Morphology-based phylogenetic binning of the lichen genera Graphis and Allographa (Ascomycota: Graphidaceae) using molecular site weight calibration

Taxon

Volumn 60, Issue 5, 2011, Pages 1450-1457

  Berger, Simon A ^a   Stamatakis, Alexandros ^a   Lücking, Robert ^b  

^a HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

Maximum likelihood; Maximum parsimony; Morphological data; Phenotype based phylogeny

Indexed keywords

CALIBRATION; CLASSIFICATION; COMPUTER SIMULATION; DATA SET; FUNCTIONAL MORPHOLOGY; LICHEN; MOLECULAR ANALYSIS; PARSIMONY ANALYSIS; PHENOTYPE; PHYLOGENETICS; PHYLOGENY; POPULATION DISTRIBUTION; SPECIES DIVERSITY; TAXONOMY;

ASCOMYCOTA; GRAPHIDACEAE; GRAPHIS; OSTROPALES;

EID: 80054923596     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.605020     Document Type: Article

References (49)

1. Baker, R.H., Yu, X. & De Salle, R. 1998. Assessing the relative contribution of molecular and morphological characters in simultaneous analysis trees. Molec. Phylog. Evol. 9: 427-436.
2. Baloch, E., Lücking, R., Lumbsch, H.T. & Wedin, M. 2010. Major clades and phylogenetic relationships between lichenized and nonlichenized lineages in Ostropales (Ascomycota: Lecanoromycetes). Taxon 59: 1483-1494.
3. Barton, N.H., Briggs, D.E.G., Eisen, J.A., Goldstein, D.B. & Patel, N.H. 2007. Evolution. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.
4. Berger, S.A. & Stamatakis, A. 2010. Accuracy of morphology-based phylogenetic fossil placement under maximum likelihood. Pp. 1-8 in: Proceedings of the 8th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-10), Hammamet, Tunisia. IEEE Computer Society.
5. Berger, S.A., Krompaß, D. & Stamatakis, A. 2011. Performance, accuracy and web-Server for evolutionary placement of short sequence reads under maximum-likelihood. Syst. Biol. 60: 291-302.
6. Bininda-Emonds, O.R.P., Brady, S.G., Sanderson, M.J. & Kim, J. 2001. Scaling of accuracy in extremely large phylogenetic trees. Pacific Symp. Biocomputing 2000: 547-558.
7. Cavalli-Sforza, L.L. & Edwards, A.W.F. 1967. Phylogenetic analysis: Models and estimation procedures. Evolution 21: 550-570.
8. Cobbett, A., Wilkinson, M. & Wills, M. 2007. Fossils impact as hard as living taxa in parsimony analyses of morphology. Syst. Biol. 56: 753-766.
9. Doyle, J.A. & Endress, P.K. 2000. Morphological phylogenetic analysis of basal angiosperms: Comparison and combination with molecular data. Int. J. Pl. Sci. 161(suppl): S121-S153.
10. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Molec. Evol. 17: 368-376.
11. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
12. Futuyma, D.J. 2005. Evolution. Sunderland, Massachusetts: Sinauer.
13. Gaubert, P., Wozencraft, W.C., Cordeiro-Estrela, P. & Veron, G. 2005. Mosaics of convergences and noise in morphological phylogenies: What's in a viverrid-like carnivoran? Syst. Biol. 54: 865-894.
14. Goloboff, P.A. 1997. Self-weighted optimization: Tree searches and character state reconstructions under implied transformation costs. Cladistics 13: 225-245.
15. Goloboff, P.A., Carpenter, J.M., Arias, J.S. & Esquivel, D.R.M. 2008. Weighting against homoplasy improves phylogenetic analysis of morphological data sets. Cladistics 24: 758.
16. Grube, M., Baloch, E. & Lumbsch, H.T. 2004. The phylogeny of Porinaceae (Ostropomycetidae) suggests a neotenic origin of perithecia in Lecanoromycetes. Mycol. Res. 108: 1111-1118.
17. Hackett, S.J., Kimball, R.T., Reddy, S., Bowie, R.C.K., Braun, E.L., Braun, M.J., Chojnowski, J.L., Cox, W.A., Han, K.-L., Harshman, J., Huddleston, C., Marks, B.D., Miglia, K.J., Moore, W.S., Sheldon, F.H., Steadman, D.W., Witt, C.C. & Yuri, T. 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320: 1763-1768.
18. Hejnol, A., Obst, M., Stamatakis, A., Ott, M., Rouse, G., Edgecombe, G., Martinez, P., Baguna, J., Bailly, X., Jondelius, U., Wiens, M., Müller, W., Seaver, E., Wheeler, W., Martindale, M., Giribet, G. & Dunn, C. 2009. Rooting the bilaterian tree with scalable phylogenomic and supercomputing tools. Proc. Roy. Soc. Biol. Sci. Ser. B. 276: 4261-4270.
19. Hibbett, D.S., Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T., Kirk, P.M., Lücking, R., Lumbsch, H.T., Lutzoni, F., Matheny, P.B., McLaughlin, D.J., Powell, M.J., Redhead, S., Schoch, C.L., Spatafora, J.W., Stalpers, J.A., Vilgalys, R., Aime, M.C., Aptroot, A., Bauer, R., Begerow, D., Benny, G.L., Castlebury, L.A., Crous, P.W., Dai, Y.C., Gams, W., Geiser, D.M., Griffith, G.W., Gueidan, C., Hawksworth, D.L., Hestmark, G., Hosaka, K., Humber, R.A., Hyde, K.D., Ironside, J.E., Koljalg, U., Kurtzman, C.P., Larsson, K.H., Lichtwardt, R., Longcore, J., Miadlikowska, J., Miller, A., Moncalvo, J.M., Mozley-Standridge, S., Oberwinkler, F., Parmasto, E., Reeb, V., Rogers, J.D., Roux, C., Ryvarden, L., Sampaio, J.P., Schussler, A., Sugiyama, J., Thorn, R.G., Tibell, L., Untereiner, W.A., Walker, C., Wang, Z., Weir, A., Weiss, M., White, M.M., Winka, K., Yao, Y.J. & Zhang, N. 2007. A higher-level phylogenetic classification of the Fungi. Mycol. Res. 111: 509-547.
20. Hillis, D.M. & Wiens, J.J. 2000. Molecules versus morphology in systematics: Conflicts, artifacts, and misconceptions. Pp. 1-19 in: Wiens, J.J. (ed.), Phylogenetic analysis of morphological data. Washington, D.C.: Smithsonian Institution Press.
21. Jenner, R.A. 2004. Accepting partnership by submission? Morphological phylogenetics in a molecular millennium. Syst. Biol. 53: 333-342.
22. Lawrey, J.D., Lücking, R., Sipman, H.J.M., Chaves, J.L., Redhead, S.A., Bungartz, F., Sikaroodi, M. & Gillevet, P.M. 2009. High concentration of basidiolichens in a single family of agaricoid mushrooms (Basidiomycota: Agaricales: Hygrophoraceae). Mycol. Res. 113: 1154-1171.
23. Lücking, R. 2009. The taxonomy of the genus Graphis sensu Staiger (Ascomycota: Ostropales: Graphidaceae). Lichenologist 41: 319-362.
24. Lücking, R. & Rivas Plata, E. 2008. Clave y guía ilustrada para géneros de Graphidaceae. Glalia 1: 1-41.
25. Lücking, R., Archer, A.W. & Aptroot, A. 2009. A world-wide key to the genus Graphis (Ostropales: Graphidaceae). Lichenologist 41: 363-452.
26. Lücking, R., Sérusiaux, E. & Vezda, A. 2005. Phylogeny and systematics of the lichen family Gomphillaceae (Ostropales) inferred from cladistic analysis of phenotype data. Lichenologist 37: 123-170.
27. Lutzoni, F., Kauff, F., Cox, C., McLaughlin, D., Celio, G., Dentinger, B., Padamsee, M., Hibbett, D., James, T.Y., Baloch, E., Grube, M., Reeb, V., Hofstetter, V., Schoch, C., Arnold, A.E., Miadlikowska, J., Spatafora, J., Johnson, D., Hambleton, S., Crockett, M., Shoemaker, R., Sung, G.-H., Lücking, R., Lumbsch, H.T., O'Donnell, K., Binder, M., Diederich, P., Ertz, D., Gueidan, C., Hansen, K., Harris, R.C., Hosaka, K., Lim, Y.-W., Matheny, B., Nishida, H., Pfister, D., Rogers, J., Rossman, A., Schmitt, I., Sipman, H., Stone, J., Sugiyama, J., Yahr, R. & Vilgalys, R. 2004. Assembling the fungal tree of life: Progress, classification, and evolution of subcellular traits. Amer. J. Bot. 91: 1446-1480.
28. Mering, C. von, Hugenholtz, P., Raes, J., Tringe, S., Doerks, T., Jensen, L., Ward, N. & Bork, P. 2007. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315: 1126-1130.
29. Moore, J. & Willmer, P. 1997. Convergent evolution in invertebrates. Biol. Rev. Cambridge Philos. Soc. 72: 1-60.
30. Moret, B.M.E., Roshan, U. & Warnow, T. 2002. Sequence-length requirements for phylogenetic methods. Pp. 343-356 in: Guigó, R. & Gusfield, D. (eds.), Proceedings of the Second International Workshop on Algorithms in Bioinformatics. London: Springer.
31. Mugambi, G.K. & Huhndorf, S.M. 2009. Parallel evolution of hysterothecial ascomata in ascolocularous fungi (Ascomycota, Fungi). Syst. Biodivers. 7: 453-464.
32. Olson, W. & Hall, B.K. 2003. Keywords and concepts in evolutionary developmental biology. Cambridge: Harvard University Press.
33. Pisani, D., Benton, M.J. & Wilkinson, M. 2007 Congruence of morphological and molecular phylogenies. Acta Biotheor. 55: 269-281.
34. Poe, S. & Wiens, J.J. 2000. Character selection and the methodology of morphological phylogenetics. Pp. 20-36 in: Wiens, J.J. (ed.), Phylogenetic analysis of morphological data. Washington, D.C.: Smithsonian Institution Press.
35. Qiu, Y.-L., Dombrovska, O., Lee, J., Li, L., Whitlock, B.A., Bernasconi-Quadroni, F., Rest, J.S., Davis, C.C., Borsch, T., Hilu, K.W., Renner, S.S., Soltis D.E., Soltis, P.S., Zanis, M.J., Cannone, J.J., Gutell, R.R., Powell, M., Savolainen, V., Chatrou, L.W. & Chase, M.W. 2005. Phylogenetic analysis of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. Int. J. Pl. Sci. 166: 815-842.
36. Rivas Plata, E., Hernández, J.E., Lücking, R., Staiger, B., Kalb, K. & Cáceres, M.E.S. 2011. Graphis is two genera - A remarkable case of parallel evolution in lichenized Ascomycota. Taxon 60: 99-107.
37. Rokas, A., Williams, B.L., King, N. & Carroll, S.B. 2003. Genomescale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
38. Schmitt, I., Del Prado, R., Grube, M. & Lumbsch, H.T. 2009. Repeated evolution of closed fruiting bodies is linked to ascoma development in the largest group of lichenized fungi (Lecanoromycetes, Ascomycota). Molec. Phylog. Evol. 52: 34-44.
39. Schoch, C.L., Sung, G.H., Lopez-Giraldez, F., Townsend, J.P., Miadlikowska, J., Hofstetter, V., Robbertse, B., Matheny, P.B., Kauff, F., Wang, Z., Gueidan, C., Andrie, R.M., Trippe, K., Ciufetti, L.M., Wynns, A., Fraker, E., Hodkinson, B.P., Bonito, G., Groenewald, J.Z., Arzanlou, M., de Hoog, G.S., Crous, P.W., Hewitt, D., Pfister, D.H., Peterson, K., Gryzenhout, M., Wingfield, M.J., Aptroot, A., Suh, S.O., Blackwell, M., Hillis, D.M., Griffith, G.W., Castlebury, L.A., Rossman, A.Y., Lumbsch, H.T., Lucking, R., Budel, B., Rauhut, A., Diederich, P., Ertz, D., Geiser, D.M., Hosaka, K., Inderbitzin, P., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Mostert, L., O'Donnell, K., Sipman, H., Rogers, J.D., Shoemaker, R.A., Sugiyama, J., Summerbell, R.C., Untereiner, W., Johnston, P.R., Stenroos, S., Zuccaro, A., Dyer, P.S., Crittenden, P.D., Cole, M.S., Hansen, K., Trappe, J.M., Yahr, R., Lutzoni, F. & Spatafora, J.W. 2009. The Ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst. Biol. 58: 224-239.
40. Scotland, R.W., Olmstead, R.G. & Bennett, J.R. 2003. Phylogeny reconstruction: The role of morphology. Syst. Biol. 52: 539-548.
41. Staiger, B. 2002. Die Flechtenfamilie Graphidaceae. Studien in Richtung einer natürlichen Gliederung. Biblioth. Lichenol. 85: 1-526.
42. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
43. Stearns, S. & Hoekstra, R. 2005. Evolution: An introduction. Oxford: Oxford University Press.
44. Strimmer, K. & Rambaut, A. 2002. Inferring confidence sets of possibly misspecified gene trees. Proc. Roy. Soc. Biol. Sci. Ser. B. 269: 137-142.
45. Wahlberg, N., Braby, M.F., Brower, A.V.Z., De Jong, R., Nylin, S., Pierce, N.E., Sperling, F.A.H., Vila, R., Warren, A.D. & Zakharov, E. 2005. Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proc. Roy. Soc. Biol. Sci. Ser. B. 272: 1577-1586.
46. Wiens, J.J. 2004. The role of morphological data in phylogeny reconstruction. Syst. Biol. 53: 653-661.
47. Wiens, J.J. & Hollingsworth, B.D. 2000. War of the iguanas: Conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards. Syst. Biol. 49: 143-159.
48. Wiley, E.O., Siegel-Causey, D., Brooks, D.R. & Funk, V.A. 1991. The compleat cladist. Lawrence: University of Kansas Museum of Natural History.
49. Wortley, A.H. & Scotland, R.W. 2006. The effect of combining molecular and morphological data in published phylogenetic analyses. Syst. Biol. 55: 677-685.