A revised dated phylogeny of the arachnid order Opiliones

Frontiers in Genetics

Volumn 5, Issue JUL, 2014, Pages

  Sharma, Prashant P ^a   Giribet, Gonzalo ^b  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Arachnids; Arthropods; Molecular dating; Node dating; Phylogenomics; Total evidence dating

Indexed keywords

ARTICLE; BAYES THEOREM; BIODIVERSITY; CALIBRATION; CARBONIFEROUS; GENETIC VARIABILITY; HORSESHOE CRAB; MOLECULAR GENETICS; MORPHOLOGY; NONHUMAN; OPILIONES; PHYLOGENETIC TREE; PHYLOGENY; TRANSCRIPTOMICS;

EID: 84906264442     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00255     Document Type: Article

References (51)

1. Benton, M. J. (1995). Testing the time axis of phylogenies. Philos. Trans. R. Soc. B Biol. Sci. 349, 5-10. doi: 10.1098/Rstb.1995.0084
2. Benton, M. J., and Donoghue, P. C. (2007). Paleontological evidence to date the Tree of Life. Mol. Biol. Evol. 24, 26-53. doi: 10.1093/molbev/msl150
3. Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540-552. doi: 10.1093/oxfordjournals.molbev.a026334
4. Donoghue, P. C., and Benton, M. J. (2007). Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends Ecol. Evol. 22, 424-431. doi: 10.1016/j.tree.2007.05.005
5. Drummond, A. J., Ho, S. Y., Phillips, M. J., and Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88. doi: 10.1371/journal.pbio.0040088
6. Dunlop, J. A. (2010). Geological history and phylogeny of Chelicerata. Arthr. Struct. Dev. 39, 124-142. doi: 10.1016/j.asd.2010.01.003
7. Dunlop, J. A., Anderson, L. I., Kerp, H., and Hass, H. (2003). Preserved organs of Devonian harvestmen. Nature 425, 916. doi: 10.1038/425916a
8. Dunlop, J. A., Anderson, L. I., Kerp, H., and Hass, H. (2004). A harvestman (Arachnida: Opiliones) from the Early Devonian Rhynie cherts, Aberdeenshire, Scotland. Trans. R. Soc. Edinburgh Earth Sci. 94, 341-354.
9. Dunlop, J. A., Scholtz, G., and Selden, P. A. (2013). "Water-to-land transitions," in Arthropod Biology and Evolution: Molecules, Development, Morphology , eds A. Minelli, G. Boxshall, and G. Fusco. (Heidelberg: Springer), 417-439. doi: 10.1007/978-3-642-36160-9_16
10. Garwood, R. J., Dunlop, J. A., Giribet, G., and Sutton, M. D. (2011). Anatomically modern Carboniferous harvestmen demonstrate early cladogenesis and stasis in Opiliones. Nature Comm. 2, 444. doi: 10.1038/ncomms1458
11. Garwood, R. J., Sharma, P. P., Dunlop, J. A., and Giribet, G. (2014). A new stem-group Palaeozoic harvestman revealed through integration of phylogenetics and development. Curr. Biol. 24, 1-7. doi: 10.1016/j.cub.2014.03.039
12. Giribet, G., and Dunlop, J. A. (2005). First identifiable Mesozoic harvestman (Opiliones: Dyspnoi) from Cretaceous Burmese amber. Proc. R. Soc. B Biol. Sci. 272, 1007-1013. doi: 10.1098/rspb.2005.3063
13. Giribet, G., Edgecombe, G. D., Wheeler, W. C., and Babbitt, C. (2002). Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data. Cladistics 18, 5-70. doi: 10.1006/Clad.2001.0185
14. Giribet, G., Sharma, P. P., Benavides, L. R., Boyer, S. L., Clouse, R. M., De Bivort, B. L.,et al. (2012a). Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement. Biol. J. Linn. Soc. 105, 92-130. doi: 10.1111/J.1095-8312.2011.01774.X
15. Giribet, G., Tourinho, A. L., Shih, C., and Ren, D. (2012b). An exquisitely preserved harvestman (Arthropoda, Arachnida, Opiliones) from the Middle Jurassic of China. Org. Divers. Evol. 12, 51-56. doi: 10.1007/s13127-011-0067-x
16. Giribet, G., Vogt, L., Pérez González, A., Sharma, P., and Kury, A. B. (2010). A multilocus approach to harvestman (Arachnida: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores. Cladistics 26, 408-437. doi: 10.1111/j.1096-0031.2009.00296.x
17. Groh, S., and Giribet, G. (2014). Polyphyly of Caddoidea, reinstatement of the family Acropsopilionidae in Dyspnoi, and a revised classification system of Palpatores (Arachnida, Opiliones). Cladistics doi: 10.1111/cla.12087
18. Guindon, S., and Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704. doi: 10.1080/10635150390235520
19. Hedin, M., Starrett, J., Akhter, S., Schönhofer, A. L., and Shultz, J. W. (2012). Phylogenomic resolution of Paleozoic divergences in harvestmen (Arachnida, Opiliones) via analysis of next- generation transcriptome data. PLoS ONE 7:e428888. doi: 10.1371/journal.pone.0042888.g001
20. Ho, S. Y. W., and Phillips, M. J. (2009). Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 58, 367-380. doi: 10.1093/sysbio/syp035
21. Kodandaramaiah, U. (2011). Tectonic calibrations in molecular dating. Curr. Zool. 57, 116-124.
22. Lartillot, N., Lepage, T., and Blanquart, S. (2009). PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286-2288. doi: 10.1093/bioinformatics/btp368
23. Lartillot, N., and Philippe, H. (2004). A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21, 1095-1109. doi: 10.1093/molbev/msh112
24. Laurin, M. (2012). Recent progress in paleontological methods for dating the Tree of Life. Front. Genet. 3:130. doi: 10.3389/fgene.2012.00130
25. Lee, M. S. Y., Soubrier, J., and Edgecombe, G. D. (2013). Rates of phenotypic and genomic evolution during the Cambrian Explosion. Curr. Biol. 23, 1-7. doi: 10.1016/j.cub.2013.07.055
26. Lepage, T., Bryant, D., Philippe, H., and Lartillot, N. (2007). A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 24, 2669-2680. doi: 10.1093/molbev/msm193
27. Lewis, P. O. (2001). A likelihood approach to estimating phylogeny from discrete morphological characters data. Syst. Biol. 50, 913-925. doi: 10.1080/106351501753462876
28. Mao, K., Milne, R. I., Zhang, L., Peng, Y., Liu, J., Thomas, P.,et al. (2012). Distribution of living Cupressaceae reflects the breakup of Pangea. Proc. Natl. Acad. Sci. U.S.A. 109, 7793-7798. doi: 10.1073/pnas.1114319109
29. Marshall, C. R. (2008). A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. Am. Nat. 171, 726-742. doi: 10.1086/587523
30. Murienne, J., Daniels, S. R., Buckley, T. R., Mayer, G., and Giribet, G. (2014). A living fossil tale of Pangaean biogeography. Proc. R. Soc. B Biol. Sci. 281, 20132648. doi: 10.1098/rspb.2013.2648
31. Murienne, J., Edgecombe, G. D., and Giribet, G. (2010). Including secondary structure, fossils and molecular dating in the centipede tree of life. Mol. Phylogenet. Evol. 57, 301-313. doi: 10.1016/j.ympev.2010.06.022
32. O'Leary, M. A., Bloch, J. I., Flynn, J. J., Gaudin, T. J., Giallombardo, A., Giannini, N. P.,et al. (2013). The placental mammal ancestor and the post-K-Pg radiation of placentals. Science 339, 662-667. doi: 10.1126/science.1229237
33. Organ, C., Nunn, C. L., Machanda, Z., and Wrangham, R. W. (2011). Phylogenetic rate shifts in feeding time during the evolution of Homo. Proc. Natl. Acad. Sci. U.S.A. 108, 14555-14559. doi: 10.1073/Pnas.1107806108
34. Parham, J. F., Donoghue, P. C. J., Bell, C. J., Calway, T. D., Head, J. J., Holroyd, P. A.,et al. (2012). Best practices for justifying fossil calibrations. Syst. Biol. 61, 346-359. doi: 10.1093/sysbio/syr107
35. Pisani, D., Poling, L. L., Lyons-Weiler, M., and Hedges, S. B. (2004). The colonization of land by animals: molecular phylogeny and divergence times among arthropods. BMC Biol. 2, 1-10. doi: 10.1186/1741-7007-2-1
36. Posada, D. (2008). jModelTest: Phylogenetic model averaging. Mol. Biol. Evol. 25, 1253-1256. doi: 10.1093/molbev/msn083
37. Posada, D., and Buckley, T. (2004). Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53, 793-808. doi: 10.1080/10635150490522304
38. Prendini, L., Francke, O. F., and Vignoli, V. (2010). Troglomorphism, trichobothriotaxy and typhlochactid phylogeny (Scorpiones, Chactoidea): more evidence that troglobitism is not an evolutionary dead-end. Cladistics 26, 117-142. doi: 10.1111/J.1096-0031.2009.00277.X
39. Pyron, R. A. (2011). Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst. Biol. 60, 466-481. doi: 10.1093/sysbio/syr047
40. Rambaut, A., and Drummond, A. J. (2009). Tracer v1.5, MCMC Trace Analysis Tool . Available at: http://beast.bio.ed.ac.uk/Tracer(accessed March 25, 2014).
41. Ronquist, F., Klopfstein, S., Vilhelmsen, L., Schulmeister, S., Murray, D. L., and Rasnitsyn, A. P. (2012a). A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst. Biol. 61, 973-999. doi: 10.1093/sysbio/sys058
42. Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D. L., Darling, A., Höhna, S.,et al. (2012b). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539-542. doi: 10.1093/sysbio/sys029
43. Rota-Stabelli, O., Daley, A. C., and Pisani, D. (2013). Molecular timetrees reveal a Cambrian colonization of land and a new scenario for ecdysozoan evolution. Curr. Biol. 23, 392-398. doi: 10.1016/J.Cub.2013.01.026
44. Sauquet, H., Ho, S. Y. W., Gandolfo, M. A., Jordan, G. J., Wilf, P., Cantrill, D. J.,et al. (2012). Testing the impact of calibration on molecular divergence times using a fossIL-rich group: the case of Nothofagus (Fagales). Syst. Biol. 61, 289-313. doi: 10.1093/Sysbio/Syr116
45. Sharma, P. P., and Giribet, G. (2011). The evolutionary and biogeographic history of the armoured harvestmen - Laniatores phylogeny based on ten molecular markers, with the description of two new families of Opiliones (Arachnida). Invertebr. Syst. 25, 106-142. doi: 10.1071/IS11002
46. Sharma, P. P., and Giribet, G. (2012). Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods. Proc. R. Soc. B Biol. Sci. 279, 3501-3509. doi: 10.1098/rspb.2012.0675
47. Signor, P. W., and Lipps, J. H. (1982). Sampling bias, gradual extinction patterns and catastrophes in the fossil record. Geol. Soc. Am. Spec. Pap. 190, 291-296. doi: 10.1130/SPE190-p291
48. 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. doi: 10.1093/oxfordjournals.molbev.a025892
49. Wang, D. Y.-C., Kumar, S., and Hedges, S. B. (1999). Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc. R. Soc. B Biol. Sci. 266, 163-171. doi: 10.1098/rspb.1999.0617
50. Wood, H. M., Matzke, N. J., Gillespie, R. G., and Griswold, C. E. (2013). Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Syst. Biol. 62, 264-284. doi: 10.1093/sysbio/sys092
51. Zuckerkandl, E., and Pauling, L. (1962). "Evolutionary divergence and convergence in proteins," in Horizons in Biochemistry, eds M. Kasha and B. Pullman. (New York: Academic Press), 189-225.