Multiple hybridization in the Aristolochia kaempferi group (Aristolochiaceae): Evidence from reproductive isolation and molecular phylogeny

American Journal of Botany

Volumn 95, Issue 7, 2008, Pages 885-896

  Watanabe, Kana ^a,b   Ohi Toma, Tetsuo ^a   Murata, Jin ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b Musashi High School   (Japan)

Author keywords

APETALA3; Aristolochiaceae; Crossing experiments; East Asia; PhyA; PISTILLATA; Reticulate evolution; Secondary contact

Indexed keywords

ANGIOSPERM; CLADISTICS; DIVERGENCE; EVOLUTION; HYBRIDIZATION; INTROGRESSION; PHYLOGENY; PHYLOGEOGRAPHY; REPRODUCTIVE ISOLATION; SPATIAL DISTRIBUTION; SPECIATION (BIOLOGY);

ARISTOLOCHIA; ARISTOLOCHIA KAEMPFERI; ARISTOLOCHIACEAE;

EID: 46249119406     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.2007331     Document Type: Article

References (67)

1. ÁLVAREZ, I., AND J. F. WENDEL. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
2. ARNOLD, M. L. 1997. Natural hybridization and evolution. Oxford University Press, New York, New York, USA.
3. AVISE, J. C. 2000. Phylogeography: The history and formation of species. Harvard University Press, Cambridge, Massachusetts, USA.
4. AVISE, J. C. 2004. Molecular markers, natural history, and evolution. Sinauer, Sunderland, Massachusetts, USA.
5. BAILEY, C. D., AND J. J. DOYLE. 1999. Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: Comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae. Molecular Phylogenetics and Evolution 13: 20-30.
6. BROWER, A. V. Z., R. DESALLE, AND A. VOGLER. 1996. Gene trees, species trees, and systematics: A cladistic perspective. Annual Review of Ecology and Systematics 27: 423-450.
7. BRUEN, T. C., H. PHILIPPE, AND D. BRYANT. 2006. A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665-2681.
8. CLEMENT, M., D. POSADA, AND K. A. CRANDALL. 2000. TCS: A computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659.
9. COMES, H. P., AND J. W. KADEREIT. 1998. The effect of Quaternary climatic changes on plant distribution and evolution. Trends in Plant Science 3: 432-438.
10. COYNE, J. A., AND H. A. ORR. 2004. Speciation. Sinauer, Sunderland, Massachusetts, USA.
11. CRONN, R., R. L. SMALL, T. HASELKORN, AND J. F. WENDEL. 2003. Cryptic repeated genomic recombination during speciation in Gossypium grossypioides. Evolution 57: 2475-2489.
12. DOBZHANSKY, T. 1937. Genetics and the origin of species. Columbia University Press, New York, New York, USA.
13. EBIHARA, A., H. ISHIKAWA, S. MATSUMOTO, S.-J. LIN, K. IWATSUKI, M. TAKAMIYA, Y. WATANO, AND M. ITO. 2005. Nuclear DNA, chloroplast DNA, and ploidy analysis clarified biological complexity of the Vandenboschia radicans complex (Hymenophyllaceae) in Japan and adjacent areas. American Journal of Botany 92: 1535-1547.
14. FARRIS, J., M. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1995. Constructing a significance test for incongruence. Systematic Biology 44: 570-572.
15. FELSENSTEIN, J. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology 22: 240-249.
16. FELSENSTEIN, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annual Review of Genetics 22: 521-565.
17. FRAJMAN, B., AND B. OXELMAN. 2007. Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences. Molecular Phylogenetics and Evolution 43: 140-155.
18. FUERTES AGUILAR, J., J. A. ROSSELLÓ, AND G. N. FELINER. 1999. Nuclear ribosomal DNA (nrDNA) concerted evolution in natural and artificial hybrids of Armeria (Plumbaginaceae). Molecular Ecology 8: 1341-1346.
19. GONZÁLEZ, F., AND D. W. STEVENSON. 2002. A phylogenetic analysis of the subfamily Aristolochioideae (Aristolochiaceae). Revista de la Academia Colombiana de Ciencias 26: 25-60.
20. GRASSLY, N. C., AND E. C. HOLMES. 1997. A likelihood method for the detection of selection and recombination using nucleotide sequences. Molecular Biology and Evolution 14: 239-247.
21. GRASSLY, N. C., AND A. RAMBAUT. 1998. PLATO: Partial likelihoods assessed through optimisation. Website http://evolve.zoo.ox. ac.uk/software/plato/.
22. HARE, M. P. 2001. Prospects for nuclear gene phylogeography. Trends in Ecology & Evolution 16: 700-706.
23. HEWITT, G. M. 2000. The genetic legacy of the Quaternary ice ages. Nature 405: 907-913.
24. HEWITT, G. M. 2001. Speciation, hybrid zones and phylogeography - Or seeing genes in space and time. Molecular Ecology 10: 537-549.
25. HEWITT, G. M. 2004. Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society of London, B, Biological Sciences 359: 183-195.
26. HOLDER, M. T., J. A. ANDERSON, AND A. K. HOLLOWAY. 2001. Difficulties in detecting hybridization. Systematic Biology 50: 978-982.
27. HOWARTH, D. G., AND D. A. BAUM. 2005. Genealogical evidence of homoploid hybrid speciation in an adaptive radiation of Scaevola (Goodeniaceae) in the Hawaiian Islands. Evolution 59: 948-961.
28. HUSON, D. H., AND D. BRYANT. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254-267.
29. IWATA, K. 1975. An essay of a naturalist. Asahi-Shinbunsha, Tokyo, Japan (in Japanese).
30. JAKOB, S. S., AND F. R. BLATTNER. 2006. A chloroplast genealogy of Hordeum (Poaceae): Long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference. Molecular Biology and Evolution 23: 1602-1612.
31. JARAMILLO, M. A., AND E. M. KRAMER. 2004. APETALA3 and PISTILLATA homologs exhibit novel expression patterns in the unique perianth of Aristolochia (Aristolochiaceae). Evolution & Development 6: 449-458.
32. KIMURA, M. 2002. Paleogeography and organisms migration of the Ryukyu Arc. Okinawa Times, Naha, Japan (in Japanese).
33. LINDER, C. R., AND L. H. RIESEBERG. 2004. Reconstructing patterns of reticulate evolution in plants. American Journal of Botany 91: 1700-1708.
34. LOWE, A., S. HARRIS, AND P. ASHTON. 2004. Ecological genetics: design, analysis, and application. Blackwell Science, Oxford, UK.
35. MALLET, J. 2007. Hybrid speciation. Nature 44: 279-283.
36. MATHEWS, S., AND M. J. DONOGHUE. 2000. Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. International Journal of Plant Sciences 161: S41-S55.
37. MAYDEN, R. L. 1997. A hierarchy of species concepts: The denouement in the saga of the species problem. In M. F. Claridge, H. A. Dawah, and M. R. Wilson [eds.], Species: The units of biodiversity, 381-424. Chapman & Hall, New York, New York, USA.
38. MAYDT, J., AND T. LENGAUER. 2006. Recco: Recombination analysis using cost optimization. Bioinformatics (Oxford, England) 22: 1064-1071.
39. MAYR, E. 1995. Species, classification, and evolution. In R. Arai, M. Kato, and Y. Doi [eds.], Biodiversity and evolution, 3-12. National Science Museum Foundation, Tokyo, Japan.
40. MCKINNON, G. E., R. E. VAILLANCOURT, H. D. JACKSON, AND B. M. POTTS. 2001. Chloroplast sharing in the Tasmanian eucalypts. Evolution 55: 703-711.
41. MOORE, W. S. 1995. Inferring phylogenies from mtDNA variation: Mitochondrial-gene trees versus nuclear-gene trees. Evolution 49: 718-726.
42. MURATA, J., T. OHI, S. WU, D. DARNAEDI, T. SUGAWARA, T. NAKANISHI, AND H. MURATA. 2001. Molecular phylogeny of Aristolochia (Aristolochiaceae) inferred from matK sequences. Acta Phytotaxonomica et Geobotanica 52: 75-83.
43. NAGATANI, A., J. W. REED, AND J. CHORY. 1993. Isolation and initial characterization of Arabidopsis mutants that are deficient in phytochrome A. Plant Physiology 102: 269-277.
44. NEINHUIS, C., S. WANKE, K. W. HILU, K. MÜLLER, AND T. BORSCH. 2005. Phylogeny of Aristolochiaceae based on parsimony, likelihood, and Bayesian analyses of trnL-trnF sequences. Plant Systematics and Evolution 250: 7-26.
45. OH, S.-H., AND D. POTTER. 2003. Phylogenetic utility of the second intron of LEAFY in Neillia and Stephanandra (Rosaceae) and implications for the origin of Stephanandra. Molecular Phylogenetics and Evolution 29: 203-215.
46. OHI-TOMA, T., T. SUGAWARA, H. MURATA, S. WANKE, C. NEINHUIS, AND J. MURATA. 2006. Molecular phylogeny of Aristolochia sensu lato (Aristolochiaceae) based on sequences of rbcL, matK, and phyA genes, with special reference to differentiation of chromosome numbers. Systematic Botany 31: 481-492.
47. PETIT, R. J., I. AGUINAGALDE, J.-L. D. BEAULIEU, C. BITTKAU, S. BREWER, R. CHEDDADI, R. ENNOS, S. FINESCHI, D. GRIVET, M. LASCOUX, A. MOHANTY, G. MÜLLER- STARCK, B. DEMESURE-MUSCH, A. PALMÉ, J. P. MARTIN, S. RENDELL, AND G. G. VENDRAMIN. 2003. Glacial refugia: Hotspots but not melting pots of genetic diversity. Science 300: 1563-1565.
48. PETIT, R. J., U. M. CSAIKL, S. BORDÁCS, K. BURG, E. COART, J. COTTRELL, B. V. DAM, ET AL. 2002. Chloroplast DNA variation in European white oaks phylogeography and patterns of diversity based on data from over 2600 populations. Forest Ecology and Management 156: 5-26.
49. POSADA, D. 2002. Evaluation of methods for detecting recombination from DNA sequences: Empirical data. Molecular Biology and Evolution 19: 708-717.
50. POSADA, D., AND K. A. CRANDALL. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics (Oxford, England) 14: 817-818.
51. POSADA, D., AND K. A. CRANDALL. 2001. Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proceedings of the National Academy of Sciences, USA 98: 13757-13762.
52. RAMBAUT, A., AND M. WOROBEY. 2001. PIST: An application for running the informative-sites test (IST), a method for detecting recombination from gene sequence data sets. Website http://evolve.zoo.ox.ac.uk/ software/pist/.
53. RIESEBERG, L. H. 1997. Hybrid origins of plant species. Annual Review of Ecology and Systematics 28: 359-389.
54. SANG, T. 2002. Utility of low-copy nuclear gene sequences in plant phylogenetics. Critical Reviews in Biochemistry and Molecular Biology 37: 121-147.
55. SANG, T., AND Y. ZHONG. 2000. Testing hybridization hypothese based on incongruent gene trees. Systematic Biology 49: 422-434.
56. SCHAAL, B. A., AND K. M. OLSEN. 2000. Gene genealogies and population variation in plants. Proceedings of the National Academy of Sciences, USA 97: 7024-7029.
57. SEEHAUSEN, O. 2004. Hybridization and adaptive radiation. Trends in Ecology & Evolution 19: 198-207.
58. SHIRAIWA, T. 1991. Arima-umanosuzukusa (Aristolochia onoei): The mysterious plant that characterizes Mt. Rokko. Kobe City Education Center, Kobe, Japan (in Japanese).
59. SMALL, R. L., R. C. CRONN, AND J. F. WENDEL. 2004. Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany 17: 145-170.
60. STELLARI, G. M., M. A. JARAMILLO, AND E. M. KRAMER. 2004. Evolution of the APETALA3 and PISTILLATA lineages of MADS-box-containing genes in the basal angiosperms. Molecular Biology and Evolution 21: 506-519.
61. SWOFFORD, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony, distance, and likelihood, version 4. Sinauer, Sunderland, Massachusetts, USA.
62. SYRING, J., A. WILLYARD, R. CRONN, AND A. LISTON. 2005. Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. American Journal of Botany 92: 2086-2100.
63. TEMPLETON, A. R., K. A. CRANDALL, AND C. F. SING. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619-633.
64. WATANABE, K., T. KAJITA, AND J. MURATA. 2006. Chloroplast DNA variation and geographical structure of the Aristolochia kaempferi group (Aristolochiaceae). American Journal of Botany 93: 442-453.
65. WENDEL, J., AND J. J. DOYLE. 1998. Phylogenetic incongruence: Window into genome history and molecular evolution. In D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants II. DNA sequencing, 265-296. Kluwer, Boston, Massachusetts, USA.
66. WOROBEY, M. 2001. A novel approach to detecting and measuring recombination: New insights into evolution in viruses, bacteria, and mitochondria. Molecular Biology and Evolution 18: 1425-1434.
67. ZHANG, D.-X., AND G. M. HEWITT. 2003. Nuclear DNA analyses in genetic studies of populations: Practice, problems and prospects. Molecular Ecology 12: 563-584.