Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns

Molecular Phylogenetics and Evolution

Volumn 48, Issue 1, 2008, Pages 176-187

  Shepherd, Lara D ^a   Holland, Barbara R ^b   Perrie, Leon R ^a  

^a MUSEUM OF NEW ZEALAND TE PAPA TONGAREWA   (New Zealand)

^b MASSEY UNIVERSITY   (New Zealand)

Author keywords

Asplenium; Chloroplast DNA; Conflict; Homoplasy; Recombination

Indexed keywords

CHLOROPLAST DNA;

ARTICLE; CHLOROPLAST; CLASSIFICATION; FERN; GENETIC RECOMBINATION; GENETICS; PHYLOGENY;

CHLOROPLASTS; DNA, CHLOROPLAST; FERNS; PHYLOGENY; RECOMBINATION, GENETIC;

ASPLENIUM; FILICOPHYTA;

EID: 44949251634     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.02.023     Document Type: Article

References (65)

1. Birky C. Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proceedings of the National Academy of Sciences USA 92 (1995) 11331-11338
2. Bollback J.P. Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution 19 (2002) 1171-1180
3. Brownlie, G., 1969. Flore de la Nouvelle-Calédonie et dépendances, no. 3, Ptéridophytes. Muséum National D'Histoire Naturelle, Paris.
4. Brownsey P.J. A taxonomic revision of the New Zealand species of Asplenium. New Zealand Journal of Botany 15 (1977) 39-86
5. Brownsey P.J. Asplenium hybrids in the New Zealand flora. New Zealand Journal of Botany 15 (1977) 601-637
6. Brownsey P.J. Asplenium lucidum Forst. f., an illegitimate name for the New Zealand shining spleenwort. New Zealand Journal of Botany 17 (1979) 217-218
7. Brownsey P.J. Aspleniaceae. Flora of Australia 48 (1998) 295-327
8. Brownsey P.J., and Smith-Dodsworth J.C. New Zealand ferns and allied plants (2000), David Bateman Ltd., Auckland, New Zealand
9. Bull J., and Charnov E. On irreversible evolution. Evolution 30 (1985) 1149-1155
10. Carvajal-Rodriguez A., Crandall K.A., and Posada D. Recombination estimation under complex evolutionary models with coalescent composite-likelihood method. Molecular Biology and Evolution 23 (2006) 817-827
11. Farris J.S., Källersjö M., Kluge A.G., and Bull C. Testing significance of incongruence. Cladistics 10 (1994) 315-319
12. Gastony G.J., and Yatskievych G. Maternal inheritance of the chloroplast and mitochondrial genomes in cheilanthoid ferns. American Journal of Botany 79 (1992) 716-722
13. Goldman N., and Whelan S. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Molecular Biology and Evolution 17 (2000) 975-978
14. Green P.S. Aspleniaceae. Flora of Australia 49 (1994) 591-597
15. Hendy M.D., Penny D., and Steel M. A discrete Fourier analysis for evolutionary trees. Proceedings of the National Academy of Sciences 91 (1994) 3339-3343
16. Huber K., Langton M., Penny D., Moulton V., and Hendy M.D. Spectronet: a package for computing spectra and median networks. Applied Bioinformatics 1 (2002) 159-161
17. Hudson R.R., and Kaplan N.L. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics (1985) 147-164
18. Huelsenbeck J.P., and Ronquist F.R. MrBayes: Bayesian inference of phylogeny. Biometrics 17 (2001) 754-755
19. Huson D.H., and Bryant D. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23 (2006) 254-267
20. Janssen T., and Schneider H. Exploring the evolution of humus collecting leaves in drynarioid ferns (Polypodiaceae, Polypodiidae) based on phylogenetic evidence. Plant Systematics and Evolution 252 (2005) 175-197
21. Kennedy M., Holland B.R., Gray R.D., and Spencer H.G. Untangling long branches: identifying phylogenetic signals using spectral analysis, neighbor-net, and consensus networks. Systematic Biology 54 (2005) 620-633
22. Khakhlova O., and Bock R. Elimination of deleterious mutations in plastid genomes by gene conversion. The Plant Journal 46 (2006) 85-94
23. Kreier H.-P., and Schneider H. Phylogeny and biogeography of the staghorn genus Platycerium (Polypodiaceae, Polypodiidae). American Journal of Botany 93 (2006) 217-225
24. Lento G., Hickson R., Chambers G., and Penny D. Use of spectral analysis to test hypotheses on the origin of pinnipeds. Molecular Biology and Evolution 12 (1995) 28-52
25. Lin Y., McLenachan P., Gore A., Phillips M., Ota R., Hendy M., and Penny D. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Molecular Biology and Evolution 19 (2002) 2060-2070
26. Lockhart P., Steel M., Barbrook A.C., Huson D.H., Charleston M.A., and Howe C.J. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Molecular Biology and Evolution 15 (1998) 1183-1188
27. Lockhart P.J., Howe C.J., Bryant D.A., Beanland T.J., and Larkum A.W.D. Substitutional bias confounds inference of organelle origins from sequence data. Journal of Molecular Evolution 34 (1992) 153-162
28. Löve, A., Löve, D., Pichi Sermolli, R.E.G., 1977. Cytotaxonomical atlas of the Pteridophyta. J. Cramer, Vaduz, Germany.
29. Marticorena C., and Rodriguez R. Flora de Chile vol. 1 (1995), Universidad de Concepción, Concepción, Chile
30. McGlone M. Goodbye Gondwana. Journal of Biogeography 32 (2005) 739-740
31. McVean G., Awadalla P., and Fearnhead P. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160 (2002) 1231-1241
32. Murakami N., Nogami S., Watanabe M., and Iwatsuki K. Phylogeny of the Aspleniaceae inferred from rbcL nucleotide sequences. American Fern Journal 89 (1999) 232-243
33. Olmstead R., and Palmer J. Chloroplast DNA systematics: a review of methods and data analysis. American Journal of Botany 81 (1994) 1205-1224
34. Perrie L.R., and Brownsey P.J. trn L intron variation in New Zealand taxa of the Asplenium obtusatum chloroplast group. Tuhinga 15 (2004) 1-5
35. Perrie L.R., and Brownsey P.J. Insights into the biogeography and polyploid evolution of New Zealand Asplenium from chloroplast DNA sequence data. American Fern Journal 95 (2005) 1-21
36. Perrie L.R., and Brownsey P.J. Molecular evidence for long-distance dispersal in the New Zealand pteridophyte flora. Journal of Biogeography 34 (2007) 2028-2038
37. Perrie L.R., Brownsey P.J., Lockhart P.J., Brown E.A., and Large M.F. Biogeography of temperate Australasian Polystichum ferns as inferred from chloroplast sequence and AFLP. Journal of Biogeography 30 (2003) 1729-1736
38. Perrie L.R., Shepherd L.D., and Brownsey P.J. Asplenium × lucrosum nothosp nov.: a sterile hybrid widely and erroneously cultivated as "Asplenium bulbiferum". Plant Systematics and Evolution 250 (2005) 243-257
39. Pirie M., Vargas M., Botermans M., Bakker F., and Chatrou L. Ancient paralogy in the cpDNA trnL-F region in the Annonaceae: implications for plant molecular systematics. American Journal of Botany 94 (2007) 1003-1016
40. Posada D., and Buckley T.R. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53 (2004) 793-808
41. Rambaut A., and Grassly N. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in the Biosciences 13 (1997) 235-238
42. Ranker T., Smith A.R., Parris B.S., Geiger J., Haufler C., Straub S., and Schneider H. Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy. Taxon 53 (2004) 415-428
43. Rokas A., Ladoukakis E., and Zouros E. Animal mitochondrial DNA recombination revisited. Trends in Ecology and Evolution 18 (2003) 411-417
44. Roux J. Lectotypification of Asplenium lucidum Burm. f. (Aspleniaceae). Taxon 43 (1994) 641-642
45. Sanmartin I., and Ronquist F. Southern Hemisphere biogeography analyzed with event-based models: plant versus animal patterns. Systematic Biology 53 (2004) 216-243
46. Schneider H., Ranker T.A., Russell S.J., Cranfill R., Geiger J.M.O., Aguraiuja R., Wood K.R., Grundmann M., Kloberdanz K., and Vogel J.C. Origin of the endemic fern genus Diella coincides with the renewal of Hawaiian terrestrial life in the Miocene. Proceedings of the Royal Society B 272 (2005) 455-460
47. Schneider H., Russell S.J., Cox C.J., Bakker F., Henderson S., Rumsey F., Barrett J., Gibby M., and Vogel J.C. Chloroplast phylogeny of Asplenioid ferns based on rbcL and trnL-F spacer sequences (Polypodiiae, Aspleniaceae) and its implications for biogeography. Systematic Botany 29 (2004) 260-274
48. Shepherd L., and Lambert D. The relationships and origins of the New Zealand wattlebirds (Passeriformes, Callaeatidae) from DNA sequence analyses. Molecular Phylogenetics and Evolution 43 (2007) 480-492
49. Shepherd L., Perrie L., and Brownsey P.J. Fire and ice: volcanic and glacial impacts on the phylogeography of the New Zealand forest fern Asplenium hookerianum. Molecular Ecology 16 (2007) 4536-4549
50. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16 (1999) 1114-1116
51. Simon C., Buckley T., Frati F., Stewart J., and Beckenbach A. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annual Review of Ecology, Evolution and Systematics 37 (2006) 545-579
52. Slowinski J.B. Molecular polytomies. Molecular Phylogenetics and Evolution 19 (2001) 114-120
53. Soltis P., Soltis D., and Chase M. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402 (1999) 402-404
54. Stuessy T. Sympatric plant speciation in islands?. Nature 443 (2006) E12
55. Swofford D., Olsen G., Waddell P., and Hillis D. Phylogenetic inference. In: Hillis D., Moritz C., and Mable B. (Eds). Molecular Systematics (1996), Sinauer, Sunderland, MA
56. * and other methods). Sinauer Associates, Sunderland, MA.
57. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24 (1997) 4876-4882
58. Tindale M.D., and Roy S.K. A cytotaxonomic survey of the Pteridophyta of Australia. Australian Systematic Botany 15 (2002) 839-937
59. Trewick S., Paterson A., and Campbell H. Hello New Zealand. Journal of Biogeography 34 (2007) 1-6
60. Vogel J.C., Russell S.J., Rumsey F.J., Barrett J.A., and Gibby M. Evidence for maternal transmission of chloroplast DNA in the genus Asplenium (Aspleniaceae, Pteridophyta). Botanica Acta 111 (1998) 247-249
61. Vogel J.C., Russell S.J., Rumsey F.J., Barrett J.A., and Gibby M. On hybrid formation in the rock fern Asplenium × alternifolium (Aspleniaceae, Pteridophyta). Botanica Acta 111 (1998) 247-249
62. Vogl C., Badger J., Kearney P., Li M., Clegg M., and Jiang T. Probabilistic analysis indicates discordant gene trees in chloroplast evolution. Journal of Molecular Evolution 56 (2003) 330-340
63. Wilcox, T., 2004. SG Runner 2.0.1: a MAC OSX shell-wrapper for Seq-Gen.
64. Wolf P., Rowe C., Sinclair R., and Hasebe M. Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Research 10 (2003) 59-65
65. Wolfe A., and Randle C. Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: implications for plant molecular systematics. Systematic Botany 29 (2004) 1011-1020