Molecular evidence for reticulate speciation in Astragalus (Fabaceae) as revealed by a case study from sect. Dissitiflori

Botany

Volumn 91, Issue 10, 2013, Pages 702-714

  Bartha, László ^a   Dragoş, Nicolae ^a,b   Molnár, Attila V ^c   Sramkó, Gábor ^c,d  

^a BABE BOLYAI UNIVERSITY   (Romania)

^b INSTITUTE OF BIOLOGICAL RESEARCH   (Romania)

^c UNIVERSITY OF DEBRECEN   (Hungary)

^d EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

Allopolyploidy; Hybridization; NrDNA ITS cloning; Reticulation; Ycf1

Indexed keywords

HYBRIDIZATION; LEGUME; MOLECULAR ANALYSIS; PHYLOGENETICS; PHYLOGENY; PLASTID; POLYPLOIDY; SPECIATION (BIOLOGY); TAXONOMY;

EID: 84885111542     PISSN: 19162804     EISSN: None     Source Type: Journal    
DOI: 10.1139/cjb-2013-0036     Document Type: Article

References (73)

1. Álvarez, I., and Wendel, J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 29(3): 417-434. doi:10.1016/s1055-7903(03)00208-2.
2. Archambault, A., and Strömvik, M.V. 2012. Evolutionary relationships in Oxytropis species, as estimated from the nuclear ribosomal internal transcribed spacer (ITS) sequences point to multiple expansions into the Arctic. Botany, 90(8): 770-779. doi:10.1139/b2012-023.
3. Barneby, R.C. 1964. Atlas of North American Astragalus. Mem. New York Bot. Gard. 13: 1-1188.
4. Bartha, L., Tóth, J.P., Molnár V., A., Dragoş, N., and Sramkó, G. 2012a. Taxonomic implications of multivariate morphometrics in selected taxa of the genus Astragalus sect. Dissitiflori. Contrib. Bot. XLVII: 59-66.
5. Bartha, L., Sramkó, G., and Dragoş, N. 2012b. New PCR primers for partial ycf1 amplification in Astragalus (Fabaceae): promising source for genus-wide phylogenies. Studia UBB Biologia, 51(1): 33-46.
6. Bennett, R.I., and Smith, A.G. 1991. Use of a genomic clone for ribosomal RNA from Brassica oleracea in RFLP analysis of Brassica species. Plant Mol. Biol. 16(4): 685-688. doi:10.1007/BF00023432.
7. Borisova, A.G., Goncharov, N.F., Gorshkova, S.G., Popov, M.G., and Vasil'chenko, I.T. 1946. Astragalus. In Flora of the U.S.S.R. Edited by V.L. Komarov and B.K. Shishkin. Izdatel'stvo Akademii Nauk S.S.S.R., Moscow, Leningrad. pp. 1-918. [Translated from Russian by Israel Prog. Sci. Trans., Jerusalem, 1965.]
8. Borza, T. 1998. Polimorfismul genetic al unor plante rare sau endemice [Genetic polymorphism of some rare or endemic plants]. Ph.D. thesis, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.
9. Bruen, T.C., Philippe, H., and Bryant, D. 2006. A simple and robust statistical test for detecting the presence of recombination. Genetics, 172(4): 2665-2681. doi:10.1534/genetics.105.048975. PMID:16489234.
10. Bunge, A. 1868. Generis Astragali species Gerontogeae. Pars prior. Claves diagnosticae. Mem. Acad. Imp. Sci. St. Petersbourg, 11(16): 1-140.
11. Campbell, C.S., Wojciechowski, M.F., Baldwin, B.G., Alice, L.A., and Donoghue, M.J. 1997. Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Mol. Biol. Evol. 14(1): 81-90. doi:10.1093/oxfordjournals.molbev.a025705. PMID:9000756.
12. Chater, A.O. 1968. Astragalus L. In Flora Europaea. Edited by T.G. Tutin, V.H. Heywood, N.A. Burges, D.H. Valentine, S.M. Walters, and D.A. Webb. Cambridge University Press, Cambridge. pp. 108-124.
13. Ciocârlan, V., and Sârbu, I. 2001. Taxonomia, variabilitatea şi rǎspândirea unor specii de Astragalus L. în Flora României. [Taxonomy, variability, and distribution of certain Astragalus L. species in the Flora of Romania.] Bul. Grad. Bot. Iaşi. 10: 59-61.
14. Clement, M., Posada, D., and Crandall, K. 2000. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9: 1657-1659. doi:10.1046/j.1365-294x. 2000.01020.x. PMID:11050560.
15. Deml, I. 1972. Revision der sektionen Acanthophace Bunge und Aegacantha Bunge der gattung Astragalus L. Boissiera, 21: 1-235.
16. Dong, W., Liu, J., Yu, J., Wang, L., and Zhou, S. 2012. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE. 7(4): e35071. doi:10.1371/journal.pone.0035071. PMID: 22511980.
17. Doyle, J.J., Doyle, J.L., Rauscher, J.T., and Brown, A.H.D. 2004. Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (Glycine subgenus Glycine). New Phytol. 161(1): 121-132. doi:10.1046/j.1469-8137. 2003.00949.x.
18. Drummond, A.J., and Rambaut, A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214-222. doi:10.1186/1471-2148-7-214. PMID:17996036.
19. Farris, J.S., Källersjö, M., Kluge, A.G., and Bult, C. 1994. Testing significance of incongruence. Cladistics. 10(3): 315-319. doi:10.1111/j.1096-0031.1994. tb00181.x.
20. Fedorov, A.A. 1969. Chromosome number of flowering plants. Komar. Bot. Inst. Academy of Science, U.S.S.R., Leningrad.
21. Ghahremani-Nejad, F. 2004. The sections of Astragalus L. with bifurcating hairs in Iran. Turk. J. Bot. 28: 101-117.
22. Grant, V. 1981. Plant speciation. Columbia University Press, New York.
23. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41: 95-98.
24. Hillis, D., Moritz, C., Porter, C., and Baker, R. 1991. Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science. 251(4991): 308-310. doi:10.1126/science.1987647. PMID:1987647.
25. Huson, D.H., and Bryant, D. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23: 254-267. doi:10.1093/molbev/msj030. PMID:16221896.
26. Javanmardi, F., Kazempour Osaloo, S., Maassoumi, A.A., and Nejadsattrai, T. 2012. Molecular phylogeny of Astragalus section Alopecuroidei (Fabaceae) and its allies based on nrDNA ITS and three cpDNAs, matK, trnT-trnY and trnHpsbA sequences. Biochem. Syst. Ecol. 45: 171-178. doi:10.1016/j.bse.2012.07. 029.
27. Judd, W.S., Campbell, C.S., Kellog, E.A., Stevens, P.F., and Donoghue, M.J. 2008. Plant systematics: a phylogenetic approach. Sinauer Associates, Sunderland, Mass.
28. Kazemi, M., Kazempour Osaloo, S., Maasoumi, A.A., and Pouyani, E.R. 2009. Molecular phylogeny of selected Old World Astragalus (Fabaceae): incongruence among chloroplast trnL-F, ndhF and nuclear ribosomal DNA ITS sequences. Nord. J. Bot. 27(5): 425-436. doi:10.1111/j.1756-1051.2009.00285.x.
29. Kazempour Osaloo, S., Maasoumi, A.A., and Murakami, N. 2003. Molecular systematics of the genus Astragalus L. (Fabaceae): phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacers and chloroplast gene ndhF sequences. Plant Syst. Evol. 242: 1-32. doi:10.1007/s00606-003-0014-1.
30. Kazempour Osaloo, S., Maasoumi, A.A., and Murakami, N. 2005. Molecular systematics of the Old World Astragalus (Fabaceae) as inferred from nrDNA ITS sequence data. Brittonia, 57(4): 367-381. doi:10.1663/0007-196X(2005)057 [0367:MSOTOW]2.0.CO;2.
31. Ledingham, G.F. 1960. Chromosome numbers in Astragalus and Oxytropis. Can. J. Genet. Cytol. 2(2): 119-128.
32. Ledingham, G.F., and Rever, B.M. 1963. Chromosome numbers of some Southwest Asian species of Astragalus and Oxytropis (Leguminosae). Can. J. Genet. Cytol. 5(1): 18-32.
33. Liston, A. 1992. Isozyme systematics of Astragalus L. sect. Leptocarpi subsect. Californici (Fabaceae). Syst. Bot. 17(3): 367-379.
34. Liu, Q., Ge, S., Tang, H., Zhang, X., Zhu, G., and Lu, B.-R. 2006. Phylogenetic relationships in Elymus (Poaceae: Triticeae) based on the nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences. New Phytol. 170(2): 411-420. doi:10.1111/j.1469-8137.2006.01665.x. PMID:16608465.
35. Lock, J.M., and Schrire, B.D. 2005. Galegeae. In Legumes of the world. Edited by G. Lewis, B. Schrire, B. Mackinder, and M. Lock. Kew, Richmond, Surrey. pp. 475-487.
36. Martin, E., Duran, A., Dinç, M., Erişen, S., and Babaoǧlu, M. 2008. Karyotype analyses of four Astragalus L. (Fabaceae) species from Turkey. Phytologia, 90(2): 147-159.
37. Masoud, S., Zarre, S., and Ismeilzadeh, J. 2009. New chromosome number reports in tragacanthic Astragalus species. Caryologia, 62(1): 30-36.
38. Nieto Feliner, G., and Roselló, J.A. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol. Phylogenet. Evol. 44(2): 911-919. doi:10.1016/j.ympev.2007.01.013.
39. Nylander, J.A.A. 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
40. O'Kane, S., Schaal, B., and Al-Shehbaz, I. 1996. The origins of Arabidopsis suecica (Brassicaceae) as indicated by nuclear rDNA sequences. Syst. Bot. 21(4): 559-566. doi:10.2307/2419615.
41. Pânzaru, P. 2006. Note sistematiche e distributive relative a Astragalus pastellianus Pollini e a A. peterfii Jáv. (Leguminosae) [Taxonomic and distributive notes on Astragalus pastellianus Pollini and A. peterfii Jáv. (Leguminosae)]. Boll. Mus. Regionale. Sci. Nat. Torino, 23: 721-727.
42. Pavlova, D., and Kozhuharov, S. 1993. Chromosome numbers of Bulgarian angiosperms. Fitologija, 44: 75-76.
43. Philippov, E.G., Kulikov, P.V., and Knjasev, M.S. 2008. Chisla khromosom vidov Astragalus i Hedysarum (Fabaceae) flory Rossii [Chromosome numbers of Astragalus and Hedysarum species of the Russian flora]. Bot. Zhl. 93(10): 1614-1619.
44. Podlech, D. 1988. Revision von Astragalus L. sect. Caprini DC. (Leguminosae). Mitteilungen der Botanischen Staatssammlung München. 25: 1-924.
45. Podlech, D. 1990. Die Typifizierung der altweltlichen Sektionender Gattung Astragalus L. (Leguminosae). Mitteilungen der Botanischen Staatssammlung München. 29: 461-494.
46. Podlech, D. 2008. The genus Astragalus L. (Fabaceae) in Europe with exclusion of the former Soviet Union. Feddes Repert. 119(5-6): 310-387. doi:10.1002/fedr. 200811171.
47. Podlech, D. 2011. Thesaurus Astragalorum: index of all taxa described within the genus Astragalus L. and other genera but belonging to the genus Astragalus. Taxa of the Old World and related taxa of the New World, Ludwig-Maximilians-Universität München.
48. Posada, D. 2006. Collapse: describing haplotypes from sequence alignments. Version 1.2 [computer program]. Available from http://darwin.uvigo.es/software/collapse.html [accessed 15 December 2011].
49. Ranjbar, M. 2004. Astragalus sect. Dissitiflori (Fabaceae) in Iran. Nord. J. Bot. 24(5): 523-531. doi:10.1111/j.1756-1051.2004.tb01634.x.
50. Riahi, M., Zarre, S., Maassoumi, A., Kazempour Osaloo, S., and Wojciechowski, M.F. 2011. Towards a phylogeny for Astragalus section Caprini (Fabaceae) and its allies based on nuclear and plastid DNA sequences. Plant Syst. Evol. 293(1-4): 119-133. doi:10.1007/s00606-011-0417-3.
51. Rieseberg, L.H., and Brunsfeld, S.J. 1992. Molecular evidence and plant introgression. In Molecular systematics of plants. Edited by P.S. Soltis, D.E. Soltis, and J.J. Doyle. Chapman & Hall, New York. pp. 151-176.
52. Sang, T. 2002. Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit. Rev. Biochem. Mol. Biol. 37(3): 121-147. doi:10.1080/10409230290771474. PMID:12139440.
53. Sang, T., Crawford, D.J., and Stuessy, T.F. 1995. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution. Proc. Natl. Acad. Sci. U.S.A. 92(15): 6813-6817. doi:10.1073/pnas.92.15. 6813. PMID:7624325.
54. Scherson, R.A., Choi, H.-K., Cook, D.R., and Sanderson, M.J. 2005. Phylogenetics of New World Astragalus: Screening of novel nuclear loci for the reconstruction of phylogenies at low taxonomic levels. Brittonia, 57(4): 354-366. doi:10. 1663/0007-196X(2005)057[0354:PONWAS]2.0.CO;2.
55. Shaw, J., Lickey, E.B., Schilling, E.E., and Small, R.L. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am. J. Bot. 94(3): 275-288. doi:10.3732/ajb.94.3.275. PMID:21636401.
56. Silvestro, D., and Michalak, I. 2012. RaxmlGUI: a graphical front-end for RAxML. Org. Divers. Evol. 12(4): 335-337. doi:10.1007/s13127-011-0056-0.
57. Sokoloff, P.C., and Gillespie, L.J. 2012. Taxonomy of Astragalus robbinsii var. fernaldii (Fabaceae): molecular and morphological analyses support transfer to Astragalus eucosmus. Botany, 90(1): 11-26. doi:10.1139/b11-077.
58. Soltis, P.S., and Soltis, D.E. 2009. The role of hybridization in plant speciation. Annu. Rev. Plant Biol. 60: 561-588. doi:10.1146/annurev.arplant.043008. 092039. PMID:19575590.
59. Spellenberg, R. 1976. Chromosome numbers and their cytotaxonomic significance for North American Astragalus (Fabaceae). Taxon, 25(4): 463-476. doi: 10.2307/1220528.
60. Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21): 2688-2690. doi:10.1093/bioinformatics/btl446. PMID:16928733.
61. Stamatakis, A., Hoover, P., and Rougemont, J. 2008. A rapid Bootstrap algorithm for the RAxML web servers. Syst. Biol. 57(5): 758-771. doi:10.1080/ 10635150802429642. PMID:18853362.
62. Swofford, D.L. 2002. PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods). Sinauer Associates, Sunderland, Mass.
63. Sytin, A.K. 1999. K sistematike Astragalus brachylobus i Astragalus varius (Fabaceae) [On the systematics of Astragalus brachylobus and Astragalus varius (Fabaceae)]. Botanicheskij Zhurnal. 84(12): 117-124.
64. Sytin, A.K. 2009. Milk-vetches (Astragalus L., Fabaceae) of Eastern Europe and the Caucasus: systematics, geography, evolution. D. Sc. thesis, Institute of Botany, Russian Academy of Sciences, Saint Petersburg, Russia.
65. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28(10): 2731-2739. doi:10.1093/molbev/msr121. PMID:21546353.
66. Watrous, K.M., and Cane, J.H. 2011. Breeding biology of the threadstalk milkvetch, Astragalus filipes (Fabaceae), with a review of the genus. Am. Midl. Nat. 165(2): 225-240. doi:10.1674/0003-0031-165.2.225.
67. Wendel, J.F., and Doyle, J.J. 1998. Phylogenetic incongruence: window into genome history and molecular evolution. In Molecular systematics of plants II: DNA sequencing. Edited by D.E. Soltis, P.S. Soltis, and J.J. Doyle. Kluwer, Dordrecht, the Netherlands. pp. 265-296.
68. White, T.J., Bruns, T., Lee, S., and Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols: a guide to methods and applications. Edited by M.A. Innis, D.H. Gelfand, J.J. Shinsky, and T.J. White. Academic Press, San Diego. pp. 315-322.
69. Willyard, A., Cronn, R., and Liston, A. 2009. Reticulate evolution and incomplete lineage sorting among the ponderosa pines. Mol. Phylogenet. Evol. 52(2): 498-511. doi:10.1016/j.ympev.2009.02.011. PMID:19249377.
70. Wojciechowski, M.F., Sanderson, M.J., Baldwin, B.G., and Donoghue, M.J. 1993. Monophyly of aneuploid Astragalus (Fabaceae): evidence from nuclear ribosomal DNA internal transcribed spacer sequences. Am. J. Bot. 80(6): 711-722. doi:10.2307/2445441.
71. Wojciechowski, M.F., Sanderson, M.J., and Hu, J. 1999. Evidence on the monophyly of Astragalus (Fabaceae) and its major subgroups based on nuclear ribosomal DNA ITS and chloroplast DNA trnL intron data. Syst. Bot. 24(3): 409-437. doi:10.2307/2419698.
72. Xu, B., Wu, N., Gao, X.-F., and Zhang, L.-B. 2012. Analysis of DNA sequences of six chloroplast and nuclear genes suggests incongruence, introgression, and incomplete lineage sorting in the evolution of Lespedeza (Fabaceae). Mol. Phylogenet. Evol. 62(1): 346-358. doi:10.1016/j.ympev.2011.10.007.
73. Zimmer, E.A., Martin, S.L., Beverley, S.M., Kan, Y.W., and Wilson, A.C. 1980. Rapid duplication and loss of genes coding for the alpha chains of hemoglobin. Proc. Natl. Acad. Sci. U.S.A. 77(4): 2158-2162. doi:10.1073/pnas.77.4.2158. PMID:6929543.