Complete CV: here (Updated October 2021)


Please note that preliminary versions of most recent publications are available on arXiv or bioRxiv, and requests for reprints can be sent by email. I do NOT use sites like Research Gate to post and distribute reprints.


Submitted/Preprints

Wicke, K., R. Haque, and L. Kubatko. 2022. Effects of gene tree variation on prioritizing species for conservation, submitted.

Wicke, K., M. Fischer, and L. Kubatko. 2021. Effects of discordance between species and gene trees on phylogenetic diversity conservation, submitted, available on arXiv

Wolfe, A.D., P. D. Blischak, and L. Kubatko. 2021. Phylogenetics of a Rapid, Continental Radiation: Diversification, Biogeography, and Circumscription of the Beardtongues (Penstemon; Plantaginaceae), submitted, available on bioRXiv.

Avenarius, M. R., L. Kubatko, H. Tu, K. Schaadt, P. Ru, Y.-S. Chang, S. Long, S. Corcoran, S. Diaz-Vazquez, D. Chappell, M. Hunt, X. Pan, J. Garee, K. Thomas, P. J. Snyder, P. Mohler, S. Koenig, P. Pancholi, and D. Jones. 2021. Emergence and persistence of a minimally mutated SARS-CoV-2 variant with Spike N501Y: Comparison with the highly mutated B.1.1.7 strain in a large surveillance set, submitted.

Tu, H., M. R. Avenarius, L. Kubatko, M. Hunt, X. Pan, P. Ru, J. Garee, K. Thomas, P. Mohler, P. Pancholi, and D. Jones. 2021. Distinct patterns of emergence of SARS-CoV-2 spike variants including N501Y in clinical samples in Columbus Ohio, available on bioRXiv.

Kubatko, L. and J. Chifman. 2020. Identifiability of speciation times under the multispecies coalescent, available on arXiv.

Cui, L. and L. Kubatko. 2014. A distance method to reconstruct species trees in the presence of gene flow, available on bioRxiv.


2023

Wascher, M. and L. S. Kubatko. 2023. On the effects of selection on species tree inference, Molecular Phylogenetics and Evolution. 179: 107650 [web link].

Wicke, K., M. Fischer, and L. Kubatko. 2023. Effects of discordance between species and gene trees on phylogenetic diversity conservation, Journal of Mathematical Biology, accepted.

Kubatko, L. S. and L. L. Knowles (eds.) 2023. Species Tree Inference: A Guide to Methods and Applications, to be published in March 2023 by Princeton University Press [web link]
Includes the following three chapters:
Knowles, L.L. and L. S. Kubatko. Introduction to species tree inference, (Chapter 1, pgs. 1-14).
Swofford, D. L. and L. S. Kubatko. Species tree estimation using site pattern frequencies (Chapter 4, pgs. 68-88).
Blischak, P. D., C. E. Thompson, E. M. Waight, L. S. Kubatko, and A. D. Wolfe. Hybridization and polyploidy in Penstemon (Chapter 9, pgs. 175-190).


2022

Gao, Y., J. Gaither, J. Chifman, and L. Kubatko. 2022. A phylogenetic approach to inferring the order in which mutations arise during cancer progression. PLoS Computational Biology, in press.

Peng, J., D. Swofford, and L. Kubatko. 2022. Estimation of speciation times under the multispecies coalescent, Bioinformatics [web link].

Zayed, A. A., J. M. Wainaina, G. Dominguez-Huerta, E. Pelletier, J. Guo, M. Mohssen, F. Tian, A. A. Pratama, B. Bolduc, O. Zablocki, D. Cronin, L. Solden, E. Delage, A. Alberti, J. M. Aury, Q. Carradec, C. da Silva, K. Labadie, J. Poulain, H. J. Ruscheweyh, G. Salazar, E. Shatoff, Tara Oceans Coordinators, R. Bundschuh, K. Fredrick, L. S. Kubatko, C. Bowler, S. Chaffron, A. Culley, D. Eveilliard, L. Guidi, E. Karsenti, H. Ogata, S. Sunagawa, J. H. Kuhn, P. Wincker, and M. B. Sullivan. 2022. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 376(6589): 156-162 [web link]

Richards, A. and L. Kubatko. 2022. Site pattern probabilities under the multispecies coalescent and a relaxed molecular clock: theory and applications, Journal of Theoretical Biology 542: 111078 [web link]

Kong, S., J. C. Pons, L. Kubatko, and K. Wicke*. 2022. Classes of explicit phylogenetic networks and their biological and mathematical significance, Journal of Mathematical Biology 84: 47 [web link]
*Senior and corresponding author


2021

Wascher, M. and L. Kubatko. 2021. Consistency of SVDQuartets and maximum likelihood for coalescent-based species tree estimation, Systematic Biology 70(1): 33-48 [web link].

Kubatko, L. 2021. Review of "A Mathematical Primer of Molecular Phylogenetics" by Xuhua Xia, Systematic Biology 70(2): 408-411 [web link].

Kong, S. and L. Kubatko. 2021. Comparative performance of popular methods for hybrid detection using genomic data, Systematic Biology 70(5): 891-907 [web link].

Peng, J., H. Rajeevan, L. Kubatko, and A. RoyChoudhury. 2021. A fast likelihood approach for estimation of large phylogenies from allele frequency data, Molecular Phylogenetics and Evolution 161: 107142 [web link].

Richards, A. and L. Kubatko. 2021. Bayesian-weighted triplet and quartet methods for species tree inference, Bulletin of Mathematical Biology 83(9): 93 [web link].

Long, C. L. and L. Kubatko. 2021. Hypothesis testing with rank conditions in phylogenetics, Frontiers in Genetics12: 664357 [web link].


2020

Sanchez-Pacheco, S. J., S. Kong, P. Pulido-Santacruz, R. W. Murphy, and L. Kubatko. 2020. Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary, Proceedings of the National Academy of Sciences 117 (17): 9241-9243. (letter in response to Forster et al. (2020))


2019

Kubatko, L. and J. Chifman. 2019. An invariants-based method for efficient identification of hybrid speciation from large-scale genomic data, BMC Evolutionary Biology 19:112 [web link].

Long, C. L. and L. Kubatko. 2019. Identifiability and reconstructibility of species phylogenies under a modified coalescent, Bulletin of Mathematical Biology 81: 408-430 [web link].

Wainaina, J. M., L. Kubatko, J. Harvey, E. Ateka, T. Makori, D. Karanja, L. M. Boykin and M. A. Kehoe. 2019. 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, PeerJ 7:e6297 [web link].

Kubatko, L. 2019. The Multispecies Coalescent, pgs. 219-245 in Handbook of Statistical Genomics, Fourth Edition, Volume 1, edited by David J. Balding, Ida Moltke and John Marioni, John Wiley & Sons Ltd.


2018

Gory, J., R. Herbei, and L. Kubatko. 2018. Bayesian inference of selection in the Wright-Fisher diffusion model, Statistical Applications in Genetics and Molecular Biology 17(3) [web link].

Blischak, P., J. Chifman, A. D. Wolfe, and L. S. Kubatko. 2018. HyDe: a Python package for genome-scale hybridization detection, Systematic Biology 67(5): 821-829 [web link].

Long, C. L. and L. S. Kubatko. 2018. The effect of gene flow on coalescent-based species tree inference, Systematic Biology 67(5): 770-785 [web link].

Wainaina, J. M., P. De Barro, L. Kubatko, M. A. Kehoe J. Harvey, D. Karanja, and L. M. Boykin. 2018. Genetic diversity, population structure and gene flow estimation of Trialeurodes vaporariorum (greenhouse whitefly), Bulletin of Entomological Research 108: 5-13 [web link].

Blischak, P. D., L. S. Kubatko, and A. D. Wolfe. 2018. SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data, Bioinformatics 34(3): 407-415 [web link].

Boykin, L., T. Kinene, J. Wainaina, A. Savill, S. Seal, H. Mugerwa, S. Macfadyen, W.T. Tay, P. De Barro, L. Kubatko, T. Alicai, C.A. Omongo, F. Tairo, J. Ndunguru and P. Sseruwagi. 2018. Review and guide to a future naming system of African Bemisia tabaci species, Systematic Entomology 43: 427-433 [web link].


2017

Tian, Y. and L. Kubatko, 2017. Rooting phylogenetic trees under the coalescent model using site pattern probabilities, BMC Evolutionary Biology 17: 263 [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 three chapters:
    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 ]