Complete CV: here

Publications

Submitted

  • Long, C. L. and L. S. Kubatko. 2017. The effect of gene flow on coalescent-based species tree inference, submitted.

  • Blischak, P., J. Chifman, A. D. Wolfe, and L. S. Kubatko. 2017. HyDe: a Python package for genome-scale hybridization detection, submitted, available on bioRXiv.

  • Wainaina, J. M., L. Kubatko, J. Harvey, E. Ateka, T. Makori, D. Karanja, L. M. Boykin and M. A. Kehoe. 2017. Phylogenomics and evolutionary insights of Bean Common Mosaic Necrosis Virus and Cowpea Aphid Borne Mosaic Virus and impacts on food security in sub Saharan Africa, submitted.

  • Long, C. L. and L. Kubatko. 2017. Identifiability and reconstructibility of species phylogenies under a modified coalescent, available on arXiv.

  • Gory, J., R. Herbei, and L. Kubatko, 2017. Bayesian inference of selection in the Wright-Fisher diffusion model, submitted.

  • Tian, Y. and L. Kubatko, 2017. Rooting phylogenetic trees under the coalescent model using site pattern probabilities, submitted.

  • Kubatko, L. and J. Chifman. 2016. An invariants-based method for efficient identification of hybrid speciation from large-scale genomic data, submitted, available on bioRxiv.

  • Cui, L. and L. Kubatko. 2017. A distance method to reconstruct species trees in the presence of gene flow, available on bioRxiv.

2017

  • Blischak, P. D., L. S. Kubatko, and A. D. Wolfe. 2017. SNP genotyping and analysis of genetic diversity in polyploids, Bioinformatics, to appear.

  • Wainaina, J. M., P. De Barro, L. Kubatko, M. A. Kehoe J. Harvey, D. Karanja, and L. M. Boykin. 2017. Genetic diversity, population structure and gene flow estimation of Trialeurodes vaporariorum (greenhouse whitefly), Bulletin of Entomological Research [web link].

  • Tian, Y. and L. Kubatko. 2017. Expected pairwise congruence among gene trees under the coalescent model, Molecular Phylogenetics and Evolution 106: 144-150 [web link].

  • Allman, E. S., L. S. Kubatko, and J. A. Rhodes. 2017. Split scores: a tool to quantify phylogenetic signal in genome-scale data, Systematic Biology 66 (4): 620-636 [web link].

2016

  • Thompson, K., C. Linnen, and L. Kubatko. 2016. Tree-based quantitative trait mapping in the presence of external covariates, Statistical Applications in Genetics and Molecular Biology 15(6): 473-490 [web link].

  • Alicai, T., Ndunguru, J., Sseruwagi, P., Tairo, F., Okao-Okuja, G., Nanvubya, R., Kiiza, L., Kehoe, M., Kubatko, L. and L. Boykin. 2016. Cassava brown streak virus has a rapidly evolving genome: implications for virus speciation, variability, diagnosis and host resistance Scientific Reports, 6: 36164 [web link].

  • Gaither, J. and L. Kubatko. 2016. Hypothesis tests for phylogenetic quartets, with applications to coalescent-based species tree inference, Journal of Theoretical Biology 408: 179-186 [web link].

  • Tian, Y. and L. Kubatko. 2016. Distribution of gene tree histories under the coalescent model with gene flow, Molecular Phylogenetics and Evolution 105: 177-192 [web link]; preliminary version available on bioRxiv.

  • Wolfe, A. D., T. NeCamp, S. Fassnacht, P. Blischak, and L. Kubatko. 2016. Conservation genetics of Penstemon albomarginatus (Plantaginaceae), a rare Mojave Desert species of deep sand habitats, Conservation Genetics 17: 1245-1255 [web link].

  • Blischak, P., L. Kubatko, and A. Wolfe. 2016. Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids, Molecular Ecology Resources 16(3): 742-754 [web link].

  • Kubatko, L. S., P. Shah, R. Herbei, and M. A. Gilchrist. 2016. A codon model of nucleotide substitution with selection on synonymous codon usage, Molecular Phylogenetics and Evolution 94: 290-297 [web link].

  • Pearl, D. and Kubatko, L. 2016. DNA Sequence Evolution. Wiley StatsRef: Statistics Reference Online. 1–14. [web link].

  • Kliman, R. (Ed.). 2016. Encyclopedia of Evolutionary Biology; L. Kubatko, Section Editor for "Phylogenetic Methods" Section, Volume 3, page 270 - Volume 4, page 255.

2015

  • Spade, D., R. Herbei, and L. Kubatko. 2015. Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths, Mathematical Biosciences 268: 9-21 [web link].

  • Chifman, J. and L. Kubatko. 2015. Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites, Journal of Theoretical Biology 374: 35-47 [web link].

  • Kubatko, L. 2015. Review of Bayesian Phylogenetics: Methods, Algorithms, and Applications, edited by Ming-Hui Chen, Lynn Kuo, and Paul O. Lewis. Journal of the American Statistical Association 110(510): 881-882.

2014

  • Chifman, J. and L. Kubatko. 2014. Quartet inference from SNP data under the coalescent model, Bioinformatics 30(23): 3317-3324 [web link].

  • Tian, Y. and L. Kubatko. 2014. Gene tree rooting methods give distributions that mimic the coalescent process, Molecular Phylogenetics and Evolution 70: 63-69 [web link].

  • Spade, D. A., R. Herbei, and L. S. Kubatko. 2014. A note on the relaxation time of two Markov chains on rooted phylogenetic tree spaces, Statistics and Probability Letters 84: 247-252 [web link].

  • Sovic, M., L. Kubatko, and P. Fuerst. 2014. The effects of locus number, genetic divergence and genotyping error on the utility of dominant markers for hybrid identification, Ecology and Evolution 4(4): 462-473, doi: 10.1002/ece3.833 [web link].

  • Wolfe, A. D., A. McMullen-Sibul, V. J. Tepedino, L. Kubatko, T. NeCamp, and S. Fassnacht. 2014. Conservation genetics and breeding system of Penstemon debilis (Plantaginaceae), a rare beardtongue endemic to oil shale talus in western Colorado, USA, Journal of Systematics and Evolution [web link].

2013

  • Thompson, K.L., and L. Kubatko. 2013. Using ancestral information to detect and localize quantitative trait loci in genome-wide association studies, BMC Bioinformatics 14: 200 [web link].

  • Hovmoller, R., L. L. Knowles, and L. S. Kubatko. 2013. Effects of missing data on species tree estimation under the coalescent, Molecular Phylogenetics and Evolution 69: 1057-1062 [web link].

  • Herbei, R. and L. Kubatko. 2013. Monte Carlo estimation of total variation distance of Markov chains on large spaces, with application to phylogenetics, Statistical Applications in Genetics and Molecular Biology, 12(1): 39-48 [web link].

  • Kubatko, L.S. and H. H. Fan. 2012. Reply to "Letter to the Editor on the article entitled "Estimating species trees using Approximate Bayesian Computation" (Fan and Kubatko, Mol. Phylogenetics Evol. 59, 354 - 363)", Molecular Phylogenetics and Evolution 66(1): 438-439 [ web link].

  • Nance, T. and L. Kubatko. 2013. Constructing an undergraduate biomath curriculum at a large univeristy, part I: Developing first year biomath coures at The Ohio State University. Undergraduate Mathematics for the Life Sciences: Processes, Models, Assessment, and Directions, edited by G. Ledder, J. P. Carpenter, and T. Comar, pages 149-154 [Link to book].

  • Kubatko, L., J. Best, T. Nance, and Y. Lou. 2013. Constructing an undergraduate biomath curriculum at a large univeristy, part II: Implementing first year biomath coures at The Ohio State University. Undergraduate Mathematics for the Life Sciences: Processes, Models, Assessment, and Directions, edited by G. Ledder, J. P. Carpenter, and T. Comar, pages 25-32 [Link to book].

2012

  • Boykin, L. M., K. Armstrong, L. Kubatko, and P. DeBarro. 2012. DNA barcoding invasive insects: Database roadblocks, Invertebrate Systematics 26: 506-514.

  • Boykin, L., K. Armstrong, L. Kubatko, and P. DeBarro. 2012. Species delimitation and global biosecurity, Evolutionary Bioinformatics 8:1-37 [web link].

2011

  • Gerard, D., H. L. Gibbs, and L. Kubatko. 2011. Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling. BMC Evolutionary Biology,11: 291 [web link].

  • Kubatko, L. S. and D. K. Pearl. 2011. Seeing the Trees in Your Terrace. Science 333 (6041): 411-412 [Reprint|Full text|Summary]

  • Kubatko, L, HL Gibbs, and EW Bloomquist. 2011. Inferring species-level phylogenies and taxonomic distinctiveness using multi- locus data in Sistrurus rattlesnakes, Systematic Biology,60(4): 393-409 [web link].

  • Fan, H. and L. S. Kubatko. 2011. Estimating Species Trees Using Approximate Bayesian Computation. Molecular Phylogenetics and Evolution, 59: 354-363 [web link].

  • Roos, C., D. Zinner, L. S. Kubatko, C. Schwarz, M. Yang, D. Meyer, S. D. Nash, J. Xing, M. A. Batzer, M. Brameier, F. H. Leendertz, T. Ziegler, D. Perwitasari-Farajallah, T. Nadler, L. Walter, and M. Osterholz. 2011. Nuclear versus Mitochondrial DNA: Evidence for Hybridization in Colobine Monkeys, BMC Evolutionary Biology 11:77 [web link].

2010

  • Boykin, LM, LS Kubatko, and TK Lowrey. 2010. Comparison of methods for rooting phylogenetic trees: A case study using Orcuttieae (Poaceae: Chloridoidea). Molecular Phylogenetics and Evolution 54: 687-700[web link].

  • Huang, H, Q He, LS Kubatko, and LL Knowles. 2010. Sources of error for species-tree estimation: Impact of mutational and coalescent effects on accuracy and implications for choosing among different methods, Systematic Biology, 59(5): 573-583 [web link].

  • Stone AC, Battistuzzi F, Kubatko LS, Perry GH, Trudeau E, Lin H & Kumar S. 2010. More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philosophical Transactions of Royal Society B 365 (1556): 3277-3288 [web link].

  • Hird, S. LS Kubatko and B. C. Carstens. 2010. Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling. Molecular Phylogenetics and Evolution 57(2): 888-898 [web link].

  • Estimating Species Trees: Practical and Theoretical Aspects, edited by L. L. Knowles and L. S. Kubatko, Wiley-Blackwell, 2010.

    Includes the following:

    • Knowles, L. L. and L. S. Kubatko. 2010. Estimating species trees: An introduction to concepts and models (Chapter 1, pgs. 1-14).

    • L. S. Kubatko and C. Meng. 2010. Accomodating hybridization in a multilocus phylogenetic framework (Chapter 6, pgs. 99-113).

    • L. S. Kubatko and H. L. Gibbs. 2010. Estimating species relationships and taxon distinctiveness in Sistrurus rattlesnakes using multilocus data (Chapter 12, pgs. 193-207).

2009

  • Meng, C and LS Kubatko. 2009. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model, Theoretical Population Biology 75:35-45. [web link].

  • Brock, G, W Beavis, and L Salter Kubatko. 2009. Fuzzy logic and related methods as a screening tool for detecting gene regulatory networks, Information Fusion 10:250-259 (special issue on Bioinformatics) [web link].

  • Kubatko, LS. 2009. Modeling the past: A resource for the future (review of the book Coalescent Theory: An Introduction by John Wakeley), Trends in Ecology and Evolution 24(3): 125-126 [web link].

  • Brock, G, V Pihur, and L Kubatko. 2009. Detecting gene regulatory networks from microarray data using fuzzy logic, pgs. 141-163, in Fuzzy Systems in Bioinformatics and Computational Biology, edited by Yaochu Jin and Lipo Wang, pages 141-164. Book info can be found here Download pdf here.

  • Kubatko, L, BC Carstens, and LL Knowles. 2009. STEM: Species Tree Estimation using Maximum likelihood for gene trees under coalescence, Bioinformatics 25(7): 971-973 [web link].

  • Liu, L, L Yu, L Kubatko, DK Pearl, and SV Edwards. 2009. Coalescent methods for estimating multilocus phylogenetic trees, Molecular Phylogenetics and Evolution 53(1): 320-328 [web link].

  • Melman, SD, ML Steinauer, C Cunningham, LS Kubatko, IN Mwangi, MW Mutuku, DMS Karanja, DG Colley, C Black, WE Secor, N Barker, GM Mkoji, and ES Loker. 2009. Reduced susceptibility of naturally occurring Schistosoma mansoni to praziquantel following repeated exposures: origin, measurement and likelihood of persistence, PLoS Neglected Tropical Diseases 3(8): e504. doi:10.1371/journal.pntd.0000504 [web lihk].

  • Kubatko, LS. 2009. Identifying Hybridization Events in the Presence of Coalescence via Model Selection, Systematic Biology 58(5): 478-488 [web link].
2008
  • Efromovich, S and L Salter Kubatko. 2008. Coalescent time distributions in trees of arbitrary size, Statistical Applications in Genetics and Molecular Biology: Vol. 7 : Iss. 1, Art. 2, Available at: http://www.bepress.com/sagmb/vol7/iss1/art2.

  • Shoff, ME, CE Joslin, EY Tu, L Kubatko, and PA Fuerst. 2008. Efficacy of contact lens systems against recent clinical and tap water Acanthamoeba isolates, Cornea 27(6): 713-719 .
2007
  • Kubatko, L and J Degnan. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence, Systematic Biology 56(1): 17-24. [ pdf ]

  • Wilbur, A, L Salter Kubatko, J Feurstein, A Hurtado, K Hill, and A Stone. 2007. Vitamin D receptor gene polymorphisms and susceptibility to M. tuberculosis in Native Paraguayans, Tuberculosis 87: 329-337. [ pdf ]

  • Kubatko, LS. 2007. Inference of Phylogenetic Trees, in "Tutorials in Mathematical Biosciences IV: Evolution and Ecology", A. Friedman (ed.), Springer-Verlag, pgs. 1-38.
2006 and earlier
  • MJ Harmon, TL VanPool, RD Leonard, CS VanPool, and L Salter. 2006. Reconstructing the Flow of Information across Time and Space: A Phylogenet ic Analysis of Ceramic Traditions from Pre-Hispanic West Mexico, North Mexico, and the U.S. Southwest, in Mapping Our Ancestors: Phylogenetic Methods in Anthropol ogy and Prehistory, edited by Carl P. Lipo, Michael J. O'Brien, Stephen Shennan, and Mark Collard, pp. 209-229.

  • Degnan, J and L Salter. 2005. Gene tree distributions under the coalescent process, Evolution 59(1): 24-37. [ pdf ]

  • Gilchrist, M, L Salter, and A Wagner. 2004. A statistical framework for interpreting high-throughput proteomic datasets, Bioinformatics 20(5): 689-700. [ pdf ]

  • Standberg, AKK and L Salter. 2004. A Comparison of Methods for Estimating the Transition:Transversion Ratio From DNA Sequences, Molecular Phylogenetics and Evolution 32(2): 495-503. [ pdf ]

  • Salter, L. 2004. Review of The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny (Edited by Marco Salemi and Anne-Mieke Vandamme. Cambridge, England: Cambridge University Press, 2003.), American Journal of Human Biology 16: 354-355.

  • Powell, A, D Jacobson, L Salter, and D Natvig. 2003. Variation among natural isolates of Neurospora on small spatial scales, Mycologia 95: 809-819. [ pdf ]

  • Pearl, D and L Salter. 2002. The Analysis of DNA Sequences, in Biostatistical Genetics and Genetic Epidemiology, edited by R. Elston, J. Olson, and L. Palmer, pp 217-227, John Wiley and Sons, New York.

  • Frankel, W, J Tranovich, L Salter, G Bumgardner, and P Baker. 2002. The Optimal Number of Biopsies to Evaluate for Liver Transplantation, Liver Transplantation, 8(11): 1044-1050. [ pdf ]

  • Wang, Q, L Salter, and D Pearl. 2002. Estimation of Evolutionary Parameters from Phylogenetic Trees, Journal of Molecular Evolution, 55(6): 684-695. [ pdf ]

  • Salter, L and D Pearl. 2001. A Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees, Systematic Biology 50(1): 7-17. [ pdf ]

  • Salter, L. 2001. Complexity of the Likelihood Surface for a Large DNA Data Set, Systematic Biology 50(6): 970-978. [ pdf ]

  • Turner, T, L Salter, and J Gold. 2001. Temporal-method Estimates of Ne From Highly Polymorphic Loci, Conservation Genetics 2: 297-308. [ pdf ]

  • Salter, L. 2000. Algorithms for Phylogenetic Tree Reconstruction. Proceeding of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Vol. 2, pgs. 459-465.[ postscript ][ pdf ]