Trans-species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): Implications for the long-term maintenance of genetic diversity in trees

American Journal of Botany

Volumn 92, Issue 1, 2005, Pages 63-73

  Bouillé, Marie ^a   Bousquet, Jean ^a  

^a UNIVERSITÉ LAVAL   (Canada)

Author keywords

Allele coalescence; Conifers; Expressed sequence tag polymorphisms; Historical demography; Intragenic recombination; Nuclear gene phylogeny; Species divergence; Spruce

Indexed keywords

CONIFEROUS TREE; GENETIC VARIATION; POLYMORPHISM;

CONIFEROPHYTA; EMBRYOPHYTA; PICEA; PINACEAE;

EID: 12244252817     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.92.1.63     Document Type: Article

References (63)

1. ARBOGAST, B. S., S. V. EDWARDS, J. WAKELEY, P. BEERLI, AND J. B. SLOWINSKI. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annual Review of Ecology and Systematics 33: 707-740.
2. AXELROD, D. I. 1998. The Eocene Thunder Mountain flora of central Idaho. University of California Publications in Geological Sciences 142: 1-61.
3. BERGMANN, F., AND W. RUETZ. 1991. Isozyme variation and heterozygosity in random tree samples and selected orchard clones from the same Norway spruce populations. Forest Ecology and Management 46: 39-47.
4. BOYLE, T. J. B., AND E. K. MORGENSTERN. 1987. Some aspects of the population structure of black spruce in central New Brunswick. Silvae Genetica 36: 53-60.
5. BURNS, R. M., AND B. H. HONKALA. 1990. Silvics of North America, vol. 1, Conifers. Agriculture Handbook 654. US Department of Agriculture, Forest Service, Washington, D.C., USA.
6. CABALLERO, A. 1994. Developments in the prediction of effective population size. Heredity 73: 657-679.
7. COLLIGNON, A.-M., H. VAN DE SYPE, AND J.-M. FAVRE. 2002. Geographical variation in random amplified DNA and quantitative traits in Norway spruce. Canadian Journal of Forest Research 32: 266-282.
8. DAVIS, M. B. 1983. Quaternary history of deciduous forests of eastern North America and Europe. Annals of the Missouri Botanical Garden 70: 550-563.
9. DVORNYK, V., A. SIRVIÖ, M. MIKKONEN, AND O. SAVOLAINEN. 2002. Low nucleotide diversity at the pall locus in the widely distributed Pinus sylvestris. Molecular Biology and Evolution 19: 179-188.
10. FAITH, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Systematic Zoology 40: 366-375.
11. FLORIN, R. 1963. The distribution of conifer and taxad genera in time and space. Acta Horti Bergiani 20: 121-312.
12. FURNIER, G. R., M. STINE, C. A. MOHN, AND M. A. CLYDE. 1991. Geographic patterns of variation in allozymes and height growth in white spruce. Canadian Journal of Forest Research 21: 707-712.
13. GAMACHE, I., J. P. JARAMILLO-COREA, S. PAYETTE, AND J. BOUSQUET. 2003. Diverging patterns of mitochondrial and nuclear DNA diversity in subarctic black spruce: imprint of a founder effect associated with postglacial colonization. Molecular Ecology 12: 891-901.
14. GARCIA-GIL, M. R., M. MIKKONEN, AND O. SAVOLAINEN. 2003. Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Molecular Ecology 12: 1195-1206.
15. HAMRICK, J. L., M. J. W. GODT, AND S. L. SHERMAN-BROYLES. 1992. Factors influencing levels of genetic diversity in woody plant species. New Forests 6: 95-124.
16. HAMRICK, J. L., AND M. J. W. GODT. 1996. Effects of life history traits on genetic diversity in plant species. Philosophical Transactions of the Royal Society of London, B, Biological Sciences 351: 1291-1298.
17. HARE, M. P., F. CIPRIANO, AND S. R. PALUMBI. 2002. Genetic evidence on the demography of speciation in allopatric dolphin species. Evolution 56: 804-816.
18. HAWLEY, G. J., AND D. H. DEHAYES. 1994. Genetic diversity and population structure of red spruce (Picea rubens). Canadian Journal of Botany 72: 1778-1786.
19. HUDSON, R. R. 1990. Gene genealogies and the coalescent process. In D. Gutuyama and J. Antonivics [eds.], Oxford surveys in evolutionary biology, vol. 7, 1-44. Oxford University Press, Oxford, UK.
20. HUDSON, R. R., AND N. L. KAPLAN. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA samples. Genetics 111: 147-164.
21. IOERGER, T. R., A. G. CLARK, AND T.-H. KAO. 1990. Polymorphism at the self-incompatibility locus in Solanaceae predates speciation. Proceedings of the National Academy of Sciences, USA 87: 9732-9735.
22. ISABEL, N., J. BEAULIEU, AND J. BOUSQUET. 1995. Complete congruence between gene diversity estimates derived from genotypic data at enzyme and random amplified polymorphic DNA loci in black spruce. Proceedings of the National Academy of Sciences, USA 92: 6369-6373.
23. ISODA, K., AND S. SHIRAISHI. 2001. Allelic sequence polymorphisms in the intron region of the nuclear-encoded GapC gene preceded the speciation of three closely related Abies species (Pinaceae). Theoretical and Applied Genetics 102: 244-250.
24. JARAMILLO-CORREA, J. P., J. BEAULIEU, AND J. BOUSQUET. 2001. Contrasting evolutionary forces driving population structure at expressed sequence tag polymorphisms, allozymes and quantitative traits in white spruce. Molecular Ecology 10: 2729-2740.
25. JOLLEY, K. A., E. J. FEIL, M.-S. CHAN, AND M. C. J. MAIDEN. 2001. Sequence type analysis and recombinational tests (START). Bioinformatics 17: 1230-1231.
26. KIMURA, M., AND T. OHTA. 1969. The average number of generations until fixation of a mutant gene in a finite population. Genetics 61: 763-771.
27. KIMURA, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120.
28. LEDIG, F. T. 1998. Genetic variation in Pinus. In D. M. Richardson [ed.], Ecology and biogeography of Pinus, 251-280. Cambridge University Press, Cambridge. UK.
29. LEDIG, F. T., B. BERMEJO-VELAZQUEZ, P. D. HODGSKISS, D. R. JOHNSON, C. FLORES-LOPEZ, AND V. JACOB-CERVANTES. 2000. The mating system and genus diversity in Martinez spruce, an extremely rare endemic of Mexico's Sierra Madre Oriental: an example of facultative selfing and survival in interglacial refugia. Canadian Journal of Forest Research 30: 1156-1164.
30. LEPAGE, B. A. 2001. New species of Picea A. Dietrich (Pinaceae) from the middle Eocene of Axel Heiberg Island, Arctic Canada. Botanical Journal of the Linnean Society 135: 137-167.
31. LI, P., AND J. BOUSQUET. 1992. Relative-rate test for nucleotide substitutions between two lineages. Molecular Biology and Evolution 9: 1185-1189.
32. MACHADO, C. A., R. M. KLIMAN, J. A. MARKERT, AND J. HEY. 2002. Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology and Evolution 19: 472-488.
33. MAGALLÓN, S., AND M. J. SANDERSON. 2002. Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages. American Journal of Botany 89: 1991-2006.
34. MAYNARD SMITH, J., AND N. H. SMITH. 1998. Detecting recombination from gene trees. Molecular Biology and Evolution 15: 590-599.
35. MIKKOLA, L. 1969. Observations on interspecific sterility in Picea. Annales Botanici Fennici 6: 285-339.
36. MILLER, C. N. 1988. The origin of modern conifer families. In C. B. Beck [ed.], Origin and evolution of the gymnosperms, 448-486. Columbia University Press. New York, New York, USA.
37. MÜLLER-STARCK, G. 1995. Genetic variation in high elevated populations of Norway spruce (Picea abies (L.) Karst.) in Switzerland. Silvae Genetica 44: 356-362.
38. NEI, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York, New York, USA.
39. NYBOM, H. 2004. Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology 13: 1143-1155.
40. PERRON, M., AND J. BOUSQUET. 1997. Natural hybridization between black spruce and red spruce. Molecular Ecology 6: 725-734.
41. PERRON, M., D. J. PERRY, C. ANDALO, AND J. BOUSQUET. 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.
42. PERRY, D. J., AND J. BOUSQUET. 1998a. Sequence-tagged-site (STS) markers of arbitrary genes: development, characterization and analysis of linkage in black spruce. Genetics 149: 1089-1098.
43. PERRY, D. J., AND J. BOUSQUET. 1998b. Sequence-tagged-site (STS) markers of arbitrary genes: the utility of black spruce-derived STS primers in other conifers. Theoretical and Applied Genetics 97: 735-743.
44. PERRY, D. J., AND J. BOUSQUET. 2001. Genetic diversity and mating system of post-fire and post-harvest black spruce: an investigation using codominant sequence-tagged-site (STS) markers. Canadian Journal of Forest Research 31: 32-40.
45. PERRY, D. J., N. ISABEL, AND J. BOUSQUET. 1999. Sequence-tagged-site (STS) markers of arbitrary genes: the amount and nature of variation revealed in Norway spruce. Heredity 83: 239-248.
46. POSADA, D., AND K. A. CRANDALL. 2002. The effect of recombination on the accuracy of phylogeny estimation. Journal of Molecular Evolution 54: 396-402.
47. PRAGER, E. M., D. P. FOWLER, AND A. C. WILSON. 1976. Rates of evolution in conifers (Pinaceae). Evolution 30: 637-649.
48. RAJORA, O. P., A. MOSSELER, AND J. E. MAJOR. 2000. Indicators of population viability in red spruce, Picea rubens. II. Genetic diversity, population structure, and mating behavior. Canadian Journal of Botany 78: 941-956.
49. ROSENBERG, N. A. 2003. The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57: 1465-1477.
50. ROSENBERG, N. A., AND M. NORDBORG. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Review Genetics 3: 380-390.
51. ROZAS, J., AND R. ROZAS. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
52. SHERRY, S. T., H. C. HARPENDING, M. A. BATZER, AND M. STONEKING. 1997. Alu evolution in human populations: using the coalescent to estimate effective population size. Genetics 147: 1977-1982.
53. SCHIERUP, M. H., AND J. HEIN. 2000. Consequences of recombination on traditional phylogenetic analysis. Genetics 156: 879-891.
54. SIGURGEIRSSON, A., AND A. E. SZMIDT. 1993. Phylogenetic and biogeographic implications of chloroplast DNA variation in Picea. Nordic Journal of Botany 13: 233-246.
55. STINE, M., B. B. SEARS, AND D. E. KEATHLEY. 1989. Inheritance of plastids in interspecific hybrids of blue spruce and white spruce. Theoretical and Applied Genetics 78: 768-774.
56. SWOFFORD, D. L. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer Associates, Sunderland, Massachusetts, USA.
57. TAJIMA, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
58. TAJIMA, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
59. WANG, R. L., J. WAKELEY, AND J. HEY. 1997. Gene flow and natural selection in the origin of Drosophila pseudoobscura and close relatives. Genetics 147: 1091-1106.
60. WANG, X.-R., Y. TSUMURA, H. YOSHIMARU, K. NAGASAKA, AND A. E. SZMIDT. 1999. Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, matK, rpl20-rps18 spacer, and trnV intron sequences. American Journal of Botany 86: 1742-1753.
61. WENG, C., AND S. T. JACKSON. 2000. Species differentiation of North American spruce (Picea) based on morphological and anatomical characteristics of needles. Canadian Journal of Botany 78: 1367-1383.
62. WOLFE, J. A. 1964. Miocene floras from Fingerrock Wash, southwestern Nevada. US Geological Survey Professional Paper 454-N: 1-36.
63. WRIGHT, J. W. 1955. Species crossability in spruce in relation to distribution and taxonomy. Forest Science 1: 319-349.