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Madison-Villar, M., Sun, C., Lau, N., Settles, M., and Mueller, R. L. 2016. Small RNAs from a big genome: the piRNA pathway and transposable elements in the salamander species Desmognathus fuscus. Journal of Molecular Evolution 83(3-4):126-136. Mohlhenrich, E. and Mueller, R. L. 2016. Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution 70(2):2865-2878. Frahry, M.B., Sun, C., Chong, R.A., and Mueller, R.L. 2015. Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders. Journal of Molecular Evolution 80:120-129. Mueller, R. L. 2015. Genome biology and the evolution of cell size diversity. In Heald, R., Hariharan, I., and Wake, D. B (Eds.), Size Control in Biology, from Organelles to Organisms. Cold Spring Harbor Press. doi: 10.1101/cshperspect.a019125. Sun, C., Feschotte, C., Wu, Z., and Mueller, R. L. 2015. DNA transposons have colonized the genome of the giant virus Pandoravirus salinus. BMC Biology 13:38. Sun, C., Wyngaard, G., Walton, D.B., Wichman, H.A., Mueller, R.L. 2014. Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development. BMC Genomics 15:186. Sun, C. and Mueller, R.L. 2014. Hellbender genome sequences shed light on genome expansion at the base of crown salamanders. Genome Biology and Evolution 6(7):1818-1829. Chong, R.A. and Mueller, R.L. 2013. Evolution along the mutation gradient within the dynamic mitochondrial genome of salamanders. Genome Biology and Evolution 5(9): 1652-1660. Chong, R.A. and Mueller, R. L. 2013. Low metabolic rates in salamanders are correlated with weak selective constraints on mitochondrial genes. Evolution 67(3):894-899. Sun, C., Lopez Arriaza, J., Mueller, R. L. 2012. Slow DNA loss in the gigantic genomes of salamanders. Genome Biology and Evolution 4(12):1340-1348. Sun, C., Shepard, D. B., Chong, R. A., Lopez-Arriaza, J., Hall, K., Castoe, T., Feschotte, C., Pollock, D., and Mueller, R. L. 2012. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biology and Evolution 4(2) 168-183. Schwartz, R. S. and Mueller, R. L. 2010. Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks. BMC Evolutionary Biology 10:5. Schwartz, R. S. and Mueller, R. L. 2010. Limited effects of among-lineage rate variation on phylogenetic performance of molecular markers. Molecular Phylogenetics and Evolution 54(3): 849-856. Mueller, R. L., T. R. Gregory, S. M. Gregory, A. Hsieh, J. L. Boore. 2008. Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamanders. Zoology 111: 218-230. Hurley, I. A., Mueller, R. L., Dunn, K. A., Schmidt, E. J., Friedman, M., Ho, R. K., Prince, V. E., Yang, Z., Thomas, M. G., Coates, M. I. 2007. A new time-scale for ray-finned fish evolution. Proceedings of the Royal Society B 274: 489-498. Mueller, R. L. 2006. Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Systematic Biology 55(2): 289-300. Mueller, R. L. and Boore, J. L. 2005. Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Molecular Biology and Evolution 22(10): 2104-2112. Mueller, R. L., Macey, J. R., Jaekel, M., Wake, D. B., Boore, J. L. 2004. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proceedings of the National Academy of Sciences 101(38): 13820-13825.