TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations

Human Molecular Genetics

Volumn 15, Issue 13, 2006, Pages 2106-2113

  Akey, Joshua M ^a   Swanson, Willie J ^a   Madeoy, Jennifer ^a   Eberle, Michael ^a   Shriver, Mark D ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM ION; DNA; ION CHANNEL; PROTEIN TRPV6; RECEPTOR PROTEIN; UNCLASSIFIED DRUG;

ALLELE; ARTICLE; CALCIUM ABSORPTION; DNA SEQUENCE; EXON; GENE FREQUENCY; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; PROBABILITY; PROTEIN FUNCTION; SINGLE NUCLEOTIDE POLYMORPHISM;

CALCIUM CHANNELS; DNA MUTATIONAL ANALYSIS; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETICS, POPULATION; GENOTYPE; GEOGRAPHY; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; TRPV CATION CHANNELS; VARIATION (GENETICS);

EID: 33745279634     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddl134     Document Type: Article

References (41)

1. Altshuler, D., Brooks, L.D., Chakravarti, A., Collins, F.S., Daly, M.J., Donnelly, P. and International HapMapConsortium (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.
2. Hinds, D.A., Stuve, L.L., Nilsen, G.B., Halperin, E., Eskin, E., Ballinger, D.G., Frazer, K.A. and Cox, D.R. (2005) Whole-genome patterns of common DNA variation in three human populations. Science, 307, 1072-1079.
3. Tishkoff, S.A., Varkonyi, R., Cahinhinan, N., Abbes, S., Argyropoulos, G., Destro-Bisol, G., Drousiotou, A., Dangerfield, B., Lefranc, G., Loiselet, J. et al. (2001) Haplotype diversity and linkage disequilibrium at human G6PD: Recent origin of alleles that confer malarial resistance. Science, 293, 455-462.
4. Akey, J.M., Zhang, G., Zhang, K., Jin, L. and Shriver, M.D. (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res., 12, 1805-1814.
5. Akey, J.M., Eberle, M.A., Rieder, M.J., Carlson, C.S., Shriver, M.D., Nickerson, D.A. and Kruglyak, L. (2004) Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes. PLoS Biol., 2, e286.
6. Sabeti, P.C., Reich, D.E., Higgins, J.M., Levine, H.Z., Richter, D.J., Schaffner, S.F., Gabriel, S.B., Platko, J.V., Patterson, N.J., McDonald, G.J. et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832-837.
7. Hamblin, M.T., Thompson, E.E. and Di Rienzo, A. (2002) Complex signatures of natural selection at the Duffy blood group locus. Am. J. Hum. Genet., 70, 369-383.
8. Rockman, M.V., Hahn, M.W., Soranzo, N., Goldstein, D.B. and Wray, G.A. (2003) Positive selection on a human-specific transcription factor binding site regulating IL4 expression. Curr. Biol., 13, 2118-2123.
9. Bersaglieri, T., Sabeti, P.C., Patterson, N., Vanderploeg, T., Schaffner, S.F., Drake, J.A., Rhodes, M., Reich, D.E. and Hirschhorn, J.N. (2004) Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet., 74, 1111-1120.
10. Thompson, E.E., Kuttab-Boulos, H., Witonsky, D., Yang, L., Roe, B.A. and Di Rienzo, A. (2004) CYP3A variation and the evolution of salt-sensitivity variants. Am. J. Hum. Genet., 75, 1059-1069.
11. Evans, P.D., Gilbert, S.L., Mekel-Bobrov, N., Vallender, E.J., Anderson, J.R., Vaez-Azizi, L.M., Tishkoff, S.A., Hudson, R.R. and Lahn, B.T. (2005) Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science, 309, 1717-1720.
12. Mekel-Bobrov, N., Gilbert, S.L., Evans, P.D., Vallender, E.J., Anderson, J.R., Hudson, R.R., Tishkoff, S.A. and Lahn, B.T. (2005) Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science, 309, 1720-1722.
13. Bamshad, M. and Wooding, S.P. (2003) Signatures of natural selection in the human genome. Nat. Rev. Genet., 4, 99-111.
14. Ronald, J. and Akey, J.M. (2005) Genome-wide scans for loci under selection in humans. Hum. Genomics, 2, 113-125.
15. Stajich, J.E. and Hahn, M.W. (2005) Disentangling the effects of demography and selection in human history. Mol. Biol. Evol., 22, 63-73.
16. Montell, C., Birnbaumer, L. and Flockerzi, V. (2002) The TRP channels, a remarkably functional family. Cell, 108, 595-598.
17. Clapham, D.E. (2003) TRP channels as cellular sensors. Nature, 426, 517-524.
18. Birnbaumer, L., Yildirim, E., Abramowitz, J. and Yidirim, E. (2003) A comparison of the genes coding for canonical TRP channels and their M, V and P relatives. Cell Calcium, 33, 419-432.
19. van de Graaf, S.F., Boullart, I., Hoenderop, J.G. and Bindels, R.J. (2004) Regulation of the epithelial Ca2+ channels TRPV5 and TRPV6 by 1-alpha,25-dihydroxy Vitamin D3 and dietary Ca2+. J. Steroid Biochem. Mol. Biol., 89-90, 303-308.
20. Nijenhuis, T., Hoenderop, J.G., Nilius, B. and Bindels, R.J. (2003) Pathophysiological implications of the novel epithelial Ca2+ channels TRPV5 and TRPV6. Pflugers Arch., 446, 401-409.
21. van de Graaf, S.F., Hoenderop, J.G., Gkika, D., Lamers, D., Prenen, J., Rescher, U., Gerke, V., Staub, O., Nilius, B. and Bindels, R.J. (2003) Functional expression of the epithelial Ca2+ channels TRPV5 and TRPV6 requires association of the S100A10-annexin 2 complex. EMBO J., 22, 1478-1487.
22. Yang, Z. (2000) Phylogenetic Analysis by Maximum Likelihood PAML. University College London, London.
23. Yang, Z. (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol., 15, 568-573.
24. Yang, Z. and Nielsen, R. (1998) Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol., 46, 409-418.
25. Yang, Z. and Nielsen, R. (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol., 19, 908-917.
26. Zhang, J. (2004) Frequent false detection of positive selection by the likelihood method with branch-site models. Mol. Biol. Evol., 21, 1332-1339.
27. Zhang, J., Nielsen, R. and Yang, Z. (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol., 22, 2472-2479.
28. Erler, I., Hirnet, D., Wissenbach, U., Flockerzi, V. and Niemeyer, B.A. (2004) Ca2+-selective transient receptor potential V channel architecture and function require a specific ankyrin repeat. J. Biol. Chem., 279, 34456-34463.
29. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
30. Fay, J.C. and Wu, C.I. (2000) Hitchhiking under positive Darwinian selection. Genetics, 155, 1405-1413.
31. Hudson, R.R. (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18, 337-338.
32. Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
33. Tishkoff, S.A. and Williams, S.M. (2002) Genetic analysis of African populations: Human evolution and complex disease. Nat. Rev. Genet., 3, 611-621.
34. Jorde, L.B., Bamshad, M. and Rogers, A.R. (1998) Using mitochondrial and nuclear DNA markers to reconstruct human evolution. BioEssays, 20, 126-136.
35. Cui, J., Bian, J.S., Kagan, A. and McDonald, T.V. (2002) CaT1 contributes to the stores-operated calcium current in Jurkat T-lymphocytes. J. Biol. Chem., 277, 47175-47183.
36. Clark, A.G., Glanowski, S., Nielsen, R., Thomas, P.D., Kejariwal, A., Todd, M.A., Tanenbaum, D.M., Civello, D., Lu, F., Murphy, B. et al. (2003) Inferring non-neutral evolution from human-chimp-mouse orthologous gene trios. Science, 12, 1960-1963.
37. Ewing, B., Hillier, L., Wendl, M.C. and Green, P. (1998) Base-calling of automated sequencer traces using phred. 1. Accuracy assessment. Genome Res., 8, 175-185.
38. Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. 2. Error probabilities. Genome Res., 8, 186-194.
39. Gordon, D., Abajian, C. and Green, P. (1998) Consed: A graphical tool for sequence finishing. Genome Res., 8, 195-202.
40. Nickerson, D.A., Tobe, V.O. and Taylor, S.L. (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res., 25, 2745-2751.
41. Schneider, S., Roessli, D. and Excoffier, L. (2000) Arlequin: A software for population genetics data analysis. Version 2.000. Genetics and Biometry Lab, Department of Anthropology, University of Geneva.