A 15-Myr-old genetic bottleneck

Molecular Biology and Evolution

Volumn 25, Issue 4, 2008, Pages 655-663

  Paape, Timothy ^a   Igic, Boris ^b   Smith, Stacey D ^c   Olmstead, Richard ^d   Bohs, Lynn ^e   Kohn, Joshua R ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^c DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

^e UNIVERSITY OF UTAH   (United States)

Author keywords

Balancing selection; Genetic bottleneck; S locus; Self incompatibility; Shared ancestral polymorphism; Solanaceae

Indexed keywords

ALLELE; ANGIOSPERM; ARTICLE; BAYES THEOREM; CLADISTICS; DNA SEQUENCE; FLOWERING; FOSSIL; GENE LOCUS; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; MOLECULAR CLOCK; NONHUMAN; PHYSALIS; PLANT GENETICS; TAXON; WITHERINGIA;

ALLELES; BAYES THEOREM; CALIBRATION; CHLOROPLASTS; EVOLUTION, MOLECULAR; FOSSILS; GENES, PLANT; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; SOLANACEAE; SPECIES SPECIFICITY; TIME FACTORS; VARIATION (GENETICS);

MAGNOLIOPHYTA; PHYSALIS; SOLANACEAE; WITHERINGIA;

EID: 40849102508     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn016     Document Type: Article

References (67)

1. Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr. 19:716-716.
2. Anderson GJ, Bernardello G, Opel MR, Santos-Guera M, Anderson M. 2006. Reproductive biology of the dioecious Canary Islands endemic Withania aristata (Solanaceae). Am J Bot. 93:1295-1305.
3. Benton MJ. 1993. The fossil record 2. London: Chapman & Hall.
4. Bergelson J, Kreitman M, Stahl EA, Tian D. 2001. Evolutionary dynamics of plant R-genes. Science. 292:2281-2285.
5. Castric V, Vekemans X. 2004. Plant self-incompatibility in natural populations: a critical assessment of recent theoretical and empirical advances. Mol Ecol. 13:2873-2889.
6. Clark AG. 1993. Evolutionary inferences from molecular characterization of self-incompatibility alleles. In: Takahata N, Clark AG, editors. Mechanisms of molecular evolution: introduction tomolecular paleopopulation biology. Sunderland (MA): Sinauer Associates. p. 79-108.
7. de Groot NG, Otting N, Doxiadis GG, Balla-Jhagjhoorsingh SS, Heeney JL, van Rood JJ, Gagneux P, Bontrop RE. 2002. Evidence for an ancient selective sweep in the MHC class I gene repertoire of chimpanzees. Proc Natl Acad Sci USA. 99:11748-11753.
8. de Nettancourt D. 1977. Incompatibility in angiosperms. Berlin: Springer.
9. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:699-710.
10. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
11. Felsenstein J. 1988. Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet. 22:521-565.
12. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 41:95-98.
13. Hasegawa M, Kishino Y, Yano Y. 1985. Dating of the humanape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160-174.
14. Igic B, Bohs L, Kohn JR. 2004. Historical inferences from the self-incompatibility locus. New Phytol. 161:97-105.
15. Igic B, Bohs L, Kohn JR. 2006. Ancient polymorphism reveals unidirectional breeding system shifts. Proc Natl Acad Sci USA. 103:1359-1363.
16. Igic B, Kohn JR. 2001. Evolutionary relationships among self-incompatibility RNases. Proc Nat Acad Sci. 98:13167-13171.
17. Igic B, Lande R, Kohn JR. 2008. Loss of self-incompatibility and its evolutionary consequences. Int J Plant Sci. 169:93-104.
18. Igic B, Smith WA, Robertson KA, Schaal BA, Kohn JR. 2007. Studies of self-incompatibility in wild tomatoes: I. S-allele diversity in Solanum chilense Dun. (Solanaceae). Heredity. 99:553-561.
19. Ioerger TR, Clark AG, Kao T-h. 1990. Polymorphism at the self-incompatibility locus in Solanaceae predates speciation. Proc Natl Acad Sci USA. 87:9732-9735.
20. Ioerger TR, Gohlke JR, Xu B, Kao T-h. 1991. Primary structural features of the self-incompatibility protein in Solanaceae. Sex Plant Reprod. 4:81-87.
21. Kaul MK, Kumar A, Sharma A. 2005. Reproductive biology of Withania somnifera (L.) Dunal. Curr Sci. 1375-1377.
22. Klein J, Satta Y, O'hUigin C, Takahata N. 1993. The molecular descent of the major histocompatibility complex. Annu Rev Immunol. 11:269-295.
23. Lawrence MJ. 2000. Population genetics of the homomorphic self-incompatibility polymorphisms in flowering plants. Ann Bot. 85:221-226.
24. Levin RA, Miller JS. 2005. Relationships within tribe Lycieae (Solanaceae): paraphyly of Lycium and multiple origins of gender dimorphism. Am J Bot. 92:2044-2053.
25. Levin RA, Shak JR, Miller JS, Bernardello G, Venter AM. 2007. Evolutionary relationships in tribe Lycieae (Solanaceae). Acta Hort. 745:225-239.
26. Lu Y. 2001. Roles of lineage sorting and phylogenetic relationship in the genetic diversity at the self-incompatibility locus of Solanaceae. Heredity. 86:195-205.
27. Magallón S, Crane PR, Herendeen PS. 1999. Phylogenetic pattern, diversity, and diversification of eudicots. Ann Mo Bot Gard. 86:297-372.
28. McClure BA. 2006. New views of S-RNase-based self-incompatibility. Curr Opin Plant Biol. 9:639-646.
29. McClure BA, Haring V, Ebert PR, Anderson MA, Simpson RJ, Sakiyama F, Clarke AE. 1989. Style self-incompatibility gene products of Nicotiana alata are ribonucleases. Nature. 342:955-957.
30. Miller JS, Levin RA, Feliciano NM. Forthcoming. 2008. A tale of two continents: Baker's rule and the maintenance of self-incompatibility in Lycium (Solanaceae). Evolution.
31. Muirhead CA, Glass NA, Slatkin M. 2002. Multilocus self-recognition systems in fungi as a cause of trans-species polymorphism. Genetics. 161:633-641.
32. Olmstead RG, Bohs L, Abdel Magid H, Santiago-Valentin E, Collier SM, Garcia VF. Forthcoming. A molecular phylogeny of the Solanaceae. Taxon.
33. Olmstead RG, Sweere JA. 1994. Combining data in phylogenetic systematics: an empirical approach using three molecular data sets in the Solanaceae. Syst Biol. 43:467-481.
34. Palmer JD. 1991. Plastid chromosome: structure and evolution. In: Bogorad L, Vasil IK, editors. The molecular biology of plastids. San Diego (CA): Academic Press. p. 5-53.
35. Posada D, Crandall KA. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics. 14:817-818.
36. Rambaut A. 1996. Se-Al: sequence alignment editor [Internet]. Available from: http://evolve.zoo.ox.ac.uk/
37. Rambaut A. 2006. FigTree [Internet]. Available from:http://evolve.zoo.ox. ac.uk/software/figtree Rambaut A, Drummond AJ. 2004. Tracer. Version 1.1 [computer program] [Internet]. Available from: http://evolve.zoo.ox.ac.uk/ software.html?id5tracer
38. Richman AD. 2000. Evolution of balanced genetic polymorphism. Mol Ecol. 9:1953-1963.
39. Richman AD, Kao T-h, Schaeffer SW, Uyenoyama MK. 1995. S-allele sequence diversity in natural populations of Solanum carolinense (Horsenettle). Heredity. 75:405-415.
40. Richman AD, Kohn JR. 1999. Self-incompatibility alleles from Physalis: implications for historical inference from balanced genetic polymorphisms. Proc Natl Acad Sci USA. 96:168-172.
41. Richman AD, Kohn JR. 2000. Evolutionary genetics of self-incompatibility in the Solanaceae. Plant Mol Biol. 42:169-179.
42. Richman AD, Uyenoyama MK, Kohn JR. 1996a. S-allele diversity in a natural population of ground cherry Physalis crassifolia (Solanaceae) assessed by RT-PCR. Heredity. 76:497-505.
43. Richman AD, Uyenoyama MK, Kohn JR. 1996b. Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae. Science. 273:1212-1216.
44. Rick CM, Chetelat R. 1991. The breakdown of self-incompatibility in Lycopersicon hirsutum. In: Hawkes L, Nee M, Estrada N, editors. Solanaceae III: taxonomy, chemistry, evolution. Richmond (United Kingdom): Royal Botanic Gardens Kew and Linnean Society of London. p. 253-256.
45. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572-1574.
46. Savage AE, Miller JS. 2006. Gametophytic self-incompatibility in Lycium parishii (Solanaceae): allelic diversity, genealogical structure, and patterns of molecular evolution. Heredity. 96:434-444.
47. Schnabel A, Wendell JF. 1998. Cladistic biogeography of Gleditsia (Leguminosae) based on ndhF and rpl16 chloroplast gene sequences. Am J Bot. 85:1753-1765.
48. Smith SD, Baum DA. 2006. Floral diversification and pollination biology for the Andean clade Iochrominae (Solanaceae). Am J Bot. 98:1140-1153.
49. Smith SD, Baum DA. 2007. Systematics of Iochrominae (Solanaceae): patterns in floral diversity and interspecific crossability. Acta Hort. 745:241-254.
50. Steinbachs JE, Holsinger KE. 2002. S-RNase-mediated gametophytic self-incompatibility is ancestral in eudicots. Mol Biol Evol. 19:825-829.
51. Stephan W, Langley CH. 1998. DNA Polymorphism in Lycopersicon and crossing-over per physical length. Genetics. 150:1585-1593.
52. Stone JL. 2002. Molecular mechanisms underlying the breakdown of gametophytic self-incompatibility. Q Rev Biol. 77:17-32.
53. Stone JL. 2004. Sheltered load associated with S-alleles in Solanum carolinense. Heredity. 92:335-342.
54. Stone JL, Pierce SE. 2005. Rapid recent radiation of S-RNase lineages in Witheringia solanacea (Solanaceae). Heredity. 94:547-555.
55. Swofford DL. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland (MA): Sinauer Associates.
56. Takahata N. 1990. A simple genealogical structure of strongly balanced allelic lines and trans-species evolution of polymorphism. Proc Natl Acad Sci USA. 87:2419-2423.
57. Takahata N, Clark AG. 1993. Mechanisms of molecular evolution: introduction to molecular paleopopulation biology. Sunderland (MA): Sinauer Associates.
58. Thorne JL, Kishino H. 2002. Divergence time estimation and rate evolution with multilocus data sets. Syst Biol. 51:689-702.
59. Thorne JL, Kishino H, Painter IS. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol Bio Evol. 15:1647-1657.
60. Uyenoyama MK. 1997. Genealogical structure among alleles regulating self-incompatibility in natural populations of flowering plants. Genetics. 147:1389-1400.
61. Uyenoyama MK. 2003. Genealogy dependent viability among self-incompatibility genotypes. Theor Popul Biol. 63:281-293.
62. Vekemans X, Slatkin M. 1994. Gene and allelic genealogies at a gametophytic self-incompatibility locus. Genetics. 137:1157-1165.
63. Wang Y, Wang X, McCubbin AG, Kao T-h. 2003. Genetic mapping and molecular characterization of the self-incompatibility (S) locus in Petunia inflata. Plant Mol Biol. 53:565-580.
64. Wikström N, Savolainen V, Chase MW. 2001. Evolution of the angiosperms: calibrating the family tree. Proc R Soc B. 268:2211-2220.
65. Wright S. 1939. The distribution of self-sterility alleles in populations. Genetics. 24:538-552.
66. Xue Y, Carpenter R, Dickinson HG, Coen ES. 1996. Origin of allelic diversity in Antirrhinum S locus RNases. Plant Cell. 8:805-814.
67. Yang Z. 2006. Molecular clock and species divergence times in computational molecular evolution. Oxford (UK): Oxford University Press. p. 248-258.