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<!DOCTYPE HTML>
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<title>The Phyleauxgenetics Lab</title>
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<h1><strong><font color=#461D7C>Phyleauxgenetics</font></strong> Lab</h1>
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<p>Phylogenetics and Molecular Evolution <br> The Lab of Jeremy M. Brown @ Louisiana State University</p>
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<p>A central tenet of modern biology</p>
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<p>P3: Phylogenetic Posterior Prediction</p>
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<h3><a href="https://github.com/treescaper">TreeScaper</a></h3>
<p>Explore and analyze sets of trees</p>
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<p>Analysis of Model Adequacy</p>
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<h2><font color=#461D7C>Publications</font></h2>
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<!-- img src="https://raw.githubusercontent.com/jembrown/websiteImages/master/Journals.jpg" alt="Journal Covers" align="left"/ -->
<p align="left">
<strong>Toups, B.</strong>, T. McGowan, <strong>J.M. Brown</strong>, K.A. Gallivan, and J.C. Wilgenbusch. 2020. CloudForest: an integrated and dynamic phylogenomic toolset for the modern age. In Review.
<br><br>
<strong>Toups, B.</strong>, and <strong>J.M. Brown</strong>. 2020. Evolution in the courtroom: Using phylogenetics to investigate legal claims of HIV transmission. In Review.
<br><br>
Hime, P.M., A.R. Lemmon, E.C.M. Lemmon, E. Scott-Prendini, <strong>J.M. Brown</strong>, R.C. Thomson, J.D. Kratovil, B.P. Noonan, R.A. Pyron, P.L.V. Peloso, M.L. Kortyna, J.S. Keogh, S.C. Donnellan, R.L. Mueller, C.J. Raxworthy, K. Kunte, S. Ron, S. Das, N. Gaitonde, D.M. Green, J. Labisko, J. Che, and D.W. Weisrock. 2020. <a href="https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syaa034/5828236">Phylogenomics reveals ancient gene tree discordance in the amphibian tree of life.</a> In Press. <i>Systematic Biology</i>
<br><br>
Thaljeh, L.F.*, J.A. Rothschild, M. Naderi, L.M. Coghill, <strong>J.M. Brown</strong>, M. Brylinski. 2019. <a href="https://www.mdpi.com/2218-273X/9/10/603">Hinge region in DNA packaging terminase pUL15 of herpes simplex virus as a potential allosteric target for antiviral drugs.</a> <i>Biomolecules</i>. 9:603.
<br><br>
Rider, P.J.F., <strong>L.M. Coghill</strong>, M. Naderi, M. Brylinski, <strong>J.M. Brown</strong>, and K.G. Kousoulas. 2019. <a href="https://www.nature.com/articles/s41598-019-50490-9">Phylogenetics and structural modeling of herpes simplex virus glycoprotein K (gK) identify functionally important domains and residues critical for alphaherpesvirus infection.</a> <i>Scientific Reports</i>. 9:14625.
<br><br>
<strong>Brown, J.M.</strong> and R.C. Thomson. 2018. <a href="https://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-110617-062249">Evaluating model performance in evolutionary biology.</a> <i>Annual Review of Ecology, Evolution, and Systematics</i>. 49:95-114.
<br><br>
Richards, E.J., <strong>J.M. Brown</strong>, A.J. Barley, R.A. Chong, and R.C. Thomson. 2018. <a href="https://academic.oup.com/sysbio/article/67/5/847/4877124">Variation across mitochondrial gene trees provides evidence for systematic error: how much gene tree variation is biological?</a> <i>Systematic Biology</i>. 67:847-860.
<br><br>
<strong>Brown, J.M.</strong> and R.C. Thomson. 2018. <a href="https://academic.oup.com/sysbio/article/67/4/729/4866058">The behavior of Metropolis-coupled Markov chains when sampling rugged phylogenetic distributions.</a> <i>Systematic Biology</i>. 67:729-734.
<br><br>
Höhna, S., <strong>L.M. Coghill, G.G. Mount</strong>, R.C. Thomson, and <strong>J.M. Brown</strong>. 2018. <a href="https://academic.oup.com/mbe/article/35/4/1028/4616601">P<sup>3</sup>: Phylogenetic Posterior Prediction in RevBayes.</a> <i>Molecular Biology and Evolution</i>. 35:1028-1034.
<br><br>
Spinks, P.Q., E. McCarteny-Melstad, T.J. Near, <strong>G.G. Mount</strong>, and H.B Shaffer. 2017. <a href="https://www.sciencedirect.com/science/article/pii/S1055790317305110">Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines).</a> <i>Molecular Phylogenetics and Evolution</i>. 115:7-15.
<br><br>
Barley, A.J., <strong>J.M. Brown</strong>, and R.C. Thomson. 2017. <a href="https://academic.oup.com/sysbio/article/67/2/269/4103348">Impact of model violations on the inference of species boundaries under the multispecies coalescent.</a> <i>Systematic Biology</i>. 67:269-284.
<br><br>
<strong>Brown, J.M.</strong> and R.C. Thomson. 2017. <a href="https://academic.oup.com/sysbio/article/66/4/517/2950896">Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses.</a> <i>Systematic Biology</i>. 66:517-530.
<br><br>
Fujimoto, K., <strong>L.M. Coghill</strong>, C.A. Weier, L.-Y. Hwang, J.Y. Kim, J.A. Schneider, M.L. Metzker, and <strong>J.M. Brown</strong>. 2017. <a href="https://www.liebertpub.com/doi/abs/10.1089/AID.2016.0228">Lack of support for socially connected HIV-1 transmission among young adult black MSM.</a> <i>AIDS Research and Human Retroviruses</i>. 33:935-940.
<br><br>
Huang, W., <strong>G. Zhou</strong>, M. Marchand, <strong>J. Ash</strong>, <strong>D. Morris</strong>, P. Van Dooren, <strong>J.M. Brown</strong>, K.A. Gallivan, and J.C. Wilgenbusch. 2016. <a href="https://academic.oup.com/mbe/article/33/12/3314/2450098">TreeScaper: visualizing and extracting phylogenetic signal from sets of trees.</a> <i>Molecular Biology and Evolution</i>. 33:3314-3316.
<br><br>
Engebretsen, K.N., L.N. Barrow, E.N. Rittmeyer, <strong>J.M. Brown+</strong>, and E.M. Lemmon+. 2016. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.2232">Quantifying the spatio-temporal dynamics in a chorus frog hybrid zone (<i>Pseudacris</i>) over 30 years.</a> <i>Ecology and Evolution</i>. 6:5013-5031.
<br>+ Co-Senior Authors
<br><br>
<strong>Andersen, J.J.</strong>, <strong>B.J. Nelson</strong>, and <strong>J.M. Brown</strong>. 2016. <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1132-4">EmpPrior: Using empirical data to inform branch-length priors for Bayesian phylogenetics.</a> <i>BMC Bioinformatics</i>. 17:253.
<br><br>
McCarteny-Melstad, E., <strong>G.G. Mount</strong>, and H.B. Shaffer. 2016. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12538">Exon capture optimization in amphibians with large genomes.</a> <i>Molecular Ecology Resources</i>. 16:1084-1094.
<br><br>
<strong>Doyle, V.P.</strong>, <strong>R.E. Young</strong>, G.J.P. Naylor, and <strong>J.M. Brown</strong>. 2015. <a href="https://academic.oup.com/sysbio/article/64/5/824/1686772">Can we identify genes with increased phylogenetic reliability?</a> <i>Systematic Biology</i>. 64:824-837.
<br><a href="http://f1000.com/prime/725583194?bd=1" target="_blank"><img alt="Access the recommendation on F1000Prime" id="bg" src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" align="left"></a>
<br><br>
<strong>Nelson, B.J.</strong>, <strong>J.J. Andersen</strong>, and <strong>J.M. Brown</strong>. 2015. <a href="https://academic.oup.com/sysbio/article/64/3/441/1632067">Deflating trees: Improving Bayesian branch-length estimates using informed priors.</a> <i>Systematic Biology</i>. 64:441-447.
<br><br>
Couturier, J., D.J. Luke, N. Agarwal, J.W. Suliburk, <strong>J.M. Brown</strong>, X. Yu, C. Nguyen, D. Iyer, C.A. Kozinetz, P.A. Overbeek, M.L. Metzker, A. Balasubramanyam, and D.E. Lewis. 2015. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4389783/">Human adipose tissue as a reservoir for HIV and activated memory CD4 T cells.</a> <i>AIDS</i>. 29:667-674.
<br><br>
<strong>Brown, J.M.</strong> 2014. <a href="https://academic.oup.com/sysbio/article/63/3/289/2848546">Predictive approaches to assessing the fit of evolutionary models.</a> <i>Systematic Biology</i>. 63: 289-292.
<br><br>
<strong>Brown, J.M.</strong> 2014. <a href="https://academic.oup.com/sysbio/article/63/3/334/1649587">Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit.</a> <i>Systematic Biology</i>. 63: 334-348.
<br><br>
<strong>Doyle, V.P.</strong>, <strong>J.J. Andersen</strong>, <strong>B.J. Nelson</strong>, M.L. Metzker, and <strong>J.M. Brown</strong>. 2014. <a href="https://www.sciencedirect.com/science/article/pii/S1055790314000815">Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster.</a> <i>Molecular Phylogenetics and Evolution</i>. 75:126-137.
<br><br>
Reid, N.M., S.M. Hird, <strong>J.M. Brown</strong>, T.A. Pelletier, J.D. McVay, J.D. Satler, and B.C. Carstens. 2014. <a href="https://academic.oup.com/sysbio/article/63/3/322/1647401">Poor fit to the multispecies coalescent is widely detectable in empirical data.</a> <i>Systematic Biology</i>. 63:322-333.
<br>* Noah Reid awarded Society of Systematic Biologist's Publisher's Award for Best Student Paper of 2014
<br><br>
Spinks, P.Q., R.C. Thomson, G.B. Pauly, C.E. Newman, <strong>G.G. Mount</strong>, and H.B. Shaffer. 2013. <a href="https://www.sciencedirect.com/science/article/pii/S1055790313001504">Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus <i>Pseudemys</i>.</a> <i>Molecular Phylogenetics and Evolution</i>. 68:269-281.
<br><br>
Fong, J.J., <strong>J.M. Brown</strong>, M.K. Fujita, and B. Boussau. 2012. <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048990">A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia.</a> <i>PLoS ONE</i> 7:e48990.
<br><br>
Boussau, B., <strong>J.M. Brown</strong>, and M.K. Fujita. 2011. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1558-5646.2011.01322.x">Nonadaptive evolution of mitochondrial genome size.</a> <i>Evolution</i>. 65:2706-2711.
<br><br>
Leitner, T., M.L. Metzker, D. Zwickl, <strong>J.M. Brown</strong>, A.M. Geretti, A. Vandamme, J. Albert, and D.M. Hillis. 2011. <a href="https://www.nature.com/articles/473284a">Forensic HIV phylogenetics.</a> <i>Nature</i>. 473:284 [Correspondence]
<br><br>
<strong>Brown, J.M.</strong>, K. Savidge*, and E.J.B. McTavish. 2010. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1755-0998.2010.02925.x">DIM SUM: Demography and Individual Migration Simulated Using a Markov chain.</a> <i>Molecular Ecology Resources</i>. 11:358-363.
<br><br>
Scaduto, D.I., <strong>J.M. Brown</strong>, W.C. Haaland, D.J. Zwickl, D.M. Hillis, and M.L. Metzker. 2010. <a href="http://www.pnas.org/content/early/2010/11/12/1015673107.short">Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences.</a> <i>Proceedings of the National Academy of Sciences USA</i>. 107:21242-21247.
<br><br>
<strong>Brown, J.M.</strong>, S.M. Hedtke, A.R. Lemmon, and E.M. Lemmon. 2009. <a href="https://academic.oup.com/sysbio/article/59/2/145/1616739">When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates.</a> <i>Systematic Biology</i>. 59:145-161.
<br><br>
<strong>Brown, J.M.</strong> and R. ElDabaje*. 2009. <a href="https://academic.oup.com/bioinformatics/article/25/4/537/249504">PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy.</a> <i>Bioinformatics</i>. 25:537-538.
<br><br>
Lemmon, A. R., <strong>J.M. Brown</strong>, K. Stanger-Hall, and E.M. Lemmon. 2009. <a href="https://academic.oup.com/sysbio/article/58/1/130/1677143">The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference.</a> <i>Systematic Biology</i>. 58:130-145.
<br><br>
Rabeling, C., <strong>J.M. Brown</strong>, and M. Verhaagh. 2008. <a href="http://www.pnas.org/content/105/39/14913.short">Newly discovered sister lineage sheds light on early ant evolution.</a> <i>Proceedings of the National Academy of Sciences USA.</i> 105:14913-14917.
<br><br>
<strong>Brown, J.M.</strong> and A.R. Lemmon. 2007. <a href="https://academic.oup.com/sysbio/article/56/4/643/1684114">The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics.</a> <i>Systematic Biology</i>. 56:643-655.
<br><br>
<strong>Brown, J.M.</strong> and G.B. Pauly. 2005. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/j.0014-3820.2005.tb00911.x">Increased rates of molecular evolution in an equatorial plant clade: an effect of environment or phylogenetic non-independence?</a> <i>Evolution</i>. 59:238-242.
<br><br>
Agrawal, A.F., <strong>J.M. Brown</strong>, and E.D. Brodie III. 2004. <a href="https://link.springer.com/article/10.1007/s00265-004-0841-2">On the social structure of offspring rearing in the burrower bug, <i>Sehirus cinctus</i> (Hemiptera: Cydnidae).</a> <i>Behavioral Ecology and Sociobiology</i>. 57:139-148.
<br><br>
<strong>Brown, J.M.</strong>, A.F. Agrawal, and E.D. Brodie III. 2003. <a href="https://link.springer.com/article/10.1023/B:JOIR.0000018317.55712.d3">An analysis of single clutch paternity in the burrower bug <i>Sehirus cinctus</i> using microsatellites.</a> <i>Journal of Insect Behavior</i>. 16:731-745.
<br><br>
Agrawal, A.F., E.D. Brodie III, and <strong>J. Brown*</strong>. 2001. <a href="http://science.sciencemag.org/content/292/5522/1710">Parent-offspring coadaptation and the dual genetic control of maternal care.</a> <i>Science</i>. 292:1710-1712.
<br><br>
* Undergraduate
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