The phylogenetic history of Selaginellaceae based on DNA sequences from the plastid and nucleus: Extreme substitution rates and rate heterogeneity

Molecular Phylogenetics and Evolution

Volumn 31, Issue 3, 2004, Pages 852-864

  Korall, Petra ^a,b   Kenrick, Paul ^c  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^c DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

26S rDNA; Bayesian inference; Long branches; Maximum parsimony; Phylogeny; Rate heterogeneity; rbcL; Selaginellaceae; Substitution rate

Indexed keywords

SELAGINELLACEAE;

EID: 2442585571     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2003.10.014     Document Type: Article

References (56)

1. Albert, V.A., Mishler, B.D., 1992. On the rationale and utility of weighting nucleotide sequence data. Cladistics 8, 73-83.
2. Andreasen, K., Baldwin, B.G., 2001. Unequal evolutionary rates between annual and perennial lineages of checker mallows (Sidalcea, Malvaceae): evidence from 18S-26S rDNA internal and external transcribed spacers. Mol. Biol. Evol. 18, 936-944.
3. Barraclough, T.G., Savolainen, V., 2001. Evolutionary rates and species diversity in flowering plants. Evolution 55, 677-683.
4. Bousquet, J., Strauss, S.H., Doerksen, A.H., Price, R.A., 1992. Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proc. Natl. Acad. Sci. USA 89, 7844-7848.
5. Bremer, K., 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795-803.
6. Britten, R.J., 1986. Rates of DNA sequence evolution differ between taxonomic groups. Science 231, 1393-1398.
7. DiMichele, W.A., Skog, J.E., 1992. The Lycopsida: a symposium. Ann. Mo. Bot. Gard. 79, 447-449.
8. Donoghue, M.J., Olmstead, R.G., Smith, J.F., Palmer, J.D., 1992. Phylogenetic relationships of Dipsacales based on rbcL sequences. Ann. Mo. Bot. Gard. 79, 333-345.
9. Douady, C.J., Delsuc, F., Boucher, Y., Doolittle, W.F., Douzery, E.J.P., 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20, 248-254.
10. Eriksson, T., 1999. AutoDecay Hypercard Program Distributed by the Author. Bergius Foundation, Royal Swedish Academy of Sciences, Stockholm.
11. Fan, C., Xiang, Q.-Y., 2001. Phylogenetic relationships within Cornus (Cornaceae) based on 26S rDNA sequences. Am. J. Bot. 88, 1131-1138.
12. Farris, J.S., Källersjö, M., Kluge, A.G., Bull, C., 1995. Testing significance of incongruence. Cladistics 90, 315-319.
13. Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
14. Fishbein, M., Hibsch-Jetter, C., Soltis, D.E., Hufford, L., 2001. Phylogeny of Saxifragales (Angiosperms, Eudicots): analysis of a rapid, ancient radiation. Syst. Biol. 50, 817-847.
15. Gaut, B.S., Morton, B.R., McCaig, B.C., Clegg, M.T., 1996. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Evolution 93, 10274-10279.
16. Holmgren, P.K., Holmgren, N.H., Barnett, L.C., 1990. Index Herbariorum 1: The herbaria of the world. Greuter W, Regnum Vegetabile. New York Botanical Garden, New York.
17. Hillis, D.M., Bull, J.J., 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42, 182-192.
18. Huelsenbeck, J.P., Larget, B., Miller, R.E., Ronquist, F., 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51, 673-688.
19. Huelsenbeck, J.P., Ronquist, F., 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
20. Jermy, A.C., 1986. Subgeneric names in Selaginella. Fern Gaz. 13, 117-118.
21. Johnson, K.P., Whiting, M.F., 2002. Multiple genes and the monophyly of Ischnocera (Insecta: Phthiraptera). Mol. Phylogenet. Evol 22, 101-110.
22. Kenrick, P., Crane, P.R., 1997. The Origin and Early Diversification of Land Plants: A Cladistic Study. Smithsonian Institution Press, Washington.
23. Korall, P., Kenrick, P., 2002. Phylogenetic relationships in selaginellaceae based on rbcL sequences. Am. J. Bot. 89, 506-517.
24. Korall, P., Kenrick, P., Therrien, J.P., 1999. Phylogeny of Selaginellaceae: evaluation of generic/subgeneric relationships based on rbcL gene sequences. Int. J. Plant Sci. 160, 585-594.
25. Kranz, H.D., Huss, V.A.R., 1996. Molecular evolution of pteridophytes and their relationships to seed plants: evidence from complete 18S rRNA gene sequences. Plant Syst. Evol. 202, 1-11.
26. Kuzoff, R.K., Sweere, J.A., Soltis, D.E., Soltis, P.S., Zimmer, E.A., 1998. The phylogenetic potential of entire 26S rDNA sequences in plants. Mol. Biol. Evol. 15, 251-263.
27. Lanave, C., Preparata, G., Saccone, C., Serio, G., 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20, 86-93.
28. Leaché, A.D., Reeder, T.W., 2002. Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Syst. Biol. 51, 44-68.
29. Manhart, J.R., 1994. Phylogenetic analysis of green plant rbcL sequences. Mol. Phylogenet. Evol. 3, 114-127.
30. Muse, S.V., 2000. Examining rates and patterns of nucleotide substitution in plants. Plant Mol. Biol. 42, 25-43.
31. Nandi, O.I., Chase, M.W., Endress, P.K., 1998. A combined cladistic analysis of angiosperms using rbcL and non-molecular data. Ann. Mo. Bot. Gard. 85, 137-212.
32. Nylander, J.A.A., 2002. MrModeltest. Version 1.0b. Computer program distributed by the author. Department of Systematic Zoology, Uppsala University, Uppsala, Sweden.
33. Ohyama, K., Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Sano, S., Umesono, K., Shiki, Y., Takeuchi, M., Chang, Z., Aota, S., Inokuchi, H., Ozeki, H., 1986. Chloroplast gene organization deduced from the complete sequence of the liverwort Marchantia polymorpha chloroplast DNA. Nature 322, 572-574.
34. Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818.
35. Rambaut, A., 1996. Se-Al, sequence alignment editor. Version 1.0 alpha 1. Department of Zoology, University of Oxford, Oxford, UK.
36. Rodríguez, F., Oliver, J.L., Marín, A., Medina, J.R., 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142, 485-501.
37. Rydin, C., Wikström, N., 2002. Phylogeny of Isoetes (Lycopsida): resolving basal relationships using rbcL sequences. Taxon 51, 83-89.
38. Savolainen, V., Chase, M.W., Hoot, S.B., Morton, C.M., Soltis, D.E., Bayer, C., Fay, M.F., De Bruijn, A.Y., Sullivan, S., Qiu, Y.-L., 2000. Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst. Biol. 49, 306-362.
39. Smedmark, J.E.E., Eriksson, T., 2002. Phylogenetic relationships of Geum (Rosaceae) and relatives inferred from the nrITS and trnL-trnF regions. Syst. Bot. 27, 303-317.
40. Staden, R., 1996. The Staden sequence analysis package. Mol. Biotechnol. 5, 233-241.
41. Stefanovic, S., Jager, M., Deutsch, J., Broutin, J., Masselot, M., 1998. Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences. Am. J. Bot. 85, 688-697.
42. Sugiura, M., Iida, Y., Oono, K., Takaiwa, F., 1985. The complete nucleotide sequence of a rice 25S rRNA gene. Gene 37, 255-259.
43. Suzuki, M., Glazko, G.V., Nei, M., 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99, 16138-16143.
44. Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, MA.
45. Tavaré, S., 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lect. Math. Life Sci. 17, 57-86.
46. Therrien, J.P., Haufler, C.H., 2000. Phylogeny and biogeography of Selaginella subg. Tetragonostachys based on nuclear ribosomal ITS sequence data. Am. J. Bot. 87, 98.
47. Therrien, J.P., Haufler, C.H., Korall, P., 1999. Phylogeny and biogeography of Selaginella subg. Tetragonostachys. In XVI International Botanical Congress, abstracts. 120. St Louis, USA.
48. Thomas, B.A., 1992. Paleozoic herbaceous lycopsids and the beginnings of extant Lycopodium sens. lat. and Selaginella sens. lat. Ann. Mo. Bot. Gard. 79, 623-631.
49. Thomas, B.A., 1997. Upper Carboniferous herbaceous lycopsids. Rev. Palaeobotan. Palynol. 95, 129-153.
50. Wikström, N., 2001. Diversification and relationships of extant homosporous lycopods. Am. Fern J. 91, 150-165.
51. Wikström, N., Kenrick, P., 1997. Phylogeny of Lycopodiaceae (Lycopsida) and the relationships of Phylloglossum drummondii Kunze based on rbcL sequences. Int. J. Plant Sci. 158, 862-871.
52. Wikström, N., Kenrick, P., 2000a. Phylogeny of epiphytic Huperzia (Lycopodiaceae): paleotropical and neotropical clades corroborated by rbcL sequences. Nordic J. Bot. 20, 165-171.
53. Wikström, N., Kenrick, P., 2000b. Relationships of Lycopodium and Lycopodiella based on combined plastid rbcL gene and trnL intron sequence data. Syst. Bot. 25, 495-510.
54. Wikström, N., Kenrick, P., 2001. Evolution of Lycopodiaceae (Lycopsida): estimating divergence times from rbcL gene sequences by use of nonparametric rate smoothing. Mol. Phylogenet. Evol. 19, 177-186.
55. Wikström, N., Kenrick, P., Chase, M., 1999. Epiphytism and terrestrialization in tropical Huperzia (Lycopodiaceae). Plant Syst. Evol. 218, 221-243.
56. Wilcox, T.P., Zwickl, D.J., Heath, T.A., Hillis, D.M., 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 25, 361-371.