A versatile and highly efficient toolkit including 102 nuclear markers for vertebrate phylogenomics, tested by resolving the higher level relationships of the caudata

Molecular Biology and Evolution

Volumn 30, Issue 10, 2013, Pages 2235-2248

  Shen, Xing Xing ^a   Liang, Dan ^a   Feng, Yan Jie ^a   Chen, Meng Yun ^a   Zhang, Peng ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

Nuclear marker; Phylogenomic; Phylogeny; Salamander; Vertebrate

Indexed keywords

AMINO ACID; MOLECULAR MARKER; PRIMER DNA;

ARTICLE; CONTROLLED STUDY; CRYPTOBRANCHOIDEA; EVOLUTIONARY DEVELOPMENTAL BIOLOGY; GENE LOCUS; GENE SEQUENCE; GENE TARGETING; GENOME; HYNOBIIDAE; MARKER GENE; MITOCHONDRIAL GENOME; MONOPHYLY; NONHUMAN; NUCLEAR PROTEIN CODING LOCUS; PARAPHYLY; PHYLOGENETIC TREE; PHYLOGENOMICS; PHYLOGENY; POLYMERASE CHAIN REACTION; SALAMANDER; TELEOST; TREE OF LIFE; VERTEBRATE;

NUCLEAR MARKER; PHYLOGENOMIC; PHYLOGENY; SALAMANDER; VERTEBRATE;

ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN; EVOLUTION, MOLECULAR; GENETIC LOCI; GENETIC MARKERS; GENOME; GENOME, HUMAN; GENOMICS; HUMANS; NUCLEAR PROTEINS; PHYLOGENY; POLYMERASE CHAIN REACTION; URODELA; VERTEBRATES;

EID: 84888624759     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst122     Document Type: Article

References (57)

1. Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. 2007. The use of coded PCR primers enables highthroughput sequencing ofmultiple homolog amplification products by 454 parallel sequencing. PLoS One 2:e197.
2. Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K, Glenn TC. 2012. More than 1000 ultraconserved elements provide evidence that turtles are the sister group to archosaurs. Biol Lett. 8: 783-786.
3. Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6:361-375.
4. Duellman WE, Trueb L. 1994. Biology of amphibians. Baltimore (MD): Johns Hopkins University Press.
5. Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749.
6. Faircloth BC, Glenn TC. 2012. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS One 7:e42543.
7. Faircloth BC, McCormack JE, Crawford NG, Brumfield RT, Glenn TC. 2012. Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales. Syst Biol. 61:717-726.
8. Fong JJ, Brown JM, Fujita MK, Boussau B. 2012. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia. PLoS One 7: e48990.
9. Fong JJ, Fujita MK. 2011. Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata. Mol Phylogenet Evol. 61:300-307.
10. Frost DR, Grant T, Faivovich J, et al. (18 co-authors). 2006. The amphibian tree of life. Bull Am Mus Nat Hist. 297:8-370.
11. Gao KQ, Shubin NH. 2001. Late Jurassic salamanders from northern China. Nature 410:574-577.
12. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximumlikelihood phylogenies: Assessing the performance of PhyML 3.0. Syst Biol. 59:307-321.
13. Hugall AF, Foster R, Lee MSY. 2007. Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Syst Biol. 56:543-563.
14. Inoue JG, Miya M, Lam K, Tay BH, Danks JA, Bell J, Walker TI, Venkatesh B. 2010. Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): A mitogenomic perspective. Mol Biol Evol. 27:2576-2586.
15. Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518.
16. Kishino H, Hasegawa M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol. 29: 170-179.
17. Künstner A, Wolf JBW, Backström N, et al. (13 co-authors). 2010. Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol. 19:266-276.
18. Lanfear R, Calcott B, Ho SYW, Guindon S. 2012. Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 29:1695-1701.
19. Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286-2288.
20. Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst Biol. 58:130-145.
21. Lemmon AR, Emme SA, Lemmon EM. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 61:727-744.
22. Li C, Ortí G, Zhang G, Lu G. 2007. A practical approach to phylogenomics: The phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol Biol. 7:44.
23. Li C, Riethoven JJ, Naylor GJ. 2012. EvolMarkers: A database for mining exon and intron markers for evolution, ecology and conservation studies. Mol Ecol Resour. 12:967-971.
24. Liu L, Yu L, Edwards SV. 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol. 10:302.
25. McCormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC. 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 22: 746-754.
26. McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT. 2013. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol. 66:526-538.
27. Meyer A, Van de Peer Y. 2005. From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). Bioessays 27:937-945.
28. Meyer M, Stenzel U, Hofreiter M. 2008. Parallel tagged sequencing on the 454 platform. Nat Protoc. 3:267-278.
29. Murphy WJ, Eizirik E, JohnsonWE, Zhang YP, Ryder OA, O'Brien SJ. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
30. Philippe H, Derelle R, Lopez P, et al. (20 co-authors). 2009. Phylogenomics revives traditional views on deep animal relationships. Curr Biol. 19:706-712.
31. Philippe H, Telford M. 2006. Large-scale sequencing and the new animal phylogeny. Trends Ecol Evol. 21:614-620.
32. Portik DM, Wood PL, Grismer JL, Stanley EL, Jackman TR. 2011. Identification of 104 rapidly-evolving nuclear protein-coding markers for amplification across scaled reptiles using genomic resources. Conserv Genet Resour. 4:1-10.
33. Pyron RA, Wiens JJ. 2011. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol Phylogenet Evol. 61: 543-583.
34. Roelants K, Gower DJ, Wilkinson M, Loader SP, Biju SD, Guillaume K, Moriau L, Bossuyt F. 2007. Global patterns of diversification in the history of modern amphibians. Proc Natl Acad Sci USA. 104: 887-892.
35. Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
36. Ronquist F, Teslenko M, Van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61:539-542.
37. Roure B, Baurain D, Philippe H. 2013. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol. 30:197-214.
38. San Mauro D. 2010. A multilocus timescale for the origin of extant amphibians. Mol Phylogenet Evol. 56:554-561.
39. San Mauro D, Vences M, Alcobendas M, Zardoya R, Meyer A. 2005. Initial diversification of living amphibians predated the breakup of Pangaea. Am Nat. 165:590-599.
40. Shen XX, Liang D, Wen JZ, Zhang P. 2011. Multiple genome alignments facilitate development of NPCL markers: A case study of tetrapod phylogeny focusing on the position of turtles. Mol Biol Evol. 28: 3237-3252.
41. Shen XX, Liang D, Zhang P. 2012. The development of three long universal nuclear protein-coding locus markers and their application to osteichthyan phylogenetics with nested PCR. PLoS One 7: e39256.
42. Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol. 51:492-508.
43. Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246-1247.
44. Song S, Liu L, Edwards SV, Wu S. 2012. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci USA. 109: 14942-14947.
45. Spinks PQ, Thomson RC, Barley AJ, Newman CE, Shaffer HB. 2010. Testing avian, squamate, and mammalian nuclear markers for cross amplification in turtles. Conserv Genet Resour. 2:127-129.
46. Spinks PQ, Thomson RC, Lovely GA, Shaffer HB. 2009. Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from Emydid turtles. BMC Evol Biol. 9:56.
47. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
48. Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW. 2009. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol. 27:1025-1031.
49. Thomson RC, Shedlock AM, Edwards SV, Shaffer HB. 2008. Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Mol Phylogenet Evol. 49:514-525.
50. Thomson RC, Wang IJ, Johnson JR. 2010. Genome-enabled development of DNA markers for ecology, evolution and conservation. Mol Ecol. 19:2184-2195.
51. Townsend TM, Alegre RE, Kelley ST, Wiens JJ, Reeder TW. 2008. Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: An example from squamate reptiles. Mol Phylogenet Evol. 47:129-142.
52. Weisrock DW, Harmon LJ, Larson A. 2005. Resolving deep phylogenetic relationships in salamanders: Analyses of mitochondrial and nuclear genomic DNA. Syst Biol. 54:758-777.
53. Wiens J, Bonett R, Chippindale P. 2005. Ontogeny discombobulates phylogeny: paedomorphosis and higher-level salamander relationships. Syst Biol. 54:91-110.
54. Wright TF, Schirtzinger EE, Matsumoto T, et al. (11 co-authors). 2008. A multilocus molecular phylogeny of the parrots (Psittaciformes): support for a Gondwanan origin during the cretaceous. Mol Biol Evol. 25:2141-2156.
55. Zhang P, Wake DB. 2009. Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogenet Evol. 53:492-508.
56. Zhang P, Zhou H, Chen YQ, Liu YF, Qu LH. 2005. Mitogenomic perspectives on the origin and phylogeny of living amphibians. Syst Biol. 54:391-400.
57. Zhou XM, Xu SX, Zhang P, Yang G. 2011. Developing a series of conservative anchor markers and their application to phylogenomics of Laurasiatherian mammals. Mol Ecol Resour. 11: 134-140.