Preprints and Submissions

Schwartz, R.S., A. Merry, M.M. Howell, and R.A. Cartwright. Strong selection is necessary for repeated evolution of blindness in cavefish. Link

Huang, N., K.A. Vigh-Conrad, R.S. Schwartz, R.A. Cartwright, and D.F. Conrad. Joint mutation calling and cell lineage inference from genome sequencing of single cells.

Wu, S., R.S. Schwartz, D. Winter, R.A. Cartwright, and D.F. Conrad. A novel method to model read counts in genomic data to reduce false positive identification of heterozygotes. Link


Harkins, K.M., Schwartz, R.S., A.C. Stone, and R.A. Cartwright. In press. Phylogenomic reconstruction supports supercontinent origins for Leishmania. Infection, Genetics and Evolution. Link

Winter, D.J., M. Andreina Pacheco, A.F. Vallejo, R.S. Schwartz, M. Arevalo-Herrera, S. Herrera, R.A. Cartwright, and A.A. Escalante. 2015. Whole genome sequencing of field isolates reveals extensive genetic diversity in Plasmodium vivax from Colombia. Link

Schwartz, R.S., K.M Harkins, A.C. Stone, and R.A. Cartwright. 2015. A composite genome approach to identify phylogenetically informative data from next-generation sequencing. BMC Bioinformatics. 16:193. Link

Lavretsky, P., R.S. Schwartz, M.R. Baerwald, and B. May. 2014. Developing Major Histocompatibility markers in a species of concern: the Sacramento Perch (Archoplites interruptus). Journal of Fish Biology. 85:1766-1776. Link

Ramu, A., M.J. Noordam, R.S. Schwartz, A. Wuster, M.E. Hurles, R.A. Cartwright, and D.F. Conrad. 2013. DeNovoGear: de novo indel and point mutation discovery and phasing. Nature Methods. 10: 985–987. Link

O’Neill, E.M., R. Schwartz, C.T. Bullock, J.S. Williams, H.B. Shaffer, X. Aguilar-Miguel, G. Parra-Olea, and D.W. Weisrock. 2013. Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex. Molecular Ecology. 22: 111-129. Link

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

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: 849–856. Link

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. Link

Schwartz, R.S. and B. May. 2008. Genetic evaluation of isolated populations for use in reintroductions reveals significant genetic bottlenecks in potential stocks of Sacramento perch. Transactions of the American Fisheries Society. 137:1764–1777. Link

Schwartz, R.S. and B. May. 2004. Characterization of microsatellite loci in Sacramento perch (Archoplites interruptus). Molecular Ecology Notes. 4:694-697. Link