Toward consilience in reptile phylogeny: MiRNAs support an archosaur, not lepidosaur, affinity for turtles

Evolution and Development

Volumn 16, Issue 4, 2014, Pages 189-196

  Field, Daniel J ^a,b   Gauthier, Jacques A ^a   King, Benjamin L ^c   Pisani, Davide ^d   Lyson, Tyler R ^a,b   Peterson, Kevin J ^e  

^a YALE UNIVERSITY   (United States)

^b DEPARTMENT OF PALEOBIOLOGY   (United States)

^c MOUNT DESERT ISLAND BIOLOGICAL LABORATORY   (United States)

^d UNIVERSITY OF BRISTOL   (United Kingdom)

^e Lamont Doherty Earth Observatory   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMMON ANCESTRY; DATA SET; GENETIC ANALYSIS; MORPHOLOGY; PHYLOGENY; REPTILE; RNA; TOPOLOGY;

MICRORNA;

ANIMAL; BIRD; CLASSIFICATION; GENETICS; PHYLOGENY; REPTILE;

ANIMALS; BIRDS; MICRORNAS; PHYLOGENY; REPTILES;

EID: 84903880424     PISSN: 1520541X     EISSN: 1525142X     Source Type: Journal    
DOI: 10.1111/ede.12081     Document Type: Article

References (50)

1. Ambros, V., et al. 2003. A uniform system for microRNA annotation. RNA 9: 277-279.
2. Becker, R. E., Valverde, R. A., and Crother, B. I. 2010. Proopiomelanocortin (POMC) and testing the phylogenetic position of turtles (Testudines). J. Zool. Syst. Evol. Res. 49: 148-159.
3. Benton, M. J., Donoghue, P. C. J., and Asher, R. J. 2009. Calibrating and constraining molecular clocks. In S. B. Hedges and S. Kumar (eds.). The Timetree of Life. Oxford University Press, Oxford, pp. 35-86.
4. Bhullar, B.-A. S., and Bever, G. S. 2009. An archosaur-like laterosphenoid in early turtles (Reptilia: Pantestudines). Breviora 518: 1-11.
5. Bremer, K. 1994. Branch support and tree stability. Cladistics 10: 295-304.
6. Carroll, R. L. 2013. Problems of the ancestry of turtles. In D. B. Brinkman, P. A. Holroy, and J. D. Gardner (eds.). Morphology and Evolution of Turtles. Springer, New York, pp. 19-36.
7. Castoe, T. A., et al. 2011. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biol. 12: 406.
8. Chiari, Y., Cahais, V., Galtier, N., and Delsuc, F. 2012. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol. 10: 65.
9. Crawford, N. G., Faircloth, B. C., McCormack, J. E., Brumfield, R. T., Winker, K., and Glenn, T. C. 2012. More than 100 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biol. Lett. 8: 783-786.
10. deBraga, M., and Rieppel, O. 1997. Reptile phylogeny and the interrelationships of turtles. Zool. J. Linn. Soc. 120: 281-354.
11. Drummond, A. J., Ho, S. Y. W., Phillips, M. J., and Rambaut, A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4: e88.
12. Drummond, A. J., Suchard, M. A., Xie, D., and Rambaut, A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29: 1969-1973.
13. Fong, J. J., Brown, J. M., Fujita, M. K., and Boussau, B. A. 2012. Phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia. PLoS ONE 7: e48990.
14. Gauthier, J., Kluge, Arnold G., and Rowe, T. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4: 105-209.
15. Gilbert, S. F., and Corfe, I. 2013. Turtle origins: picking up speed. Dev. Cell 25: 326-328.
16. Hedges, S. B., and Poling, L. L. 1999. A molecular phylogeny of reptiles. Science 283: 998-1000.
17. Iwabe, N., et al. 2005. Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins. Mol. Biol. Evol. 22: 810-813.
18. Jeffroy, O., Brinkmann, H., Delsuc, F., and Philippe, H. 2006. Phylogenomics: the beginning of incongruence? Trends Genet. 22: 225-231.
19. Kozomara, A., and Griffiths-Jones, S. 2011. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39: D152-D157.
20. Kumazawa, Y., and Nishida, M. 1999. Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: statistical evidence for archosaurian affinity of turtles. Mol. Biol. Evol. 16: 784-792.
21. Lartillot, N., Lepage, T., and Blanquart, S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25: 2286-2288.
22. Lee, M. S. Y. 1997. Reptile relationships turn turtle. Nature 389: 246-246.
23. Lee, M. S. Y. 2013. Turtle origins: insights from phylogenetic retrofitting and molecular scaffolds. J. Evol. Biol. 26: 2729-2738.
24. Lee, M. S. Y., Hugall, A. F., Lawson, R., and Scanlon, J. D. 2007. Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood, Bayesian and parsimony analyses. Syst. Biodiv. 5: 371-389.
25. Li, C., Wu, X.-C., Rieppel, O., and Wang, L.-T. 2008. An ancestral turtle from the Late Triassic of southwestern China. Nature 456: 497-501.
26. Lu, B., Yang, W., Dai, Q., and Fu, J. 2013. Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles. PLoS ONE 8: e79348.
27. Lyson, T. R., Bever, G. S., Bhullar, B.-A. S., Joyce, W. G., and Gauthier, J. A. 2010. Transitional fossils and the origin of turtles. Biol. Lett. 6: 453-455.
28. Lyson, T. R., Sperling, E. A., Heimberg, A. M., Gauthier, J. A., King, B. L., and Peterson, K. J. 2012. MicroRNAs support a turtle+lizard clade. Biol. Lett. 8: 104-107.
29. Lyson, T. R., Bever, G. S., Scheyer, T. M., Hsiang, A. Y., and Gauthier, J. A. 2013a. Evolutionary origin of the turtle shell. Curr. Biol. 23: 1113-1119.
30. Lyson, T. R., et al. 2013b. Homology of the enigmatic nuchal bone reveals novel reorganization of the shoulder girdle in the evolution of the turtle shell. Evol. Dev. 15: 317-325.
31. Maddison, D. R., and Maddison, W. P. 2005. MacClade 4. Sinauer Associates, Sunderland.
32. Matsuda, Y., et al. 2005. Highly conserved linkage homology between birds and turtles: bird and turtle chromosomes are precise counterparts of each other. Chromosome Res. 13: 601-615.
33. Rieppel, O., and deBraga, M. 1996. Turtles as diapsid reptiles. Nature 384: 453-455.
34. Rieppel, O., and Reisz, R. R. 1999. The origin and early evolution of turtles. Ann. Rev. Ecol. Syst. 30: 1-22.
35. Salichos, L., and Rokas, A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327-331.
36. Shaffer, H. B., et al. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol. 1: R:28.
37. Shapiro, M. D., et al. 2013. Genomic diversity and evolution of the head crest in the rock pigeon. Science 339: 1063-1067.
38. Shedlock, A. M., et al. 2007. Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc. Nat. Acad. Sci. USA 104: 2767-2772.
39. Shen, X.-X., Liang, D., Wen, J.-Z., and 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.
40. Sperling, E. A., and Peterson, K. J. 2009. microRNAs and metazoan phylogeny: big trees from little genes. In M. J. Telford and D. T. J. Littlewood (eds.). Animal evolution-genomes, trees and fossils. Oxford University Press, Oxford, pp. 157-170.
41. St John, J. A., et al. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol. 13: 415.
42. Swofford, D. L. 2002. PAUP* phylogenetic analysis using parsimony (* and other methods) v.4.0b10 for Macintosh. Sinauer Associates, Sunderland.
43. Tarver, J. E., Donoghue, P. C. J., and Peterson, K. J. 2012. Do miRNAs have a deep evolutionary history? Bioessays 34: 857-866.
44. Tarver, J. E., et al. 2013. miRNAs: small genes with big potential in metazoan phylogenetics. Mol. Biol. Evol. 30: 2369-2382.
45. Thorne, J. L., Kishino, H., and Painter, I. S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15: 1647-1657.
46. Tzika, A. C., Helaers, R., Schramm, G., and Milinkovitch, M. 2011. Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles. Evodevo 2: 19.
47. Wang, Z., et al. 2013. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat. Genet. 45: 701-706.
48. Werneburg, I., and Sánchez-Villagra, M. R. 2009. Timing of organogenesis support basal position of turtles in the amniote tree of life. BMC Evol. Biol. 9: 82.
49. Wheeler, B. M., et al. 2009. The deep evolution of metazoan microRNAs. Evol. Dev. 11: 50-68.
50. Zardoya, R., and Meyer, A. 1998. Complete mitochondrial genome suggests diapsid affinities of turtles. Proc. Nat. Acad. Sci. USA 95: 14226-14231.