Extending coalescent theory to autotetraploids

Genetics

Volumn 192, Issue 1, 2012, Pages 195-204

  Arnold, B ^a   Bomblies, K ^a   Wakeley, J ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOTETRAPLOID; COALESCENT SIMULATION; DNA SEQUENCE; HAPLOIDY; HUMAN; INHERITANCE; POLYPLOIDY; POPULATION; PRIORITY JOURNAL; SIMULATION; TETRASOMY;

BASE SEQUENCE; EVOLUTION, MOLECULAR; GENETIC VARIATION; MARKOV CHAINS; MODELS, GENETIC; TETRAPLOIDY;

EID: 84866100854     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.140582     Document Type: Article

References (80)

1. Bever, J., and F. Felber, 1992 The theoretical population genetics of autopolyploids. Oxf. Surv. Evol. Biol. 8: 185-217.
2. Butruille, D. V., and L. S. Boiteux, 2000 Selection-mutation balance in polysomic tetraploids: impact of double reduction and gametophytic selection on the frequency and subchromosomal localization of deleterious mutations. Proc. Natl. Acad. Sci. USA 97: 6608-6613.
3. Cannings, C., 1974 The latent roots of certain Markov chains arising in genetics: a new approach. I. Haploid models. Adv. Appl. Probab. 6: 260-290.
4. Ciu, L., P. K. Wall, J. H. Leebens-Mack, B. G. Lindsay, D. E. Soltis et al., 2006 Widespread genome duplications throughout the history of flowering plants. Genome Res. 16: 738-749.
5. Comai, L., 2005 The advantages and disadvantages of being polyploidy. Nat. Rev. Genet. 6: 836-846.
6. Crow, J. F., 1954 Random mating with linkage in polysomics. Am. Nat. 88: 431-434.
7. Ewing, G., and J. Hermisson, 2010 MSMS: a coalescent simulation program including recombination, demographic structure, and selection at a single locus. Bioinformatics 26: 2064-2065.
8. Felber, F., and J. Bever, 1997 Effect of triploid fitness on the coexistence of diploids and tetraploids. Biol. J. Linn. Soc. Lond. 60: 95-106.
9. Gallardo, M., J. Bickham, R. Honeycutt, R. Ojeda, and N. Köhler, 1999 Discovery of tetraploidy in a mammal. Nature 401: 341.
10. Grant, V., 1981 Plant Speciation. Columbia University Press, New York.
11. Gregory, T. R., and B. K. Mable, 2005 Polyploidy in animals, pp. 427-517 in The Evolution of the Genome, edited by T. R. Gregory. Elsevier, San Diego.
12. Grinstead, C. M., and J. L. Snell, 1997 Introduction to Probability, Ed. 2. American Mathematical Society, Providence, RI.
13. Haldane, J., 1930 Theoretical genetics of autopolyploids. J. Genet. 22: 359-372.
14. Hudson, R., 1983 Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23: 183-201.
15. Hudson, R., 2002 Generating samples under a Wright-Fisher neutral model. Bioinformatics 18: 337-338.
16. Husband, B., 2004 The role of triploid hybrids in the evolutionary dynamics of mixed-ploidy populations. Biol. J. Linn. Soc. Lond. 82: 537-546.
17. Jørgensen, M., D. Ehrich, R. Schmickl, M. Koch, and A. Brysting, 2011 Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae). BMC Evol. Biol. 11: 346.
18. Kingman, J. F. C., 1982a The coalescent. Stoch. Proc. Appl. 13: 235-248.
19. Kingman, J. F. C., 1982b On the genealogy of large populations. J. Appl. Probab. 19A: 27-43.
20. Leggatt, R. A., and G. K. Iwama, 2003 Occurrence of polyploidy in the fishes. Rev. Fish Biol. Fish. 13: 237-246.
21. Li, H., and R. Durbin, 2011 Inference of human population history form individual whole-genome sequences. Nature 475: 493-496.
22. Luo, Z. W., Z. Zhang, R. Zhang, M. Pandey, O. Gailing et al., 2006 Modeling population genetic data in autotetraploid species. Genetics 172: 639-646.
23. Masterson, J., 1994 Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms. Science 264: 421-424.
24. Mather, K., 1935 Reductional and equational separation of the chromosomes in bivalents and multivalents. J. Genet. 30: 53-78.
25. Mather, K., 1936 Segregation and linkage in autotetraploids. J. Genet. 32: 287-314.
26. Möhle, M., 1998a A convergence theorem for Markov chains arising in population genetics and the coalescent with selfing. Adv. Appl. Probab. 30: 493-512.
27. Möhle, M., 1998b Coalescent results for two-sex population models. Adv. Appl. Probab. 30: 513-520.
28. Möhle, M., 1998c Robustness results for the coalescent. J. Appl. Probab. 35: 438-447.
29. Möhle, M., and S. Sagitov, 2001 A classification of coalescent processes for haploid exchangeable population models. Ann. Appl. Probab. 29: 1547-1562.
30. Moody, M., L. Mueller, and D. Soltis, 1993 Genetic variation and random drift in autotetraploid populations. Genetics 134: 649-657.
31. Nordborg, M., and P. Donnelly, 1997 The coalescent process with selfing. Genetics 146: 1185-1195.
32. Otto, S. P., and J. Whitton, 2000 2000 Polyploid incidence and evolution. Annu. Rev. Genet. 34: 401-437.
33. Ptacek, M., H. Gerhardt, and R. Sage, 1994 Speciation by polyploidy in treefrogs: multiple origins of the tetraploid, Hyla versicolor. Evolution 48(3): 898-908.
34. Ramsey, J., and D. Schemske, 1998 Pathways, mechanisms, and rates of polyploidy formation in flowering plants. Annu. Rev. Ecol. Syst. 29: 467-501.
35. Rodriguez, D. J., 1996 A model for the establishment of polyploidy in plants. Am. Nat. 147(1): 33-46.
36. Ronfort, J., E. Jenczewski, T. Bataillon, and F. Rousset, 1998 Analysis of population structure in autotetraploid species. Genetics 150: 921-930.
37. Sexton, O., 1980 Polyploidy in animal evolution: summary, pp. 379-381 in Polyploidy, Biological Relevance, edited by W. H. Lewis. Plenum, New York.
38. Sjödin, P., I. Kaj, S. Krone, M. Lascoux, and M. Nordborg, 2005 On the meaning and existence of an effective population size. Genetics 169: 1061-1070.
39. Soltis, D. E., P. S. Soltis, and B. D. Ness, 1989 Chloroplast-DNA variation and multiple origins of autopolyploidy in Heuchera micrantha (Saxifragaceae). Evolution 43(3): 650-656.
40. Soltis, D. E., P. S. Soltis, D. W. Schemske, J. F. Hancock, J. N. Thompson et al., 2007 Autopolyploidy in angiosperms: Have we grossly underestimated the number of species? Taxon 56: 13-30.
41. Stebbins, G., 1947 Types of polyploids: their classification and significance. Adv. Genet. 1: 403-429.
42. Stebbins, G., 1950 Variation and Evolution in Plants. Columbia University Press, New York.
43. Stift, M., C. Berenos, P. Kuperus, and P. H. van Tienderen, 2008 Segregation models for disomic, tetrasomic and intermediate inheritance in tetraploids: a general procedure applied to Rorippa (yellow cress) microsatellite data. Genetics 179: 2113-2123.
44. St. Onge, K., J. Foxe, J. Li, H. Li, K. Holm et al., 2012 Coalescentbased analysis distinguishes between allo-and autopolyploid origin in Sheperd's Purse (Capsella bursa-pastoris). Mol. Biol. Evol. 29(7): 1721-1733.
45. Tajima, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
46. Tiffin, P., and B. Gaut, 2001 Sequence diversity in the tetraploid Zea perennis and the closely related diploid Z. diploperennis: insights from four nuclear loci. Genetics 158: 401-412.
47. Wakeley, J., 1999 Non-equilibrium migration in human history. Genetics 153: 1863-1871.
48. Wakeley, J., 2008 Coalescent Theory: An Introduction. Roberts, Greenwood Village, CO.
49. Wakeley, J., and N. Aliacar, 2001 Gene genealogies in a metapopulation. Genetics 159: 893-905.
50. Wolf, P., D. Soltis, and P. Soltis, 1990 Chloroplast-DNA and allozymic variation in diploid and autotetraploid Heuchera grossulariifolia (Saxifragaceae). Am. J. Bot. 77(2): 232-244.
51. Wood, T. E., N. Takebayashi, M. S. Barker, I. Mayrose, P. B. Greenspoon et al., 2009 The frequency of polyploid speciation in vascular plants. Proc. Natl. Acad. Sci. USA 106: 13875-13879.
52. Wright, S., 1938 The distribution of gene frequencies in population of polyploids. Proc. Natl. Acad. Sci. USA 24: 372-377.
53. Mandal, A.K., Ennos, R.A. and Fagg, C.W. (1994) Mating system analysis in a natural population of Acacia nilotica subspecies leiocarpa. Theor Appl Genet 89:931---935.
54. Huang, H., Dane, F., Wang, Z., Jiang, Z., Huang, R. and Wang, S. (1997) Isozyme inheritance and variation in Actinidia. Heredity 78: 328-336.
55. Rieseberg, L.H. and Doyle, M.F. (1989). Tetrasomic segregation in the naturally occurring autotetraploid Allium nevii (Alliaceae). Hereditas 111: 31---36.
56. Mable, B.K., Beland, J., and Di Berardo, C. (2004) Inheritance and dominance of self---incompatibility alleles in polyploid Arabidopsis lyrata. Heredity 93: 476---486.
57. Manton I. (1934) The problem of Biscutella laevigata L. Z. Indukt. Abstammungs---Vererbungsl. 67: 41-57.
58. Manton I. (1937) The problem of Biscutella laevigata L. II. The evidence from meisois. Ann. Bot. 1: 439-462.
59. Hardy, O.J., Vanderhoeven, S., De Loose, M. and Meerts, P. (2000) Ecological, morphological and allozymic differentiation between diploid and tetraploid knapweeds (Centaurea jacea) from a contact zone in the Belgian Ardennes. New Phytol. 146: 281---29
60. Watanabe, K. (1983) Studies on the control of diploid---like meiosis in polyploidy taxa of Chrysanthemum. Theor Appl Genet 66:9---14.
61. Bousalem, M., Arnau, G., Hochu, I., Arnolin, R., Viader, V., Santoni, S. and David, J. (2006) Microsatellite segregation analysis and cytogenetic evidence for tetrasomic inheritance in the American yam Dioscorea trifida and a new basic chromosome number in the Dioscoreae. Theor Appl Genet 113: 439---451.
62. Mosquin, T. (1967) Evidence for Autopolyploidy in Epilobium angustifolium (Onagraceae). Evolution 21: 713---719.
63. Husband, B.C. and Schemske, D.W. (1997) The Effect of Inbreeding in Diploid and Tetraploid Populations of Epilobium angustifolium (Onagraceae): Implications for the Genetic Basis of Inbreeding Depression. Evolution 51: 737---746.
64. Wolf, P.G., Soltis, P.S., and Soltis, D.E. (1989). Tetrasomic inheritance and chromosome pairing behaviour in the naturally occurring autotetraploid Heuchera grossulariifolia (Saxifragaceae). Genome 32: 655---659.
65. Soltis, D.E. and Soltis, P.S. (1989) Tetrasomic inheritance in Heuchera micrantha (Saxifragaceae). J Hered 80: 123---126.
66. Dawson, C.D.R. (1941) Tetrasomic inheritance in Lotus corniculatus L. J Genet 42: 49---73.
67. Fjellstrom, R.G., Beuselinck, P.R. and Steiner, J.J. (2001) RFLP marker analysis supports tetrasomic inheritance in Lotus corniculatus L. Theor Appl Genet 102:718---725
68. Laushman, R.H., Schnabel, A., and Hamrick, J.L. (1990). Electrophoretic Evidence for tetrasomic inheritance in the dioecious tree Maclura pomifera (Raf.) Schneid. J Hered, 87: 469---473.
69. Quiros, C.F. (1982) Tetrasomic segregation for multiple alleles in alfalfa. Genetics 101; 117---127.
70. Stein, J., Quarin, C.L., Matínez, E.J., Pessino, S.C., and Ortiz, J.P.A. (2004) Tetraploid races of Paspalum notatum show polysomic inheritance and preferential chromosome pairing around the apospory---controlling locus. Theor Appl Genet 109:186---191.
71. Pupilli, F., Caceres, M.E., Quarin, C.L. and Arcioni, S. (1997) Segregation analysis of RFLP markers reveals a tetrasomic inheritance in apomictic Paspalum simplex. Genome 40: 822---828.
72. Leinemann, L. (2000) Inheritance analysis of isozyme phenotypes in tetraploid species using single plant progenies. An example in black thorn (Prunus spinosa L.). Forest Genetics 7: 205---209.
73. Stift, M., Berenos, C., Kuperus, P. and van Tienderen, P.H. (2008) Segregation models for disomic, tetrasomic and intermediate inheritance in tetraploids: A general procedure applied to Rorippa (Yellow Cress) microsatellite data. Genetics 179: 2113---2123.
74. Brown, A.H.D. and Young, A.G. (2000) Genetic diversity in tetraploid populations of the endangered daisy Rutidosis leptorrhynchoides and implications for its conservation. Heredity 85: 122---129.
75. Landergott, U., Naciri, Y., Schneller, J.J., and Holderegger, R. (2006) Allelic configurations and polysomic inheritance of highly variable microsatellites in tetraploid gynodioecious Thymus praecox agg. Theor Appl Genet 113: 453---465.
76. Soltis, D.E. and Rieseberg, L.H. Autopolyploidy in Tolmiea menziesii (Saxifragaceae): Genetic insights from enzyme electrophoresis. Am J Bot 73: 310---318.
77. Tamari, F., Khosravi, D., Hilliker, A.J. and Shore, J.S. (2005) Inheritance of spontaneous mutant homostyles in Turnera subulata x krapovickasii and in autotetraploid T. scabra (Turneraceae). Heredity 94: 207---216.
78. Fernández, A. (1987). Estudios cromosómicos en Turnera y Piriqueta (Turneraceae). Bonplandia 6: 1---21.
79. Jelenkovic, G., and Hough, L.F. (1970). Chromosome associations in the first meiotic division in three tetraploid clones of Vaccinium corymbosum L. Can J Genet Cytol 12: 316-324.
80. Krebs, S.L. and Hancock, J.F. (1989). Tetrasomic inheritance of isoenzyme markers in the highbush blueberry Vaccinium corymbosum L. Heredity 63: 11-18.