Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)

Molecular Phylogenetics and Evolution

Volumn 66, Issue 3, 2013, Pages 748-756

  Luan, Peng Tao ^a   Ryder, Oliver A ^b   Davis, Heidi ^b   Zhang, Ya Ping ^a,c   Yu, Li ^a  

^a YUNNAN UNIVERSITY   (China)

^b INSTITUTE FOR CONSERVATION RESEARCH   (United States)

^c KUNMING INSTITUTE OF ZOOLOGY   (China)

Author keywords

Arctoidea; Indel coding; Insertion deletion events; Phylogenetic analyses

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CARNIVORA; CLASSIFICATION; DNA SEQUENCE; GENETICS; INDEL MUTATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; CARNIVORA; CLASSIFICATION; INDEL MUTATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

CARNIVORA; MAMMALIA; PINNIPEDIA; URSIDAE;

EID: 84873193284     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.10.023     Document Type: Article

References (62)

1. Agnarsson I., Kuntner M., May-Collado L.J. Dogs, cats, and kin: a molecular species-level phylogeny of Carnivora. Mol. Phylogenet. Evol. 2010, 54:726-745.
2. Akaike H. A new look at the statistical model identification. Autom. Control, IEEE Trans. 1974, 19:716-723.
3. Arnason U., Gullberg A., Janke A., Kullberg M. Mitogenomic analyses of caniform relationships. Mol. Phylogenet. Evol. 2007, 45:863-874.
4. Baker R.H., DeSalle R. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst. Biol. 1997, 46:654-673.
5. Belinky F., Cohen O., Huchon D. Large-scale parsimony analysis of metazoan indels in protein-coding genes. Mol. Biol. Evol. 2010, 27:441-451.
6. Benavides E., Baum R., McClellan D., Sites J.W. Molecular phylogenetics of the lizard genus Microlophus (squamata: tropiduridae): aligning and retrieving indel signal from nuclear introns. Syst. Biol. 2007, 56:776-797.
7. Bininda-Emonds O.R.P., Russell A.P. A morphological perspective on the phylogenetic relationships of the extant phocid seals (Mammalia: Carnivora: Phocidae). Bonner Zool. Monogr. 1996, 41:1-256.
8. Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 1988, 42:795-803.
9. Bremer K. Branch support and tree stability. Cladistics 1994, 10:295-304.
10. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17:540-552.
11. Cline M., Hughey R., Karplus K. Predicting reliable regions in protein sequence alignments. Bioinformatics 2002, 18:306-314.
12. Creer S., Pook C.E., Malhotra A., Thorpe R.S. Optimal intron analyses in the trimeresurus radiation of Asian pitvipers. Syst. Biol. 2006, 55:57-72.
13. Creer S. Choosing and using introns in molecular phylogenetics. Evol. Bioinformatics 2007, 3:99.
14. Delisle I., Strobeck C. A phylogeny of the Caniformia (order Carnivora) based on 12 complete protein-coding mitochondrial genes. Mol. Phylogenet. Evol. 2005, 37:192-201.
15. Dessimoz C., Gil M. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol. 2010, 11:R37.
16. Dwivedi B., Gadagkar S.R. Phylogenetic inference under varying proportions of indel-induced alignment gaps. BMC Evol. Biol. 2009, 9:211.
17. Egan A.N., Crandall K.A. Incorporating gaps as phylogenetic characters across eight DNA regions: ramifications for North American Psoraleeae (Leguminosae). Mol. Phylogenet. Evol. 2008, 46:532-546.
18. Eizirik E., Murphy W.J., Koepfli K.P., Johnson W.E., Dragoo J.W., Wayne R.K., O'Brien S.J. Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Mol. Phylogenet. Evol. 2010, 56:49-63.
19. Flower W.H. The Homologies and Notation of the Teeth of Mammalia. J. Anat. Physiol. 1869, 3:262-278.
20. Flynn J.J., Nedbal M.A. Phylogeny of the Carnivora (Mammalia): congruence vs incompatibility among multiple data sets. Mol. Phylogenet. Evol. 1998, 9:414-426.
21. Flynn J.J., Finarelli J.A., Zehr S., Hsu J., Nedbal M.A. Molecular phylogeny of the carnivora (mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst. Biol. 2005, 54:317-337.
22. Fulton T.L., Strobeck C. Molecular phylogeny of the Arctoidea (Carnivora): effect of missing data on supertree and supermatrix analyses of multiple gene data sets. Mol. Phylogenet. Evol. 2006, 41:165-181.
23. Fulton T.L., Strobeck C. Novel phylogeny of the raccoon family (Procyonidae: Carnivora) based on nuclear and mitochondrial DNA evidence. Mol. Phylogenet. Evol. 2007, 43:1171-1177.
24. Giribet G., Wheeler W.C. On gaps. Mol. Phylogenet. Evol. 1999, 13:132-143.
25. González D., Cubeta M.A., Vilgalys R. Phylogenetic utility of indels within ribosomal DNA and β-tubulin sequences from fungi in the Rhizoctonia solani species complex. Mol. Phylogenet. Evol. 2006, 40:459-470.
26. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
27. Hunt, R.M., Barnes, L.G., 1994. Basicranial Evidence for Ursid Affinity of the Oldest Pinnipeds, pp. 57-67.
28. Löytynoja A., Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Natl. Acad. Sci. USA 2005, 102:10557-10562.
29. Löytynoja A., Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 2008, 320:1632-1635.
30. Landan G., Graur D. Heads or tails: a simple reliability check for multiple sequence alignments. Mol. Biol. Evol. 2007, 24:1380-1383.
31. Malhotra A., Creer S., Pook C.E., Thorpe R.S. Inclusion of nuclear intron sequence data helps to identify the Asian sister group of New World pitvipers. Mol. Phylogenet. Evol. 2010, 54:172-178.
32. Morrison D.A. Multiple sequence alignment for phylogenetic purposes. Aust. Syst. Bot. 2006, 19:479-539.
33. Müller K. SeqState: primer design and sequence statistics for phylogenetic DNA datasets. Appl. Bioinformatics 2005, 4:65-69.
34. Müller K. Incorporating information from length-mutational events into phylogenetic analysis. Mol. Phylogenet. Evol. 2006, 38:667-676.
35. Ogden T.H., Rosenberg M.S. How should gaps be treated in parsimony? A comparison of approaches using simulation. Mol. Phylogenet. Evol. 2007, 42:817-826.
36. Peng R., Zeng B., Meng X., Yue B., Zhang Z., Zou F. The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca). Genetica 2007, 397:76-83.
37. Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: advantages of akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 2004, 53:793-808.
38. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
39. Posada D. Selection of models of DNA evolution with jModelTest. Methods Mol. Biol. 2009, 537:93-112.
40. Rokas A., Holland P.W. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 2000, 15:454-459.
41. Rambaut, A., Drummond, A.J., 2007. Tracer v1.5. http://beast.bio.ed.ac.uk/software/tracer.
42. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
43. Sato J.J., Wolsan M., Suzuki H., Hosoda T., Yamaguchi Y., Hiyama K., Kobayashi M., Minami S. Evidence from nuclear DNA sequences sheds light on the phylogenetic relationships of Pinnipedia: single origin with affinity to Musteloidea. Zool. Sci. 2006, 23:125-146.
44. Sato J.J., Wolsan M., Minami S., Hosoda T., Sinaga M.H., Hiyama K., Yamaguchi Y., Suzuki H. Deciphering and dating the red panda's ancestry and early adaptive radiation of Musteloidea. Mol. Phylogenet. Evol. 2009, 53:907-922.
45. Schröder C., Bleidorn C., Hartmann S., Tiedemann R. Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives. Genetica 2009, 448:221-226.
46. Shimodaira H., Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17:1246-1247.
47. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 2002, 51:492-508.
48. Silvestro, D., Michalak, I., 2010. raxmlGUI: A Graphical Front-end for RAxML. http://sourceforge.net/projects/raxmlgui/.
49. Simmons M.P., Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 2000, 49:369-381.
50. Simmons M.P., Ochoterena H., Carr T.G. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Syst. Biol. 2001, 50:454-462.
51. Simmons M.P., Muller K., Norton A.P. The relative performance of indel-coding methods in simulations. Mol. Phylogenet. Evol. 2007, 44:724-740.
52. Sorenson M.D., Franzosa E.A. TreeRot, Version 3 2007, Boston University, Boston, MA.
53. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
54. Swofford, D.L., 2002. PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
55. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Phylogenet. Evol. 2011, 28:2731-2739.
56. Templeton A.R. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 1983, 37:221-244.
57. Wolsan M. Phylogeny and classification of early European Mustelida (Mammalia: Carnivora). Acta Theriol. 1993, 38:345-384.
58. Wyss A.R., Flynn J.J. A phylogenetic analysis and definition of the Carnivora. Mammal Phylogeny: Placentals 1993, 32-52. Springer-Verlag, New York. F.S. Szalay, M.J. Novacek, M.C. McKenna (Eds.).
59. Yu L., Li Q.W., Ryder O.A., Zhang Y.P. Phylogenetic relationships within mammalian order Carnivora indicated by sequences of two nuclear DNA genes. Mol. Phylogenet. Evol. 2004, 33:694-705.
60. Yu L., Zhang Y.P. Phylogeny of the caniform carnivora: evidence from multiple genes. Genetica 2006, 127:65-79.
61. Yu L., Liu J., Luan P.T., Lee H., Lee M., Min M.S., Ryder O.A., Chemnick L., Davis H., Zhang Y.P. New insights into the evolution of intronic sequences of the beta-fibrinogen gene and their application in reconstructing mustelid phylogeny. Zool. Sci. 2008, 25:662-672.
62. Yu L., Luan P.T., Jin W., Ryder O.A., Chemnick L.G., Davis H.A., Zhang Y.P. Phylogenetic utility of nuclear introns in interfamilial relationships of caniformia (order carnivora). Syst. Biol. 2011, 60:175-187.