Patterns of genetic diversity and candidate genes for ecological divergence in a homoploid hybrid sunflower, Helianthus anomalus

Molecular Ecology

Volumn 16, Issue 23, 2007, Pages 5017-5029

  Sapir, Yuval ^a,b   Moody, Michael L ^b   Brouillette, Larry C ^c   Donovan, Lisa A ^c   Rieseberg, Loren H ^b,d  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^b INDIANA UNIVERSITY   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Ecological divergence; EST based microsatellite markers; Homoploid hybrid speciation; Natural selection

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; EXPRESSED SEQUENCE TAG; GENE; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; HYBRIDIZATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SPECIES DIFFERENTIATION; SUNFLOWER;

BIODIVERSITY; EXPRESSED SEQUENCE TAGS; GENES, PLANT; GENETIC SPECIATION; GENOTYPE; HELIANTHUS; HYBRIDIZATION, GENETIC; MICROSATELLITE REPEATS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; SELECTION (GENETICS); VARIATION (GENETICS);

HELIANTHUS; HELIANTHUS ANOMALUS;

EID: 36349004877     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03557.x     Document Type: Article

References (77)

1. Aldrich PR, Hamrick JL, Chavarriaga P, Kochert G (1998) Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera. Molecular Ecology, 7, 933 944.
2. Altschul SF, Madden TL, Schäffer AA et al 1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389 3402.
3. Anderson E (1949) Introgressive Hybridization. John Wiley, New York.
4. Arnold ML (2006) Evolution Through Genetic Exchange. Oxford University Press, Oxford.
5. Barton NH (2001) The role of hybridization in evolution. Molecular Ecology, 10, 551 568.
6. ST tell us? Trends in Ecology and Evolution, 20, 435 440.
7. Brouillette LC, Gebremedhin DM, Donovan LA (2006) Testing hypothesized evolutionary shifts toward stress tolerance in hybrid Helianthus species. West North American Naturalist, 66, 409 419.
8. Buerkle CA, Morris RJ, Asmussen MA, Rieseberg LH (2000) The likelihood of homoploid hybrid speciation. Heredity, 84, 441 451.
9. Burke JM, Tang S, Knapp SJ, Rieseberg LH (2002) Genetic analysis of sunflower domestication. Genetics, 161, 1257 1267.
10. Coyne JA, Orr HA (2004) Speciation. Sinauer Associates, Sunderland, MA.
11. Dieringer D, Schlötterer C (2003) microsatellite analyser (msa): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167 169.
12. Dieringer D, Nolte V, Schlötterer C (2005) Population structure in African Drosophila melanogaster revealed by microsatellite analysis. Molecular Ecology, 14, 563 573.
13. Don R, Cox P, Wainwright B, Baker K, Mattick J (1991) Touchdown PCR to circumvent spurious priming during gene amplification. Nucleic Acids Research, 19, 4008 4008.
14. Edelist C, Lexer C, Dillmann C, Sicard D, Rieseberg LH (2006) Microsatellite signature of ecological selection for salt tolerance in a wild sunflower hybrid species, Helianthus paradoxus. Molecular Ecology, 15, 4623 4634.
15. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
16. Farazi TA, Waksman G, Gordon JI (2001) The biology and enzymology of protein N-Myristoylation. Journal of Biological Chemistry, 276, 39501 39504.
17. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915 925.
18. Grant V (1981) Plant Speciation, 2nd edn. Columbia University Press, New York.
19. Gross BL, Rieseberg LH (2005) The ecological genetics of homoploid hybrid speciation. Journal of Heredity, 96, 241 252.
20. Harr B, Kauer M, Schlötterer C (2002) Hitchhiking mapping: a population-based fine-mapping strategy for adaptive mutations in Drosophila melanogaster. Proceedings of the National Academy of Sciences, USA, 99, 12949 12954.
21. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution, 59, 1633 1638.
22. Hoekstra HE, Hirschmann RJ, Bundey RA, Insel PA, Crossland JP (2006) A single amino acid mutation contributes to adaptive beach mouse color pattern. Science, 313, 101 104.
23. Hulo N, Bairoch A, Bulliard V et al 2006) The prosite database. Nucleic Acids Research 34 (Database Issue), D227 D230.
24. Ishitani M, Liu J, Halfter U et al 2000) SOS3 function in plant salt tolerance requires N-myristoylation and calcium binding. Plant Cell, 12, 1667 1677.
25. Kim Y, Stephan W (2002) Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics, 160, 765 777.
26. Lai Z, Nakazato T, Salmaso M et al 2005) Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species. Genetics, 171, 291 303.
27. Lexer C, Welch ME, Raymond O, Rieseberg LH (2003) The origin of ecological divergence in Helianthus paradoxus (Asteraceae): Selection on transgressive characters in a novel hybrid habitat. Evolution, 57, 1989 2000.
28. Ludwig F, Rosenthal DM, Johnston JA et al 2004) Selection on leaf ecophysiological traits in a desert hybrid Helianthus species and early-generation hybrids. Evolution, 58, 2682 2692.
29. Maddison D, Maddison W (2000) Macclade 4: Analysis of Phylogeny and Character Evolution, Version 4. Sinauer Associates, Sunderland, MA.
30. Maurer-Stroh S, Eisenhaber B, Eisenhaber F (2002) N-terminal N-Myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. Journal of Molecular Biology, 317, 523 540.
31. Maynard-Smith J, Haigh J (1974) The hitch-hiking effect of a favorable gene. Genetical Research, 23, 23 35.
32. McCarthy EM, Asmussen MA, Anderson WW (1995) A theoretical assessment of recombinational speciation. Heredity, 74, 502 509.
33. McDaniel SF, Shaw AJ (2005) Selective sweeps and intercontinental migration in the cosmopolitan moss Ceratodon purpureus (Hedw.) Brid. Molecular Ecology, 14, 1121 1132.
34. Moran MD (2003) Arguments for rejecting the sequential Bonferroni in ecological studies. Oikos, 100, 403 405.
35. Morjan CL, Rieseberg LH (2004) How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles. Molecular Ecology, 13, 1341 1356.
36. Muir G, Schlötterer C (2005) Evidence for shared ancestral polymorphism rather than recurrent gene flow at microsatellite loci differentiating two hybridizing oaks (Quercus spp.). Molecular Ecology, 14, 549 561.
37. Nalefski EA, Falke JJ (1996) The C2 domain calcium-binding motif: Structural and functional diversity. Protein Science, 5, 2375 2390.
38. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution, 3, 418 426.
39. Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, Oxford.
40. Nei M, Li W-H (1979) Mathematical model for studying genetic variation in terms of restriction nucleases. Proceedings of the National Academy of Sciences, USA, 76, 5269 5273.
41. Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148, 929 936.
42. Ohta T, Kimura M (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genetical Research, 22, 201 204.
43. Orr HA, Coyne JA (1992) The genetics of adaptation: a reassessment. American Naturalist, 140, 725 742.
44. Peakall R, Smouse PE (2006) GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288 295.
45. Rice WR (1989) Analyzing tables of statistical tests. Evolution, 43, 223 225.
46. Rieseberg LH (1991) Homoploid reticulate evolution in Helianthus (Asteraceae): evidence from ribosomal genes. American Journal of Botany, 78, 1218 1237.
47. Rieseberg LH (1997) Hybrid origins of plant species. Annual Review of Ecology and Systematics, 28, 359 389.
48. Rieseberg LH, Raymond O, Rosenthal DM et al 2003) Major ecological transitions in wild sunflowers facilitated by hybridization. Science, 301, 1211 1216.
49. Rosenthal DM, Schwarzbach AE, Donovan LA, Raymond O, Rieseberg LH (2002) Phenotypic differentiation between three ancient hybrid taxa and their parental species. International Journal of Plant Sciences, 163, 387 398.
50. Rosenthal DM, Rieseberg LH, Donovan LA (2005) Re-creating ancient hybrid species' complex phenotypes from early-generation synthetic hybrids: three examples using wild sunflowers. American Naturalist, 166, 26 41.
51. Rost B, Yachdav G, Liu J (2003) The PredictProtein Server. Nucleic Acids Research, 32 (Web Server Issue), W321 W326.
52. Rozas JS, Ánchez-Delbarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
53. Sáez AG, Tatarenkov A, Barrio E, Becerra NH, Ayala FJ (2003) Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: Unraveling the footprint of a recent selective sweep. Proceedings of the National Academy of Sciences, USA, 100, 1793 1798.
54. Schlötterer C (2002) A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics, 160, 753 763.
55. Schlötterer C, Dieringer D (2005) A novel test statistic for the identification of local selective sweeps based on microsatellite gene diversity. In : Selective Sweep (ed. Nurminsky D pp. 55 64. Landes Bioscience, Georgetown, TX.
56. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18, 233 234.
57. Schwarzbach AE, Rieseberg LH (2002) Likely multiple origins of a diploid hybrid sunflower species. Molecular Ecology, 11, 1703 1715.
58. Schwarzbach AE, Donovan LA, Rieseberg LH (2001) Transgressive character expression in a hybrid sunflower species. American Journal of Botany, 88, 270 277.
59. Song B-H, Clauss MJ, Pepper A, Mitchell-Olds T (2006) Geographic patterns of microsatellite variation in Boechera stricta, a close relative of Arabidopsis. Molecular Ecology, 15, 357 369.
60. Storz JF (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology, 14, 671 688.
61. Suzuki Y, Gojobori T (1999) A method for detecting positive selection at single amino acid sites. Molecular Biology and Evolution, 16, 1315 1328.
62. Swofford D (2000) Phylogenetic Analysis Using Parsimony, Version 4.0. Sinauer Associates, Sunderland, MA.
63. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585 595.
64. Tang SYuJK, Slabaugh MB, Shintani DK, Knapp SJ (2002) Simple sequence repeat map of the sunflower genome. Theoretical and Applied Genetics, 105, 1124 1136.
65. The Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nature Genetics, 25, 25 29.
66. The InterPro Consortium (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research, 29, 37 40.
67. Towler DA, Gordon JI, Adams SP, Glaser L (1988) The biology and enzymology of eukaryotic protein acylation. Annual Review of Biochemistry, 57, 69 99.
68. Ungerer MC, Baird SJE, Pan J, Rieseberg LH (1998) Rapid hybrid speciation in wild sunflowers. Proceedings of the National Academy of Sciences, USA, 95, 11757 11762.
69. Vigouroux Y, Jaqueth JS, Matsuoka Y et al 2002) Rate and pattern of mutation at microsatellite loci in maize. Molecular Biology and Evolution, 19, 1251 1260.
70. de Vries JS, Andriotis VM, Wu AJ, Rathjen JP (2006) Tomato Pto encodes a functional N-myristoylation motif that is required for signal transduction in Nicotiana benthamiana. Plant Journal, 45, 31 45.
71. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358 1370.
72. Wiehe T, Nolte V, Zivkovic D, Schlötterer C (2007) Identification of Selective Sweeps Using a Dynamically Adjusted Number of Linked Microsatellites. Genetics, 175, 207 218.
73. Wong W, Goldman N, Nielsen R (2004) Accuracy and Power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics, 168, 1041 1051.
74. Yang Z (2000) Phylogenetic Analysis by Maximum Likelihood (PAML), Version 3.14. University College, London.
75. Yang Z, Nielsen R, Goldman N, Pedersen A-M (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 155, 431 449.
76. Yatabe Y, Kane NC, Scotti-Saintagne C, Rieseberg LH (2007) Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, Helianthus annuus and H. petiolaris. Genetics, 175, 1883 1893.
77. Zdobnov EM, Apweiler R (2001) InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847 848.