Rachel Lockridge Mueller

Department of Biology, Colorado State University, Fort Collins, CO 80523

E-mail: rlm@colostate.edu

Web: http://rydberg.biology.colostate.edu/muellerlab/index.html

Phone: (970) 491-6717

Position

2007-            Assistant Professor, Colorado State University Department of Biology

2007-             Faculty Member, Graduate Degree Program in Ecology, CSU

Research Interests

Phylogenetic systematics, molecular evolution, mitochondrial and nuclear genome evolution, vertebrate biology, herpetology, genomics

Education

2005            Ph.D. in Integrative Biology, University of California, Berkeley

                    “Genome evolution, morphological homoplasy, and the phylogeny of plethodontid salamanders”

1995             B.A. with Honors in Integrative Biology, University of California, Berkeley

                    “Locomotion energetics of nocturnal geckos”

2001-2005    Guest graduate student researcher, DOE Joint Genome Institute

1999            Neotropical Herpetology, Institute for Tropical Ecology and Conservation

1993            Tropical Rainforest Ecology and Management, School for Field Studies

Prior Appointments

2005-2006     National Institutes of Health Post-doctoral Fellow, The University of Chicago “A microarray-based analysis of hematopoietic gene function in zebrafish”

2004              Graduate Student Researcher, NSF AmphibiaTree Project, UC Berkeley

2001, 2003    Graduate Student Instructor, Evolution, UC Berkeley

2000              Lab Manager, Evolutionary Genetics Laboratory, UC Berkeley

1999              Graduate Student Instructor, General Biology, UC Berkeley

1995-1997     Staff Research Associate, Ocular Oncology Laboratory, UC San Francisco

Academic Honors

2006    Publisher’s Award, Best Student Paper in Systematic Biology, Society of Systematic Biologists

2003    Best Student Paper Award, Division of Systematic and Evolutionary Biology, Society for Integrative and Comparative         Biology

2002    Outstanding Graduate Student Instructor Award, UC Berkeley

1995    Departmental Citation for Outstanding Undergraduate Achievement, UC Berkeley

1995    Highest Honors, B.A., Integrative Biology, UC Berkeley

1995    High Distinction in General Scholarship, UC Berkeley

Grants, Scholarships, and Awards

2012    NSF DDIG “Impacts of metabolic differences on cytonuclear coevolution” with Co-PI Becky Chong

2010    NSF award, Evolutionary Processes cluster. “Genome evolution in plethodontid salamanders: Molecular analysis of

            genomic gigantism” & REU supplement (2012) 

2005    NIH postdoctoral fellowship in cardiology, The University of Chicago       

2004    Annie Alexander Fellowship, UC Berkeley

2003     Programs for Genomic Applications Short Course: “Bioinformatics tools for comparative genomics,” Lawrence Berkeley National Laboratory and National Heart, Lung, and Blood Institute

2001    Doctoral Dissertation Improvement Grant, National Science Foundation

2001    Summer Block Grant, UC Berkeley Department of Integrative Biology

2000    Grant-in-aid of Research, Sigma Xi

2000    Grant-in-aid of Basic Research, UC Berkeley

1999    National Institutes of Health Pre-doctoral Fellowship: UC Berkeley NRSA Institutional Training Grant in Genetics, 2 years

1998    National Science Foundation Pre-doctoral Fellowship, 3 years

1998    Louisa M. Kellogg Grant-in-aid, UC Berkeley 

1996    That Man May See Foundation Research Grant, P.I. Joan M. O’Brien, M.D., University of California, San Francisco; Co P.I. Rachel L. Mueller

1994    General Honorary Scholarship, UC Berkeley

1994    Howard Hughes Summer Institute in Molecular and Cell Biology, University of California, Santa Cruz

Publications

Parrie, L.M., Renfrew, E.M., Mueller, R.L., Garrity, D.M. Zebrafish tbx5 paralogs demonstrate independent essential requirements in cardiac and pectoral fin development. Submitted.

Sun, C., Lopez Arriaza, J., Mueller, R.L. DNA loss is slow in the gigantic genomes of salamanders. In revision.

Chong, R.A. and Mueller, R.L. Low metabolic rates in salamanders are correlated with weak selective constraints on mitochondrial genes. Evolution, in press.

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 Evolution 4(2):168-183.

Mueller, R.L., Huang, C., Ho, R.K. 2010. Spatio-temporal regulation of Wnt and retinoic acid signaling by tbx16/spadetail during zebrafish mesoderm differentiation. BMC Genomics 11:492.

Schwartz, R.S. and Mueller, R.L. 2010. Variation in DNA substitution rates among lineages erroneously inferred from simulated clock-like data. PLoS ONE 5(3):e9649.

Schwartz, R.S. and R.L. Mueller. 2010. Limited effects of among-lineage rate variation on the phylogenetic performance of molecular markers. Molecular Phylogenetics and Evolution 54(3): 849 - 856.

Schwartz, R.S. and R.L. Mueller. 2010. Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks. BMC Evolutionary Biology 10:5.

Kuchta, S. R., Parks, D., Mueller, R. L., and Wake, D. B. 2009. Closing the ring: Historical biogeography of the salamander ring species Ensatina eschscholtzii. Journal of Biogeography 36: 992-995. (cover)

Ebert, A. M., McAnelly, C. A., Mueller, R. L., Horne, W. A., and Garrity, D. M. 2008. Genomic organization, expression and phylogenetic analysis of Ca2+ channel β4 (CACNB4) genes in thirteen vertebrate species. Physiological Genomics 35: 133-144.

Ebert, A. M., McAnelly, C. A., Srinivasan, A., Mueller, R. L., Garrity, D. B., and Garrity, D. M. 2008. The calcium channel 2 (CACNB2) subunit repertoire in teleosts. 2008. BMC Molecular Biology 9: 38.

Mueller, R. L., Gregory, T. R., Gregory, S. M., Hsieh, A., Boore, J. L. 2008. Genome size, cell size, and the evolution of enucleated red blood cells in attenuate salamanders. Zoology 111(3): 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. *authors contributed equally

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.

Bonnet, R. M., Mueller, R. L., Wake, D. B. 2005. Why should reacquisition of larval stages by desmognathine salamanders surprise us? Herpetological Review 36(2): 112-113.

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.

Tsai, T., Fulton, L., Mueller, R. L., Smith, B. J., Gonzalez, G., O’Brien, J. M. 2004. Rapid identification of germline mutations in retinoblastoma by protein truncation testing. Archives of Ophthalmology 122: 239-248.

Mueller, R. L. 2000. Who needs a nucleus?  Red blood cells in the genus Batrachoseps.  American Zoologist 40(6): 1142.

Autumn, K., Jindrich, D., DeNardo, D., Mueller, R. 1999. Locomotor performance at low temperature and the evolution of nocturnality in geckos.  Evolution 53(2): 580-599.

Murray, T. G., Cicciarelli, N., O'Brien, J. M., Hernandez, E., Mueller, R. L., Smith, B. J., Feuer, W. 1997. Subconjunctival carboplatin therapy and cryotherapy in the treatment of transgenic murine retinoblastoma.  Archives of Ophthalmology 115(10): 1286-1290.

Mueller, R. L., Gordon, K. B., Smith, B. J., O'Brien, J. M. 1997. Genetic markers for second tumor susceptibility in retinoblastoma.  Investigative Ophthalmology & Visual Science 38(4): S795.

Courses Taught

Herpetology, Spring 2008, 2009, 2011, 2012

Life 102: Attributes of Living Systems, Fall 2008, 2010, 2012

Molecular and Genomic Evolution, Spring 2010, 2012

Basic Bioinformatics, Spring 2009, 2011

Invited Seminars and Lectures

2011    American Genetics Association symposium on Genomics and Biodiversity

            Exploring the largest vertebrate genomes: causes and consequences of genomic gigantism in salamanders

2011    University of Colorado Department of Ecology and Evolutionary Biology Student Symposium Keynote

            Genomic gigantism in salamanders

2011    University of Denver Department of Biological Sciences

            Genomic gigantism in salamanders

2010    University of Northern Colorado — Biology Departmental Seminar Series

            Mitochondrial and nuclear genome expansion in plethodontid salamanders   

2008    Humboldt State University — Biology Departmental Seminar Series

            Genome Evolution in Plethodontid Salamanders

2008    University of Wyoming Summer Institute in Bioinformatics

            Incorporating Bioinformatics into Evolutionary Biology Research – An Example from Salamanders

2008    Colorado State University Workshop on Bioinformatics

            Genomic expansion in plethodontid salamanders.

2007    Bioagricultural Sciences and Pest Management Departmental Seminar Series, CSU

            Salamanders, genome evolution, and the tree of life

2005    Assembling the Tree of Life (AToL) Workshop: “Phylogenetic analysis of life history evolution in urodeles: consensus and controversy,” Am. Soc. Ichth. Herp.

            Life history of plethodontid salamanders inferred from mitochondrial genomes

2005    Integrative Biology Departmental Seminar Series, UC Berkeley

            Mitochondrial genome evolution and the phylogeny of plethodontid salamanders

2005    Fish Group Seminar Series, University of Chicago

            Mitochondrial genome evolution and the phylogeny of plethodontid salamanders

2004    Museum of Vertebrate Zoology Seminar Series, UC Berkeley

            Plethodontid salamander mitochondrial genome evolution

2004    Evolution Course, UC Berkeley

            The evolution of genome size

2002    Herpetology Group Seminar Series, UC Berkeley

            Enucleated red blood cells in the genus Batrachoseps: footprint of an evolutionary constraint?

2002    Amphibians of the San Francisco Bay Area Workshop, Sonoma State University

            Natural history of Batrachoseps attenuatus

2002    Evolution Course, UC Berkeley

            Developmental biology and the evolution of morphological novelty

2002    Herpetology Course, UC Berkeley

            Genome size evolution in amphibians

2001    Evolution Course, UC Berkeley

            The evolution of morphological novelty

Contributed Presentations

2012    DNA loss and transposable element proliferation in the largest tetrapod genomes. Soc. Study Evol

2009    Genomic expansion in plethodontid salamanders. Soc. Study Evol.

2007  Salamander mitochondrial genomes and the Tree of Life. Rocky Mountain Bioinformatics Conference.

2006  Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic   analysis. Soc. Study Evol.

2003    Phylogenetic relationships of plethodontid salamanders inferred from mitochondrial genomes. Soc. Study Evol.

2003    Evolution of salamander mitochondrial genomes:  duplication, rearrangement, and phylogenetic implications.  Soc. Mol. Biol. Evol

2003    Mueller, R. L.  Genome size, cell size, and the evolution of enucleated red blood cells in the salamander genus Batrachoseps.  Soc. Integrat. Comp. Biol.

2002    The evolution of enucleated red blood cells in the salamander genus Batrachoseps. Soc. Study Evol.

2001    Who needs a nucleus?  Red blood cells in the genus Batrachoseps. Soc. Integrat. Comp. Biol.