Recent population decline and selection shape diversity of taxol-related genes

Molecular Ecology

Volumn 21, Issue 12, 2012, Pages 3006-3021

  Burgarella, C ^a,e   NavascuEs M ^b   Zabal Aguirre, M ^a   Berganzo, E ^c   Riba, M ^c   Mayol, M ^c   Vendramin, G G ^d   Gonzalez MartInez S C ^a  

^a INIA   (Spain)

^b CENTRE DE BIOLOGIE ET DE GESTION DES POPULATIONS   (France)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^d CNR   (Italy)

^e UMR AGAP   (France)

Author keywords

ABC inference; bottleneck; natural selection; neutrality tests; taxol genes; Taxus baccata (European yew)

Indexed keywords

MICROSATELLITE DNA; TAXOID;

ARTICLE; DNA SEQUENCE; GENE FREQUENCY; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOTYPE; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT GENE; SPAIN; TAXUS;

BASE SEQUENCE; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENES, PLANT; GENETIC VARIATION; GENOTYPE; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA; SPAIN; TAXOIDS; TAXUS;

SANDFLY FEVER SICILIAN VIRUS; TAXUS; TAXUS BACCATA;

EID: 84862000553     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05532.x     Document Type: Article

References (79)

1. Akashi H, (1999) Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination. Genetics, 151, 221-238.
2. Akey JM, Eberle MA, Rieder MJ, et al. (2004) Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biology, 2, e286.
3. Baudry E, Depaulis F, (2003) Effect of misoriented sites on neutrality tests with outgroup. Genetics, 165, 1619-1622.
4. Beaumont MA, (2010) Approximate Bayesian Computation in evolution and ecology. Annual Review of Ecology, Evolution, and Systematics, 41, 379-406.
5. Bierne N, Eyre-Walker A, (2004) The genomic rate of adaptive amino acid substitution in Drosophila. Molecular Biology and Evolution, 21, 1350-1360.
6. Cornuet J-M, Ravigné V, Estoup A, (2010) Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). BMC Bioinformatics, 11, 401.
7. Croteau R, Ketchum REB, Long RM, Kaspera R, Wildung MR, (2006) Taxol biosynthesis and molecular genetics. Phytochemistry Reviews, 5, 75-97.
8. Daniewski WM, Gumulka M, Anczewski W, Masnyk M, Bloszyk E, Gupta KK, (1998) Why the yew tree (Taxus baccata) is not attacked by insects. Phytochemistry, 49, 1279-1282.
9. Dempsey D, Hook I, (2000) Yew (Taxus) species-chemical and morphological variations. Pharmaceutical Biology, 38, 274-280.
10. Dubreuil M, Sebastiani F, Mayol M, González-Martínez SC, Riba M, Vendramin GG, (2008) Isolation and characterization of polymorphic nuclear microsatellite loci in Taxus baccata L. Conservation Genetics, 9, 1665-1668.
11. Dubreuil M, Riba M, González-Martínez SC, Vendramin GG, Sebastiani F, Mayol M, (2010) Genetic effects of chronic habitat fragmentation revisited: strong genetic structure in a temperate tree, Taxus baccata (Taxaceae), with great dispersal capability. American Journal of Botany, 97, 303-310.
12. Eckert AJ, van Heerwaarden J, Wegrzyn JL, et al. (2010) Patterns of population structure and environmental associations to aridity across the range of Loblolly pine (Pinus taeda L., Pinaceae). Genetics, 185, 969-982.
13. Egea R, Casillas S, Barbadilla A, (2008) Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites. Nucleic Acids Research, 36, W157-162.
14. Elmer W, Mattina M, MacEachern G, (1994) Sensitivity of plant pathogenic fungi to taxane extracts from ornamental yews. Phytopathology, 84, 1179-1185.
15. Ersoz ES, Wright MH, González-Martínez SC, Langley CH, Neale DB, (2010) Evolution of disease response genes in Loblolly pine: insights from candidate genes. PLoS ONE, 5, e14234.
16. 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.
17. Excoffier L, Lischer HEL, (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
18. Eyre-Walker A, Keightley PD, (2009) Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Molecular Biology and Evolution, 26, 2097-2108.
19. Fay JC, Wu CI, (2001) The neutral theory in the genomic era. Current Opinion in Genetics & Development, 11, 642-646.
20. Frense D, (2006) Taxanes: perspectives for biotechnological production. Applied Microbiology and Biotechnology, 73, 1233-1240.
21. Garza JC, Williamson EG, (2001) Detection of reduction in population size using data from microsatellite loci. Molecular Ecology, 10, 305-318.
22. Gershenzon J, (1994) Metabolic costs of terpenoid accumulation in higher plants. Journal of Chemical Ecology, 20, 1281-1328.
23. Gershenzon J, Dudareva N, (2007) The function of terpene natural products in the natural world. Nature Chemical Biology, 3, 408-414.
24. González-Martínez SC, Dubreuil M, Riba M, Vendramin GG, Sebastiani F, Mayol M, (2010) Spatial genetic structure of Taxus baccata L. in the western Mediterranean Basin: past and present limits to gene movement over a broad geographic scale. Molecular Phylogenetics and Evolution, 55, 805-815.
25. Grivet D, Sebastiani F, Alía R, et al. (2011) Molecular footprints of local adaptation in two Mediterranean conifers. Molecular Biology and Evolution, 28, 101-116.
26. Hao DC, Yang L, Huang B, (2008) Molecular evolution of paclitaxel biosynthetic genes TS and DBAT of Taxus species. Genetica, 135, 123-135.
27. Hershberg R, Petrov DA, (2008) Selection on codon bias. Annual Review of Genetics, 42, 287-299.
28. Heuertz M, De Paoli E, Kallman T, et al. (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics, 174, 2095-2105.
29. Hilfiker K, Holderegger R, Rotach P, Gugerli F, (2004) Dynamics of genetic variation in Taxus baccata: local versus regional perspectives. Canadian Journal of Botany, 82, 219-227.
30. Holliday JA, Yuen M, Ritland K, Aitken SN, (2010) Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests. Molecular Ecology, 19, 3857-3864.
31. Hook I, Poupat C, Ahond A, et al. (1999) Seasonal variation of neutral and basic taxoid contents in shoots of European Yew (Taxus baccata). Phytochemistry, 52, 1041-1045.
32. Hudson RR, (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18, 337-338.
33. Hudson RR, Kreitman M, Aguade M, (1987) A test of neutral molecular evolution based on nucleotide data. Genetics, 116, 153-159.
34. Ingvarsson PK, (2005) Molecular population genetics of herbivore-induced protease inhibitor genes in European aspen (Populus tremula L., Salicaceae). Molecular Biology and Evolution, 22, 1802-1812.
35. 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, 23, 1801-1806.
36. Jaramillo-Correa J, Verdu M, González-Martínez SC, (2010) The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms. BMC Evolutionary Biology, 10, 22.
37. Jennewein S, Wildung MR, Chau M, Walker K, Croteau R, (2004) Random sequencing of an induced Taxus cell cDNA library for identification of clones involved in Taxol biosynthesis. Proceedings of the National Academy of Sciences of the United States of America, 101, 9149-9154.
38. Keeling CI, Bohlmann J, (2006) Genes, enzymes and chemicals of terpenoid diversity in the constitutive and induced defence of conifers against insects and pathogens. New Phytologist, 170, 657-675.
39. Keeling CI, Weisshaar S, Lin RPC, Bohlmann J, (2008) Functional plasticity of paralogous diterpene synthases involved in conifer defense. Proceedings of the National Academy of Sciences, 105, 1085-1090.
40. Külheim C, Yeoh SH, Wallis IR, Laffan S, Moran GF, Foley WJ, (2011) The molecular basis of quantitative variation in foliar secondary metabolites in Eucalyptus globulus. New Phytologist, 191, 1041-1053.
41. Leimu R, Fischer M, (2008) A meta-analysis of local adaptation in plants. PLoS ONE, 3, e4010.
42. Li J, Davis C, Del Tredici P, Donoghue M, (2001) Phylogeny and biogeography of Taxus (Taxaceae) inferred from sequences of the internal transcribed spacer region of nuclear ribosomal DNA. Harvard Papers in Botany, 6, 267-274.
43. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
44. McDonald JH, Kreitman M, (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 652-654.
45. McVean G, Awadalla P, Fearnhead P, (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics, 160, 1231-1241.
46. de Meaux J, Mitchell-Olds T, (2003) Evolution of plant resistance at the molecular level: ecological context of species interactions. Heredity, 91, 345-352.
47. Ng PC, Henikoff S, (2001) Predicting deleterious amino acid substitutions. Genome Research, 11, 863-874.
48. Nielsen R, (2005) Molecular signatures of natural selection. Annual Review of Genetics, 39, 197-218.
49. Palmé AE, Wright M, Savolainen O, (2008) Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps. Molecular Biology and Evolution, 25, 2567-2577.
50. Palmé AE, Pyhäjärvi T, Wachowiak W, Savolainen O, (2009) Selection on nuclear genes in a Pinus phylogeny. Molecular Biology and Evolution, 26, 893-905.
51. Paradis E, (2010) pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics, 26, 419-420.
52. Parc G, Canaguier A, Landré P, Hocquemiller R, Chriqui D, Meyer M, (2002) Production of taxoids with biological activity by plants and callus culture from selected Taxus genotypes. Phytochemistry, 59, 725-730.
53. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
54. Pyhäjärvi T, García-Gil MR, Knürr T, Mikkonen M, Wachowiak W, Savolainen O, (2007) Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics, 177, 1713-1724.
55. R Development Core Team (2009) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
56. Ralph SG, Yueh H, Friedmann M, et al. (2006) Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-scale changes of the host transcriptome. Plant, Cell and Environment, 29, 1545-1570.
57. Ramsay H, Rieseberg LH, Ritland K, (2009) The correlation of evolutionary rate with pathway position in plant terpenoid biosynthesis. Molecular Biology and Evolution, 26, 1045-1053.
58. Roberts SC, (2007) Production and engineering of terpenoids in plant cell culture. Nature Chemical Biology, 3, 387-395.
59. van Rozendaal ELM, Lelyveld GP, van Beek TA, (2000) Screening of the needles of different yew species and cultivars for paclitaxel and related taxoids. Phytochemistry, 53, 383-389.
60. Sanz R, Pulido F, Nogués-Bravo D, (2009) Predicting mechanisms across scales: amplified effects of abiotic constraints on the recruitment of yew Taxus baccata. Ecography, 32, 993-1000.
61. Savolainen O, Pyhäjärvi T, Knürr T, (2007) Gene flow and local adaptation in trees. Annual Review of Ecology, Evolution, and Systematics, 38, 595-619.
62. Slotte T, Foxe JP, Hazzouri KM, Wright SI, (2010) Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Molecular Biology and Evolution, 27, 1813-1821.
63. Stapley J, Reger J, Feulner PGD, et al. (2010) Adaptation genomics: the next generation. Trends in Ecology & Evolution, 25, 705-712.
64. Strasburg JL, Scotti-Saintagne C, Scotti I, Lai Z, Rieseberg LH, (2009) Genomic patterns of adaptive divergence between chromosomally differentiated sunflower species. Molecular Biology and Evolution, 26, 1341-1355.
65. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
66. Thomas PA, Polwart A, (2003) Biological flora of the British Isles: Taxus baccata L. Journal of Ecology, 91, 489-524.
67. Thrall PH, Burdon JJ, (2002) Evolution of gene-for-gene systems in metapopulations: the effect of spatial scale of host and pathogen dispersal. Plant Pathology, 51, 169-184.
68. Tiffin P, Moeller DA, (2006) Molecular evolution of plant immune system genes. Trends in Genetics, 22, 662-670.
69. Trapp SC, Croteau R, (2001) Genomic organization of plant terpene synthases and molecular evolutionary implications. Genetics, 158, 811-832.
70. Watterson GA, (1978) The homozygosity test of neutrality. Genetics, 88, 405-417.
71. Wilson DJ, McVean G, (2006) Estimating diversifying selection and functional constraint in the presence of recombination. Genetics, 172, 1411-1425.
72. Wright F, (1990) The 'effective number of codons' used in a gene. Gene, 87, 23-29.
73. Wright SI, Andolfatto P, (2008) The impact of natural selection on the genome: emerging patterns in Drosophila and Arabidopsis. Annual Review of Ecology, Evolution, and Systematics, 39, 193-213.
74. Wright SI, Yau CBK, Looseley M, Meyers BC, (2004) Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Molecular Biology and Evolution, 21, 1719-1726.
75. Young DH, Michelotti EL, Swindell CS, Krauss NE, (1992) Antifungal properties of taxol and various analogues. Cellular and Molecular Life Sciences, 48, 882-885.
76. Zeng K, Fu YX, Shi S, Wu CI, (2006) Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics, 174, 1431-1439.
77. Zeng K, Mano S, Shi S, Wu CI, (2007a) Comparisons of site- and haplotype-frequency methods for detecting positive selection. Molecular Biology and Evolution, 24, 1562-1574.
78. Zeng K, Shi S, Wu CI, (2007b) Compound tests for the detection of hitchhiking under positive selection. Molecular Biology and Evolution, 24, 1898-1908.
79. Zhai W, Nielsen R, Slatkin M, (2009) An investigation of the statistical power of neutrality tests based on comparative and population genetic data. Molecular Biology and Evolution, 26, 273-283.