Genetic diversity and multiple origins of polyploid Atriplex nummularia Lindl. (Chenopodiaceae)

Biological Journal of the Linnean Society

Volumn 105, Issue 1, 2012, Pages 218-230

  Sampson, Jane F ^a,b   Byrne, Margaret ^a,b  

^a Crop Variety Testing Group   (Australia)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Allopolyploid; Conservation; Genetic differentiation; Genetic risk; Hybridization; Microsatellites; Octoploid; Speciation

Indexed keywords

BAYESIAN ANALYSIS; CLUSTER ANALYSIS; CONSERVATION GENETICS; ECONOMIC ANALYSIS; GENETIC DIFFERENTIATION; GENETIC MARKER; HERB; HYBRIDIZATION; MOLECULAR ANALYSIS; PERENNIAL PLANT; POLYPLOIDY; POPULATION STRUCTURE; SPECIATION (BIOLOGY); TAXONOMY;

AUSTRALIA;

EID: 83155182552     PISSN: 00244066     EISSN: 10958312     Source Type: Journal    
DOI: 10.1111/j.1095-8312.2011.01787.x     Document Type: Article

References (64)

1. Ainouche ML, Baumel A, Salmon A, Yannic G. 2004. Hybridization, polyploidy and speciation in Spartina (Poaceae). New Phytologist 161: 165-172.
2. Albach DC. 2007. Amplified fragment length polymorphisms and sequence data in the phylogenetic analysis of polyploids: multiple origins of Veronica cymbalaria (Plantaginaceae). New Phytologist 176: 481-498.
3. Bennett MD. 2004. Perspectives on polyploidy in plants - ancient and neo. Biological Journal of the Linnean Society 82: 411-423.
4. Bruvo R, Michiels NK, D'Souza TG, Schulenburg H. 2004. A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level. Molecular Ecology 13: 2101-2106.
5. Byrne M, Hankinson M, Sampson JF, Stankowski S. 2008a. Microsatellite markers isolated from a polyploid saltbush, Atriplex nummularia Lindl. (Chenopodiaceae). Molecular Ecology Resources 8: 1426-1428.
6. Byrne M, Stone L, Millar MA. 2011. Assessing genetic risk in revegetation. Journal of Applied Ecology (in press).
7. Byrne M, Yeates DK, Joseph L, Kearney M, Bowler J, Williams MAJ, Cooper S, Donnellan SC, Keogh JS, Leys R, Melville J, Murphy DJ, Porch N, Wyrwoll K-H. 2008b. Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota. Molecular Ecology 17: 4398-4417.
8. Clark LV, Jasieniuk M. 2011. POLYSAT: an R package for polyploid microsatellite analysis. Molecular Ecology Resources 11: 562-566.
9. Dixon CJ, Schönswetter P, Suda J, Wiedermann MM, Schneeweiss GM. 2009. Reciprocal Pleistocene origin and postglacial range formation of an allopolyploid and its sympatric ancestors (Androsace adfinis group, Primulaceae). Molecular Phylogenetics and Evolution 50: 74-83.
10. Duminil J, Hardy OJ, Petit RJ. 2009. Plant traits correlated with generation time directly affect inbreeding depression and mating system and indirectly genetic structure. BMC Evolutionary Biology 9: 177.
11. Earl DA, von Holdt BM. 2011. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources (in press).
12. Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611-2620.
13. Excoffier L, Laval G, Schneider S. 2005. Arlequin ver 3.0: an integrated software package for population genetic data analysis. Evolutionary Bioinformatics Online 1: 47-50.
14. Excoffier L, Smouse P, Quattro J. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
15. Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
16. Falush D, Stephens M, Pritchard JK. 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 7: 574-578.
17. Felsenstein J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics: The International Journal of the Willi Hennig Society 5: 164-166.
18. Ferguson D, Sang T. 2001. Speciation through homoploid hybridization between allotetraploids in peonies (Paeonia). Proceedings of the National Academy of Sciences of the United States of America 98: 3915-3919.
19. Fjellheim S, Holten Jørgensen M, Kjos M, Borgen L. 2009. A molecular study of hybridization and homoploid hybrid speciation in Argyranthemum (Asteraceae) on Tenerife, the Canary Islands. Botanical Journal of the Linnean Society 159: 19-31.
20. Flores H, Davis JI. 2001. A cladistic analysis of Atripliceae (Chenopodiaceae) based on morphological data. Journal of the Torrey Botanical Society 128: 297-319.
21. Fortune PM, Schierenbeck K, Ayres D, Bortolus A, Catrice O, Brown S, Ainouche ML. 2008. The enigmatic invasive Spartina densiflora: a history of hybridizations in a polyploidy context. Molecular Ecology 17: 4304-4316.
22. Grant V. 1981. Plant speciation. New York: Columbia University Press.
23. Halverson K, Heard SB, Nason JD, Stireman JO. 2008. Origins, distribution, and local co-occurrence of polyploidy cytotypes in Solidago altissima (Asteraceae). American Journal of Botany 95: 50-58.
24. Hamrick JL, Godt MJW. 1989. Allozyme diversity in plant species. In: Brown AHD, Clegg MT, Kahler AL, Weir BS, eds. Plant Population Genetics, Breeding and Genetic Resources. Sunderland, MA: Sinauer, 43-63.
25. Hamrick JL, Godt MJW. 1996. Effects of life history traits on genetic diversity in plant species. Philosophical Transactions of the Royal Society of London Series B 351: 1291-1298.
26. Hegarty MJ, Hiscock SJ. 2005. Hybrid speciation in plants: new insights from molecular studies. New Phytologist 165: 411-423.
27. Hopper SD, Gioia P. 2004. The Southwest Australian Floristic Region: evolution and conservation of a global hot spot of biodiversity. Annual Review of Ecology, Evolution and Systematics 35: 623-650.
28. Jacobs SWL. 2000. Chenopodiaceae. In: Harden GJ, ed. Flora of New South Wales. Revised Edition 1. Sydney: New South Wales University Press, 211.
29. Jakobsson M, Rosenberg NA. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics (Oxford, England) 23: 1801-1806.
30. Jørgensen MH, Carlsen T, Skrede I, Elven R. 2008. Microsatellites resolve the taxonomy of the polyploidy Cardamine digitata aggregate (Brassicaceae). Taxon 57: 882-892.
31. 4 photosynthesis. American Journal of Botany 97: 1664-1687.
32. Kloda JM, Dean PDG, Maddren C, MacDonald DW, Mayes S. 2008. Using principal component analysis to compare genetic diversity across polyploidy levels within plant complexes: an example from British Restharrows (Ononis spinosa and Ononis repens). Heredity 100: 253-260.
33. Kosman E, Leonard KJ. 2005. Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploidy species. Molecular Ecology 14: 415-424.
34. Luttikhuizen PC, Stift M, Kuperus P, Van Tienderen PH. 2007. Genetic diversity in diploid vs. tetraploid Rorippa amphibia (Brassicaceae). Molecular Ecology 16: 3544-3553.
35. Lynch M, Milligan BG. 1994. Analysis of population genetic structure with RAPD markers. Molecular Ecology 3: 91-99.
36. McGlaughlin ME, Friar EA. 2011. Evolutionary diversification and geographical isolation in Dubautia laxa (Asteraceae), a widespread member of the Hawaiian silversword alliance. Annals of Botany 107: 357-370.
37. McKenna DJ, Bennell M, Mazanec R. 2009. Review of Atriplex nummularia (OldMan Saltbush) and its potential for domestication as a fodder plant in Australian dryland farming systems. In: Hobbs TJ, Bartle J, Bennell M, eds. Domestication Potential of High Priority Species (Acacia saligna, Atriplex nummularia and Eucalyptus rudis) for Woody Biomass Crops in Lower Rainfall southern Australia. Florasearch 3b. RIRDC Publication No. 09/043. Barton, Australia: Rural Industries Research and Development Corporation, 81-124.
38. Nei M. 1972. Genetic distance between populations. American Naturalist 106: 283-292.
39. Nobs MA. 1980. Chromosome numbers in Australian species of Atriplex. Carnegie Institute Yearbook 79: 164-169.
40. Nybom H. 2004. Comparison of different nuclear DNA markers for estimation of intraspecific genetic diversity in plants. Molecular Ecology 13: 1143-1155.
41. Obbard DJ, Harris SA, Pannell JR. 2006. Simple allelic phenotype diversity and differentiation statistics for allopolyploids. Heredity 97: 297-303.
42. Ortíz-Dorda J, Martínez-Mora C, Correal E, Simón B, Cenis JL. 2005. Genetic structure of Atriplex halimus populations in the Mediterranean Basin. Annals of Botany 95: 827-834.
43. Ostrowski MF, David J, Santoni S, Mckhann H, Reboud X, Le Corre V, Camilleri C, Brunel D, Bouchez D, Faure B, Bataillon T. 2006. Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium. Molecular Ecology 15: 1507-1517.
44. Otto SP, Whitton J. 2000. Polyploid incidence and evolution. Annual Review of Genetics 34: 401-437.
45. Palop-Esteban M, Segarra-Moragues JG, González-Candelas F. 2007. Historical and biological determinants of genetic diversity in the highly endemic triploid sea lavender Limonium dufourii (Plumbaginaceae). Molecular Ecology 16: 3814-3827.
46. Parr-Smith GA. 1982. Biogeography and evolution in the shrubby Australian species of Atriplex (Chenopodiaceae). In: Barker WR, Greenslade PJM, eds. Evolution of the Flora and Fauna of Arid Australia. Frewville, SA: Peacock Publications, 291-299.
47. Peakall R, Smouse PE. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288-295.
48. Pérez-Collazos E, Catalán P. 2006. Paleopolyploidy, spatial structure and conservation genetics of the narrow steppe plant Vella pseudocytisus subsp. paui (Vellinae, Cruciferae). Annals of Botany 97: 635-647.
49. Perrie LR, Shepherd LD, De Lange PJ, Brownsey PJ. 2010. Parallel polyploid speciation: distinct sympatric gene-pools of recurrently derived allo-octoploid Asplenium ferns. Molecular Ecology 19: 2916-2932.
50. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure from multilocus genotype data. Genetics 155: 945-959.
51. Pritchard JK, Wen X, Falush D. 2009. Documentation for structure software. Version 2.3. Available at:.
52. Rieseberg LH, Willis JH. 2007. Plant speciation. Science 317: 910-914.
53. Robertson A, Newton AC, Ennos RA. 2004. Multiple hybrid origins, genetic diversity and population genetic structure of two endemic Sorbus taxa on the Isle of Arran, Scotland. Molecular Ecology 13: 123-134.
54. Robertson A, Rich TCG, Allen AM, Houston L, Roberts C, Bridle JR, Harris SA, Hiscock SJ. 2010. Hybridization and polyploidy as drivers of continuing evolution and speciation in Sorbus. Molecular Ecology 19: 1675-1690.
55. Rosenberg NA. 2004. DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes 4: 137-138.
56. Saltonstall K. 2002. Cryptic invasion by a non-native genotype of the common reed, Phragmites australis, into North America. Proceedings of the National Academy of Sciences of the United States of America 99: 2445-2449.
57. Schwarzbach AE, Rieseberg LH. 2002. Likely multiple origins of a diploid hybrid sunflower species. Molecular Ecology 11: 1703-1715.
58. Sherman NA, Burke JM. 2009. Population genetic analysis reveals a homoploid hybrid origin of Stephanomeria diegensis (Asteraceae). Molecular Ecology 18: 4049-4060.
59. Soltis PS, Plunkett GM, Novak SJ, Soltis DE. 1995. Genetic variation in Tragopogon species: additional origins of the allotetraploids T. mirus and T. miscellus (Compositae). American Journal of Botany 82: 1329-1341.
60. Soltis PS, Soltis DE. 2000. The role of genetic and genomic attributes in the success of polyploids. Proceedings of the National Academy of Sciences of the United States of America 97: 7051-7057.
61. Soltis PS, Soltis DE. 2009. The role of hybridization in plant speciation. Annual Review of Plant Biology 60: 561-588.
62. Španiel S, Marhold K, Filová B, Zozomová-Lihová J. 2011. Genetic and morphological variation in the diploid-polyploid Alyssum montanum in Central Europe: taxonomic and evolutionary considerations. Plant Systematics and Evolution 294: 1-25.
63. Stebbins GL. 1950. Variation and Evolution in Plants. New York: Columbia University Press.
64. Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I. 2002. Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology 11: 139-151.