The importance of taxon sampling in genomic studies: An example from the cyclooxygenases of teleost fishes

Molecular Phylogenetics and Evolution

Volumn 56, Issue 1, 2010, Pages 451-455

  Havird, Justin C ^a   Miyamoto, Michael M ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

Comparative genomics; COX; Gene phylogeny; Incomplete sampling

Indexed keywords

PROSTAGLANDIN SYNTHASE;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; FISH; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; COMPARATIVE GENOMIC HYBRIDIZATION; EVOLUTION, MOLECULAR; FISHES; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; PROSTAGLANDIN-ENDOPEROXIDE SYNTHASES; SEQUENCE ANALYSIS, DNA;

TELEOSTEI;

EID: 77953139578     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.04.003     Document Type: Article

References (27)

1. Alfaro M.E., and Holder M.T. The posterior and the prior in Bayesian phylogenetics. Annu. Rev. Ecol. Syst. 37 (2006) 19-42
2. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., and Wheeler D.L. Genbank. Nucleic Acids Res. 36 (2008) D25-D30
3. Flicek P., Aken B.L., Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., Down T., Dyer S.C., Eyre T., Fitzgerald S., Fernandez-Banet J., Gräf S., Haider S., Hammond M., Holland R., Howe K.L., Howe K., Johnson N., Jenkinson A., Kähäri A., Keefe D., Kokocinski F., Kulesha E., Lawson D., Longden I., Megy K., Meidl P., Overduin B., Parker A., Pritchard B., Prlic A., Rice S., Rios D., Schuster M., Sealy I., Slater G., Smedley D., Spudich G., Trevanion S., Vilella A.J., Vogel J., White S., Wood M., Birney E., Cox T., Curwen V., Durbin R., Fernandez-Suarez X.M., Herrero J., Hubbard T.J.P., Kasprzyk A., Proctor G., Smith J., Ureta-Vidal A., and Searle S. Ensembl 2008. Nucleic Acids Res. 36 (2007) D707-D714
4. Gibson G., and Muse S.V. A Primer of Genome Science. third ed. (2009), Sinauer Association, Sunderland, MA
5. Goldman N., Anderson J.P., and Rodrigo A.G. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49 (2000) 652-670
6. Goodman M., Czelusniak J., Moore G.W., Romero-Herrera A.E., and Matsuda G. Fitting the gene lineage into its species lineage. A parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28 (1979) 132-163
7. Havird J.C., Miyamoto M.M., Choe K.P., and Evans D.H. Gene duplications and losses within the cyclooxygenase family of teleosts and other chordates. Mol. Biol. Evol. 25 (2008) 2349-2359
8. Heath T.A., Zwickl D.J., Kim J., and Hillis D.M. Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst. Biol. 57 (2008) 160-166
9. Hedtke S.M., Townsend T.M., and Hillis D.M. Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst. Biol. 55 (2006) 522-529
10. Hurley I.A., Mueller R.L., Dunn K.A., Schmidt E.J., Friedman M., Ho R.K., Prince V.E., Yang Z., Thomas M.G., and Coates M.I. A new time-scale for ray-finned fish evolution. Proc. R. Soc. B 274 (2007) 489-498
11. Ishikawa T.O., Griffin K.J., Banerjee U., and Herschman H.R. The zebrafish genome contains two inducible, functional cyclooxygenase-2 genes. Biochem. Biophys. Res. Commun. 352 (2007) 181-187
12. Ishikawa T.O., and Herschman H.R. Two inducible, functional cyclooxygenase-2 genes are present in the rainbow trout genome. J. Cell. Biochem. 102 (2007) 1486-1492
13. Kass R.E., and Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 90 (1995) 773-795
14. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., and Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics 23 (2007) 2947-2948
15. Lartillot N., and Philippe H. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55 (2006) 195-207
16. Lecointre G., Philippe H., Vân Lê H.L., and Le Guyader H. Species sampling has a major impact on phylogenetic inference. Mol. Phylogenet. Evol. 2 (1993) 205-224
17. Lynch M. The Origins of Genome Architecture (2007), Sinauer Association, Sunderland, MA
18. Moyle P.B., and Cech J.J. Fishes: An Introduction to Ichthyology. fifth ed. (2003), Prentice Hall, Inc., Upper Saddle River, NJ
19. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., and Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53 (2004) 47-67
20. Rokas A., and Abbot P. Harnessing genomics for evolutionary studies. Trends Ecol. Evol. 24 (2009) 192-200
21. Ronquist F., and Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
22. Rouzer C.A., and Marnett L.J. Cyclooxygenases: structural and functional insights. J. Lipid Res. 50 (2009) S29-S34
23. Taylor J.S., Baasch I., Frickey T., Meyer A., and Van de Peer Y. Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res. 13 (2003) 382-390
24. Thornton J.W., and DeSalle R. Gene family evolution and homology: genomics meets phylogenetics. Annu. Rev. Genomics Hum. Genet. 1 (2000) 41-73
25. Volff J.-N. Vertebrate genomes. Genome Dynam. 2 (2006) 1-216
26. Yang Z. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24 (2007) 1586-1591
27. Zwickl, D.J., 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph. D. Dissertation, The University of Texas, Austin, TX.