The research in our lab centers on questions in evolution and ecology. We are currently studying (1) the use of multidimensional site frequency spectra to make ecological and evolutionary inferences about recently invasive species; (2) the evolution of codon usage bias in Cryptococcus neoformans; and (3) queen conch conservation and demography.

Research Overview    top

The research in our lab involves evolutionary and ecological genetics. Most recently, we are developing structured coalescent models to predict the multidimensional site frequency spectra (i.e., spectra of character state frequencies at polymorphic sites and accumulation of fixed differences between populations) of recently founded populations relative to their source populations. This work involves computer simulations and direct mathematical modeling, with the ultimate aim of infering demographics and adaptive evolution of invasive species using population genomic data.

We also study the causes of variation in synonymous codon usage within and among genes. Part of our reason for studying codon bias is to better understand the relationship between genetic recombination and (a) genetic diversity and (b) the effectiveness of natural selection.

Finally, we have carried out research on the demographics and the population/ecological genetics of queen conch, Aliger gigas (right; photo by Judy Malitsch), in Belize, in collaboration with Dr. John Cigliano. The research has combined field work in Belize (e.g., population surveys and tagging), laboratory work (mainly DNA sequencing), and statistical analysis. The genetics component of the research program has been supported by The Conservation International Foundation. The field work has been supported by The Earthwatch Institute. Our work has included a Before-After-Control-Impact study of the effectiveness of the recently created Sapodilla Cayes Marine Reserve with respect to queen conch abundance and age-structure. We have most recently obtained population genomic data for 43 queen conch and 7 milk conch for use in demographic analyses.

Current lab members:
Isabella Neto

Journal Articles with Undergraduate authors (in red)    top

McDermott, S.R. & R.M. Kliman (2008). Estimation of isolation times of the island species in the Drosophila simulans complex from multilocus DNA sequence data. PLoS ONE 3:e2442. Link to 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.

Kliman, R.M. & C.A. Bernal (2005) Unusual usage of AGG and TTG codons in humans and their viruses. Gene 352:92-99.

Kliman, R.M. & A.N. Henry (2005) Inference of codon preferences in Arabidopsis thaliana. International Journal of Plant Sciences 166:3-11.

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.

Presentations by Undergraduates (in red)    top

Neto, I., K. Kelly, K. Parham & R. Kliman (2024) Pennsylvania Academy of Sciences, Messiah University, Mechanicsburg, PA. No DNA sequence variation in three protein coding nuclear genes of spotted lanternflies. Related presentation at the 2024 Lehigh Valley Ecology and Evolution Symposium, Moravian University, Bethlehem, PA.

Reed, K., I. Neto, K. Parham., G. Sodano & R. Kliman (2023) Lehigh Valley Ecology and Evolution Symposium, DeSales University, Center Valley, PA. Low DNA sequence variation in spotted lanternflies, Lycorma delicatula.

House, S., D. Schwartz & R. Kliman (2018) Lehigh Valley Ecology and Evolution Symposium, Cedar Crest College, Allentown, PA. Differences in lineage merger probabilities in Wright-Fisher and coalescent models in flushing populations.

Gill, R.V. & R.M. Kliman (2017) Lehigh Valley Ecology and Evolution Symposium, Desales University, Center Valley, PA. Host origin of human papillomaviruses.

Schwab, J., J. Cigliano & R. Kliman (2012) Lehigh Valley Ecology and Evolution Symposium, Desales University, Center Valley, PA. Genetic analysis of unusual conch collected in Belize. Related presentation at the 2012 meeting of the Pennsylvania Academy of Science.

Bachert, B., J. Klecha, J. Schwab, J. Ory, L. Cotroneo & R. Kliman (2011) Society for the Study of Evolution, Norman, OK. Inference of preferred codons in Cryptococcus neoformans var. neoformans.

J. Klecha, S. Coombe, B. Bachert, S. McGaugh, L. Cotroneo & R. Kliman (2011) Society for the Study of Evolution, Norman, OK. Population genomic analysis of natural selection on codon usage in Drosophila pseudoobscura.

Smith, M.J. & R.M. Kliman (2008) Society for the Study of Evolution, Minneapolis, MN. Evidence for changing base composition in human papillomaviruses. Related presentation at the 2008 Lehigh Valley Ecology and Evolution Symposium.

Vereneck, R.M., J.A. Cigliano & R.M. Kliman (2008) Society for the Study of Evolution, Minneapolis, MN. DNA sequence variation at the COI locus of Strombus gigas and S. costatus.

Vereneck, R., P. Miller, M. Sandridge, J. Cigliano & R. Kliman (2008) Lehigh Valley Ecology and Evolution Symposium, Lafayette College, Easton, PA. Assessment of the genetic population structure of the queen conch, Strombus gigas.

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.

Burgett, K. & R. Kliman (2007) Lehigh Valley Evolution and Ecology Symposium, DeSales University, Center Valley, PA. Does natural selection produce a codon bias peak within the genes of Drosophila?

Dittmar, E., P. Miller, D. Skinner, R. Vereneck & R. Kliman (2007) Lehigh Valley Evolution and Ecology Symposium, DeSales University, Center Valley, PA. Assessment of DNA sequence variation and population structure in queen conch of Belize.

Mabille, A., J. Shaffer & R. Kliman (2007) Lehigh Valley Evolution and Ecology Symposium, DeSales University, Center Valley, PA. Testing for ongoing selection on synonymous codon usage in Drosophila.

McDermott, S. & R. Kliman (2007) Lehigh Valley Evolution and Ecology Symposium, DeSales University, Center Valley, PA. Inference of isolation times of island species from multilocus DNA sequence data.

Tillette, A. & R. Kliman (2007) Lehigh Valley Evolution and Ecology Symposium, DeSales University, Center Valley, PA. Codon usage and base composition trends along the genes of three fungal species.

Burgett, K., A. Mabille, J. Shaffer & R. Kliman (2006) Society for the Study of Evolution, Stony Brook, NY. Testing for ongoing selection on codon usage in Drosophila. Related presentation at the 2006 meeting of the Lehigh Valley Ecology and Evolution Society.

McDermott, S., P. Miller & R. Kliman (2006) Society for the Study of Evolution, Stony Brook, NY. Testing the strict isolation model in the Drosophila simulans species complex. Related presentation at the 2006 meeting of the Lehigh Valley Ecology and Evolution Society.

Donigan, M.A. & R.M. Kliman (2005) Lehigh Valley Ecology and Evolution Society, Muhlenberg College, Allentown, PA. Development of population genetic markers in queen conch Strombus gigas. Related presentation at the 2005 meeting of the Pennsylvania Academy of Sciences.

Bernal, C.A. & R.M. Kliman (2004) Society for the Study of Evolution, Fort Collins, CO. Codon usage trends of humans and their viruses.

Botens, C.M. & R.M. Kliman (2004) Society for the Study of Evolution, Fort Collins, CO. Synonymous codon variation in human papillomaviruses. Related presentations at the 2005 meetings of the Pennsylvania Academy of Sciences and Lehigh Valley Ecology and Evolution Society, along with the 2005 Northeast Ecology and Evolution Conference.

Hild, R.A. & R.M. Kliman (2004) Society for the Study of Evolution, Fort Collins, CO. Preferred codon usage trends within eukaryote genes. Related presentations at the 2005 meeting of the Pennsylvania Academy of Sciences and the 2005 Northeast Ecology and Evolution Conference.

Miede, K.A. & R.M. Kliman (2004) Society for the Study of Evolution, Fort Collins, CO. Bacteriophage codon usage reflects host codon usage. Related presentations at the 2005 meeting of the Pennsylvania Academy of Sciences and the 2005 Northeast Ecology and Evolution Conference.

Santiago, M., N. Irving & R.M. Kliman (2002). Society for the Study of Evolution, Urbana, IL. Patterns of codon usage in the yeast genome.

Lab Alums    top

Laurie Cotroneo (Cedar Crest College), postdoc (2011).

Rebecca Anewalt (Cedar Crest College), codon bias in Cryptococcus neoformans.
Beth Bachert (Cedar Crest College), Cryptococcus codon usage and gene expression.
Cheryl Bernal (Cedar Crest College), codon usage in humans and viruses.
Chelsey Bihlear (Cedar Crest College), scuttle fly population genetics.
Katelyn Burgett (Cedar Crest College), Drosophila population genetics: codon bias.
Cristy Botens (Cedar Crest College), codon usage in bacteria.
Emily Dittmar (Cedar Crest College), queen conch population genetics.
Melissa Donigan (Cedar Crest College), queen conch population genetics.
Kaleigh Fernald (Cedar Crest College), Cryptococcus codon usage and gene expression.
Amanda Gilbert (Cedar Crest College), Drosophila population genetics.
Regina Gill (Cedar Crest College), genomics, evolution of human papillomaviruses.
Jeremy Goodin (Radford University), Drosophila population genetics.
Nicole Hess (Cedar Crest College), Drosophila population genetics: gene flow.
Ashley Henry (Cedar Crest College), codon usage in eukaryotes.
Rebecca Hild (Cedar Crest College), within-gene codon usage trends in eukaryotes.
Naheelah Irving (Kean University), yeast codon usage.
Aelén Mabillé (Cedar Crest College), Drosophila population genetics: codon bias.
Shannon McDermott (Cedar Crest College), Drosophila population genetics: isolation model testing.
Mercedes Melo (Cedar Crest College), avian microbiome analysis.
Kimberly Miede (Cedar Crest College), bacteria/phage codon usage coevolution.
Paula Miller (Cedar Crest College), queen conch population genetics.
Rose Moran (Cedar Crest College), Drosophila population genetics.
Kimeal Parham (Cedar Crest College), spotted lanternfly population genetics.
Matthew Petrus (Radford University), Drosophila population genetics.
Kelly Reid (Cedar Crest College), spotted lanternfly population genetics.
Mindy Sandridge (Cedar Crest College), queen conch population genetics.
Maria Santiago (Kean University), yeast codon usage.
Jennifer Schwab (Cedar Crest College), queen conch genetics and natural history.
Christine Seay (Radford University), Drosophila quantitative genetics.
Jennifer Shaffer (Cedar Crest College), Drosophila population genetics: codon bias.
Danielle Skinner (Cedar Crest College), queen conch population genetics.
Elizabeth Smith (Cedar Crest College), Drosophila population genetics.
Melanie Smith (Cedar Crest College), bioinformatics: evolution of human papillomaviruses.
Ted Stevens (Radford University), Drosophila population genetics.
Brandi Strauch (Cedar Crest College), queen conch population genetics.
Ashley Tillette (Cedar Crest College), genomics: influences on codon usage.
Nino Velasco (Kean University), Drosophila population genetics.
Rachel Vereneck (Cedar Crest College), queen conch population genetics.