Professor
Department of Biological Sciences
Cedar Crest College
100 College Drive
Allentown, PA 18104-6196
(610) 606-4666 ext 3501
rmkliman@cedarcrest.edu
www.cedarcrest.edu/rmkliman
Education
- A.B., Colby College (Biology & Music), 1984
- Ph.D., Wesleyan University (Biology), 1990
Previous Professional Experience
- High School Teacher, Sprinfield, VT, 1984-1985
- Postdoctoral Fellow, Rutgers University, 1990-1993
- Postdoctoral Fellow, Harvard University, 1993-1994
- Assistant Professor, Radford University, 1994-1998
- Research Associate, Rutgers University, 1998-1999
- Assistant Professor, Kean University, 1999-2002
- Assistant Professor, Cedar Crest College, 2002-2005
- Associate Professor, Cedar Crest College, 2005-2011
- Program Director, National Science Foundation, Division of Environmental Biology, Evolutionary Processes Cluster, 2011
Professional Workshops
- Short Course in Experimental Medical and Mammalian Genetics, The Jackson Laboratory, 1988
- Workshop in Molecular Evolution, Marine Biological Laboratory, 1992
- Summer Institute in Statistical Genetics, North Carolina State University, 2003
Courses taught
CCC, Cedar Crest College; KU, Kean University; RU, Radford University
- Advanced Bioinformatics (lecture/applications), CCC
- Advanced Mendelian and Population Genetics (lecture), CCC
- Advanced Recombinant DNA Techniques (lecture), CCC
- Cell and Molecular Biology (lab), CCC
- Concepts in Ecology and Environmental Issues (lecture/lab, non-majors), CCC
- Concepts in Human Biology and Health Issues (lecture/lab, non-majors), CCC
- Ecology (lecture/lab), CCC
- Ecology, Evolution & Genetics (lecture/lab), CCC
- Evolution (lecture), RU
- Genetics (lecture/lab), RU, KU, CCC
- Independent Research, RU, KU, CCC
- Introduction to Bioinformatics (lecture/applications), CCC
- Junior Colloquium (lecture/seminar), CCC
- Law & Science (Political Science course; lecture), CCC
- Medical Genetics and Genomics (lecture), CCC
- Molecular Biology (lecture/lab), RU
- Neurobiology (lecture), RU
- Nucleic Acid Sequencing/Sequence Analysis (graduate; lecture/lab), KU
- Principles of Biology (for majors; lecture/lab), CCC
- Principles of Biology (for non-majors; lecture/lab), RU
- Principles of Biology (mixed majors, non-majors; lecture/lab), KU
- Pseudoscience, Junk Science & Skepticism (Honors course; lecture), CCC
- Science, Ethics and Society (seminar), CCC
Research Support
I. Extramural Support - Grants
- Virginia Academy of Sciences, "Estimation of components of genetic variance in Drosophila sechellia." 1995-1996
- Jeffress Memorial Trust, "Genealogical analysis of species formation in the Drosophila simulans species complex." 1995-1998
- NIH (R15), "Analysis of eukaryotic compositional and codon biases." 2001-2004
- NIH (R15), "Assessment of codon usage at the gene and genome levels." 2004-2007
- Conservation International Foundation (Dr. John Cigliano, Cedar Crest College, co-PI), "Assessment of DNA sequence variation and population structure in queen conch of Belize." 2006-2009
- NIH (R15) (Dr. Amy Reese, Cedar Crest College, co-PI), "Empirical analysis of natural selection on codon usage in eukaryotes." 2007-2010
- NIH (R01) (Multiple-PI with Dr. Mohamed Noor, Duke), "Fine-scale recombination, variation, divergence, and codon bias in Drosophila." 2009-2013
- NIH (R01, ARRA supplemental) (Multiple-PI with Dr. Mohamed Noor, Duke), "Fine-scale recombination, variation, divergence, and codon bias in Drosophila." 2009-2011
- Earthwatch Institute (with Dr. John Cigliano), 2008, 2010-2012
- Oceanic Society (with Dr. John Cigliano), 2008
- Busch Postdoctoral Fellowship (Rutgers University), 1990-1993
- Radford University (Seed Grant), 1994-1995
- Kean University Untenured Faculty Research Initiative, 2000-2001
- Cedar Crest College Faculty Development Grants, 2002-2004, 2005-2010, 2012-2013
Current Professional Memberships
- American Association for the Advancement of Science
- Genetics Society of America
- National Center for Science Education
- Society for the Study of Evolution
Current and Ongoing Service and Activities
- Associate Editor, Journal of Molecular Evolution, 2004-2010, 2012-present
- Committee on Undergraduate Education, 2013-present
- Director, Biology Major, 2010-present
- Athletic Advisory Board, 2006-present
- Tri-Beta, Faculty Advisor, 2005-present
- Student/Faculty Rock Band, Co-founder and Faculty Advisor, 2008-present
- Co-organizer of NSF-sponsored program to increase undergraduate diversity at the annual Evolution meeting, 2003-present
- Reviewer: Behavior Genetics; BMC Journals; Evolution; Genetica; Genome Biology; Genome Biology and Evolution; Genetics; International Journal of Plant Sciences; Journal of Molecular Evolution; Journal of Theoretical Biology; Molecular Biology and Evolution; Molecular Ecology; Molecular Phylogenetics and Evolution; PLoS Genetics; PLoS ONE; Proceedings of the National Academy of Science; Proceedings of the Royal Society; Proteins: Structure, Function and Genetics; Science. Guest Associate Editor for Evolution.
- NSF grant review panelist (4 panels) and ad hoc reviewer.
- NIH study section member (2 special study sections).
Past Service and Activities (selected list)
- Associate Editor, Genetica, 2001-2007
- Lead Editor, Population, Quantitative and Evolutionary Genetics, Nature Education (a.k.a., Scitable), 2007-2009
- Cedar Crest College (College-level): Curriculum and Academic Policy Committee, 2007-2010, 2012-2013 (committee chair and representative to the Faculty Council); Institutional Review Board, 2005-2008; Graduate Programs Committee, 2006; Grievance Committee, 2005-2006
- Cedar Crest College (Department-level): Director, Bioinformatics Program, 2002-2008
- Kean University (University-level): Information Technology Strategic Plan Task Force; Technology Institute for Professionals (Instructor, technical and pedagogical aspects of course web site design)
- Kean University (College-level): ad hoc Major Equipment Committee; M.S. Biotechnology Steering Committee
- Kean University, (Department-level): Curriculum Committee; Grievance Committee; Tri-Beta (faculty advisor)
- Radford University (University-level): Academic Policies and Procedures Committee
- Radford University (College-level): Curriculum Committee; Liaison to the Honors Program
- Radford University (Department-level): Curriculum Committee (chair); Graduate School Assessment Committee (chair); Biology Club (faculty advisor)
Software Developed
- EvolGenius Population Genetics Simulation. Two-locus population genetics simulation for instruction and research.
- LU1, LU2 and CODON10. Used to construct "lookup tables" of protein-coding genes in NCBI genome files, and to then analyze codon usage and base composition (see Kliman et al., JME 2003)
- MONTECOD. Used to test for natural selection on codon usage (see Llopart et al., JME 2008)
- ISOLATION. Used to estimate species isolation times and other parameters from multilocus DNA sequence data (see McDermott and Kliman, PLoS One 2008)
- MicroScan_rk2. Perl program to find microsatellites in Fasta libraries (modification of MicroScan by Mohamed Noor)
- New software in development for current research in population genomics
Patent
- Barany, F., M. Zirvi, N.P. Gerry, R. Favis & R. Kliman. "Method of designing an addressable array suitable for detection of nucleic acid sequence differences using the ligase detection reaction and addressable arrays."
Publications and Presentations
I. Research Articles
Manuscripts in preparation deal with (1) diversity estimation using population genomic data; (2) inference of Hill-Robertson interference using population genomic data; and (3) inference of the action of natural selection on synonymous codon usage.
- Cigliano, J.A. & R.M. Kliman (submitted) Density, age structure, and length of queen conch (Strombus gigas) in shallow-water aggregations in the Sapodilla Cayes Marine Reserve, Belize.
- McDermott, S.R. & R.M. Kliman (2008) Estimation of isolation times of the island species in the D. simulans complex from multilocus DNA sequence data. PLoS One 3:e2442. Abstract | Full-text
- Llopart, A., A. Mabille, J.R. Peters-Hall, J.M. Comeron & R.M. Kliman (2008) A new test for selection applied to codon usage in Drosophila simulans and D. mauritiana. Journal of Molecular Evolution 66:224-231. Abstract
- Cirulli, E.T., R.M. Kliman & M.A.F. Noor (2007) Fine-scale crossover rate heterogeneity in Drosophila pseudoobscura. Journal of Molecular Evolution 64:129-135. Abstract
- Kliman, R.M. & C.A. Bernal (2005) Unusual usage of AGG and TTG codons in humans and their viruses. Gene 352:92-99. Abstract
- Kliman, R.M. & A.N. Henry (2005) Inference of codon preferences in Arabidopsis thaliana. International Journal of Plant Sciences 166:3-11. Abstract
- Kliman, R.M., N. Irving & M Santiago (2003) Selection conflicts, gene expression and codon usage trends in yeast. Journal of Molecular Evolution 57:98-109. Abstract
- Kliman, R.M. & J. Hey (2003) Hill-Robertson interference in Drosophila melanogaster: reply to Marais, Mouchiroud & Duret. Genetical Research 81:89-90. Abstract
- Noor, M.A.F. & R.M. Kliman (2003) Variability on the dot chromosome in the Drosophila simulans clade. Genetica 118:51-58. Abstract
- Machado, C.A., R.M. Kliman, J. Markert & J. Hey (2002) Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology and Evolution 19:472-488. Abstract | Full-text
- Hey, J. & R.M. Kliman (2002) Interactions between natural selection, recombination, and gene density in the genes of Drosophila. Genetics 160:595-608. Abstract | Full-text
- Noor, M.A.F., R.M. Kliman & C. Machado (2001) Evolutionary history of microsatellites in the obscura group of Drosophila. Molecular Biology and Evolution 18:551-556. Abstract | Full-text
- Kliman, R.M., P. Andolfatto, J.A. Coyne, F. Depaulis, M. Kreitman, A.J. Berry, J. McCarter, J. Wakeley & J. Hey (2000) The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156:1913-1931. Abstract | Full-text
- Kliman, R.M. (1999) Recent selection on synonymous codon usage in Drosophila. Journal of Molecular Evolution 49:343-351. Abstract
- Kliman, R.M. & A. Eyre-Walker (1998) Patterns of base composition within the genes of Drosophila melanogaster. Journal of Molecular Evolution 46:534-541. Abstract
- Kliman, R.M. & J. Hey (1994) The effects of mutation and natural selection on codon bias in the genes of Drosophila. Genetics 137:1049-1056. Abstract | Full-text
- Hilton, H., R.M. Kliman & J. Hey (1994) Using hitchhiking genes to study adaptation and divergence during speciation within the Drosophila melanogaster species complex. Evolution 48:1900-1913. Abstract
- Kliman, R.M. & J. Hey (1993) Reduced natural selection associated with low recombination in Drosophila melanogaster. Molecular Biology and Evolution 10:1239-1258. Abstract | Full-text
- Hey, J. & R.M. Kliman (1993) Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex. Molecular Biology and Evolution 10:804-822. Abstract | Full-text
- Kliman, R.M. & J. Hey (1993) DNA sequence variation at the period locus within and among species of the Drosophila melanogaster complex. Genetics 133:375-387. Abstract | Full-text
- Kliman, R.M. & G.R. Lynch (1992) Evidence for genetic variation in the occurrence of the photoresponse of the Djungarian hamster, Phodopus sungorus. Journal of Biological Rhythms 7:161-173. Abstract
- Kliman, R.M. & G.R. Lynch (1991) Evidence for independence of circadian characters and the extent of photoresponsiveness in the Djungarian hamster, Phodopus sungorus. Journal of Biological Rhythms 6:159-166. Abstract
- Lynch, G.R., C.B. Lynch & R.M. Kliman (1989) Genetic analyses of photoresponsiveness in the Djungarian hamster, Phodopus sungorus. Journal of Comparative Physiology A 164:475-481. Abstract
- Puchalski, W.R., R. Kliman & G.R. Lynch (1988) Differential effects of short day pretreatment on melatonin-induced adjustments in Djungarian hamsters. Life Science 43:1005-1012. Abstract
- Kliman, R.M. (2008) Book Review: Theories of Population Variation in Genes and Genomes, by F.B. Christiansen. Quarterly Review of Biology 83:407.
- Comeron, J.M., A. Williford & R.M. Kliman (2008) The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations. Heredity 100:19-31. Abstract
- Kliman, R.M., F. Barany, N. Cohen & R. Favis (2007) Association studies: practical and theoretical considerations for drug discovery, evaluation, and beyond. In Biochips as Pathways to Drug Discovery (eds. A. Carmen & G. Hardimann), pp. 169-192. CRC Press, New York.
- Kliman, R.M. & N.A. Johnson (2005) What every undergraduate should know about evolution (and why). BioScience 55:926-927. Full-text
- Kirk, B.W., M. Feinsod, R. Favis, R.M. Kliman & F. Barany (2002) Single nucleotide polymorphism seeking long term association with complex disease. Nucleic Acids Research 30:3295-3311. Abstract | Full-text
- Johnson, N.A. & R.M. Kliman (2002) Hidden evolution: progress and limitations in detecting multifarious natural selection. Genetica 114:281-291. Abstract
- Kliman, R.M., B.T. Rogers & M.A.F. Noor (2001) Differences in (G+C) content between species: a commentary on Forsdyke's "chromosomal viewpoint" of speciation. Journal of Theoretical Biology 209:131-141. Abstract | Full-text PDF
- Akashi, H., R.M. Kliman & A. Eyre-Walker (1998) Mutation pressure, natural selection, and the evolution of base composition in Drosophila. Genetica 102/103:49-60. Abstract
- Hey, J. & R.M. Kliman (1994) Genealogical portraits of speciation in the Drosophila melanogaster species complex. In Non-neutral evolution: Theories and Molecular Data (ed. G.B. Golding), pp. 208-216. Chapman and Hall, New York and London.
- Kliman, R.M. (2008) The EvolGenius population genetics computer simulation: how it works. Nature Education 1(3). | Full-text
- Kliman, R., B. Sheehy & J. Schultz (2008) Genetic drift and effective population size. Nature Education 1(3). | Full-text
- Kliman, R.M. (2001) A project-based approach to teaching complex population genetics to undergraduates. Bioscene: The Journal of College Biology Teaching 27:13-20. Full-text
- Kliman, R., J. Cigliano & R. Vereneck (2010) Science to Action Symposium (Marine Management Area Science Project), Belize City, Belize. Genetic variation within and among queen conch populations.
- Kliman, R.M. (2008) Forensic Science Training Institute, Cedar Crest College. Workshop on Bayesian approaches in forensic science.
- Kliman, R.M. (2005) VIII Simposio de Genetica, Sao Jose do Rio Preto, Brazil. Inferring natural history of closely related species from multilocus DNA sequence data. Also taught a 3-day postgraduate course in Molecular Population Genetics.
- Kliman, R.M. (2005) Entomology Seminar, University of Massachusetts - Amherst. Reconstructing the history of divergence of closely related Drosophila species.
- Kliman, R.M. (2004) Biology Department Seminar, Louisiana State University. Codon usage as a model for the study of selection conflicts.
- Kliman, R.M. (2003) Johnson & Johnson Pharmaceutical Research and Development, Dept. of Pharmacogenomics. Caveats in association studies: a population genetics perspective.
- Kliman, R., S. McGaugh & J. Schwab (2012) American Genetics Association Annual Symposium, Durham, NC. A weak relationship between recombination rate and the effectiveness of natural selection on codon usage in Drosophila pseudoobscura.
- Goldstein, S., S. McGaugh, R. Kliman, M.A.F. Noor, L. Loewe (2012) American Genetics Association Annual Symposium, Durham, NC. Quantifying dips in diversity around selective sweeps.
- Kliman, R., S. McGaugh & M. Noor (2012) 1st Joint Congress on Evolutionary Biology, Ottawa, ON, Canada. Population genomic analysis of codon usage along genes of Drosophila.
- Bachert, B., J. Klecha, J. Schwab, J. Ory, L. Cotroneo & R. Kliman (2011) Evolution 2011, Norman, OK. Inference of preferred codons in Cryptococcus neoformans var. neoformans.
- Klecha, J., S. Coombe, B. Bachert, S. McGaugh, L. Cotroneo & R. Kliman (2011) Evolution 2011, Norman, OK. Population genomic analysis of natural selection on codon usage in Drosophila pseudoobscura.
- Kliman, R.M. (2009) Lehigh Valley Ecology and Evolution Society, Allentown, PA. Absence of mitochondrial population structure in queen conch.
- Kliman, R.M. & S.M. McDermott (2008) Evolution 2008, Minneapolis, MN. Genetic evidence for contemporaneous origin of Drosophila sechellia and D. mauritiana.
- Smith, M.J. & R.M. Kliman (2008) Evolution 2008, Minneapolis, MN. Evidence for changing base composition in human papillomaviruses.
- Vereneck, R.M., J.A. Cigliano & R.M. Kliman (2008) Evolution 2008, Minneapolis, MN. DNA sequence variation at the COI locus of Strombus gigas and S. costatus.
- Vereneck, R., M. Sandridge, P. Miller, J. Cigliano & R. Kliman (2007) 3rd International Conservation Genetics Symposium, American Museum of Natural History, New York, NY. DNA sequence variation within and among populations of queen conch in Belize.
- Kliman, R. & K. Miede (2007) Lehigh Valley Evolution and Ecology Symposium, Center Valley, PA. Coevolution of bacteriophage and host codon and amino acid usage.
- Kliman, R.M. & S.M. McDermott (2007) Drosophila Research Conference, Philadelphia, PA. The divergence population genetics of the D. simulans species complex.
- Kliman, R.M. & J.A. Cigliano (2006) Evolution 2006, Stony Brook, NY. The Cow Diversity Project: molecular population genetics for undergraduates.
- Burgett, K., A. Mabille, J. Shaffer & R. Kliman (2006) Evolution 2006, Stony Brook, NY. Testing for ongoing selection on codon usage in Drosophila.
- McDermott, S., P. Miller & R. Kliman (2006) Evolution 2006, Stony Brook, NY. Testing the strict isolation model in the Drosophila simulans species complex.
- Kliman, R.M. (2005) Evolution 2005, Fairbanks, AK. DNA sequence variation at the wds and cdc37 loci within and among species of the Drosophila simulans complex.
- Kliman, R.M. (2004) Evolution 2004, Fort Collins, CO. Preferred codon usage as it relates to gene density.
- Bernal, C.A. & R.M. Kliman (2004) Evolution 2004, Fort Collins, CO. Codon usage trends of humans and their viruses.
- Botens, C.M. & R.M. Kliman (2004) Evolution 2004, Fort Collins, CO. Synonymous codon variation in human papillomaviruses.
- Hild, R.A. & R.M. Kliman (2004) Evolution 2004, Fort Collins, CO. Preferred codon usage trends within eukaryote genes.
- Miede, K.A. & R.M. Kliman (2004) Evolution 2004, Fort Collins, CO. Bacteriophage codon usage reflects host codon usage.
- Kliman, R.M. (2004) Lehigh Valley Ecology and Evolution Society, Allentown, PA. Selection conflicts from linkage and pleiotropy.
- Kliman, R.M. & M.A.F. Noor (2003) Society for Molecular Biology and Evolution, Newport Beach, CA. Is a strict isolation model appopriate for the Drosophila simulans species complex?
- Kliman, R.M., N. Irving & M. Santiago. (2002). Gordon Research Conference on Genomics and Structural/Evolutionary Bioinformatics, South Hadley, MA. Codon usage in Saccharomyces cerevisiae reflects gene expression, gene spacing and compositional biases.
- Santiago, M., N. Irving & R.M. Kliman (2002). Evolution 2002, Urbana, IL. Patterns of codon usage in the yeast genome.
- Kliman, R.M. & J. Hey (2001). New England Molecular Evolutionary Biologists, Northampton, MA. Hill-Robertson interference and regulatory conflicts in Drosophila.
- Kliman, R.M. & J. Hey (2001). Evolution 2001, Bloomington, IN. Inference of Hill-Robertson interference on codon usage in Drosophila.
- Kliman, R.M. et al. (2000). Evolution 2000, Knoxville, TN. The population genetics of the origin and divergence of the Drosophila simulans complex species.