Polymorphism and divergence in two willow species, Salix viminalis L. and Salix schwerinii E. wolf

G3: Genes, Genomes, Genetics

Volumn 1, Issue 5, 2011, Pages 387-400

  Berlin, Sofia ^a   Fogelqvist, Johan ^a,b   Lascoux, Martin ^c   Lagercrantz, Ulf ^b   Rönnberg Wästljung, Ann Christin ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

^c MAX PLANCK INSTITUTE   (Germany)

Author keywords

Gene flow; Linkage disequilibrium; Nucleotide polymorphism; Salix; Species divergence

Indexed keywords

EID: 84874251121     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.111.000539     Document Type: Article

References (56)

1. Alström-Rapaport, C., M. Lascoux, and U. Gullberg, 1997 Sex determination and sex ratio in the dioecious shrub Salix viminalis L. Theor. Appl. Genet. 94: 493-497.
2. Becquet, C., and M. Przeworski, 2009 Learning about modes of speciation by computational approaches. Evolution 63: 2547-2562.
3. Berlin, S., U. Lagercrantz, S. von Arnold, T. Öst, and A. C. Rönnberg-Wästljung, 2010 High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus. BMC Genomics 11: 129.
4. Blum, M. G. B., and O. Francois, 2010 Non-linear regression models for Approximate Bayesian Computation. Stat. Comput. 20: 63-73.
5. Brubaker, L. B., P. M. Anderson, M. E. Edwards, and A. V. Lozhkin, 2005 Beringia as a glacial refugium for boreal trees and shrubs: new perspectives from mapped pollen data. J. Biogeogr. 32: 833-848.
6. Darwin, C., 1865 Darwin to M. E. Wichura, 3 Feb 1865 [letter 4675a]. Darwin Correspondence Database. Available at: www.darwinproject.ac. uk/entry-4765a. Accessed: 11/07/2010.
7. Evanno, G., S. Regnaut, and J. Goudet, 2005 Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611-2620.
8. Excoffier, L., G. Laval, and S. Schneider, 2005 Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1: 47-50.
9. Frisse, L., R. R. Hudson, A. Bartoszewicz, J. D. Wall, J. Donfack et al., 2001 Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet. 69: 831-843.
10. Gilchrist, E. J., G. W. Haughn, C. C. Ying, S. P. Otto, J. Zhuang et al., 2006 Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol. Ecol. 15: 1367-1378.
11. Hanley, S., A. Barker, W. Van Ooijen, C. Aldam, L. Harris et al., 2002 A genetic linkage map of willow (Salix viminalis) based on AFLP and microsatellite markers. Theor. Appl. Genet. 105: 1087-1096.
12. Hanley, S. J., M. D. Mallott, and A. Karp, 2007 Alignment of a Salix linkage map to the Populus genomic sequence reveals macrosynteny between willow and poplar genomes. Tree Genet. Genomes 3: 35-48.
13. Hill, W. G., and A. Robertson, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38: 226-231.
14. Hill, W. G., and B. S. Weir, 1988 Variances and covariances of squared linkage disequilibria in finite populations. Theor. Popul. Biol. 33: 54-78.
15. Hudson, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
16. Hudson, R. R., and J. A. Coyne, 2002 Mathematical consequences of the genealogical species concept. Evolution 56: 1557-1565.
17. Ingvarsson, P. K., 2005 Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics 169: 945-953.
18. Ingvarsson, P. K., 2008 Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics 180: 329-340.
19. Karp, A., S. J. Hanley, S. O. Trybush, W. Macalpine, M. Pei et al., 2011 Genetic improvement of willow for bioenergy and biofuels. J. Integr. Plant Biol. 53: 151-165.
20. Kehl, A., G. Aas, and G. Rambold, 2008 Genotypical and multiple phenotypical traits discriminate Salix x rubens Schrank clearly from its parent species. Plant Syst. Evol. 275: 169-179.
21. Keller, S. R., M. S. Olson, S. Silim, W. Schroeder, and P. Tiffin, 2010 Genomic diversity, population structure, and migration following rapid range expansion in the Balsam Poplar, Populus balsamifera. Mol. Ecol. 19: 1212-1226.
22. Kim, S., V. Plagnol, T. T. Hu, C. Toomajian, R. M. Clark et al., 2007 Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 39: 1151-1155.
23. Larsson, G., and B. Bremer, 1991 Korgviden -nyttoväxter förr och nu. Sven. Bot. Tidskr. 85: 185-200.
24. Lascoux, M., J. Thorsen, and U. Gullberg, 1996 Population structure of a riparian willow species, Salix viminalis L. Genet. Res. 68: 45-54.
25. Librado, P., and J. Rozas, 2009 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
26. Mueller, J. C., 2004 Linkage disequilibrium for different scales and applications. Brief. Bioinform. 5: 355-364.
27. Nei, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
28. Olson, M. S., A. L. Robertson, N. Takebayashi, S. Silim, W. R. Schroeder et al., 2010 Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera). New Phytol. 186: 526-536.
29. Ossowski, S., K. Schneeberger, J. I. Lucas-Lledo, N. Warthmann, R. M. Clark et al., 2010 The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94.
30. Peeters, L., and O. Totland, 1999 Wind to insect pollination ratios and floral traits in five alpine Salix species. Can. J. Bot. 77: 556-563.
31. Petit, R. J., and L. Excoffier, 2009 Gene flow and species delimitation. Trends Ecol. Evol. 24: 386-393.
32. Pritchard, J. K., and M. Przeworski, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
33. Pritchard, J. K., M. Stephens, and P. Donnelly, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
34. Reich, D. E., M. Cargill, S. Bolk, J. Ireland, P. C. Sabeti et al., 2001 Linkage disequilibrium in the human genome. Nature 411: 199-204.
35. Rönnberg-Wästljung, A. C., C. Glynn, and M. Weih, 2005 QTL analyses of drought tolerance and growth for a Salix dasyclados x Salix viminalis hybrid in contrasting water regimes. Theor. Appl. Genet. 110: 537-549.
36. Rönnberg-Wästljung, A. C., V. Tsarouhas, V. Semerikov, and U. Lagercrantz, 2003 A genetic linkage map of a tetraploid Salix viminalis x S. dasyclados hybrid based on AFLP markers. For. Genet. 10: 185-194.
37. Siol, M., S. I. Wright, and S. C. Barrett, 2010 The population genomics of plant adaptation. New Phytol. 188: 313-332.
38. Skvortsov, A. K., 1968 Willows of the USSR and Adjacent Lands. Multilingual Service Division, Bureau No. 125754, Ottawa, Canada.
39. Stephens, M., and P. Donnelly, 2003 A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet. 73: 1162-1169.
40. Stephens, M., N. J. Smith, and P. Donnelly, 2001 A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68: 978-989.
41. Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
42. Tamura, K., J. Dudley, M. Nei, and S. Kumar, 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599.
43. Thompson, J. D., D. G. Higgins, and T. J. Gibson, 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
44. Thornton, K., 2003 Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
45. Triest, L., L. Q. Trung, A. K. M. M. H. Talukder, and K. Van Puyvelde, 2009 Nuclear cyp73 intron fragment length polymorphism supports morphological analysis of Salix species and hybrids. Plant Biosyst. 143: 555-563.
46. Tsarouhas, V., U. Gullberg, and U. Lagercrantz, 2002 An AFLP and RFLP linkage map and quantitative trait locus (QTL) analysis of growth traits in Salix. Theor. Appl. Genet. 105: 277-288.
47. Tsarouhas, V., U. Gullberg, and U. Lagercrantz, 2003 Mapping of quantitative trait loci controlling timing of bud flush in Salix. Hereditas 138: 172-178.
48. Tsarouhas, V., U. Gullberg, and U. Lagercrantz, 2004 Mapping of quantitative trait loci (QTLs) affecting autumn freezing resistance and phenology in Salix. Theor. Appl. Genet. 108: 1335-1342.
49. Tuskan, G. A., S. Difazio, S. Jansson, J. Bohlmann, I. Grigoriev et al., 2006 The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
50. Ueno, N., Y. Suyama, and K. Seiwa, 2007 What makes the sex ratio femalebiased in the dioecious tree Salix sachalinensis? J. Ecol. 95: 951-959.
51. Untergasser, A., H. Nijveen, X. Rao, T. Bisseling, R. Geurts et al., 2007 Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 35: W71-74.
52. Voight, B. F., A. M. Adams, L. A. Frisse, Y. Qian, R. R. Hudson et al., 2005 Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc. Natl. Acad. Sci. USA 102: 18508-18513.
53. Watterson, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
54. Weih, M., A. C. Rönnberg-Wästljung, and C. Glynn, 2006 Genetic basis of phenotypic correlations among growth traits in hybrid willow (Salix dasyclados x S. viminalis) grown under two water regimes. New Phytol. 170: 467-477.
55. Wichura, M. E., 1865 Die Bastardbefruchtung im Pflanzenreich erläutert an den Bastarden der Weiden. Verlag von E Morgenstern, Breslau.
56. Xia, X., and Z. Xie, 2001 DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92: 371-373.