Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

Molecular Phylogenetics and Evolution

Volumn 92, Issue , 2015, Pages 140-146

  Gilbert, Princess S ^a   Chang, Jonathan ^a   Pan, Calvin ^a   Sobel, Eric M ^b   Sinsheimer, Janet S ^a,b   Faircloth, Brant C ^c   Alfaro, Michael E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

Molecular evolution; Next generation sequencing; Non coding DNA; Phylogenetic informativeness; Phylogenomics; Ultraconserved elements

Indexed keywords

PERCOMORPHA; PISCES;

GENETIC MARKER; NUCLEOTIDE;

ANIMAL; CONFIDENCE INTERVAL; CONSERVED SEQUENCE; FISH; GENE LOCUS; GENETIC DATABASE; GENETIC MARKER; GENETICS; GENOME; OPEN READING FRAME; PHYLOGENY; REPRODUCIBILITY; STATISTICAL MODEL;

ANIMALS; CONFIDENCE INTERVALS; CONSERVED SEQUENCE; DATABASES, GENETIC; FISHES; GENETIC LOCI; GENETIC MARKERS; GENOME; LINEAR MODELS; NUCLEOTIDES; OPEN READING FRAMES; PHYLOGENY; REPRODUCIBILITY OF RESULTS;

EID: 84936932932     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2015.05.027     Document Type: Article

References (52)

1. Abascal F., Zardoya R., Telford M.J. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucl. Acids Res. 2010, 38:W7-W13.
2. Bejerano G., Pheasant M., Makunin I., Stephen S., Kent W.J., Mattick J.S., Haussler D. Ultraconserved elements in the human genome. Science 2004, 304:1321-1325.
3. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucl. Acids Res. 2005, 33:D34-D38.
4. Betancur-R R., Broughton R.E., Wiley E.O., Carpenter K., Lopez J.A., Li C., Holcroft N.I., Arcila D., Sanciangco M., Cureton Ii J.C., Zhang F., Buser T., Campbell M.A., Ballesteros J.A., Roa-Varon A., Willis S., Borden W.C., Rowley T., Reneau P.C., Hough D.J., Lu G., Grande T., Arratia G., Orti G. The tree of life and a new classification of bony fishes. PLoS Curr. 2013, 5. 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288.
5. Broughton R.E., Betancur-R R., Li C., Arratia G., Ortí G. Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLoS Curr. 2013, 5. 10.1371/currents.tol.2ca8041495ffafd0c92756e75247483e.
6. Chen W.-J., Santini F., Carnevale G., Chen J.-N., Liu S.-H., Lavoué S., Mayden R.L. New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha). Front. Mar. Sci. 2014, 1. 10.3389/fmars.2014.00053.
7. Crawford, N.G., Faircloth, B.C., 2014. Cloudforest: Code to Calculate Species Trees from Large Genomic Datasets. doi:. doi:10.5281/zenodo.12259.
8. Crawford N.G., Faircloth B.C., McCormack J.E., Brumfield R.T., Winker K., Glenn T.C. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of Archosaurs. Biol. Lett. 2012, 8:783-786.
9. Derti A., Roth F.P., Church G.M., Wu C.T. Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nat. Genet. 2006, 38:1216-1220.
10. Dornburg A., Townsend J.P., Friedman M., Near T.J. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Evol. Bio. 2014, 14:169. 10.1186/s12862-014-0169-0.
11. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 2004, 32:1792-1797.
12. Faircloth B.C., Branstetter M.G., White N.D., Brady S.G. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Mol. Ecol. Res. 2014, 15:489-501. 10.1111/1755-0998.12328.
13. Faircloth, B.C., Chang, J., Alfaro, M.E., 2012a. TAPIR Enables High-throughput Estimation and Comparison of Phylogenetic Informativeness using Locus-specific Substitution Models. arXiv preprint arXiv:12021215 2012, p. 1215.
14. Faircloth B.C., McCormack J.E., Crawford N.G., Harvey M.G., Brumfield R.T., Glenn T.C. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 2012, 61:717-726.
15. Faircloth B.C., Sorenson L., Santini F., Alfaro M.E. A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS One 2013, 8:e65923.
16. Harrell F.E., Dupont M.C. R Package Hmisc 2014, R Foundation for Statistical Computing, Vienna, Austria.
17. Harris R.S. Improved Pairwise Alignment of Genomic DNA. Computer Science and Engineering 2007, The Pennsylvania State University, PA, USA.
18. Hubbard T.J., Aken B.L., Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., Down T., Dyer S.C., Fitzgerald S., Fernandez-Banet J., Graf S., Haider S., Hammond M., Herrero J., Holland R., Howe K., Howe K., Johnson N., Kahari A., Keefe D., Kokocinski F., Kulesha E., Lawson D., Longden I., Melsopp C., Megy K., Meidl P., Ouverdin B., Parker A., Prlic A., Rice S., Rios D., Schuster M., Sealy I., Severin J., Slater G., Smedley D., Spudich G., Trevanion S., Vilella A., Vogel J., White S., Wood M., Cox T., Curwen V., Durbin R., Fernandez-Suarez X.M., Flicek P., Kasprzyk A., Proctor G., Searle S., Smith J., Ureta-Vidal A., Birney E. Ensembl 2007. Nucl. Acids Res. 2007, 35:D610-617.
19. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755.
20. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., Haussler David. The human genome browser at UCSC. Genome Res. 2002, 12:996-1006.
21. Klopfstein S., Kropf C., Quicke D.L. An evaluation of phylogenetic informativeness profiles and the molecular phylogeny of diplazontinae (Hymenoptera, Ichneumonidae). Syst. Biol. 2010, 59:226-241.
22. Li B., Dettai A., Cruaud C., Couloux A., Desoutter-Meniger M., Lecointre G. RNF213, a new nuclear marker for acanthomorph phylogeny. Mol. Phylog. Evol. 2009, 50:345-363.
23. Li C., Lu G., Orti G. Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci. Syst. Biol. 2008, 57:519-539.
24. Li C., Orti G., Zhang G., Lu G. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol. Biol. 2007, 7:44.
25. Lopez-Giraldez F., Moeller A.H., Townsend J.P. Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets. Biomed. Res. Int. 2013, 2013:621604. 10.1155/2013/621604.
26. Lopez-Giraldez F., Townsend J.P. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evol. Biol. 2011, 11:152.
27. McCormack J.E., Faircloth B.C., Crawford N.G., Gowaty P.A., Brumfield R.T., Glenn T.C. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 2012, 22:746-754.
28. McCormack J.E., Harvey M.G., Faircloth B.C., Crawford N.G., Glenn T.C., Brumfield R.T. A phylogeny of birds based on over 1500 loci collected by target enrichment and high-throughput sequencing. PLoS One 2013, 8:e54848.
29. Miller W., Rosenbloom K., Hardison R.C., Hou M., Taylor J., Raney B., Burhans R., King D.C., Baertsch R., Blankenberg D., Kosakovsky Pond S.L., Nekrutenko A., Giardine B., Harris R.S., Tyekucheva S., Diekhans M., Pringle T.H., Murphy W.J., Lesk A., Weinstock G.M., Lindblad-Toh K., Gibbs R.A., Lander E.S., Siepel A., Haussler D., Kent W.J. 28-Way vertebrate alignment and conservation track in the UCSC genome browser. Genome Res. 2007, 17:1797-1808.
30. Near T.J., Dornburg A., Eytan R.I., Keck B.P., Smith W.L., Kuhn K.L., Moore J.A., Price S.A., Burbrink F.T., Friedman M., Wainwright P.C. Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proc. Natl. Acad. Sci. USA 2013, 110:12738-12743.
31. Near T.J., Dornburg A., Kuhn K.L., Eastman J.T., Pennington J.N., Patarnello T., Zane L., Fernández D.A., Jones C.D. Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes. Proc. Natl. Acad. Sci. 2012, 109:3434-3439.
32. Pond S.L., Frost S.D., Muse S.V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005, 21:676-679.
33. Rambaut, A., Suchard, M.A., Xie, D., Drummond, A.J., 2014. Tracer v.16- MCMC Trace Analysis Tool. http://beast.bio.ed.ac.uk/Tracer.
34. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
35. Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2012, 61:539-542.
36. Santini F., Harmon L.J., Carnevale G., Alfaro M.E. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evol. Biol. 2009, 9:194.
37. Santini F., Nguyen M.T.T., Sorenson L., Waltzek T.B., Lynch Alfaro J.W., Eastman J.M., Alfaro M.E. Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae). J. Evol. Biol. 2013, 26:1003-1018.
38. 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. The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst. Biol. 2009, 58:224-239.
39. Siepel A., Bejerano G., Pedersen J.S., Hinrichs A.S., Hou M., Rosenbloom K., Clawson H., Spieth J., Hillier L.W., Richards S., Weinstock G.M., Wilson R.K., Gibbs R.A., Kent W.J., Miller W., Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005, 15:1034-1050.
40. Simons C., Pheasant M., Makunin I.V., Mattick J.S. Transposon-free regions in mammalian genomes. Genome Res. 2006, 16:164-172.
41. Smith B.T., Harvey M.G., Faircloth B.C., Glenn T.C., Brumfield R.T. Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst. Biol. 2014, 63:83-95.
42. Smith W.L., Craig M.T., Quattro J.M. Casting the Percomorph Net Widely: the importance of broad taxonomic sampling in the search for the placement of Serranid and Percid fishes. Copeia 2007, 1:35-55.
43. Stephen S., Pheasant M., Makunin I.V., Mattick J.S. Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Mol. Biol. Evol. 2008, 25:402-408.
44. Sun K., Meiklejohn K.A., Faircloth B.C., Glenn T.C., Braun E.L., Kimball R.T. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Proc. Roy. Soc. B 2014, 281. 10.1098/rspb.2014.0823.
45. R Core Team, 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
46. Townsend J.P. Profiling phylogenetic informativeness. Syst. Biol. 2007, 56:222-231.
47. Townsend J.P., Leuenberger C. Taxon sampling and the optimal rates of evolution for phylogenetic inference. Syst. Biol. 2011, 60:358-365.
48. Townsend J.P., Lopez-Giraldez F., Friedman R. The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. J. Mol. Evol. 2008, 67:437-447.
49. Wainwright P.C., Smith W.L., Price S.A., Tang K.L., Sparks J.S., Ferry L.A., Kuhn K.L., Eytan R.I., Near T.J. The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Syst. Biol. 2012, 61:1001-1027.
50. Warnes, G.R., Bolker, B., Lumley T., 2014. Gtools: Various R Programming Tools. R Package Version 3.4.1. http://CRAN.R-project.org/package=gtools.
51. Wickham H. ggplot2: Elegant Graphics for Data Analysis 2009, Springer, New York.
52. Wickham H. The split-apply-combine strategy for data analysis. J. Stat. Softw. 2011, 40:1-29.