Contrasting microsatellite variation between subalpine and western larch, two closely related species with different distribution patterns

Molecular Ecology

Volumn 15, Issue 13, 2006, Pages 3907-3918

  Khasa, Damase P ^a   Jaramillo Correa, Juan P ^a   Jaquish, Barry ^b   Bousquet, Jean ^a  

^a UNIVERSITÉ LAVAL   (Canada)

^b RESEARCH BRANCH   (Canada)

Author keywords

Comparative population genetics; Conservation genetics; Larch; Microsatellites

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; CANADA; COMPARATIVE STUDY; EVOLUTION; GENETIC VARIABILITY; GENETICS; LARIX; POPULATION GENETICS;

BIOLOGICAL EVOLUTION; CANADA; EVOLUTION; GENETIC VARIATION; GENETICS, POPULATION; LARIX; MICROSATELLITE REPEATS; VARIATION (GENETICS);

LARIX; LARIX LYALLII; LARIX OCCIDENTALIS;

EID: 33750209510     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2006.03066.x     Document Type: Article

References (72)

1. Amarasinghe V, Carlson JE (2002) The development of microsatellite DNA markers for genetic analysis in Douglas-Fir. Canadian Journal of Forest Research, 32, 1904-1915.
2. Arno SF (1990) Alpine larch. In: Silvics of North America, Vol. 1. Agricultural Handbook, Conifers, 654, 152-159.
3. Arno SF, Habeck JR (1972) Ecology of alpine larch (Larix lyallii Parl.) in the Pacific Northwest. Ecological Monographs, 42, 417-450.
4. Barnosky CW, Anderson PM, Bartlein PJ (1987) The northwestern U.S. during deglaciation; vegetational history and paleoclimatic implications. In: North America and Adjacent Oceans During the Last Deglaciation. The Geology of North America, K-3 (eds Ruddiman WF, Wright HE Jr), pp. 289-321. Geological Society of North America, Boulder, Colorado.
5. Bouillé M, Bousquet L (2005) Trans-species shared polymorphisms at orthologous nuclear loci among distant species in the conifer Picea (Pinaceae): implications for the long-term maintenance of genetic diversity in trees. American Journal of Botany, 92, 63-73.
6. Bruno D, Brinegar C (2004) Microsatellite markers in coast redwood (Sequoia sempervirens). Molecular Ecology Notes, 4, 482-484.
7. Carlson CE (1995) Natural hybrids of western larch and alpine larch. In: Ecology and Management of Larix Forests: a Look Ahead (eds Schmidt WC, McDonald KJ), pp. 473-474. Intermountain Research Station, USDA Forest Service, General Technical Report GTR-I.
8. Casgrain P, Legendre P (2000) The R package for Multivariate and Spatial Analysis, Version 4.0. D1. User's Manual. Département des sciences biologiques. Université de Montréal, Canada. (http://www.fas. umontreal.ca/biol/legendre/).
9. Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis models and estimation procedures. American Journal of Human Genetics, 19, 233-257.
10. Cheliak WM, Wang J, Pitel JA (1988) Population structure and genetic diversity in tamarack, Larix laricina (Du Roi) K. Koch. Canadian Journal of Forest Research, 18, 1318-1324.
11. Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144, 2001-2014.
12. Di Rienzo AD, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB (1994) Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences, USA, 91, 3166-3170.
13. El-Kassaby YA, Jaquish B (1996) Population density and mating pattern in western larch. Journal of Heredity, 87, 438-443.
14. England PR, Usher AV, Whelan RJ, Ayre DJ (2002) Microsatellite diversity and genetic structure of fragmented populations of the rare, fire-dependent shrub Grevillea macleayana. Molecular Ecology, 11, 967-977.
15. Estoup A, Garnery L, Solignac M, Cornuet JM (1995) Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models. Genetics, 145, 679-695.
16. Estoup A, Jarne P, Cornuet JM (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Molecular Ecology, 11, 1591-1604.
17. Farrar JL (1995) Trees in Canada. Fitzhenry and Whiteside, Markham, Ontario.
18. Felsenstein J (1993) PHYLIP (phylogeny inference package), version 3.5c. Sinauer Associates, Sunderland, Massachusetts.
19. Fins L, Seeb LW (1986) Genetic variation in allozymes of western larch. Canadian Journal of Forest Research, 16, 1013-1018.
20. Fowler DP, Morris RW (1977) Genetic diversity in red pine: evidence of low genetic heterozygosity. Canadian Journal of Forest Research, 7, 343-347.
21. Godbout J, Jaramillo-Correa JP, Beaulieu J, Bousquet J (2005) A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad range North American conifer. Molecular Ecology, 14, 3497-3512.
22. Goldstein DB, Pollock DD (1997) Launching microsatellites: a review of mutation processes and methods of phylogenetic inference. Journal of Heredity, 88, 335-342.
23. ST CALC : a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance. Molecular Ecology, 6, 881-885.
24. Gros-Louis MC, Bousquet J, Pâques LE, Isabel I (2005) Species diagnostic markers in Larix spp. based on nuclear, cpDNA, and mtDNA gene sequences, and their phylogenetic implications. Tree Genetics and Genomes, 1, 50-63.
25. Hamrick JL, Godt MJW (1996) Effects of life history on genetic diversity in plant species. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 351, 1291-1298.
26. Hewitt GM (1996) Post-glacial re-colonization of European biota. Biological Journal of the Linnean Society, 68, 67-112.
27. Isabel N, Beaulieu J, Bousquet J (1995) Complete congruence between gene diversity estimates derived from genotypic data at enzyme and random amplified DNA loci in black spruce. Proceedings of the National Academy of Sciences, USA, 92, 6369-6373.
28. Jaquish B, El-Kassaby YA (1998) Genetic variation of western larch in British Columbia and its conservation. Journal of Heredity, 89, 248-253.
29. Jaramillo-Correa JP, Beaulieu J, Bousquet J (2004) Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer. Molecular Ecology, 13, 2735-2747.
30. Khasa PD, Newton C, Rahman M, Jaquish B, Dancik BP (2000) Isolation, characterization and inheritance of microsatellite loci in alpine larch and western larch. Genome, 43, 439-448.
31. Knowles P, Furnier GR, Aleksuik MA, Perry DJ (1987) Significant levels of self-fertilization in natural populations of tamarack. Canadian Journal of Botany, 65, 1087-1091.
32. Ledig FT, Capó-Arteaga M, Hodgskiss Sbay H, Flores-López C, Conkle MT, Bermejo-Velázquez B (2001) Genic diversity and the mating system of a rare mexican piñon, Pinus pinceana, and a comparison with Pinus maximartinezii (Pinaceae). American Journal of Botany, 88, 1977-1987.
33. Lewis PO, Zaykin D (2001) Genetic Data Analysis: Computer Program for the Analysis of Allelic Data, Version 1.0 (d16c). Free program distributed by the authors over the Internet from. http://lewis.eeb.uconn.edu/lewishome/software. html.
34. Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics, 74, 175-195.
35. Luikart G, Cornuet JM (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology, 12, 228-237.
36. Manly BFJ (1985) The Statistics of Natural Selection in Animal Populations. Chapman & Hall, London.
37. Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants: salient statistical tools and considerations. Crop Science, 43, 1235-1248.
38. Molina-Freaner F, Delgado P, Piñero D, Pérez-Nasser N, Alvarez-Buylla E (2001) Do rare pines need different conservation strategies? Evidence from three mexican rare species. Canadian Journal of Botany, 79, 131-138.
39. Nadeem S, Jaquish B, Newton C, Khasa PD (2003) Use of diagnostic SSR markers for identification of Larix lyallii and L. occidentalis (Pinaceae). Edinburgh Journal of Botany, 60, 49-56.
40. Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends in Plant Science, 9, 325-330.
41. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583-590.
42. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
43. Newton AC, Allnutt TR, Gillies ACM, Lowe AJ, Ennos RA (2003) Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends in Ecology & Evolution, 14, 140-145.
44. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology, 13, 1143-1155.
45. O'Connell LM, Ritland CE (2000) Characterization of microsatellites in western redcedar (Thuja plicata). Molecular Ecology, 9, 1920-1921.
46. Perron M, Perry DJ, Andalo C, Bousquet J (2000) Evidence from sequence-tagged-site markers of a recent progenitor-derivative species pair in conifers. Proceedings of the National Academy of Sciences USA, 97, 11331-11336.
47. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conservation Biology, 12, 844-855.
48. Piry S, Luikart G, Cornuet J-M (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity, 90, 502-503.
49. Rahman M, Jaquish B, Khasa PD (2000) Optimization of PCR protocol in microsatellite analysis with silver and SYBR stains. Plant Molecular Biology Reporter, 18, 339-348.
50. Rajora OH, Rahman MH, Buchert GP, Dancik BP (2000) Microsatellite DNA analysis of genetic effects of harvesting in old-growth eastern white pine (Pinus strobus) in Ontario, Canada. Molecular Ecology, 9, 339-348.
51. Rehfeldt GE (1995) Genetic variation, climate models and ecological genetics of Larix occidentalis. Forest Ecology and Management, 78, 21-37.
52. Richardson BA, Brunsfeld SJ, Klopfenstein NB (2002) DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetics structure of whitebark pine (Pinus albicaulis). Molecular Ecology, 11, 215-227.
53. Ritland K (2002) Extensions of models for the estimation of mating systems using n independent loci. Heredity, 88, 221-228.
54. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogentic trees. Molecular Biology and Evolution, 4, 406-425.
55. Salgueiro F, Caron H, De Souza MIF, Kremer A, Margis R (2005) Characterization of nuclear microsatellite loci in South American Araucariaceae species. Molecular Ecology Notes, 5, 256-258.
56. Schmidt WC, Shearer RC (1990) Larix occidentalis, western larch. In: Silvics of North America, Vol. 1. Conifers. Agricultural Handbook, 654, 227-237.
57. Semerikov VL, Lascoux M (1999) Genetic relationships among Eurasian and American Larix species based on allozymes. Heredity, 83, 62-70.
58. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics, 139, 457-462.
59. Slatkin M, Barton NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution, 43, 1349-1368.
60. Sneath RR, Sokal RR (1973) Numerical Taxonomy. W.H. Freeman, San Francisco, California.
61. Soltis DE, Gitzendanner MA, Strenge DD, Soltis PS (1997) Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Systematics and Evolution, 206, 353-373.
62. Strauss SH, Libby WJ (1987) Allozyme heterosis in radiata pine is poorly explained by overdominance. American Naturalist, 120, 879-890.
63. Strong WL, Hills LV (2003) Post-hypsithermal plant disjunctions in western Alberta, Canada. Journal of Biogeography, 30, 419-430.
64. Swofford DL, Selander RB (1989) BIOSYS-1: a Fortran program for comprehensive analysis for electrophoretic data in population genetics and systematics. Journal of Heredity, 72, 281-283.
65. Takezaki N, Nei N (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics, 144, 389-399.
66. Thomas BR, MacDonald SE, Hick M, Adams DL, Hodgetts RB (1999) Effects of reforestation methods on genetic diversity of lodgepole pine: an assessment using microsatellite and randomly amplified polymorphic DNA markers. Theoretical and Applied Genetics, 98, 793-801.
67. Viard F, Frank P, Dubois MP, Estoup A, Jarne P (1998) Variation of microsatellite size homoplasy across electromorphs, loci, and populations in three invertebrate species. Journal of Molecular Evolution, 47, 42-51.
68. Walter R, Epperson BK (2001) Geographic pattern of genetic variation in Pinus resinosa: area of greatest diversity is not the origin of postglacial populations. Molecular Ecology, 10, 103-111.
69. Weir BS (1996) Genetic Data Analysis II. Sinauer Associates, Sunderland, Massachusetts.
70. Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution, 19, 395-420.
71. Ying L, Morgenstern EK (1991) The population structure of Larix laricina in New Brunswick, Canada. Silvae Genetica, 40, 180-184.
72. Zar JH (1984) Biostatistical Analysis, 2nd edn. Prentice Hall, Englewood Cliffs, New Jersey.