Phylogenetics and reticulate evolution in Pistacia (Anacardiaceae)

American Journal of Botany

Volumn 95, Issue 2, 2008, Pages 241-251

  Yi, Tingshuang ^a   Wen, Jun ^b,c   Golan Goldhirsh, Avi ^d   Parfitt, Dan E ^e  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b DEPARTMENT OF PALEOBIOLOGY   (United States)

^c INSTITUTE OF BOTANY   (China)

^d BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Anacardiaceae; ITS; ndhF; NIA i3; Phylogenetics; Pistacia; trnC trnD; trnL F

Indexed keywords

BAYESIAN ANALYSIS; DATA SET; GENETIC ANALYSIS; HYBRID; PARSIMONY ANALYSIS; PHYLOGENETICS; PHYLOGENY; PLASTID; TAXONOMY;

ANACARDIACEAE; NIA; PISTACIA; PISTACIA LENTISCUS; PISTACIA TEREBINTHUS; PISTACIA VERA;

EID: 38849102893     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.95.2.241     Document Type: Article

References (78)

1. ADANSON, M. 1763. Familles des plantes. Vincent, Paris, France.
2. ÁLVAREZ, I., AND J. F. WENDEL. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
3. BALDWIN, B. G., M. J. SANDERSON, J. M. PORTER, M. F. WOJCIECHOWSKI, C. S. CAMPBELL, AND M. J. DONOGHUE. 1995. The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden 82: 247-277.
4. BARRETT, M., M. J. DONOGHUE, AND E. SOBER. 1991. Against congruence. Systematic Zoology 40: 486-493.
5. BAUM, D. A., R. L. SMALL, AND J. F. WENDEL. 1998. Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets. Systematic Biology 47: 181-207.
6. BAUMEL, A., M. L. AINOUCHE, AND J. E. LEVASSEUR. 2001. Molecular investigations in populations of Spartina anglica C. E. Hubbard (Poaceae) invading coastal Brittany (France). Molecular Ecology 10: 1689-1701.
7. BROCHMANN, C., T. NILSSON, AND T. M. GABRIELSEN. 1996. A classic example of postglacial allopolyploid speciation re-examined using RAPD markers and nucleotide sequences: Saxifraga osloensis (Saxifragaceae). Symbolae Botanicae Upsalienses 31: 75-89.
8. BURNAT, E. 1896. Flores des Alpes maritimes on catalogue Raisonné. Vol. II, 54. Georg & Cie., Lyon, France.
9. CRANE, J. C., AND H. I. FORDE. 1976. Effects of four rootstocks on yield and quality of pistachio nuts. Journal of the American Society for Horticultural Science 101: 604-606.
10. CRANE, J. C., AND B. T. IWAKIRI. 1986. Pistachio yield and quality as affected by rootstock. HortScience 21: 1139-1140.
11. CRONN, R. C., R. L. SMALL, AND J. F. WENDEL. 1999. Duplicated genes evolve independently after polyploid formation in cotton. Proceedings of the National Academy of Sciences, USA 96: 14406-14411.
12. CUNNINGHAM, C. W. 1997. Can three incongruence tests predict when data should be combined? Molecular Biology and Evolution 14: 733-740.
13. DOYLE, J. J., AND J. L. DOYLE. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
14. EICHLER, A. W. 1875-1878. Bluthendiagramme construirirt und erlautert, vol. 2. Wilhelm Engelmann, Leipzig, Germany.
15. ENGLER, A. 1876. Anacardiaceae. In C. F. P. Martius [eds.], Flora Brasiliensis, vol. 12, part 2, 367-418. F. Fleischer, Munchen and Leipzig, Germany.
16. ENGLER, A. 1883. Anacardiaceae. In A. P. and A. C. De Candolle [eds.], Monographie Phanerogamarum, vol. 4, 171-546. G. Masson, Paris, France.
17. ENGLER, A. 1892. Anacardiaceae. In A. Engler and K. Prantl [eds.], Die natürlichen Pflanzenfamilien, vol III, part 5, 138-178. W. Engelmann, Leipzig, Germany.
18. ENGLER, A. 1936. Syllabus der Pflanzenfamilien, vol 11. Gebriider Borntraeger, Berlin, Germany.
19. FARRIS, J. S., M. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1994. Testing significance of incongruence. Cladistics 10: 315-319.
20. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution; International Journal of Organic Evolution 39: 783-791.
21. FERGUSON, C. J., F. KRÄMER, AND R. K. JANSEN. 1999. Relationships of eastern North American Phlox (Polemoniaeae) based on ITS sequence data. Systematic Botany 24: 616-631.
22. FRANZKE, A., AND K. MUMMENHOFF. 1999. Recent hybrid speciation in Cardamine (Brassicaceae) - Conversion of nuclear ribosomal ITS sequences in statu nascendi. Theoretical and Applied Genetics 98: 831-834.
23. FUERTES AGUILAR, J., J. A. ROSSELLÓ, AND G. NIETO FELINER. 1999a. Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae). Systematic Biology 48: 735-754.
24. FUERTES AGUILAR, J., J. A. ROSSELLÓ, AND G. NIETO FELINER. 1999b. Nuclear ribosomal DNA (nrDNA) concerted evolution in natural and artificial hybrids of Armeria (Plubaginaceae). Molecular Ecology 8: 1341-1346.
25. GOLAN-GOLDHIRSH, A., O. BARAZANI, Z. S. WANG, D. K. KHADKA, J. A. SAUNDERS, V. KOSTIUKOVSKY, AND L. J. ROWLAND. 2004. Genetic relationships among Mediterranean Pistacia species evaluated by RAPD and AFLP markers. Plant Systematics and Evolution 246: 9-18.
26. GRUNDWAG, M., AND E. WEAKER. 1976. Comparative wood anatomy as an aid to identification of Pistacia L. species. Israel Journal of Botany 25: 152-167.
27. HIPP, A. L., J. C. HALL, AND K. J. SYTSMA. 2004. Congruence versus phylogenetic accuracy: Revisiting the incongruence length difference test. Systematic Biology 53: 81-89.
28. HOWARTH, D. G., AND D. A. BAUM. 2002. Phylogenetic utility of a nuclear intron from nitrate reductase for the study of closely related plant species. Molecular Phylogenetics and Evolution 23: 525-528.
29. HUELSENBECK, J. P., AND F. RONQUIST. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England) 17: 754-755.
30. KAFKAS, S. 2006. Phylogenetic analysis of the genus Pistacia by AFLP markers. Plant Systematics and Evolution 262: 113-124.
31. KAFKAS, S., AND R. PERL-TREVES. 2001. Morphological and molecular phylogeny of Pistacia species in Turkey. Theoretical and Applied Genetics 102: 908-915.
32. KAFKAS, S., AND R. PERL-TREVES. 2002. Interspecific relationships in Pistacia based on RAPD fingerprinting. HortScience 37: 168-171.
33. KATSIOTIS, A., M. HAGIDIMITRIOU, A. DROSSOU, C. PONTIKIS, AND M. LOUKAS. 2003. Genetic relationships among species and cultivars of Pistacia using RAPDs and AFLPs. Euphytica 132: 279-286.
34. KIMURA, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120.
35. KOKWARO, J. O., AND J. B. GILLETT. 1980. Notes on the Anacardiaceae of eastern Africa. Kew Bulletin 34: 745-760.
36. LEE, C., AND J. WEN. 2004. Phylogeny of Panax using chloroplast trnC-trnD intergenic region and the utility of trnC-trnD in interspecific studies of plants. Molecular Phylogenetics and Evolution 31: 894-903.
37. MABBERLEY, D. J. 1997. The plant book. Cambridge Uinversity Press, Cambridge, UK.
38. MARCHAND, N. L. 1869. Révision du groupe des Anacardiacées. J. B. Bailliére & Sons, Paris, France.
39. MITCHELL, J. D., D. C. DALY, S. K. PELL, AND A. RANDRIANASOLO. 2006. Poupartiopsis gen. nov. and its context in Anacardiaceae classification. Systematic Botany 31: 337-348.
40. MITCHELL, J. D., AND S. A. MORI. 1987. The cashew and its relatives (Anacardium: Anacardiaceae). Memoirs of the New York Botanical Garden 42: 1-76.
41. MORGAN, D. P., L. EPSTEIN, AND L. FERGUSON. 1992. Verticillium wilt resistance in pistachio rootstock cultivars: Assays and an assessment of two interspecific hybrids. Plant Disease 76: 310-313.
42. OLMSTEAD, R. G., AND J. A. SWEERE. 1994. Combining data in phylogenetic systematics: An empirical approach using three molecular data sets in the Solanaceae. Systematic Biology 43: 467-481.
43. PARFITT, D. E. 2003. 'Bonsai' ornamental pistachio. HortScience 38: 1260-1261.
44. PARFITT, D. E., AND M. L. BADENES. 1997. Phylogeny of the genus Pistacia as determined from analysis of the chloroplast genome. Proceedings of the National Academy of Sciences, USA 94: 7987-7992.
45. PARFITT, D. E., AND M. L. BADENES. 1998. Molecular phylogenetic analysis of the genus Pistacia. Acta Horticulturae 470: 143-151.
46. PELL, S. K. 2004. Molecular systematics of the cashew family (Anacardiaceae). Ph.D. dissertation, Louisiana State University, Baton Rouge, Louisiana, USA.
47. POSADA, D., AND K. A. CRANDALL. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics (Oxford, England) 14: 817-818.
48. RIESEBERG, L. H. 1991. Homoploid reticulate evolution in Helianthus (Asteraceae): Evidence from ribosomal genes. American Journal of Botany 78: 1218-1237.
49. RIESEBERG, L. H. 1997. Hybrid origins of plant species. Annual Review of Ecology and Systematics 28: 359-389.
50. RIESEBERG, L. H., AND N. C. ELLSTRAND. 1993. What can molecular and morphological markers tell us about plant hybridization? Critical Reviews in Plant Sciences 12: 213-241.
51. RIESEBERG, L. H., AND J. WENDEL. 1993. Introgression and its consequences in plants. In R. Harrison [eds.], Hybrid zones and the evolutionary process, 70-109. Oxford University Press, New York, New York, USA.
52. ROELOFS, D., J. VAN VELZEN, P. KUPERUS, AND K. BACHMANN. 1997. Molecular evidence for an extinct parent of tetraploid species Microseris acuminata and M. campestris (Asteraceae, Lactuceae). Molecular Ecology 6: 641-649.
53. nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA.
54. SANG, T., AND Y. ZHONG. 2000. Testing hybridization hypotheses based on incongruent gene trees. Systematic Biology 49: 422-434.
55. SENCHINA, D. S., I. ALVAREZ, R. C. CRONN, B. LIU, J. RONG, R. D. NOYES, A. H. PATERSON, R. A. WING, T. A. WILKINS, AND J. F. WENDEL. 2003. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Molecular Biology and Evolution 20: 633-643.
56. SHIMODAIRA, H., AND M. HASEGAWA. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16: 1114-1116.
57. SIMMONS, M. P., AND H. OCHOTERENA. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.
58. SOLTIS, P. S., G. M. PLUNKETT, S. J. NOVAK, AND D. E. SOLTIS. 1995. Genetic variation in Tragopogon species: Additional origins of the allotetraploids T. mirus and T. miscellus (Compositae). American Journal of Botany 82: 1329-1341.
59. SOLTIS, P. S., AND D. E. SOLTIS. 1991. Multiple origins of the allotetraploid Tragopogon mirus (Compositae): rDNA evidence. Systematic Botany 16: 407-413.
60. SWOFFORD, D. L. 2003. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer, Sunderland, Massachusetts, USA.
61. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference. In D. M. Hillis, C. Moritz, and B. K. Mable [eds.], Molecular systematics, 2nd ed., 407-514. Sinauer, Sunderland, Massachusetts, USA.
62. TABERLET, P., L. GIELLY, G. PAUTON, AND J. BOUVET. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17: 1105-1109.
63. TAKHTAJAN, A. 1987. System of Magnoliophyta. Academy of Sciences U.S.S.R, Leningrad, Russia.
64. TAKHTAJAN, A. 1997. Diversity and classification of flowering plants. Columbia University Press, New York, New York, USA.
65. TEMPLETON, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution; International Journal of Organic Evolution 37: 221-244.
66. TERRAZAS, T. 1994. Wood anatomy of the Anacardiaceae: Ecological and phylogenetic interpretation. Ph.D. dissertation, University of North Carolina, Chapel Hill, North Carolina, USA.
67. TOURNEFORT, J. P. 1700. Institutiones rei herbariae. Typographia Regia, Paris, France.
68. WANNAN, B. S., AND C. J. QUINN. 1991. Floral structure and evolution in the Anacardiaceae. Botanical Journal of the Linnean Society 107: 349-385.
69. WENDEL, J. F. 2000. Genome evolution in polyploids. Plant Molecular Biology 42: 225-249.
70. WERNER, O., P. SÁNCHEZ-GÓMEZ, J. GUERRA, AND J. F. MARTÍNEZ. 2001. Identification of Pistacia x saportae Burnat (Anacardiaceae) by RAPD analysis and morphological characters. Scientia Horticulturae 91: 179-186.
71. WHITE, T. J., T. BRUNS, S. LEE, AND J. TAYLOR. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White [eds.], PCR protocols: A guide to methods and applications, 315-322. Academic Press, San Diego, California, USA.
72. WOLFE, A. D., Q. Y. XIANG, AND S. R. KEPHART. 1998. Diploid hybrid speciation in Penstemon (Scrophulariaceae). Proceedings of the National Academy of Sciences, USA 95: 5112-5115.
73. YALTIRIK, F. 1967. Anacardiaceae. In P. H. Davis [eds.], Flora of Turkey, vol. 2, 544-548. Edinburgh University Press, Edingburgh, UK.
74. YI, T., A. J. MILLER, AND J. WEN. 2004. Phylogenetic and biogeographic diversification of Rhus (Anacardiaceae) in the northern hemisphere. Molecular Phylogenetics and Evolution 33: 861-879.
75. YI, T., A. J. MILLER, AND J. WEN. 2007. Phylogeny of Rhus (Anacardiaceae) based on sequences of nuclear NIA-i3 intron and chloroplast trnC-trnD. Systematic Botany 32: 379-391.
76. ZHANG, L., T. J. VISION, AND B. S. GAUT. 2002. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Molecular Biology and Evolution 19: 1464-1473.
77. ZOHARY, M. 1952. A monographical study of the genus Pistacia. Palestine Journal of Botany 5: 187-228.
78. ZOHARY, M. 1972. Pistacia L. Flora Palestina 2: 297-300. Israel Academy of Sciences and Humanities, Jerusalem, Israel.