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Phylogenetic Information

McManus, H. A., K. Fučíková, P. O. Lewis, L. A. Lewis, and K. G. Karol. 2018. Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life. American Journal of Botany 105(3):315–329. [doi:10.1002/ajb2.1066]

Wang, Y.-B., M.-H. Chen, L. Kuo, and P. O. Lewis. 2018. A new Monte Carlo method for estimating marginal likelihoods. Bayesian Analysis 13(2):311-333. [doi:10.1214/17-BA1049]

Neupane, S., P. O. Lewis, S. Dessein, H. Shanks, S. Paudyal, and F. Lens. 2017. Evolution of woody life form on tropical mountains in the tribe Spermacoceae (Rubiaceae). American Journal of Botany 104(3):419-438. [doi:10.3732/ajb.1600248]

Mitchell, N., P. O. Lewis, E. M. Lemmon, A. R. Lemmon, and K. E. Holsinger. 2017. Anchored phylogenomics improves evolutionary relationships in the rapid radiation of Protea L. (Proteaceae). American Journal of Botany 104(1):102-115. [doi:10.3732/ajb.1600227]

Lewis, P. O., M.-H. Chen, L. Kuo, L. A. Lewis, K. Fučíková, S. Neupane, Y.-B. Wang, and D. Shi. 2016. Estimating Bayesian phylogenetic information content. Systematic Biology 65(6):1009-1023. [doi:10.1093/sysbio/syw042]

Watanabe, S., K. Fučíková, L. A. Lewis, and P. O. Lewis. 2016. Hiding in plain sight: Koshicola spirodelophila gen. et sp. nov. (Chaetopeltidales, Chlorophyceae), a novel green alga associated with the aquatic angiosperm Spirodela polyrhiza. American Journal of Botany 103:865875. [doi:10.3732/ajb.1500481]

Neupane, S., S. Dessein, N. Wikström, P. O. Lewis, C. Long, B. Bremer, and T. Motley. 2015. The Hedyotis-Oldenlandia complex (Rubiaceae: Spermacoceae) in Asia and the Pacific: phylogeny revisited with new generic delimitations. Taxon 64(2):299-322 [doi:10.12705/642.8]

Lewis, P. O., M. T. Holder, D. L. Swofford. 2015. Phycas: software for Bayesian phylogenetic analysis. Systematic Biology 64(3):525531 [doi:10.1093/sysbio/syu132].

Fučíková, K., F. Leliaert, E. D. Cooper, P. Škaloud, S. D’Hondt, O. De Clerck, C. F. D. Gurgel, L. A. Lewis, P. O. Lewis, J. M. Lopez-Bautista, C. F. Delwiche, and H. Verbruggen. 2014. New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data. Frontiers in Ecology and Evolution 2(63):1-12 [doi:10.3389/fevo.2014.00063].

American Journal of Botany cover image
New green algal genus Koshicola

Fučíková, K., P. O. Lewis and L. A. Lewis. 2014. Widespread desert affiliations of trebouxiophyte algae (Trebouxiophyceae, Chlorophyta), including discovery of three new desert lineages. Phycological Research 62(4):294-305 [doi:10.1111/pre.12062].

Wu, R., M.-H. Chen, L. Kuo, and P. O. Lewis. 2014. A new method for tracking configuration for Dirichlet process sampling. Sri Lankan Journal of Applied Statistics. Special Issue: Modern Statistical Methodologies in the Cutting Edge of Science. pp. 1-16. [doi:10.4038/sljastats.v5i4.7781].

Fučíková, K., P. O. Lewis, D. González-Halphen, and L. A. Lewis. 2014. Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of Sphaeropleales (Chlorophyta). Genome Biology and Evolution 6(8):2170-2180. [doi:10.1093/gbe/evu172]

Cover image from Chen, Kuo and Lewis 2014 edited volume
Cover of Chen, Kuo and Lewis 2014

Chen, M.-H., L. Kuo, and P. O. Lewis (eds.). 2014. Bayesian phylogenetics: methods, algorithms, and applications. Chapman & Hall/CRC Mathematical and Computational Biology. 396 pages.

Holder, M. T., P. O. Lewis, D. L. Swofford, and D. Bryant. 2014. Variable tree topology stepping-stone marginal likelihood estimation . Pp. 95-112 in: Chen, M.-H., L. Kuo, and P. O. Lewis (eds.). 2014. Bayesian phylogenetics: methods, algorithms, and applications. Chapman & Hall/CRC Mathematical and Computational Biology.

Wu, R., M.-H. Chen, L. Kuo, and P. O. Lewis. 2014. Consistency of marginal likelihood estimation when topology varies. Pp. 113-128 in: Chen, M.-H., L. Kuo, and P. O. Lewis (eds.). 2014. Bayesian phylogenetics: methods, algorithms, and applications. Chapman & Hall/CRC Mathematical and Computational Biology.

Lewis, P. O., W. Xie, M.-H. Chen, Y. Fan, L. Kuo. 2014. Posterior predictive Bayesian phylogenetic model selection. Systematic Biology 63(3): 309-321. [doi:10.1093/sysbio/syt068]

Fučíková, K., P. O. Lewis, and L. A. Lewis. 2014. Putting insertae sedis taxa in their place: a proposal for ten new families and three new genera in Sphaeropleales (Chlorophyceae, Chlorophyta). J. Phycology 50:14-25. [doi:10.1111/jpy.12118]

Fan, Y., R. Wu, M.-H. Chen, L. Kuo, and P. O. Lewis. 2013. A conditional autoregressive model for detecting natural selection in protein-coding DNA sequences. Pages 203-212 in Hu, Mingxiu, Liu, Yi, and Lin, Jianchang (editors), Topics in Applied Statistics: 2012 Symposium of the International Chinese Statistical Association. Springer, New York.

Tippery, N. P., K. Fucikova, P. O. Lewis, and L. A. Lewis. 2012. Probing the monophyly of the directly opposite flagellar apparatus group in Chlorophyceae using data from five genes. Journal of Phycology 48:1482–1493. [doi:10.1111/jpy.12003]

Ayres, D. L., A. Darling, D. J. Zwickl, P. Beerli, M. T. Holder, P. O. Lewis, J. P. Huelsenbeck, F. Ronquist, D. L. Swofford, M. P. Cummings, A. Rambaut and M. A. Suchard. 2011. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology 61(1):170–173. [doi: 10.1093/sysbio/syr100]

Cover of Systematic Biology 60(2)
Issue containing Xie et al. 2011 paper on the stepping-stone method.

Xie, W., P. O. Lewis, Y. Fan, L. Kuo, and M.-H. Chen. 2011. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Systematic Biology 60:150-160. [doi:10.1093/sysbio/syq085]

Fan, Y., R. Wu, M.-H. Chen, L. Kuo and P. O. Lewis. 2011. Choosing among partition models in Bayesian phylogenetics. Molecular Biology and Evolution 28(1):523-532. [doi:10.1093/molbev/msq224] [pdf]

Holder, M. T., P. O. Lewis, and D. L. Swofford. 2010. The Akaike Information Criterion will not choose the No Common Mechanism model. Systematic Biology 59(4):477-485. [doi:10.1093/sysbio/syq028]

Holder, M. T., J. Sukumaran, and P. O. Lewis. 2008. A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics. Systematic Biology 57:814–821. [doi:10.1080/10635150802422308]

Wickett, N. J., Y. Fan, P. O. Lewis, and B. Goffinet. 2008. Distribution and evolution of pseudogenes, gene losses and a gene rearrangement in the plastid genome of the non-photosynthetic liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida). Journal of Molecular Evolution 67(1):111-122. [doi:10.1007/s00239-008-9133-1]

Lapp, H., S. Bala, J. P. Balhoff, A. Bouck, N. Goto, M. Holder, R. Holland, A. Holloway, T. Katayama, P. O. Lewis, A. J. Mackey, B. I. Osborne, W. H. Piel, S. L. Kosakovsky Pond, A. F. Y. Poon, W-G Qiu, J. E. Stajich, A. Stoltzfus, T. Thierer, A. J. Vilella, R. A. Vos, C. M. Zmasek, D. J. Zwickl and T. J Vision. 2007. The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics 3: 357-366.

Gelfand, A. E., J. A. Silander Jr., S. Wu, A. Latimer, P. O. Lewis, A. G. Rebelo and M. Holder. 2006. Explaining species distribution patterns through hierarchical modeling. Bayesian Analysis 1(1): 41-92. [doi:10.1214/06-BA102]

Duran, K. L., T. K. Lowrey, R. R. Parmenter and P. O. Lewis. 2005. Genetic diversity in Chihuahuan desert populations of creosotebush (Zygophyllaceae: Larrea tridentata). American Journal of Botany 92(4): 722-729. [doi:10.3732/ajb.92.4.722]

Holder, Mark T., P. O. Lewis, D. L. Swofford, and B. Larget. 2005. Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics. Systematic Biology 54(6): 961-965. [doi:10.1080/10635150500354670]

Lewis, L. A., and P. O. Lewis. 2005. Unearthing the molecular phylodiversity of desert soil green algae (Chlorophyta). Systematic Biology 54(6): 936-947. [doi:10.1080/10635150500354852]

Lewis, P. O., M. T. Holder and K. E. Holsinger. 2005. Polytomies and Bayesian phylogenetic inference. Systematic Biology 54(2): 241-253. [doi:10.1080/10635150590924208]

Holder, M. T. and P. O. Lewis. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews Genetics 4: 275-284. [doi:10.1038/nrg1044[pdf]

Lewis, P. O. 2003. NCL: a C++ class library for interpreting data files in NEXUS format. Bioinformatics 19 (17): 2330-2331. [doi:10.1093/bioinformatics/btg319]  [SourceForge]

Brauer, M. J., M. T. Holder, L. A. Dries, D. J. Zwickl, P. O. Lewis, and D. M. Hillis. 2002. Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference.Molecular Biology and Evolution 19: 1717-1726.

Holsinger, K. E., P. O. Lewis, and D. K. Dey. 2002. A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology 11: 1157-1164. [doi:10.1046/j.1365-294X.2002.01512.x]

Conant, G. C., and P. O. Lewis. 2001. Effects of nucleotide composition bias on the success of the parsimony critierion in phylogenetic inference. Molecular Biology and Evolution18: 1024-1033.

Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50:913-925. [doi:10.1080/106351501753462876]

Lewis, P. O. 2001. Phylogenetic systematics turns over a new leaf. Trends in Ecology and Evolution 16:30-37. [doi:10.1016/S0169-5347(00)02025-5[pdf]
Reprinted from TRENDS in Ecology & Evolution, volume 16, copyright 2001, with permission from Elsevier Science

Lewis, P. O., and D. L. Swofford. 2001. Back to the future: Bayesian inference arrives in phylogenetics. Trends in Ecology and Evolution 16: 600-601. (conference report) [doi:10.1016/S0169-5347(01)02322-9]

Swofford, D. L., P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology 50: 525-539. [doi:10.1080/106351501750435086]

Lewis, P. O. 1998. Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data. Pages 132-163 in: Soltis, D. E., Soltis, P. S., and Doyle, J. J., Molecular Systematics of Plants II. Kluwer, Boston.

Lewis, P. O. 1998. A genetic algorithm for maximum likelihood phylogeny inference using nucleotide sequence data. Molecular Biology and Evolution 15:277-283.

Gaut, B. S., and P. O. Lewis. 1995. Success of maximum likelihood phylogeny inference in the four-taxon case. Molecular Biology and Evolution 12:152-162. [doi:10.1093/oxfordjournals.molbev.a040183]

Lewis, P. O., and D. J. Crawford. 1995. Pleistocene refugium endemics exhibit greater allozymic diversity than widespread congeners in the genus Polygonella (Polygonaceae).American Journal of Botany 82:141-149. [doi:10.2307/2445522]

Williams, C. G., J. L. Hamrick, and P. O. Lewis. 1995. Multiple-population versus hierarchical conifer breeding programs: a comparison of genetic diversity levels. Theoretical and Applied Genetics 90: 584-594. [doi:10.1007/BF00222007]

Lewis, P. O., and L. A. Lewis. 1995. MEGA: Molecular evolutionary genetics analysis, version 1.02. Systematic Biology 44: 576-577. (software review)

Kaplan, N.L., P. O. Lewis, and B. S. Weir. 1994. Age of cystic fibrosis mutation. Nature Genetics 8: 216. [doi:10.1038/ng1194-216a]

Snow, A. A., and P. O. Lewis. 1993. Reproductive traits and male fertility in plants: empirical approaches. Annual Review of Ecology and Systematics 24: 331-351. [doi:10.1146/]

Govindaraju, D., P. O. Lewis, and C. Cullis. 1992. Phylogenetic analysis of pines using ribosomal DNA restriction fragment length polymorphisms. Plant Systematics and Evolution179: 141-153. [doi:10.1007/BF00937592]

Lewis, P. O., and A. A. Snow. 1992. Deterministic paternity exclusion using RAPD markers. Molecular Ecology 1:155-160. [doi:10.1111/j.1365-294X.1992.tb00171.x]

Lewis, P. O. 1991. Allozyme variation in the rate Gulf Coast endemic Polygonella macrophylla Small (Polygonaceae). Plant Species Biology 6: 1-10. [doi:10.1111/j.1442-1984.1991.tb00204.x]

Lewis, P. O., and E. T. Browne, Jr.  1991. The vascular flora of Haywood County, Tennessee. Journal of the Tennessee Academy of Science 66: 37–44.

Lewis, P. 1990. PeaStats:  a computer program for use with introductory plant biology courses. Plant Science Bulletin 36: 8. []

Lewis, P. O., and R. Whitkus. 1989. GENESTAT for microcomputers. American Society of Plant Taxonomists Newsletter 2: 15–16.

Bates, V., L. M. Wilson and P. Lewis. 1985. Notes and new distributional records for several Tennessee orchids. Journal of the Tennessee Academy of Science 60: 45–48.

Bates, V., and P. Lewis. 1984. Rediscovery of  Stylisma humistrata  (Convolvulaceae) in Tennessee. Rhodora   86: 393–394.

Lewis, P., and G. Nesom. 1984. Label writing program in MBasic for microcomputers. Herbarium News (Missouri Botanical Garden) 4: 6–7.

Browne, E. T., Jr., K. Broyles and P. Lewis. 1983.  Trianthema portulacastrum  L. (Aizoaceae) in Tennessee. Castanea 48: 238. []

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