Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate


The evolution and great diversity of genome size has been of long-standing interest to biologists, but has seldom been investigated on a broad phylogenetic scale. Here we present a comparative quantitative analysis of factors shaping genome size evolution in amphibians, the extant class of vertebrates with the largest variation in genome size. We find that amphibian genomes have undergone saltations in size, although these are rare and the evolutionary history of genome size in amphibians has otherwise been one of gradual, time-dependent variation (that is, Brownian motion). This macroevolutionary homogeneity is remarkable given the evolutionary and ecological diversity of most other aspects of the natural history of amphibians. Contrary to previous claims, we find no evidence for associations between life cycle complexity and genome size despite the high diversity of reproductive modes and the multiple events of independent evolution of divergent life cycles in the group. Climate (temperature and humidity) affects genome size indirectly, at least in frogs, as a consequence of its effect on premetamorphic developmental period, although directionality of the relationship between developmental period and genome size is not unequivocal.

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Fig. 1: Amphibian phylogeny with clades painted to reflect shifts in Ornstein–Uhlenbeck parameters according to the best performing 1lou model for genome size evolution.
Fig. 2: Phenogram showing ancestral state reconstructions for genome size evolution in amphibians under the two best performing mvMORPH models (two-trait mean Brownian motion in colour, three-trait mean Brownian motion underlain in grey).
Fig. 3: Rate estimates for genome size evolution for the three amphibian orders showing posterior distributions as estimated by BAMM showing mean rates per clade and through time.
Fig. 4: Best-scoring phylogenetic path analysis models.

Data availability

All genome size measurements generated for this study are available in the supplementary information.


  1. 1.

    Mirsky, A. E. & Ris, H. The desoxyribonucleic acid content of animal cells and its evolutionary significance. J. Gen. Physiol. 34, 451–462 (1951).

    CAS  Article  Google Scholar 

  2. 2.

    Thomas, C. A. The genetic organization of chromosomes. Annu. Rev. Genet. 5, 237–256 (1971).

    CAS  Article  Google Scholar 

  3. 3.

    Lynch, M. The Origins of Genome Architecture (Sinauer Associates, Sunderland, 2007).

  4. 4.

    Lynch, M. & Conery, J. S. The origins of genome complexity. Science 302, 1401–1404 (2003).

    CAS  Article  Google Scholar 

  5. 5.

    Gregory, T. R. Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol. Rev. Camb. Philos. Soc. 76, 65–101 (2001).

    CAS  Article  Google Scholar 

  6. 6.

    Elliott, T. A. & Gregory, T. R. What's in a genome? The C-value enigma and the evolution of eukaryotic genome content. Phil. Trans. R. Soc. B 370, 20140331-10 (2015).

    Article  Google Scholar 

  7. 7.

    Olmo, E., Capriglione, T. & Odierna, G. Genome size evolution in vertebrates: trends and constraints. Comp. Biochem. Phys. C 92B, 447–453 (1989).

    Google Scholar 

  8. 8.

    Kang, M. et al. Adaptive and nonadaptive genome size evolution in Karst endemic flora of China. New. Phytol. 202, 1371–1381 (2014).

    CAS  Article  Google Scholar 

  9. 9.

    Petrov, D. A. Evolution of genome size: new approaches to an old problem. Trends Genet. 17, 23–28 (2001).

    CAS  Article  Google Scholar 

  10. 10.

    Whitney, K. D. & Garland, T. Did genetic drift drive increases in genome complexity? PLoS Genet. 6, e1001080 (2010).

    Article  Google Scholar 

  11. 11.

    Lynch, M. Statistical inference on the mechanisms of genome evolution. PLoS Genet. 7(6), e1001389 (2011).

    CAS  Article  Google Scholar 

  12. 12.

    Gregory, T. R. (ed.) The Evolution of the Genome (Academic/Elsevier, Burlington, 2005).

  13. 13.

    Ogata, H., Fujibuchi, W. & Kanehisa, M. The size differences among mammalian introns are due to the accumulation of small deletions. FEBS Lett. 390, 99–103 (1996).

    CAS  Article  Google Scholar 

  14. 14.

    Sun, C., Lopez Arriaza, J. R. & Mueller, R. L. Slow DNA loss in the gigantic genomes of salamanders. Genome Biol. Evol. 4, 1340–1348 (2012).

    Article  Google Scholar 

  15. 15.

    Smith, J. J. et al. Genic regions of a large salamander genome contain long introns and novel genes. BMC Genomics 10, 19–11 (2009).

    CAS  Article  Google Scholar 

  16. 16.

    Schlötterer, C. & Harr, B. Drosophila virilis has long and highly polymorphic microsatellites. Mol. Biol. Evol. 17, 1641–1646 (2000).

    Article  Google Scholar 

  17. 17.

    Tenaillon, M. I., Hollister, J. D. & Gaut, B. S. A triptych of the evolution of plant transposable elements. Trends Plant Sci. 15, 471–478 (2010).

    CAS  Article  Google Scholar 

  18. 18.

    Sun, C. & Mueller, R. L. Hellbender genome sequences shed light on genomic expansion at the base of crown salamanders. Genome Biol. Evol. 6, 1818–1829 (2014).

    Article  Google Scholar 

  19. 19.

    Sun, C. et al. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biol. Evol. 4, 168–183 (2012).

    Article  Google Scholar 

  20. 20.

    Kapusta, A., Suh, A. & Feschotte, C. Dynamics of genome size evolution in birds and mammals. Proc. Natl Acad. Sci. USA 114, E1460–E1469 (2017).

    CAS  Article  Google Scholar 

  21. 21.

    Crollius, H. R. et al. Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis. Genome Res. 10, 939–949 (2000).

    Article  Google Scholar 

  22. 22.

    Lower, S. S. et al. Genome size in North American fireflies: substantial variation likely driven by neutral processes. Genome Biol. Evol. 9, 1499–1512 (2017).

    CAS  Article  Google Scholar 

  23. 23.

    Lefébure, T. et al. Less effective selection leads to larger genomes. Genome Res. 27, 1016–1028 (2017).

    Article  Google Scholar 

  24. 24.

    Talla, V. et al. Rapid increase in genome size as a consequence of transposable element hyperactivity in Wood-White (Leptidea) butterflies. Genome Biol. Evol. 9, 2491–2505 (2017).

    CAS  Article  Google Scholar 

  25. 25.

    Olmo, E. & Morescalchi, A. Genome and cell sizes in frogs: a comparison with salamanders. Experientia 34, 44–46 (1978).

    CAS  Article  Google Scholar 

  26. 26.

    Gregory, T. R. The bigger the C-value, the larger the cell: genome size and red blood cell size in vertebrates. Blood Cell Mol. Dis. 27, 830–843 (2001).

    CAS  Article  Google Scholar 

  27. 27.

    Guignard, M. S. et al. Genome size and ploidy influence angiosperm species’ biomass under nitrogen and phosphorus limitation. New Phytol. 210, 1195–1206 (2016).

    Article  Google Scholar 

  28. 28.

    Gregory, T. R. Genome size and developmental complexity. Genetica 115, 131–146 (2002).

    Article  Google Scholar 

  29. 29.

    Vinogradov, A. E. Nucleotypic effect in homeotherms: body-mass independent resting metabolic rate of passerine birds is related to genome size. Evolution 51, 220–225 (1997).

    Article  Google Scholar 

  30. 30.

    Sessions, S. K. & Larson, A. Developmental correlates of genome size in Plethodontid salamanders and their implications for genome evolution. Evolution 41, 1239–1251 (1987).

    Article  Google Scholar 

  31. 31.

    Jockusch, E. L. An evolutionary correlate of genome size change in plethodontid salamanders. Proc. R. Soc. Lond. B 264, 597–604 (1997).

    CAS  Article  Google Scholar 

  32. 32.

    Wyngaard, G. A., Rasch, E. M., Manning, N. M., Gasser, K. & Domangue, R. The relationship between genome size, development rate, and body size in copepods. Hydrobiologia 532, 123–137 (2005).

    CAS  Article  Google Scholar 

  33. 33.

    Alfsnes, K., Leinaas, H. P. & Hessen, D. O. Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans. Ecol. Evol. 44, 498–499 (2017).

    Google Scholar 

  34. 34.

    Xia, X. Body temperature, rate of biosynthesis, and evolution of genome size. Mol. Biol. Evol. 12, 834–842 (1995).

    CAS  PubMed  Google Scholar 

  35. 35.

    Wells, K. D. The Ecology and Behavior of Amphibians (Univ. Chicago Press, Chicago, 2007).

  36. 36.

    Gomez-Mestre, I., Pyron, R. A. & Wiens, J. J. Phylogenetic analyses reveal unexpected patterns in the evolution of reproductive modes in frogs. Evolution 66, 3687–3700 (2012).

    Article  Google Scholar 

  37. 37.

    Mohlhenrich, E. R. & Mueller, R. L. Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution 70, 2865–2878 (2016).

    CAS  Article  Google Scholar 

  38. 38.

    Bennett, M. D., Lewis, R. K. & Harbert, D. J. The time and duration of meiosis. Phil. Trans. R. Soc. Lond. B 277, 201–226 (1977).

    CAS  Article  Google Scholar 

  39. 39.

    Knight, C. A. & Ackerly, D. D. Variation in nuclear DNA content across environmental gradients: a quantile regression analysis. Ecol. Lett. 5, 66–76 (2002).

    Article  Google Scholar 

  40. 40.

    White, M. M. & McLaren, I. A. Copepod development rates in relation to genome size and 18S rDNA copy number. Génome 43, 750–755 (2000).

    CAS  Article  Google Scholar 

  41. 41.

    Camper, J. D., Ruedas, L. A., Bickham, J. W. & Dixon, J. R. The relationship of genome size with developmental rates and reproductive strategies in five families of neotropical bufonoid frogs. Genetics 12, 79–87 (1993).

    Google Scholar 

  42. 42.

    Wilkinson, M., San Mauro, D., Sherratt, E. & Gower, D. J. A nine-family classification of caecilians (Amphibia: Gymnophiona). Zootaxa 2874, 41–64 (2011).

    Article  Google Scholar 

  43. 43.

    Kamei, R. G. et al. Discovery of a new family of amphibians from northeast India with ancient links to Africa. Proc. Biol. Sci. 279, 2396–2401 (2012).

    Article  Google Scholar 

  44. 44.

    Khabbazian, M., Kriebel, R., Rohe, K. & Ané, C. Fast and accurate detection of evolutionary shifts in Ornstein–Uhlenbeck models. Methods Ecol. Evol. 7, 811–824 (2016).

    Article  Google Scholar 

  45. 45.

    Clavel, J., Escarguel, G. & Merceron, G. mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data. Methods Ecol. Evol. 6, 1311–1319 (2015).

    Article  Google Scholar 

  46. 46.

    Rabosky, D. L. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS One 9, e89543 (2014).

    Article  Google Scholar 

  47. 47.

    Harmon, L. J., Weir, J. T., Brock, C. D., Glor, R. E. & Challenger, W. GEIGER: investigating evolutionary radiations. Bioinformatics 24, 129–131 (2008).

    CAS  Article  Google Scholar 

  48. 48.

    Duchen, P. et al. Inference of evolutionary jumps in large phylogenies using Levy processes. Syst. Biol. 66, 950–963 (2017).

    Article  Google Scholar 

  49. 49.

    Gonzalez-Voyer, A. & Hardenberg, A. V. Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology (ed. Garamszegi, L. Z.) 201–229 (Springer, Berlin, 2014).

  50. 50.

    Thomson, K. S. & Muraszko, K. Estimation of cell-size and DNA content in fossil fishes and amphibians. J. Exp. Zool. 205, 315–320 (1978).

    CAS  Article  Google Scholar 

  51. 51.

    Chipman, A. D., Khaner, O., Haas, A. & Tchernov, E. The evolution of genome size: what can be learned from anuran development? J. Exp. Zool. 291, 365–374 (2001).

    CAS  Article  Google Scholar 

  52. 52.

    Laurin, M., Canoville, A., Struble, M., Organ, C. & de Buffrénil, V. Early genome size increase in urodeles. CR Palevol. 15, 74–82 (2016).

    Article  Google Scholar 

  53. 53.

    Canapa, A., Barucca, M., Biscotti, M. A., Forconi, M. & Olmo, E. Transposons, genome size, and evolutionary insights in animals. Cytogenet. Genome. Res. 147, 217–239 (2016).

    Article  Google Scholar 

  54. 54.

    Pagel, M. & Johnstone, R. A. Variation across species in the size of the nuclear genome supports the junk-DNA explanation for the C-value paradox. Proc. Biol. Sci. 249, 119–124 (1992).

    CAS  Article  Google Scholar 

  55. 55.

    Zeng, C., Gomez-Mestre, I. & Wiens, J. J. Evolution of rapid development in spadefoot toads is unrelated to arid environments. PLoS One 9, e96637 (2014).

    Article  Google Scholar 

  56. 56.

    Lynch, M., Bobay, L.-M., Catania, F., Gout, J.-F. & Rho, M. The repatterning of eukaryotic genomes by random genetic drift. Annu. Rev. Genom. Hum. Genet. 12, 347–366 (2011).

    CAS  Article  Google Scholar 

  57. 57.

    Evans, T., Wade, C. M., Chapman, F. A., Johnson, A. D. & Loose, M. Acquisition of germ plasm accelerates vertebrate evolution. Science 344, 200–203 (2014).

    CAS  Article  Google Scholar 

  58. 58.

    Romiguier, J. et al. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature 515, 261–263 (2014).

    CAS  Article  Google Scholar 

  59. 59.

    Chrtek, J. I. Jr, Zahradnek, J., Krak, K. & Fehrer, J. Genome size in Hieracium subgenus Hieracium (Asteraceae) is strongly correlated with major phylogenetic groups. Ann. Bot. 104, 161–178 (2009).

    CAS  Article  Google Scholar 

  60. 60.

    Weiss-Schneeweiss, H., Greilhuber, J. & Schneeweiss, G. M. Genome size evolution in holoparasitic Orobanche (Orobanchaceae) and related genera. Am. J. Bot. 93, 148–156 (2006).

    CAS  Article  Google Scholar 

  61. 61.

    Leitch, I. J. et al. Punctuated genome size evolution in Liliaceae. J. Evol. Biol. 20, 2296–2308 (2007).

    CAS  Article  Google Scholar 

  62. 62.

    Johnston, J. S. et al. Evolution of genome size in Brassicaceae. Ann. Bot. 95, 229–235 (2005).

    CAS  Article  Google Scholar 

  63. 63.

    Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009).

    Article  Google Scholar 

  64. 64.

    Sanmiguel, P. & Bennetzen, J. L. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 82, 37–44 (1998).

    CAS  Article  Google Scholar 

  65. 65.

    Pyron, R. A. Biogeographic analysis reveals ancient continental vicariance and recent oceanic dispersal in amphibians. Syst. Biol. 63, 779–797 (2014).

    Article  Google Scholar 

  66. 66.

    Frost, D. R. Amphibian Species of the World: An Online Reference Version 6.0 (American Museum of Natural History, New York, 2018);

  67. 67.

    Hardie, D. C., Gregory, T. R. & Hebert, P. D. N. From pixels to picograms: a beginners’ guide to genome quantification by Feulgen image analysis densitometry. J. Histochem. Cytochem. 50, 735–749 (2002).

    CAS  Article  Google Scholar 

  68. 68.

    Bivand, R. S., Pebesma, E. & Gómez-Rubio, V. Applied Spatial Data Analysis with R (Springer, New York, 2013).

  69. 69.

    Hijmans, R. J. raster: Geographic Data Analysis and Modeling R Package Version 2.5-8 (2016);

  70. 70.

    Bivand, R. S. & Lewin-Koh, N. maptools: Tools for Reading and Handling Spatial Objects R Package Version 0.9-2 (2017);

  71. 71.

    Jeffery, N. W. & Gregory, T. R. Genome size estimates for crustaceans using Feulgen image analysis densitometry of ethanol-preserved tissues. Cytometry 85, 862–868 (2014).

    Article  Google Scholar 

  72. 72.

    Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    CAS  Article  Google Scholar 

  73. 73.

    Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).

    Article  Google Scholar 

  74. 74.

    Rabosky, D. L. et al. BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods Ecol. Evol. 5, 701–707 (2014).

    Article  Google Scholar 

  75. 75.

    Plummer, M., Best, N., Cowles, K. & Vines, K. CODA: convergence diagnosis and output analysis for MCMC. R News 6, 7–11 (2006).

    Google Scholar 

  76. 76.

    van der Bijl, W. phylopath: easy phylogenetic path analysis in R. PeerJ 6, e4718 (2018).

    Article  Google Scholar 

  77. 77.

    San Mauro, D. et al. Life-history evolution and mitogenomic phylogeny of caecilian amphibians. Mol. Phylogenet. Evol. 73, 177–189 (2014).

    Article  Google Scholar 

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We would like to thank C. Spencer at the Museum of Vertebrate Zoology (Berkeley), M.-O. Rödel and F. Tillack at the Museum für Naturkunde (Berlin), S. Loader and J. Streicher at the Natural History Museum (London), B. Alvarez and I. Martinez-Solano at the Museo Nacional de Ciencias Naturales (Madrid), V. Gvoždík at the Academy of Sciences (Brno) for tissue loans and L. Asencio Vazquez for assistance with laboratory work. M.W. and D.J.G. thank the many persons and organizations that have facilitated the collection of caecilian materials used in this work, especially S. Maddock and the Direction de l’Environment, de l’Aménagement et du Logement and the Conseil Scientifique Régional du Patrimonie Naturel (Guyane). Funding was provided by Spanish National Research Plan (CGL2017-83407-P) awarded to I.G.-M., Swiss National Science Fund (P2BSP3_158846) awarded to H.C.L. and the Darwin Initiative (19-002) awarded to D.J.G.

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H.C.L., I.G.-M., D.J.G. and M.W. were all involved in planning and executing the project. D.J.G. and M.W. contributed key samples and H.C.L. obtained de novo genome size estimates and performed data analyses with input from I.G.-M. H.C.L. wrote the first version of the manuscript, to which all other authors thereafter contributed.

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Correspondence to Ivan Gomez-Mestre.

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Liedtke, H.C., Gower, D.J., Wilkinson, M. et al. Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate. Nat Ecol Evol 2, 1792–1799 (2018).

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