Rachel Mueller

Rachel MuellerAssociate Professor
Office: Biology 434
Phone: 970-491-6717
Website: http://wp.natsci.colostate.edu/muellerlab
Education: Ph.D., University of California, Berkeley
Email: rlm@colostate.edu

I am interested in three basic questions in evolutionary biology: (1) How do genomes evolve, particularly those at the extremes of genome size? (2) How do transposable elements shape genome biology and evolution? (3) How does genome size impact phenotype and the evolutionary trajectories of lineages? My lab focuses primarily on the nuclear and mitochondrial genomes of salamanders, both of which are greatly expanded relative to other vertebrate species. Currently, we also work on copepods and giant viruses. Our research combines genomic sequence data, simulations, phylogenetics, natural history collections, and fieldwork. CV_Mueller

Selected Publications

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.