular genetics of special tuning in New World monkey color vision. J. Mol. Evol. 46: 697-702.
26. TAKAHATA, N., 1989 Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122: 957-966.
27. TAKAHATA, N., 1990 A simple genealogical structure of strongly balanced allelic lines and trans-species polymorphism. Proc. Natl. Acad. Sci. USA 87: 2419-2423.
28. TAN, Y., and W.-H. LI, 1999 Trichromatic vision in prosimians. Nature 402: 36.
29. TAVARÉ, S., 1984 Line-of-descent and genealogical processes, and their applications in population genetic models. Theor. Popul. Biol. 26: 119-164.
30. VEKEMANS, X., and M. SLATKIN, 1994 Gene and allelic genealogies at a gametophytic self-incompatibility locus. Genetics 137: 1157-1165.
31. VINCEK, V., C. O'HUIGIN, Y. SATTA, N. TAKAHATA, P. T. BOAG et al., 1997 How large was the founding population of Darwin's finches? Proc. R. Soc. Lond. Ser. B 264: 111-118.
32. WIUF, C., and J. HEIN, 2000 The coalescent with gene conversion. Genetics 155: 451-462.