Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree

Molecular Phylogenetics and Evolution

Volumn 28, Issue 2, 2003, Pages 328-340

  De Jong, Wilfried W ^a,b   Van Dijk, Marjon A M ^a   Poux, Céline ^a   Kappé, Guido ^a   Van Rheede, Teun ^a   Madsen, Ole ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EDENTATA; EUTHERIA; MURIDAE; RODENTIA;

ATAXIN 1; ATAXIN-1; BACTERIAL PROTEIN; HEAT SHOCK PROTEIN; HSPB PROTEIN, HELICOBACTER PYLORI; NERVE PROTEIN; NUCLEAR PROTEIN; PRIMER DNA; TUMOR NECROSIS FACTOR ALPHA;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BAYES THEOREM; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; MAMMAL; MOLECULAR GENETICS; PHYLOGENY; POINT MUTATION; STATISTICAL MODEL;

AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; BAYES THEOREM; DNA PRIMERS; HEAT-SHOCK PROTEINS; LIKELIHOOD FUNCTIONS; MAMMALS; MOLECULAR SEQUENCE DATA; NERVE TISSUE PROTEINS; NUCLEAR PROTEINS; PHYLOGENY; POINT MUTATION; TUMOR NECROSIS FACTOR-ALPHA;

EID: 0141721403     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(03)00116-7     Document Type: Conference Paper

References (48)

1. Adkins, R.M., Gelke, E.L., Rowe, D., Honeycutt, R.L., 2001. Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Mol. Biol. Evol. 18, 777-791.
2. Amrine-Madsen, H., Koepfli, K.-P., Wayne, R.K., Springer, M.S., 2003. A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships. Mol. Phylogenet. Evol. 28, 225-240.
3. Arnason, U., Adegoke, J.A., Bodin, K., Born, E.W., Esa, Y.B., Gullberg, A., Nilsson, M., Short, R.V., Xu, X., Janke, A., 2002. Mammalian mitogenomic relationships and the root of the eutherian tree. Proc. Natl. Acad. Sci. USA 99, 8151-8156.
4. Bapteste, E., Philippe, H., 2002. The potential value of indels as phylogenetic markers: position of trichomonads as a case study. Mol. Biol. Evol. 19, 972-977.
5. Delsuc, F., Scally, M., Madsen, O., Stanhope, M.J., de Jong, W.W., Catzeflis, F.M., Springer, M.S., Douzery, E.J.P., 2002. Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting. Mol. Biol. Evol. 19, 1656-1671.
6. Douady, C., Chatelier, P., Madsen, O., de Jong, W.W., Catzeflis, F., Springer, M.S., Stanhope, M.J., 2002. Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews. Mol. Phylogenet. Evol. 25, 200-209.
7. Giribet, G., Wheeler, W.C., 1999. On gaps. Mol. Phylogenet. Evol. 13, 132-143.
8. Graur, D., Li, W.-H., 1999. Fundamentals of Molecular Evolution. Sinauer, Sunderland.
9. Gu, X., Li, W.-H., 1995. The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J. Mol. Evol. 40, 464-473.
10. Gupta, R.S., 2001. The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int. Microbiol. 4, 187-202.
11. Huchon, D., Madsen, O., Sibbald, M.J., Ament, K., Stanhope, M.J., Catzeflis, F., de Jong, W.W., Douzery, E.J.P., 2002. Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes. Mol. Biol. Evol. 19, 1053-1065.
12. Huelsenbeck, J.P., Ronquist, F., 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
13. Janke, A., Magnell, O., Wieczorek, G., Westerman, M., Arnason, U., 2002. Phylogenetic analysis of 18S rRNA and the mitochondrial genomes of the wombat, Vombatus ursinus, and the spiny anteater, Tachyglossus aculeatus: increased support for the Marsupionta hypothesis. J. Mol. Evol. 54, 71-80.
14. Kappé, G., Franck, E., Verschuure, P., Boelens, W.C., Leunissen, J.A.M., de Jong, W.W., in press. The human genome encodes ten α-crystallin-related small heat shock protein. Cell Stress Chaperon 8, 53-61.
15. Keeling, P.J., Palmer, J.D., 2000. Parabasalian flagellates are ancient eukaryotes. Nature 405, 635-637.
16. Keeling, P.J., Palmer, J.D., 2001. Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase. Proc. Natl. Acad. Sci. USA 98, 10745-10750.
17. Lin, Y.-H., McLenachan, P.A., Gore, A.R., Phillips, M.J., Ota, R., Hendy, M., Penny, D., 2002a. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Mol. Biol. Evol. 19, 2060-2070.
18. Lin, Y.-H., Waddell, P.J., Penny, D., 2002b. Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires. Gene 294, 119-129.
19. Madsen, O., Scally, M., Douady, C.J., Kao, D.J., DeBry, R.W., Adkins, R., Amrine, H.M., Stanhope, M.J., de Jong, W.W., Springer, M.S., 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409, 610-614.
20. Matthee, C.A., Burzlaff, J.D., Taylor, J.F., Davis, S.K., 2001. Mining the mammalian genome for artiodactyl systematics. Syst. Biol. 50, 367-390.
21. McGuire, G., Denham, M.C., Balding, D.J., 2001. Models of sequence evolution for DNA sequences containing gaps. Mol. Biol. Evol. 18, 481-490.
22. Misawa, K., Janke, A., 2003. Revisiting the Glires concept - phylogenetic analysis of nuclear sequences. Mol. Phylogenet. Evol. 28, 320-327.
23. Misawa, K., Nei, M., 2003. Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests over-credibility of Bayesian trees. J. Mol. Evol., in press.
24. Murphy, W.J., Eizirik, E., Johnson, W.E., Zhang, Y.P., Ryder, O.A., O'Brien, S.J., 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 409, 614-618.
25. Murphy, W.J., Eizirik, E., O'Brien, S.J., Madsen, O., Scally, M., Douady, C.J., Teeling, E., Ryder, O.A., Stanhope, M.J., de Jong, W.W., Springer, M.S., 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294, 2348-2351.
26. Nei, M., Kumar, S., 2000. Molecular Evolution and Phylogenetics. Oxford University Press, Oxford.
27. Nei, M., Glazko, G.V., 2002. Estimation of divergence times for a few mammalian and several primate species. J. Hered. 93, 157-164.
28. Nikaido, M., Cao, Y., Harada, M., Okada, N., Hasegawa, M., 2003. Mitochondrial phylogeny of hedgehogs and their relation to Eulipotyphla based on maximum likelihood analysis. Mol. Phylogenet. Evol. 28, 276-284.
29. Ophir, R., Graur, D., 1997. Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene 205, 191-202.
30. Phillips, A., Janies, D., Wheeler, W., 2000. Multiple sequence alignment in phylogenetic analysis. Mol. Phylogenet. Evol. 16, 317-330.
31. Poux, C., van Rheede, T., Madsen, O., de Jong, W.W., 2002. Sequence gaps join mice and men: phylogenetic evidence from deletions in two proteins. Mol. Biol. Evol. 19, 2035-2037.
32. Posoda, D., Crandall, K.A., 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818.
33. Qian, B., Goldstein, R.A., 2001. Distribution of indel lengths. Proteins 45, 102-104.
34. Reyes, A., Pesole, G., Saccone, C., 2000. Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny. Gene 259, 177-187.
35. Rokas, A., Holland, P.W., 2000. Rare genomic changes as a tool for phylogenetics. Trends. Ecol. Evol. 15, 454-459.
36. Rosenberg, M.S., Kumar, S., 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 98, 10751-10756.
37. Scally, M., Madsen, O., Douady, C.J., de Jong, W.W., Stanhope, M.J., Springer, M.S., 2001. Molecular evidence for the major clades of placental mammals. J. Mammal. Evol. 8, 239-277.
38. Schatzl, H.M., Da Costa, M., Taylor, L., Cohen, F.E., Prusiner, S.B., 1995. Prion protein gene variation among primates. J. Mol. Biol. 245, 362-374.
39. Simmons, M.P., Ochoterena, H., 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49, 369-381.
40. Schmitz, J., Ohme, M., Zischler, H., 2002. The complete mitochondrial sequence of Tarsius bancanus: evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA. Mol. Biol. Evol. 19, 544-553.
41. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (* and other Methods), Version 4.0b10. Sunderland, Massachusetts: Sinauer Associates.
42. Teeling, E.C., Madsen, O., Stanhope, M.J., de Jong, W.W., Van Den Bussche, R., Springer, M.S., 2002. Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats. Proc. Natl. Acad. Sci. USA 99, 1432-1436.
43. van Dijk, M.A.M., Paradis, E., Catzeflis, F., de Jong, W.W., 1999. The virtues of gaps: xenarthran (edentate) monophyly supported by a unique deletion in αA-crystallin. Syst. Biol. 48, 94-106.
44. van Rheede, T., Smolenaars, M.M.W., Madsen, O., de Jong, W.W., 2003. Molecular evolution of the mammalian prion protein. Mol. Biol. Evol. 20, 111-121.
45. Venkatesh, B., Erdmann, M.V., Brenner, S., 2001. Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proc. Natl. Acad. Sci. USA 98, 11382-11387.
46. Waddell, P.J., Kishino, H., 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Inform. Ser. Workshop Genome Inform. 12, 141-154.
47. Waddell, P.J., Shelley, S., Sorenson, M., 2003. Testing placental interordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA plus Metropolis coupled MCMC optimized GTR amino acid and codon models. Mol. Phylogenet. Evol. 28, 197-224.
48. Wopfner, F., Weidenhofer, G., Schneider, R., von Brunn, A., Gilch, S., Schwarz, T.F., Werner, T., Schatzl, H.M., 1999. Analysis of 27 mammalian and 9 avian PrPs reveals high conservation of flexible regions of the prion protein. J. Mol. Biol. 289, 1163-1178.