Table of Contents
International Journal of Evolutionary Biology
Volume 2013, Article ID 628467, 12 pages
http://dx.doi.org/10.1155/2013/628467
Research Article

Undersampling Taxa Will Underestimate Molecular Divergence Dates: An Example from the South American Lizard Clade Liolaemini

Department of Biology, 8 Clarkson Avenue, Clarkson University, Potsdam, NY 13699, USA

Received 11 March 2013; Revised 30 August 2013; Accepted 31 August 2013

Academic Editor: Hirohisa Kishino

Copyright © 2013 James A. Schulte II. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. Poe and D. L. Swofford, “Taxon sampling revisited,” Nature, vol. 398, no. 6725, pp. 299–300, 1999. View at Google Scholar · View at Scopus
  2. D. D. Pollock, D. J. Zwickl, J. A. McGuire, and D. M. Hillis, “Increased taxon sampling is advantageous for phylogenetic inference,” Systematic Biology, vol. 51, no. 4, pp. 664–671, 2002. View at Publisher · View at Google Scholar · View at Scopus
  3. D. J. Zwickl and D. M. Hillis, “Increased taxon sampling greatly reduces phylogenetic error,” Systematic Biology, vol. 51, no. 4, pp. 588–598, 2002. View at Publisher · View at Google Scholar · View at Scopus
  4. H. P. Linder, C. R. Hardy, and F. Rutschmann, “Taxon sampling effects in molecular clock dating: an example from the African Restionaceae,” Molecular Phylogenetics and Evolution, vol. 35, no. 3, pp. 569–582, 2005. View at Publisher · View at Google Scholar · View at Scopus
  5. P. C. J. Donoghue and M. J. Benton, “Rocks and clocks: calibrating the Tree of Life using fossils and molecules,” Trends in Ecology and Evolution, vol. 22, no. 8, pp. 424–431, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. J. F. Parham, P. C. J. Donoghue, C. J. Bell et al., “Best practices for justifying fossil calibrations,” Systematic Biology, vol. 61, no. 2, pp. 346–359, 2012. View at Publisher · View at Google Scholar · View at Scopus
  7. H. Sauquet, S. Y. W. Ho, M. A. Gandolfo et al., “Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales),” Systematic Biology, vol. 61, no. 2, pp. 289–313, 2012. View at Publisher · View at Google Scholar · View at Scopus
  8. J. A. Schulte II, J. R. Macey, R. E. Espinoza, and A. Larson, “Phylogenetic relationships in the iguanid lizard genus Liolaemus: multiple origins of viviparous reproduction and evidence for recurring Andean vicariance and dispersal,” Biological Journal of the Linnean Society, vol. 69, no. 1, pp. 75–102, 2000. View at Publisher · View at Google Scholar · View at Scopus
  9. J. A. Schulte II and F. Moreno-Roark, “Live birth among Iguanian lizards predates pliocene-pleistocene glaciations,” Biology Letters, vol. 6, no. 2, pp. 216–218, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. F. M. Fontanella, M. Olave, L. J. Avila, J. W. Sites Jr., and M. Morando, “Molecular dating and diversification of the South American lizard genus Liolaemus (sub-genus Eulaemus) based on nuclear and mitochondrial DNA sequences,” Zoological Journal of the Linnean Society, vol. 164, no. 4, pp. 825–835, 2012. View at Publisher · View at Google Scholar · View at Scopus
  11. A. Dornburg, M. C. Brandley, M. R. McGowen, and T. J. Near, “Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea),” Molecular Biology and Evolution, vol. 29, no. 2, pp. 721–736, 2012. View at Publisher · View at Google Scholar · View at Scopus
  12. W. P. Maddison and D. R. Maddison, “Mesquite: a modular system for evolutionary analysis,” Version 2.75, 2011, http://mesquiteproject.org/mesquite/mesquite.html.
  13. A. Stamatakis, P. Hoover, and J. Rougemont, “A rapid bootstrap algorithm for the RAxML web servers,” Systematic Biology, vol. 57, no. 5, pp. 758–771, 2008. View at Publisher · View at Google Scholar · View at Scopus
  14. M. A. Miller, W. Pfeiffer, and T. Schwartz, “Creating the CIPRES Science Gateway for inference of large phylogenetic trees,” in Proceedings of the Gateway Computing Environments Workshop (GCE '10), pp. 1–8, New Orleans, LA, USA, November 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. R. Lanfear, B. Calcott, S. Y. W. Ho, and S. Guindon, “PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses,” Molecular Biology and Evolution, vol. 29, pp. 1695–1701, 2012. View at Google Scholar
  16. J. Felsenstein and H. Kishino, “Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull,” Systematic Biology, vol. 42, no. 2, pp. 193–200, 1993. View at Google Scholar · View at Scopus
  17. F. Ronquist, M. Teslenko, P. van der Mark et al., “Mrbayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space,” Systematic Biology, vol. 61, no. 3, pp. 539–542, 2012. View at Publisher · View at Google Scholar · View at Scopus
  18. A. Rambaut and A. J. Drummond, “Tracer v1.4 2003–2007 MCMC trace analysis package,” 2007, http://tree.bio.ed.ac.uk/software/tracer/.
  19. M. E. Alfaro, S. Zoller, and F. Lutzoni, “Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence,” Molecular Biology and Evolution, vol. 20, no. 2, pp. 255–266, 2003. View at Publisher · View at Google Scholar · View at Scopus
  20. C. J. Douady, F. Delsuc, Y. Boucher, W. F. Doolittle, and E. J. P. Douzery, “Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability,” Molecular Biology and Evolution, vol. 20, no. 2, pp. 248–254, 2003. View at Publisher · View at Google Scholar · View at Scopus
  21. P. O. Lewis, M. T. Holder, and K. E. Holsinger, “Polytomies and bayesian phylogenetic inference,” Systematic Biology, vol. 54, no. 2, pp. 241–253, 2005. View at Publisher · View at Google Scholar · View at Scopus
  22. M. J. Sanderson, “r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock,” Bioinformatics, vol. 19, no. 2, pp. 301–302, 2003. View at Publisher · View at Google Scholar · View at Scopus
  23. M. J. Sanderson, “Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach,” Molecular Biology and Evolution, vol. 19, no. 1, pp. 101–109, 2002. View at Google Scholar · View at Scopus
  24. S. B. Hedges, J. E. Blair, M. L. Venturi, and J. L. Shoe, “A molecular timescale of eukaryote evolution and the rise of complex multicellular life,” BMC Evolutionary Biology, vol. 4, article 2, 2004. View at Publisher · View at Google Scholar · View at Scopus
  25. D. Pisani, L. L. Poling, M. Lyons-Weiler, and S. B. Hedges, “The colonization of land by animals: Molecular phylogeny and divergence times among arthropods,” BMC Biology, vol. 2, article 1, 2004. View at Google Scholar · View at Scopus
  26. S. Y. W. Ho, M. J. Phillips, A. J. Drummond, and A. Cooper, “Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation,” Molecular Biology and Evolution, vol. 22, no. 5, pp. 1355–1363, 2005. View at Publisher · View at Google Scholar · View at Scopus
  27. T. J. Near, P. A. Meylan, and H. B. Shaffer, “Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles,” American Naturalist, vol. 165, no. 2, pp. 137–146, 2005. View at Publisher · View at Google Scholar · View at Scopus
  28. D. L. Swofford, PAUP*. Phylogenetic Analysis Using Parsimony* (and Other Methods), Version 4.0, Sinauer Associates, Sunderland, Mass, USA, 2003.
  29. J. L. Thorne and H. Kishino, “Divergence time and evolutionary rate estimation with multilocus data,” Systematic Biology, vol. 51, no. 5, pp. 689–702, 2002. View at Publisher · View at Google Scholar · View at Scopus
  30. J. P. Huelsenbeck, B. Larget, and D. Swofford, “A compound Poisson process for relaxing the molecular clock,” Genetics, vol. 154, no. 4, pp. 1879–1892, 2000. View at Google Scholar · View at Scopus
  31. T. Lepage, D. Bryant, H. Philippe, and N. Lartillot, “A general comparison of relaxed molecular clock models,” Molecular Biology and Evolution, vol. 24, no. 12, pp. 2669–2680, 2007. View at Publisher · View at Google Scholar · View at Scopus
  32. J. L. Thorne, H. Kishino, and I. S. Painter, “Estimating the rate of evolution of the rate of molecular evolution,” Molecular Biology and Evolution, vol. 15, no. 12, pp. 1647–1657, 1998. View at Google Scholar · View at Scopus
  33. N. Lartillot and H. Philippe, “A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process,” Molecular Biology and Evolution, vol. 21, no. 6, pp. 1095–1109, 2004. View at Publisher · View at Google Scholar · View at Scopus
  34. E. Paradis, J. Claude, and K. Strimmer, “APE: analyses of phylogenetics and evolution in R language,” Bioinformatics, vol. 20, no. 2, pp. 289–290, 2004. View at Publisher · View at Google Scholar · View at Scopus
  35. M. J. Sanderson and J. A. Doyle, “Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data,” American Journal of Botany, vol. 88, pp. 1499–1516, 2001. View at Google Scholar
  36. A. M. Albino, “Lagartos iguanios del Colhuehuapense (Mioceno Temprano) de Gaiman (Provincia del Chubut, Argentina),” Ameghiniana, vol. 45, pp. 775–782, 2008. View at Google Scholar
  37. L. J. Harmon, J. A. Schulte II, A. Larson, and J. B. Losos, “Tempo and mode of evolutionary radiation in iguanian lizards,” Science, vol. 301, no. 5635, pp. 961–964, 2003. View at Publisher · View at Google Scholar · View at Scopus
  38. A. M. Albino, “Evolution of squamata reptiles in Patagonia based on the fossil record,” Biological Journal of the Linnean Society, vol. 103, no. 2, pp. 441–457, 2011. View at Publisher · View at Google Scholar · View at Scopus
  39. M. Li, Y. Tian, Y. Zhao, and W. Bu, “Higher level phylogeny and the first divergence time estimation of heteroptera (Insecta: Hemiptera) based on multiple genes,” PLoS ONE, vol. 7, no. 2, Article ID e32152, 2012. View at Publisher · View at Google Scholar · View at Scopus
  40. D. G. Mulcahy, B. P. Noonan, T. Moss et al., “Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles,” Molecular Phylogenetics and Evolution, vol. 65, pp. 974–991, 2012. View at Google Scholar
  41. Y. Okajima and Y. Kumazawa, “Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications,” BMC Evolutionary Biology, vol. 10, no. 1, article 141, 2010. View at Publisher · View at Google Scholar · View at Scopus
  42. T. M. Townsend, D. G. Mulcahy, B. P. Noonan et al., “Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation,” Molecular Phylogenetics and Evolution, vol. 61, no. 2, pp. 363–380, 2011. View at Publisher · View at Google Scholar · View at Scopus
  43. N. Vidal and S. B. Hedges, “The molecular evolutionary tree of lizards, snakes, and amphisbaenians,” Comptes Rendus, vol. 332, no. 2-3, pp. 129–139, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. M. F. Breitman, L. J. Avila, J. W. Sites, and M. Morando, “Lizards from the end of the world: phylogenetic relationships of the Liolaemus lineomaculatus section (Squamata: Iguania: Liolaemini),” Molecular Phylogenetics and Evolution, vol. 59, no. 2, pp. 364–376, 2011. View at Publisher · View at Google Scholar · View at Scopus
  45. M. F. Breitman, L. J. Avila, M. Parra, J. W. Sites Jr., and M. Morando, “How lizards survived blizzards: phylogeography of the Liolaemus lineomaculatus group (Liolaemidae) reveals multiple breaks and refugia in southern Patagonia, and their concordance with other co-distributed taxa,” Molecular Ecology, vol. 21, pp. 6068–6085, 2012. View at Google Scholar
  46. F. Fontanella, N. Feltrin, L. J. Avila, J. W. Sites Jr., and M. Morando, “Early stages of divergence: phylogeography, climate modeling, and niche differentiation in the South American lizard Liolaemus petrophilus (Squamata: Liolaemidae),” Ecology and Evolution, vol. 2, pp. 792–808, 2012. View at Google Scholar
  47. I. Vera-Escalona, G. D’Elía, N. Gouin et al., “Lizards on ice: evidence for multiple refugia in Liolaemus pictus (Squamata: Liolaemidae) during the last glacial maximum in the southern Andean beech forests,” Public Library of Science ONE, vol. 7, Article ID e48358, 2012. View at Google Scholar
  48. J. J. Wiens, M. C. Brandley, and T. W. Reeder, “Why does a trait evolve multiple times within a clade? Repeated evolution of snakelike body form in squamate reptiles,” Evolution, vol. 60, no. 1, pp. 123–141, 2006. View at Publisher · View at Google Scholar · View at Scopus
  49. Y. Okajima and Y. Kumazawa, “Mitogenomic perspectives into iguanid phylogeny and biogeography: gondwanan vicariance for the origin of Madagascan oplurines,” Gene, vol. 441, no. 1-2, pp. 28–35, 2009. View at Publisher · View at Google Scholar · View at Scopus
  50. A. F. Hugall, R. Foster, and M. S. Y. Lee, “Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1,” Systematic Biology, vol. 56, no. 4, pp. 543–563, 2007. View at Publisher · View at Google Scholar · View at Scopus
  51. H.-D. Sues and P. E. Olsen, “Triassic vertebrates of Gondwanan aspect from the Richmond basin of Virginia,” Science, vol. 249, no. 4972, pp. 1020–1023, 1990. View at Google Scholar · View at Scopus
  52. J. A. Holman, “Herpetofauna of the Calf Creek local fauna (Lower Oligocene: Cypress Hills Formation) of Saskatchewan,” Canadian Journal of Earth Sciences, vol. 9, pp. 1612–1631, 1972. View at Google Scholar
  53. R. Estes, “The fossil record and early distribution of lizards,” in Advances in Herpetology and Evolutionary Biology: Essays in Honour of Ernest E. Williams, A. G. J. Rhodin and K. Miyata, Eds., pp. 365–398, Museum of Comparative Zoology, Cambridge, Mass, USA, 1983. View at Google Scholar
  54. M. D. Robinson and T. R. van Devender, “Miocene lizards from Wyoming and Nebraska,” Copeia, no. 4, pp. 698–704, 1973. View at Google Scholar
  55. J. A. Holman, “Some amphibians and reptiles from the Oligocene of northeastern Colorado,” Dakoterra, vol. 3, pp. 16–21, 1987. View at Google Scholar
  56. D. A. Yatkola, “Mid-Miocene lizards from western Nebraska,” Copeia, vol. 1976, pp. 645–654, 1976. View at Google Scholar
  57. K. T. Smith, “A new lizard assemblage from the earliest Eocene (zone Wa0) of the Bighorn Basin, Wyoming, USA: biogeography during the warmest interval of the Cenozoic,” Journal of Systematic Palaeontology, vol. 7, no. 3, pp. 299–358, 2009. View at Publisher · View at Google Scholar · View at Scopus
  58. K. T. Smith, “A diverse new assemblage of Late Eocene squamates (Reptilia) from the Chadron Formation of North Dakota, U.S.A.,” Palaeontologia Electronica, vol. 9, no. 2, pp. 1–44, 2006. View at Google Scholar · View at Scopus