Evolution of multiple paralogous adenosine kinase genes in the moss genus Hygroamblystegium: Phylogenetic implications

Molecular Phylogenetics and Evolution

Volumn 31, Issue 2, 2004, Pages 505-516

  Vanderpoorten, Alain ^a,b   Shaw, A Jonathan ^a   Cox, Cymon J ^a  

^a DUKE UNIVERSITY   (United States)

^b UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Adenosine kinase gene; Gene duplication; Gene trees; Hygroamblystegium; Moss; Paralogy; Polyploids

Indexed keywords

BRYOPHYTA; HYGROAMBLYSTEGIUM; HYGROAMBLYSTEGIUM TENAX;

EID: 1542371109     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2003.09.020     Document Type: Article

References (46)

1. Avise, J.C., 2000. Phylogeography. Harvard University Press, Cambridge.
2. Buck, W.R., Goffinet, B., Shaw, A.J., 2000. Testing morphological concepts of orders of pleurocarpous mosses (Bryophyta) using phylogenetic reconstructions based on trnL-trnF and rps4 sequences. Mol. Phylogenet. Evol. 16, 180-198.
3. Campbell, C.S., Wojciechowski, M.F., Baldwin, B.G., Alice, L.A., Donoghue, M.J., 1997. Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Mol. Biol. Evol. 14, 81-90.
4. Crum, H.A., Anderson, L.E., 1981. In: Mosses of Eastern North America, vol. 2. Columbia University Press, New York.
5. De Luna, E., Buck, W.R., Akiyama, H., Arikawa, T., Tsubota, H., Gonzalez, D., Newton, A.E., Shaw, A.J., 2000. Ordinal phylogeny within the Hypnobryalean pleurocarpous mosses inferred from cladistic analyses of three chloroplast DNA sequence data sets: trnL-F, rps4, and rbcL. Bryologist 103, 242-256.
6. D'Erchia, H., Gissi, C., Pesole, G., Saccone, C., Arnason, U., 1996. The guinea-pig is not a rodent. Nature 381, 597-600.
7. Derda, G., Wyatt, R., 2000. Isozyme evidence regarding the origins of the allopolyploid species of Polytrichastrum (Polytrichaceae, Bryophyta). Plant Syst. Evol. 220, 37-53.
8. Fritsch, R., 1982. Index to chromosome numbers - Bryophyta. Junk, The Hague.
9. Gornall, R.J., 1999. Population genetic structure in agamospermous plants. In: Hollingsworth, P.M., Bateman, R.M., Gornall, R.J. (Eds.), Molecular Systematics and Plant Evolution. Taylor & Francis, London, pp. 118-138.
10. Hasegawa, M., Kishino, K., Yano, T., 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNH. J. Mol. Evol. 22, 160-174.
11. Hedin, M.C., Maddison, W.P., 2001. Phylogenetic utility and evidence for multiple copies of elongation factor-1 alpha in the spider genus Habronattus (Araneae: Salticidae). Mol. Biol. Evol. 18, 1512-1521.
12. Huelsenbeck, J.P., Ronquist, F., Nielsen, R., Bollack, J.P., 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310-2314.
13. Hugall, A., Stanton, J., Moritz, C., 1999. Reticulate evolution and the origins of ribosomal transcribed spacer diversity in apomictic Melaidogyne. Mol. Biol. Evol. 16, 157-164.
14. Ignatov, M.S., Huttunen, S., 2002. Brachytheciaceae (Bryophyta) - a family of sibling genera. Arctoa 11, 245-296.
15. Levin, D.H., 2000. The origin, expansion, and demise of plant species. Oxford Series in Ecology and Evolution.
16. Maddison, W.P., 1997. Gene trees in species trees. Syst. Biol. 46, 523-536.
17. Mason-Gamer, R., Kellogg, E., 1996. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 45, 524-545.
18. McDaniel, S., Shaw, A.J., 2003. Phylogeographic structure and cryptic speciation in the trans-antarctic moss Pyrrhobryum minoides. Evolution 57, 205-215.
19. Miadlikowska, J., Lutzoni, F., 2000. Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical, and large subunit nuclear ribosomal DNA. Int. J. Plant Sci. 161, 925-958.
20. Moffatt, B.A., Wang, L., Allen, M.S., Stevens, Y.Y., Qin, W., Snider, J., von Schwarzenberg, K., 2000. Adenosine kinase of Arabidopsis. Kinetic properties and gene expression. Plant Physiol. 124, 1775-1785.
21. Ochyra, R., Matteri, C.M., 2001. Bryophyta, Musci: Amblystegiaceae. Flora Cryptogamica de Tierra del Fuego 14, 1-95.
22. Ochyra, R., Streimann, H., 2001. Studies on austral Amblystegiaceae: I. Australian taxa. Nova Hedwigia 73, 453-460.
23. Otto, S.P., Whitton, J., 2000. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401-437.
24. Page, R.D.M., 1998. GeneTree: comparing gene and species trees using reconciled trees. Bioinformatics 14, 819-820.
25. Page, R.D.M., 2000. Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny. Mol. Phylogenet. Evol. 14, 89-106.
26. Page, R.D.M., Charleston, M.A., 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7, 231-240.
27. Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818.
28. Quandt, D., Tangney, R.S., Frahm, J.-P., Frey, W., 2000. A molecular contribution for understanding the Lembophyllaceae (Bryopsida) based on noncoding chloroplast regions (cpDNA) and ITS2 (nrDNA) sequence data-studies in austral temperate rain forest bryophytes 8. J. Hatt. Bot. Lab. 89, 71-92.
29. Rodriguez, F., Oliver, J.F., Marin, A., Medina, J.R., 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142, 485-501.
30. Schomberg, D., Stephan, D., 1997. Adenosine kinase. In: Schomberg, D., Stephan, D. (Eds.), Enzyme Handbook, vol. 13. Springer Verlag, Berlin, pp. 1-9.
31. Shaw, A.J., Allen, B., 2000. Phylogenetic relationships, morphological incongruence, and geographic speciation in the Fontinalaceae (Bryophyta). Mol. Phylogenet. Evol. 16, 225-237.
32. Shaw, A.J., McDaniel, S.F., Werner, O., Ros, R.M., 2002. New frontiers in bryology and lichenology - phylogeography and phylodemography. Bryologist 105, 373-383.
33. Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
34. Simmons, M.P., Donovan Bailey, C., Nixon, K.C., 2000. Phylogeny reconstruction using duplicate genes. Mol. Biol. Evol. 17, 469-473.
35. Soltis, D.E., Soltis, P.S., Doyle, J.J. (Eds.), 1998. Molecular Systematics of Plants II: DNA Sequencing. Kluwer Academic Publishers, Boston.
36. Suh, Y., Thien, L.B., Reeve, H.E., Zimmer, E.H., 1993. Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of ribosomal DNA in Winteraceae. Am. J. Bot. 80, 1042-1055.
37. Swofford, D.L., 2001. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland.
38. Vanderpoorten, A., Jacquemart, A.-L., 2003. Evolutionary mode, tempo, and phylogenetic association of continuous morphological traits in the aquatic moss genus, Amblystegium. J. Evol. Biol., in press.
39. Vanderpoorten, A., Shaw, A.J., Goffinet, B., 2001. Testing controversial alignments in Hygroamblystegium and related genera (Amblystegiaceae: Bryopsida). Evidence from rDNA ITS sequences. Syst. Bot. 28, 470-479.
40. Vanderpoorten, A., Hedenäs, L., Cox, C.J., Shaw, A.J., 2002a. Phylogeny and morphological evolution of the Amblystegiaceae (Bryopsida). Mol. Phylogenet. Evol. 23, 1-21.
41. Vanderpoorten, A., Hedenäs, L., Cox, C.J., Shaw, A.J., 2002b. Circumscription, phylogenetic relationships and taxonomy of Amblystegiaceae inferred from nr and cpDNA sequence data and morphology. Taxon 51, 115-122.
42. Vanderpoorten, A., Goffinet, B., Hedenäs, L., Cox, C.J., Shaw, A.J., 2003. A taxonomic reassessment of the Vittiaceae (Hypnales, Bryopsida): evidence from phylogenetic analyses of combined chloroplast and nuclear sequence data. Plant Syst. Evol. 241, 1-12.
43. von Schwartzenberg, K., Kruse, S., Reski, R., Moffatt, B., Laloue, M., 1998. Cloning and characterization of an adenosine kinase from Physcomitrella involved in cytokinin metabolism. Plant J. 13, 249-257.
44. Wall, D.P., 2002. Use of the nuclear gene glyceraldehyde 3-phosphate dehydrogenase for phylogeny reconstruction of recently diverged lineages in Mitthyridium (Musci: Calymperaceae). Mol. Phylogenet. Evol. 25, 10-26.
45. Wendel, J.F., 2000. Genome evolution in polyploids. Plant Mol. Biol. 42, 225-249.
46. Williams, P., and multiple authors, 1999. Gnuplot 3.71. Distributed by the authors.