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<div id="sitetitle" class="sixteen columns"><a href="index.html">The Hahn Lab</a></div>
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<li><a href="research.html">Research</a></li>
<li><a href="publications.html">Publications</a></li>
<li><a href="people.html">People</a></li>
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<ul class="pubmenu">
<li><strong>· <a href="#pub">Publications</a> · <a href="#spub">Post-Doc and Student Publications</a> · </strong><strong><a href="#books">Books</a> ·</strong></li>
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<div class="fourteen columns bluebox" >
<p><strong>Publications</strong></p>
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<div id="pagecontent" class="fourteen columns">
<ul class="publist">
<li><strong>2026</strong></li>
<li>
<p>Mo, Y.K. and M.W. Hahn (<em>in press</em>) Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees. <em>Evolutionary Journal of the Linnean Society</em>. </p>
<p>Smith, M.L. and M.W. Hahn (<em>in press</em>) Using gene trees with lineage-specific duplicates for phylogenetic inference mitigates the effects of long-branch attraction. <em>Systematic Biology</em>. </p>
<p>Rickert, D.A., W.-T. Fan, and M.W Hahn (<em>in press</em>) Inconsistency of parsimony under the multispecies coalescent. <em>Theoretical Population Biology</em>. </p>
<p>Larson, D.A., M.W. Itgen, R.D. Denton, and M.W. Hahn (2026) Reconsidering cytonuclear discordance in the genomic age. <em>Evolution</em> 80:1-14. <a href="Publications/Larson_etal2026.pdf">PDF</a></p>
<p id="NoDEAR">Hahn, M.W. and S.R. Mishra (2026) Estimating recombination using only the allele frequency spectrum. <em>Genetics</em> 232:iyaf108. <a href="Publications/HahnMishra2026.pdf">PDF</a></p>
<li><strong>2025</strong></li>
<li>
<p>Peña-García, Y., R.J. Wang, M. Raveendran, R.A. Harris, P.B. Samollow, J. Rogers, and M.W. Hahn (2025) Low mutation rate but high male-bias in the germline of a short-lived opossum. <em>Genetics</em> 231:iyaf17. <a href="Publications/Pena-Garcia_etal2025.pdf">PDF</a></p>
<p>Jeffries, D., C. Benvenuto, A. Böhne, C. Fraisse, S. Garcia, P. Jay, L. Kratochvíl, C.E. McDonough-Goldstein, A. Ruiz-Herrera, C.G. Sotero-Caio, N. Valenzuela, M.A. Wilson, Tree of Sex Consortium, K.S. Jaron (2025) The Tree of Sex consortium: A global initiative for studying the evolution of reproduction in eukaryotes. <em>Journal of Evolutionary Biology</em> 38:861-886. <a href="Publications/Jeffries_etal2025.pdf">PDF</a></p>
<p>Lipshutz, S.E., M.S. Hibbins, A.B. Bentz, A.M. Buechlein, T.A. Empson, E.M. George, M.E. Hauber, D.B. Rusch, W.M. Schelsky, Q.K. Thomas, S.J. Torneo, A.M. Turner, S.E. Wolf, M.J. Woodruff, M.W. Hahn, and K.A. Rosvall (2025) Repeated behavioral evolution is associated with convergence of gene expression in cavity-nesting songbirds. <em>Nature Ecology & Evolution</em> 9:845-856. <a href="Publications/Lipshutz_etal2025.pdf">PDF</a></p>
<p>Pinseel, E., E. C. Ruck, T. Nakov, P. R. Jonsson, O. Kourtchenko, A. Kremp, M. I. M. Pinder, W. R. Roberts, C. Sjoqvist, M. Topel, A. Godhe, M. W. Hahn, and A. J. Alverson (2025) Genome-wide adaptation to a complex environmental gradient in a keystone phytoplankton species. <em>Molecular Ecology</em> 34:e17817. <a href="Publications/Pinseel_etal2025.pdf">PDF</a></p>
<p>Larson, D.A., M.E. Staton, B. Kapoor, N. Islam-Faridi, T. Zhebentyayeva, S. Fan, J. Stork, A. Thomas, A.S. Ahmed, E.C. Stanton, A. Houston, S.E. Schlarbaum, M.W. Hahn, J.E. Carlson, A.G. Abbott, S. DeBolt, and C.D. Nelson (2025) A haplotype-resolved reference genome of <em>Quercus alba</em> sheds light on the evolutionary history of oaks. <em>New Phytologist</em> 246:331-348. <a href="Publications/Larson_etal2025.pdf">PDF</a></p>
<p>Orkin, J.D., L.F.K. Kuderna, N. Hermosilla-Albala, C. Fontsere, M.L. Aylward, M. Janiak, N. Andriaholinirina, P. Balaresque, M.E. Blair, J.-L. Fausser, I.G. Gut, M. Gut, M.W. Hahn, R.A. Harris, J.E. Horvath, C. Keyser, A.C. Kitchener, M.D. Le, E. Lizano, S. Merker, T. Nadler, G.H. Perry, C.J. Rabarivola, M. Raveendran, C. Roos, D.D. Wu, A. Zaramody, G. Zhang, D. Zinner, L. Pozzi, J. Rogers, K.K.-H. Farh, T. Marques Bonet (2025) Genomic diversity and demographic history of the non-anthropoid primates. <em>Nature Ecology & Evolution</em> 9:42-56. <a href="Publications/Orkin_etal2025.pdf">PDF</a></p>
<p>Wang, R.J., Y. Peña-García, R. Muthuswamy, R.A. Harris, T.-T. Nguyen, M.-C. Gingras, Y. Wu, L. Perez, A.D. Yoder, J.H. Simmons, J. Rogers, and M.W. Hahn (2025) Unprecedented female mutation bias in the aye-aye, a highly unusual lemur from Madagascar. <em>PLOS Biology</em> 23:e3003015. <a href="Publications/Wang_etal2025.pdf">PDF</a></p>
<li><strong>2024</strong></li>
<li>
<p>Lanfear, R. and M.W. Hahn (2024) The meaning and measure of concordance factors in phylogenomics. <em>Molecular Biology and Evolution</em> 41:msae214. <a href="Publications/LanfearHahn2024.pdf">PDF</a> </p>
<p>Smith, M.L. and M.W. Hahn (2024) Selection leads to false inferences of introgression using popular methods. <em>Genetics</em> 227:iyae089. <a href="Publications/SmithHahn2024.pdf">PDF</a></p>
<p>Wong, T.K.F., C. Cherryh, A.G. Rodrigo, M.W. Hahn, B.Q. Minh, and R. Lanfear (2024) MAST: Phylogenetic inference with mixtures across sites and trees. <em>Systematic Biology</em> 73:375-391. <a href="Publications/Wong_etal2024.pdf">PDF</a></p>
<p>Khan, R.R., R.F. Guerrero, R.J. Wapner, M.W. Hahn, A. Raja, A. Salleb-Aouissi, W.A. Grobman, H. Simhan, R. Silver, J.H. Chung, U.M. Reddy, P. Radivojac, I. Pe’er, and D.M. Haas (2024) Genetic polymorphisms associated with adverse pregnancy outcomes in nulliparas. <em>Scientific Reports</em> 14:10514. <a href="Publications/Khan_etal2024.pdf">PDF</a></p>
<p>Mo, Y.K., M.W. Hahn, and M.L. Smith (2024) Applications of machine learning in phylogenetics. <em>Molecular Phylogenetics and Evolution</em> 196:108066. <a href="Publications/Mo_etal2024.pdf">PDF</a> </p>
<p>Hibbins, M.S. and M.W. Hahn (2024) Distinguishing between histories of speciation and introgression using genomic data. <em>Bulletin of the Society of Systematic Biologists</em> 3: https://doi.org/10.18061/bssb.v3i1.9227. <a href="Publications/HibbinsHahn2024.pdf">PDF</a></p>
</li>
<li><strong>2023</strong></li>
<li>
<p>Hahn, M.W., Y. Peña-Garcia, and R.J. Wang (2023) The “faulty male” hypothesis for sex-biased mutation and disease. <em>Current Biology</em> 33:R1166-R1172. <a href="Publications/Hahn_etal2023.pdf">PDF</a> </p>
<p id="phyloGAN">Smith. M.L. and M.W. Hahn (2023) Phylogenetic inference using generative adversarial networks. <em>Bioinformatics</em> 39:btad543. <a href="Publications/SmithHahn2023.pdf">PDF</a></p>
<p>Yan, Q., R.F. Guerrero, R.R. Khan, A.A. Surujnarine, R.J. Wapner, M.W. Hahn, A. Raja, A. Salleb-Aouissi, W.A. Grobman, H. Simhan, N. Blue, R. Silver, J.H. Chung, U.M. Reddy, P. Radivojac, I. Pe’er, and D.M. Haas (2023) Searching and visualizing genetics associations of pregnancy traits by using GnuMoM2b. <em>Genetics</em> 225:iyad151. <a href="Publications/Yan_etal2023.pdf">PDF</a></p>
<p>Wang, R.J., J. Rogers, and M.W. Hahn (2023) Robust inference of historical human generation times. <em>bioRxiv</em> 2023.07.20.549788. <a href="Publications/Wang_etal2023b.pdf">PDF</a> [Permanent version]</p>
<p id="seastaR">Hibbins, M.S., L.C. Breithaupt, and M.W. Hahn (2023) Phylogenomic comparative methods: accurate evolutionary inferences in the presence of gene tree discordance. <em>Proceedings of the National Academy of Sciences</em> 120:e2220389120. <a href="Publications/Hibbins_etal2023.pdf">PDF</a></p>
<p id="CAGEE">Bertram, J. B. Fulton, J. Tourigny, Y. Peña-Garcia, L.C. Moyle, and M.W. Hahn (2023) CAGEE: computational analysis of gene expression evolution. <em>Molecular Biology and Evolution</em> 40:msad106. <a href="Publications/Bertram_etal2023.pdf">PDF</a></p>
<p>Wang, R.J., S.I. Al-Saffar, J. Rogers, and M.W. Hahn (2023) Human generation times across the past 250,000 years. <em>Science Advances</em> 9:eabm7047. <a href="Publications/Wang_etal2023combined.pdf">PDF</a></p>
<p id="sCFl">Mo, Y.K., R. Lanfear, M.W. Hahn, and B.Q. Minh (2023) Updated site concordance factors minimize effects of homoplasy and taxon sampling. <em>Bioinformatics</em> 39:btac741. <a href="Publications/Mo_etal2023.pdf">PDF</a></p>
<li><strong>2022</strong></li>
<li>
<p>Wang, R.J., Y. Peña-Garcia, M.G. Bibby, M. Raveendran, R.A. Harris, H.T. Jansen, C.T. Robbins, J. Rogers, J.L. Kelley, and M.W. Hahn (2022b) Examining the effect of hibernation on germline mutation rates in grizzly bears. <em>Genome Biology and Evolution</em> 14:evac148. <a href="Publications/Wang_etal2022b.pdf">PDF</a></p>
<p>Rusch, D.B., J. Huang, C. Hemmerich, and M.W. Hahn (2022) High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS. <em>ISME Communications</em> 2:99. <a href="Publications/Rusch_etal2022.pdf">PDF</a></p>
<p>Pagel, K. A., H. Chu, R. Ramola, R.F. Guerrero, J.H. Chung, S. Parry, U.M. Reddy, R.M. Silver, J.G. Steller, L.M. Yee, R.J. Wapner, M.W. Hahn, S. Natarajan, D.M. Haas, and P. Radivojac (2022) Association of genetic predisposition and physical activity with risk of gestational diabetes in nulliparous women. <em>JAMA Network Open</em> 5:e2229158. <a href="Publications/Pagel_etal2022.pdf">PDF</a></p>
<p>Al-Saffar, S.I. and M.W. Hahn (2022) Evaluating methods for estimating the proportion of adaptive amino acid substitutions. <em>bioRxiv</em> 2022.08.15.504017. <a href="Publications/Al-SaffarHahn2022.pdf">PDF</a> [Permanent version]</p>
<p>Wang, R.J., M. Raveendran, R.A. Harris, W.J. Murphy, L.A. Lyons, J. Rogers, and M.W. Hahn (2022a) <em>De novo</em> mutations in domestic cat are consistent with an effect of reproductive longevity on both the rate and spectrum of mutations. <em>Molecular Biology and Evolution</em> 39:msac147. <a href="Publications/Wang_etal2022.pdf">PDF</a></p>
<p>Smith, M.L. and M.W. Hahn (2022) The frequency and topology of pseudoorthologs. <em>Systematic Biology</em> 71:649-659. <a href="Publications/SmithHahn2022.pdf">PDF</a></p>
<p>Smith, M.L., D. Vanderpool, and M.W. Hahn (2022) Using all gene families vastly expands data available for phylogenomic inference. <em>Molecular Biology and Evolution</em> 39:msac112. <a href="Publications/Smith_etal2022.pdf">PDF</a></p>
<p>Hibbins, M.S. and M.W. Hahn (2022) Phylogenomic approaches to detecting and characterizing introgression. <em>Genetics</em> 220:iyab173. <a href="Publications/HibbinsHahn2022.pdf">PDF</a></p>
<p>Bergeron, L. A., S. Besenbacher, T. N. Turner, C. J. Versoza, R. J. Wang, A. L. Price, E. Armstrong, M. Riera, J. Carlson, H.-y. Chen, M. W. Hahn, K. Harris, A. Snøfrid Kleppe, E. H. López-Nandam, P. Moorjani, S. P. Pfeifer, G. P. Tiley, A. D. Yoder, G. Zhang, and M. H. Schierup (2022) Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates. <em>eLife</em> 11:e73577. <a href="Publications/Bergeron_etal2022.pdf">PDF</a></p>
<p>Rosenzweig, B., A.D. Kern, and M.W. Hahn (2022) Accurate detection of incomplete lineage sorting via supervised machine learning. <em>bioRxiv</em> 2022.11.09.515828. <a href="Publications/Rosenzweig_etal2022.pdf">PDF</a> [Permanent version] </p>
<p>Yan, Z., M.L. Smith, P. Du, M.W. Hahn, and L. Nakhleh (2022) Species tree inference methods intended to deal with incomplete lineage sorting are robust to the presence of paralogs. <em>Systematic Biology</em> 71:367-381. <a href="Publications/Yan_etal2022.pdf">PDF</a></p>
<li><strong>2021</strong></li>
<li>
<p>Hibbins, M.S. and M.W. Hahn (2021) The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes. <em>PLoS Genetics</em> 17:e1009892. <a href="Publications/HibbinsHahn2021.pdf">PDF</a></p>
<p>Alcalay, Y., S. Fuchs, R. Galizi, F. Bernardini, R.E. Haghighat-Khah, D.B. Rusch, J.R. Adrion, M.W. Hahn, P. Tortosa, and P.A. Papathanos (2021) The potential for a released autosomal X-shredder becoming a driving-Y chromosome and invasively suppressing wild populations of malaria mosquitoes. <em>Frontiers in Bioengineering and Biotechnology</em> 9:752253. <a href="Publications/Alcalay_etal2021.pdf">PDF</a></p>
<p>Albecker, M.A., L.G.E. Wilkins, S.A. Krueger-Hadfield, S.M. Bashevkin, M.W. Hahn, M.P. Hare, H.K. Kindsvater, M.A. Sewell, K.E. Lotterhos, and A.M. Reitzel (2021) Does a complex life cycle affect adaptation to environmental change? Genome-informed approaches for characterizing selection across life cycle stages. <em>Proceedings of the Royal Society B</em> 288:20212122. <a href="Publications/Albecker_etal2021.pdf">PDF</a></p>
<p>Wu, M., D.C. Haak, G.J. Anderson, M.W. Hahn, L.C. Moyle, and R.F. Guerrero (2021) Inferring the genetic basis of sex determination from the genome of a dioecious nightshade. <em>Molecular Biology and Evolution</em> 38:2946-2957. <a href="Publications/Wu_etal2021.pdf">PDF</a></p>
<p>Broz, A., A. Simpson-Van Dam, A. Tovar-Méndez, M.W. Hahn, B.A. McClure, and P. Bedinger (2021) Spread of self-compatibility constrained by an intrapopulation crossing barrier. <em>New Phytologist</em> 231:878-891. <a href="Publications/Broz_etal2021.pdf">PDF</a></p>
<p>Thomas, G.W.C., R.J. Wang, J. Nguyen, R.A. Harris, M. Raveendran, J. Rogers, and M.W. Hahn (2021) Origins and long-term patterns of copy-number variation in rhesus macaques. <em>Molecular Biology and Evolution</em> 38:1460-1471. <a href="Publications/Thomas_etal2021.pdf">PDF</a></p>
<p>Wang, R.J., P. Radivojac, and M.W. Hahn (2021) Distinct error rates for reference and non-reference genotypes estimated by pedigree analysis. <em>Genetics</em> 217:iyaa014. <a href="Publications/Wang_etal2021.pdf">PDF</a></p>
<p>Sun, C., J. Huang, Y. Wang, X. Zhao, L. Su, G. W. C. Thomas, M. Zhao, X. Zhang, I. Jungreis, M. Kellis, S. Vicario, I. V. Sharakhov, S. M. Bondarenko, M. Hasselmann, C. N. Kim, B. Paten, L. Penso-Dolfin, L. Wang, Y. Chang, Q. Gao, L. Ma, L. Ma, Z. Zhang, H. Zhang, H. Zhang, L. Ruzzante, H. M. Robertson, Y. Zhu, Y. Liu, H. Yang, L. Ding, Q. Wang, W. Xu, C. Liang, M. W. Itgen, L. Mee, B. M. Sadd, G. Cao, Z. Zhang, M. W. Hahn, S. Schaack, S. M. Barribeau, P. H. Williams, R. M. Waterhouse, and R. L. Mueller (2021) Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. <em>Molecular Biology and Evolution</em> 38:486-501. <a href="Publications/Sun_etal2021.pdf">PDF</a></p>
<p>Smith, M.L. and M.W. Hahn (2021) New approaches for inferring phylogenies in the presence of paralogs. <em>Trends in Genetics</em> 37:156-169. <a href="Publications/SmithHahn2021.pdf">PDF</a></p>
<li><strong>2020</strong></li>
<li>
<p id="CAFE5">Mendes, F.K., D. Vanderpool, B. Fulton, and M.W. Hahn (2020) CAFE 5 models variation in evolutionary rates among gene families. <em>Bioinformatics</em> 36:5516-5518. <a href="Publications/Mendes_etal2020.pdf">PDF</a></p>
<p id="Heist">Hibbins, M.S., M.J.S. Gibson, and M.W. Hahn (2020) Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression. <em>eLife</em> 9:e63753. <a href="Publications/Hibbins_etal2020.pdf">PDF</a></p>
<p>Vanderpool, D., B.Q. Minh, R. Lanfear, D. Hughes, S. Murali, R.A. Harris, M. Raveendran, D.M. Muzny, M.S. Hibbins, R.J. Williamson, R.A. Gibbs, K.C. Worley, J. Rogers, and M.W. Hahn (2020) Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. <em>PLoS Biology</em> 18: e3000954. <a href="Publications/Vanderpool_etal2020.pdf">PDF</a></p>
<p>Small, S.T., F. Labbé, N.F. Lobo, L.L. Koekemoer, C.H. Sikaala, D.E. Neafsey, M.W. Hahn, M.C. Fontaine, and N.J. Besansky (2020) Radiation with reticulation marks the origin of a major malaria vector. <em>Proceedings of the National Academy of Sciences</em> 117: 31583–31590. <a href="Publications/Small_etal2020.pdf">PDF</a></p>
<p>The <em>Anopheles gambiae</em> 1000 Genomes Consortium (2020) Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species <em>Anopheles gambiae</em> and <em>Anopheles coluzzii</em>. <em>Genome Research</em> 30:1533-1546. <a href="Publications/Clarkson_etal2020.pdf">PDF</a></p>
<p>Wang, R.J., G.W.C. Thomas, M. Raveendran, R.A. Harris, H. Doddapaneni, D.M.
Muzny, J.P. Capitanio, P. Radivojac, J. Rogers, and M.W. Hahn (2020) Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability. <em>Genome Research</em> 30:826–834. <a href="Publications/Wang_etal2020.pdf">PDF</a></p>
<p id="sCF">Minh, B.Q., M.W. Hahn, and R. Lanfear (2020) New methods to calculate concordance factors for phylogenomic datasets. <em>Molecular Biology and Evolution</em> 37:2727-2733. <a href="Publications/Minh_etal2020.pdf">PDF</a></p>
<p>Stamboulian, M., R.F. Guerrero, M.W. Hahn, and P. Radivojac (2020) The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. <em>Bioinformatics (ISMB 2020)</em> 36:i219–i226. <a href="Publications/Stamboulian_etal2020.pdf">PDF</a></p>
<p>Bryant, D. and M.W. Hahn (2020) The concatenation question. In: <em>Phylogenetics in the Genomic Era</em>. Pp. 3.4:1-3.4:23 C. Scornavacca, F. Delsuc, and N. Galtier, eds. No commercial publisher | Authors open access book. <a href="Publications/BryantHahn2020.pdf">PDF</a></p>
<p>Thomas, G.W.C., E. Dohmen, D.S.T. Hughes, S.C. Murali, M. Poelchau, K. Glastad, C.A. Anstead, N.A. Ayoub, P. Batterham, M. Bellair, G.J. Binford, H. Chao, Y.H. Chen, C. Childers, H. Dinh, H. Doddapaneni, J.J. Duan, S. Dugan, L.A. Esposito, M. Friedrich, J. Garb, R.B.B. Gasser, M.A.D. Goodisman, D.E. Gundersen-Rindal, Y. Han, A.M. Handler, M. Hatakeyama, L. Hering, W.B. Hunter, P. Ioannidis, J.C. Jayaseelan, D. Kalra, A. Khila, P.K. Korhonen, C.E. Lee, S.L. Lee, Y. Li, A.R.I. Lindsey, G. Mayer, A.P. McGregor, D.D. McKenna, B. Misof, M. Munidasa, M. Munoz-Torres, D.M. Muzny, O. Niehuis, N. Osuji-Lacy, S.R. Palli, K.A. Panfilio, M. Pechmann, T. Perry, R.S. Peters, H.C. Poynton, N.-M. Prpic, J. Qu, D. Rotenberg, C. Schal, S.D. Schoville, E.D. Scully, E. Skinner, D.B. Sloan, R. Stouthamer, M.R. Strand, N.U. Szucsich, A. Wijeratne, N.D. Young, E.E. Zattara, J.B. Benoit, E.M. Zdobnov, M.E. Pfrender, K.J. Hackett, J.H. Werren, K.C. Worley, R.A. Gibbs, A.D. Chipman, R.M. Waterhouse, E. Bornberg-Bauer, M.W. Hahn, and S. Richards (2020) Gene content evolution in arthropods. <em>Genome Biology</em> 21:15. <a href="Publications/Thomas_etal2020.pdf">PDF</a></p>
<p> Waterhouse, R.M., S. Aganezov, Y. Anselmetti, J. Lee, L. Ruzzante, M.J. Reijnders, R. Feron, S. Bèrard, P. George, M.W. Hahn, P.I. Howell, M. Kamali, S. Koren, D. Lawson, G. Maslen, A. Peery, A.M. Phillippy, M.V. Sharakhova, E. Tannier, M.F. Unger, S.V. Zhang, M.A. Alekseyev, N.J. Besansky, C. Chauve, S.J. Emrich, and I.V. Sharakhov (2020) Evolutionary superscaffolding and chromosome anchoring to improve <em>Anopheles</em> genome assemblies. <em>BMC Biology</em> 18:1. <a href="Publications/Waterhouse_etal2020.pdf">PDF</a> </p>
<li><strong>2019</strong></li>
<li>
<p>M.W. Hahn and M.S. Hibbins (2019) A three-sample test for introgression. <em>Molecular Biology and Evolution</em> 12:2878-2882.<a href="Publications/HahnHibbins2019.pdf">PDF</a> </p>
<p id="Referee">Thomas, G.W.C. and M.W. Hahn (2019) Referee: reference assembly quality scores. <em>Genome Biology and Evolution</em> 11:1483-1486. <a href="Publications/ThomasHahn2019.pdf">PDF</a></p>
<p>Yang, R., Y. Jiang, S. Mathews, E.A. Housworth, M.W. Hahn, and P. Radivojac (2019) A new class of metrics for learning on real-valued and structured data. <em>Data Mining and Knowledge Discovery</em> 33:995-1016. <a href="Publications/Yang_etal2019.pdf">PDF</a></p>
<p>Mendes, F.K., A.P. Livera, and M.W. Hahn (2019) The perils of intralocus recombination for inferences of molecular convergence. <em>Philosophical Transactions of the Royal Society B</em> 374:20180244. <a href="Publications/Mendes_etal2019.pdf">PDF</a></p>
<p>Adrion, J.R., D.J. Begun, and M.W. Hahn (2019) Patterns of transposable element variation and clinality in <em>Drosophila</em>. <em>Molecular Ecology</em> 28:1523-1536. <a href="Publications/Adrion_etal2019.pdf">PDF</a></p>
<p>Ayala, D., S. Zhang, M. Chateau, C. Fouet, I. Morlais, C. Costantini, M.W. Hahn, and N.J. Besansky (2019) Association mapping desiccation resistance within chromosomal inversions in the African malaria vector <em>Anopheles gambiae</em>. <em>Molecular Ecology</em> 28:1333–1342. <a href="Publications/Ayala_etal2019.pdf">PDF</a></p>
<p>Rogers, J., R. Muthuswamy, R. A. Harris, T. Mailund, K. Leppälä, G. Athanasiadis, M.H. Schierup, J. Cheng, K. Munch, J.A. Walker, M. Konkel, V. Jordan, C. Steely, T. Beckstrom, C. Bergey, A. Burrell, D. Schrempf, A. Noll, M. Kothe, G.H. Kopp, Y. Liu, S. Murali, K. Billis, F. J. Martin, M. Muffato, L. Cox, J. Else, T. Disotell, D.M. Muzny, J. Phillips-Conroy, B. Aken, E.E. Eichler, T. Marques-Bonet, C. Kosiol, M.A. Batzer, M.W. Hahn, J. Tung, D. Zinner, C. Roos, C.J. Jolly, R.A. Gibbs, K.C. Worley and the Baboon Genome Analysis Consortium (2019) The comparative genomics and complex population history of <em>Papio</em> baboons. <em>Science Advances</em> 5:eaau6947. <a href="Publications/Rogers_etal2019.pdf">PDF</a></p>
<p>Hibbins, M.S. and M.W. Hahn (2019) The timing and direction of introgression under the multispecies network coalescent. <em>Genetics</em> 211:1059-1073. <a href="Publications/HibbinsHahn2019.pdf">PDF</a></p>
<li><strong>2018</strong></li>
<li>
<p id="PePo">Guerrero, R.F. and M.W. Hahn (2018) Quantifying the risk of hemiplasy in phylogenetic inference. <em>Proceedings of the National Academy of Sciences</em> 115:12787-12792. <a href="Publications/GuerreroHahn2018.pdf">PDF</a> <a href="Publications/GuerreroHahn2018_supp.pdf"> Appendix</a></p>
<p>Thomas, G.W.C., R. J. Wang, A. Puri, R.A. Harris, M. Raveendran, D. Hughes, S. Murali, L. Williams, H. Doddapaneni, D. Muzny, R.A. Gibbs, C. Abee, M. R. Galinski, K.C. Worley, J. Rogers, P. Radivojac, and M.W. Hahn (2018) Reproductive longevity predicts mutation rates in primates. <em>Current Biology</em> 28:3193-3197. <a href="Publications/Thomas_etal2018.pdf">PDF</a></p>
<p>Wang, R.J. and M.W. Hahn (2018) Speciation genes are more likely to have discordant gene trees. <em>Evolution Letters</em> 2:281-296. <a href="Publications/WangHahn2018.pdf">PDF</a></p>
<p>Cheng, C., J.C. Tan, M.W. Hahn, and N.J. Besansky (2018) A systems genetic analysis of inversion polymorphisms in the malaria mosquito <em>Anopheles gambiae</em>. <em>Proceedings of the National Academy of Sciences</em> 115:E7005-E7014. <a href="Publications/Cheng_etal2018.pdf">PDF</a></p>
<p> Wu, M., J.L. Kostyun, M.W. Hahn, and L.C. Moyle (2018) Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance. <em>Molecular Ecology</em> 27:3301-3316. <a href="Publications/Wu_etal2018.pdf">PDF</a></p>
<p>Mendes, F.K., J.A. Fuentes-González, J.G. Schraiber, and M.W. Hahn (2018) A multispecies coalescent model for quantitative traits. <em>eLife</em> 7:e36482. <a href="Publications/Mendes_etal2018.pdf">PDF</a></p>
<p>Venkat, A., M.W. Hahn, and J.W. Thornton (2018) Multinucleotide mutations cause false inferences of lineage-specific positive selection. <em>Nature Ecology & Evolution</em> 2:1280-1288. <a href="Publications/Venkat_etal2018.pdf">PDF</a></p>
<p>Kern, A.D. and M.W. Hahn (2018) The neutral theory in light of natural selection. <em>Molecular Biology and Evolution</em> 35:1366-1371. <a href="Publications/KernHahn2018.pdf">PDF</a></p>
<p>House, G.L. and M.W. Hahn (2018) Evaluating methods to visualize patterns of genetic differentiation on a landscape. <em> Molecular Ecology Resources </em>18:448-460. <a href="Publications/HouseHahn2018.pdf">PDF</a></p>
<p>Ramalho, R.F., S. Li, P. Radivojac, and M.W. Hahn (2018) Proteomic evidence for in-frame and out-of-frame alternatively spliced isoforms in human and mouse. <em>IEEE-ACM Transactions on Computational Biology and Bioinformatics </em> 15:1284-1289 <a href="Publications/Ramalho_etal2018.pdf">PDF</a></p>
<p>Warren, W.C., R. García-Pérez, S. Xu, K.P. Lampert, D. Chalopin, M. Stöck, L. Kuderna, P. Minx, M.J. Montague, C. Tomlinson, L.W. Hillier, D.N. Murphy, J. Wang, Z. Wang, T. Marques-Bonet, C.M. Garcia, G.W.C. Thomas, M.W. Hahn, J.-N. Volff, F. Farias, B. Aken, K.D. Pruitt, S. Kneitz, M. Lynch, and M. Schartl (2018) Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly. <em>Nature Ecology & Evolution </em>2:669-679. <a href="Publications/Warren_etal2018.pdf">PDF</a></p>
<p>Palesch, D., S. E. Bosinger, G. K. Tharp, T. H. Vanderford, M. Paiardini, A. M. Chahroudi, Z. P. Johnson, F. Kirchhoff, B. Hahn, R. B. Norgren Jr, H. RA, S. Murali, Y. Liu, M. Raveendran, G. W. C. Thomas, M. W. Hahn, L. Pipes, C. E. Mason, D. Muzny, R. A. Gibbs, K. C. Worley, J. Rogers, and G. Silvestri (2018) Sooty mangabey genome sequence reveals new insights into mechanisms of disease resistance in natural hosts of SIV. <em>Nature</em> 553:77-81.<a href="Publications/Palesch_etal2018.pdf">PDF</a></p>
<p>Mendes, F.K. and M.W. Hahn (2018) Why concatenation fails near the anomaly zone. <em>Systematic Biology </em>67:158-169. <a href="Publications/MendesHahn2018.pdf">PDF</a> <a href="Publications/MendesHahn2018_Appendix.pdf"> Appendix</a>
</p>
<li><strong>2017</strong></li>
<li>
<p>Guerrero, R.F. and M.W. Hahn (2017) Speciation as a sieve for ancestral polymorphism. <em>Molecular Ecology </em>26:5362-5368. <a href="Publications/GuerreroHahn2017.pdf">PDF</a></p>
<p>The <em>Anopheles gambiae</em> 1000 Genomes Consortium (2017) Natural diversity of the malaria vector <em>Anopheles gambiae</em>. <em>Nature</em> 552:96-100. <a href="Publications/Miles_etal2017.pdf">PDF</a></p>
<p id="GRAMPA">Thomas, G.W.C, S.H. Ather, and M.W. Hahn (2017) Gene-tree reconciliation with MUL-trees to resolve polyploidy events. <em>Systematic Biology</em> 66:1007-1018.
<a href="Publications/Thomas_etal2017b.pdf">PDF</a></p>
<p id="TEFLoN">Adrion, J.R., M. Song, D.R. Schrider, M.W. Hahn, and S. Schaack (2017) Genome-wide estimates of transposable element insertion and deletion rates in <em>Drosophila melanogaster</em>. <em>Genome Biology and Evolution </em>9:1329-1340. <a href="Publications/Adrion_etal2017.pdf">PDF</a></p>
<p>Roda, F., F.K. Mendes, M.W. Hahn, and R. Hopkins (2017) Genomic evidence of gene flow during reinforcement in Texas <em>Phlox</em>. <em>Molecular Ecology </em>26:2317-2330. <a href="Publications/Roda_etal2017.pdf">PDF</a></p>
<p>Thomas, G.W.C, M.W. Hahn, and Y. Hahn (2017) The effects of increasing the number of taxa on inferences of molecular convergence. <em>Genome Biology and Evolution </em>9:213-221. <a href="Publications/Thomas_etal2017.pdf">PDF</a></p>
<p>Broz, A.K., R.F. Guerrero, A.M. Randle, Y.S. Baek, M.W. Hahn, P.A. Bedinger (2017) Linking gene expression to unilateral pollen-pistil reproductive barriers. <em>BMC Plant Biology</em> 17:81. <a href="Publications/Broz_etal2017.pdf">PDF</a></p>
<p>Bromberg, Y., M.W. Hahn, and P. Radivojac (2017) Computational approaches to understanding the evolution of molecular function. <em>Pacific Symposium on Biocomputing</em> 22:1-2. <a href="Publications/Bromberg_etal2017.pdf">PDF</a><br>
</p>
</li>
<li><strong>2016</strong></li>
<li>
<p>Mendes, F.K., Y. Hahn, and M.W. Hahn (2016) Gene tree discordance can generate patterns of diminishing convergence over time. <em>Molecular Biology and Evolution </em>33:3299-3307. <a href="Publications/Mendes_etal2016.pdf">PDF</a></p>
<p id="AGOUTI">Zhang, S.V., L. Zhuo, and M.W. Hahn (2016) AGOUTI: improving genome assembly and annotation using transcriptome data. <em>GigaScience </em>5:31. <a href="Publications/Zhang_etal2016.pdf">PDF</a></p>
<p>Mendes, F.K. and M.W. Hahn (2016) Gene tree discordance causes apparent substitution rate variation. <em>Systematic Biology </em>65:711-721. <a href="Publications/MendesHahn2016.pdf">PDF</a></p>
<p>Pease, J.B., R.F. Guerrero, N.A. Sherman, M.W. Hahn, and L.C. Moyle (2016) Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis. <em>Molecular Ecology </em>25:2592-2608. <a href="Publications/Pease_etal2016b.pdf">PDF</a></p>
<p>Rosenzweig, B.K., J.B. Pease, N.J. Besansky, and M.W. Hahn (2016) Powerful methods for detecting introgressed regions from population genomic data. <em>Molecular Ecology </em>25:2387-2397. <a href="Publications/Rosenzweig_etal2016.pdf">PDF</a></p>
<p>Wen, D., Y. Yu, M.W. Hahn, and L. Nakhleh (2016) Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis. <em>Molecular Ecology </em>25:2361-2372. <a href="Publications/Wen_etal2016.pdf">PDF</a></p>
<p>Schrider, D.R., M.W. Hahn, and D.J. Begun (2016) Parallel evolution of copy-number variation across continents in <em>Drosophila melanogaster</em>. <em>Molecular Biology and Evolution </em>33:1308-1316<em>.</em> <a href="Publications/Schrider_etal2016.pdf">PDF</a></p>
<p>Guerrero, R.F., A.L. Posto, L.C. Moyle, and M.W. Hahn (2016) Genome-wide patterns of regulatory divergence revealed by introgression lines. <em>Evolution </em>70:696-706. <a href="Publications/Guerrero_etal2016.pdf">PDF</a></p>
<p>Hall A.B., P.-A. Papathanos, A. Sharma, C. Cheng, O.S. Akbari, L.A. Assour, N.H. Bergman, A. Cagnetti, A. Crisanti, T. Dottorini, E. Fiorentini, R. Galizi, J. Hnath, X. Jiang, S. Koren, T. Nolan, D. Radune, M.V. Sharakhova, A. Steele, V.A. Timoshevskiy, N. Windbichler, S.V. Zhang, M.W. Hahn, A.M. Phillippy, S.J. Emrich, I.V. Sharakhov, Z. Tu, and N.J. Besansky (2016) Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. <em>Proceedings of the National Academy of Sciences </em>113:E2114-E2123. <a href="Publications/Hall_etal2016.pdf">PDF</a></p>
<p>Hahn, M.W. and L. Nakhleh (2016) Irrational exuberance for resolved species trees. <em>Evolution </em>70:7-17. <a href="Publications/HahnNakhleh2016.pdf">PDF</a></p>
<p>Mallet, J., N.J. Besansky, and M.W. Hahn (2016) How reticulated are species? <em>BioEssays </em>38:140-149<em>.</em> <a href="Publications/Mallet_etal2016.pdf">PDF</a></p>
</li>
<li>Pease, J.B., D.C. Haak, M.W. Hahn, and L.C. Moyle (2016) Phylogenomics reveals three sources of adaptive variation during a rapid radiation. <em>PLoS Biology </em>14:e1002379<em>.</em> <a href="Publications/Pease_etal2016.pdf">PDF</a></li>
<li><strong>2015</strong></li>
<li>
<p>Muir, C.D. and M.W. Hahn (2015) The limited contribution of reciprocal gene loss to increased speciation rates following whole genome duplication. <em>The American Naturalist</em>. 185:70-86. <a href="Publications/MuirHahn2015.pdf">PDF</a></p>
<p>Warren W.C…G.W.C. Thomas, M.W. Hahn…et al. (2015) The genome of the vervet (<em>Chlorocebus aethiops sabaeus</em>). <em>Genome Research</em>. 25:1921-1933. <a href="Publications/Warren_etal2015.pdf">PDF</a></p>
<p>Cooper, B.S., C.R. Burrus, C. Ji, M.W. Hahn, and K.L. Montooth (2015) Similar efficacies of selection shape mitochondrial and nuclear genes in both <em>Drosophila melanogaster </em>and <em>Homo sapiens. G3.</em> 5:2165-2176. <a href="Publications/Cooper_etal2015.pdf">PDF</a></p>
<li id="dfoil"><p>Pease, J.B. and M.W. Hahn (2015) Detection and polarization of introgression in a five-taxon phylogeny.<em> Systematic Biology.</em> 64:651-662. <a href="Publications/PeaseHahn2015.pdf">PDF</a></p>
<p>Adrion, J.R., M.W. Hahn, and B.S. Cooper (2015) Revisiting classic clines in <em>Drosophila melanogaster </em>in the age of genomics. <em>Trends in Genetics</em>. 31:434-444. <a href="Publications/Adrion_etal2015.pdf">PDF</a></p>
<p>Schrider, D.R., F.K. Mendes, M.W. Hahn, and A.D. Kern (2015) Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps<em>.</em> <em>Genetics</em>. 200:267-284. <a href="Publications/Schrider_etal2015.pdf">PDF</a></p>
<p>Thomas, G.W.C. and M.W. Hahn (2015) Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals. <em>Molecular Biology and Evolution.</em> 32:1232-1236. <a href="Publications/ThomasHahn2015.pdf">PDF</a></p>
<p>Aganezov, S., N. Sitdykova, The <em>Anopheles </em>Genomes Cluster Consortium, and M.A. Alekseyev (2015) Scaffold assembly based on genome rearrangement analysis. <em>Computational Biology and Chemistry</em>. 57:46-53. <a href="Publications/Aganezov_etal2015.pdf">PDF</a></p>
<p>Foote, A.D., Y. Liu, G.W.C. Thomas, T. Vinar, J. Alföldi, J. Deng, S. Dugan, N. van Elk, V. Joshi, Z. Khan, C. Kovar, S.L. Lee, K. Lindblad-Toh, A. Mancia, R. Nielsen, X. Qin, J. Qu, B.J. Raney, N. Vijay, J.B.W. Wolf, M.W. Hahn, D.M. Muzny, K.C. Worley, M.T.P. Gilbert, R.A. Gibbs. (2015) Convergent evolution of the genomes of marine mammals. <em>Nature Genetics.</em> 47:272-275. <a href="Publications/Foote_etal2015.pdf">PDF</a></p>
</li>
<li>
<p>Neafsey, D.E….G.W.C. Thomas, M.W. Hahn…et al. (2015) Highly evolvable malaria vectors: the genomes of 16 <em>Anopheles</em> mosquitoes. <em>Science</em>. 347:1258522. <a href="Publications/Neafsey_etal2015.pdf">PDF</a> <a href="Publications/Neafsey_etal2015_SOM.pdf">Supplementary Materials</a></p>
<p>Fontaine, M.C., J.B. Pease, A. Steele, R.M. Waterhouse, D.E. Neafsey, I.V. Sharakhov, X. Jiang, A.B. Hall, F. Catteruccia, E. Kakani, S.N. Mitchell, Y.-C. Wu, H.A. Smith, R.R. Love, M.K.N. Lawniczak, M.A. Slotman, S.J. Emrich, M.W. Hahn, N.J. Besansky (2015) Extensive introgression in a malaria vector species complex revealed by phylogenomics. <em>Science.</em> 347:1258524. <a href="Publications/Fontaine_etal2015.pdf">PDF</a> <a href="Publications/Fontaine_etal2015_SOM_final.pdf">Supplementary Materials</a></p>
</li>
<li><strong>2014</strong></li>
<li>Denton, J.F., J. Lugo Martinez, A.E. Tucker, D.R. Schrider, W.C. Warren, and M.W. Hahn (2014) Extensive error in the number of genes inferred from draft genome assemblies. <em>PLoS Computational Biology. </em>10:e1003998. <a href="Publications/Denton_etal2014.pdf">PDF</a></li>
<li>
<p>Montague, M.J., G. Li, B. Gandolfi, R. Khan, B.L. Aken, S.M.J. Searle, P. Minx, L. Hillier, D. Kolboldt, B.W. Davis, C.A. Driscoll, C. Barr, K. Blackistone, J. Quilez, B. Lorente-Galdos, T. Marques-Bonet, C. Alkan, G.W.C. Thomas, M.W. Hahn, M. Menotti-Raymond, S.J. O’Brien, R.K. Wilson, L.A. Lyons, W.J. Murphy, and W.C. Warren (2014) Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. <em>Proceedings of the National Academy of Sciences.</em> 111:17230-17235. <a href="Publications/Montague_etal2014.pdf">PDF</a></p>
</li>
<li>Carbone, L....G.W.C. Thomas, M.W. Hahn...et al. (2014) Gibbon genome and the fast karyotype evolution of small apes. <em>Nature</em>. 513:195-201. <a href="Publications/Carbone_etal2014.pdf">PDF</a></li>
<li>The Marmoset Genome Sequencing and Analysis Consortium (2014) The common marmoset genome provides insight into primate biology and evolution. <em>Nature Genetics.</em> 46:850-857. <a href="Publications/Marmoset2014.pdf">PDF</a></li>
<li>Cruickshank, T.C. and M.W. Hahn (2014) Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. <em>Molecular Ecology</em>. 23:3133-3157. <a href="Publications/CruickshankHahn2014.pdf">PDF</a></li>
<li>Bachtrog, D., J.E. Mank, C.L. Peichel, M. Kirkpatrick, S.P. Otto, T.-L. Ashman, M.W. Hahn, J. Kitano, I. Mayrose, R. Ming, N. Perrin, L. Ross, N. Valenzuela, and J.C. Vamosi. (2014) Sex determination: Why so many ways of doing it? <em>PLoS Biology</em>.12:e1001899. <a href="Publications/Bachtrog_etal2014.pdf">PDF</a></li>
<li>The Tree of Sex Consortium (2014) Tree of Sex: A database of sexual systems. <em>Scientific Data. </em>1:140015. <a href="Publications/TreeOfSex2014.pdf">PDF</a></li>
<li>Cassone, B.J., C. Kamdem, C. Cheng, J.C. Tan, M.W. Hahn, C. Costantini, and N.J. Besansky (2014) Gene expression divergence between malaria vector sibling species Anopheles gambiae and An. coluzzii from rural and urban Yaounde Cameroon. <em>Molecular Ecology</em>. 23:2242-2259. <a href="Publications/Cassone_etal2014.pdf">PDF</a></a></li>
<li id="RPGC">Hahn, M.W., Zhang, S.V., and L.C. Moyle. (2014) Sequencing, assembling, and correcting draft genomes using recombinant populations. <em>G3</em> 4:669-679. <a href="Publications/Hahn_etal2014.pdf">PDF</a></li>
<li>Thomas, G.W.C. and M.W. Hahn (2014) The human mutation rate is increasing, even as it slows. <em>Molecular Biology and Evolution</em>. 31:253-257. <a href="Publications/ThomasHahn2014_combined.pdf">PDF</a></li>
<li><strong>2013</strong></li>
<li id="CAFE3">Han, M.V., G.W.C. Thomas, J. Lugo-Martinez, and M.W. Hahn (2013) Estimating gene gain and loss rates in the presence of genome assembly and annotation error using CAFE 3. <em>Molecular Biology and Evolution</em>. 30:1987-1997. <a href="Publications/Han_etal2013.pdf">PDF</a></li>
<li>Schrider, D.R., D. Houle, M. Lynch, and M.W. Hahn (2013) Rates and genomic consequences of spontaneous mutational events in <em>Drosophila melanogaster</em>. <em>Genetics</em>. 194:937-954. <a href="Publications/Schrider_etal2013c.pdf">PDF</a></li>
<li>Neafsey, D.E., G.K. Christophides, F.H. Collins, S.J. Emrich, M.C. Fontaine, W. Gelbart, M.W. Hahn, P.I. Howell, F.C. Kafatos, D. Lawson, M.A.T. Muskavitch, R.M. Waterhouse, L.J. Williams, and N.J. Besansky (2013) The evolution of the <em>Anopheles</em> 16 genomes project. <em>G3</em>. 3:1191-1194. <a href="Publications/Neafsey_etal2013.pdf">PDF</a></li>
<li>Pease, J.B. and M.W. Hahn (2013) More accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting. <em>Evolution</em>. 67:2376-2384. <a href="Publications/PeaseHahn2013.pdf">PDF</a></li>
<li>Schrider, D.R., F.C.P. Navarro, P.A.F. Galante, R.B. Parmigiani, A.A. Camargo, M.W. Hahn, and S.J. de Souza (2013) Gene copy-number polymorphism caused by retrotransposition in humans. <em>PLoS Genetics.</em> 9:e1003242. <a href="Publications/Schrider_etal2013b.pdf">PDF</a></li>
<li>Schrider, D.R., D.J. Begun, and M.W. Hahn (2013) Detecting highly differentiated copy-number variants from pooled population sequencing. <em>Pacific Symposium on Biocomputing</em>. 18:344-355. <a href="Publications/Schrider_etal2013a.pdf">PDF</a></li>
<li><strong>2012</strong></li>
<li>Casola, C., G.C. Conant, and M.W. Hahn (2012) Very low rate of gene conversion in the yeast genome. <em>Molecular Biology and Evolution</em>. 29:3817-3826. <a href="Publications/Casola_etal2012b.pdf">PDF</a></li>
<li>Langley, C.H., K.S. Stevens, C. Cardeno, Y.C.G. Lee, D.R. Schrider, J.E. Pool, S.A. Langley, C. Suarez, R. Detig-Corbett, B. Kolaczkowski, S. Fang, P.M. Nista, A.K. Holloway, A.D. Kern, C.N. Dewey, Y.S. Song, M.W. Hahn, and D.J. Begun (2012) Genomic variation in natural populations of <em>Drosophila melanogaster</em>. <em>Genetics</em>. 192:533-598. <a href="Publications/Langley_etal2012.pdf">PDF</a></li>
<li>Pease, J.B. and M.W. Hahn (2012) Sex chromosomes evolved from independent ancestral linkage groups in winged insects. <em>Molecular Biology and Evolution</em>. 29:1645-1653. <a href="Publications/PeaseHahn2012.pdf">PDF</a></li>
<li>Cheng, C., B.J. White, C. Camdem, K. Mockaitis, C. Costantini, M.W. Hahn, and N.J. Besansky (2012) Ecological genomics of <em>Anopheles gambiae </em>along a latitudinal cline in Cameroon: a population resequencing approach. <em>Genetics</em>. 190:1417-1432. <a href="Publications/Cheng_etal2012.pdf">PDF</a></li>
<li>Casola, C., U. Zekonyte, A.D. Phillips, D.N. Cooper, and M.W. Hahn (2012) Interlocus gene conversion events introduce deleterious mutations in at least 1% of human genes associated with inherited disease. <em>Genome Research</em>. 22:429-435. <a href="Publications/Casola_etal2012.pdf">PDF</a></li>
<li>Han, M.V. and M.W. Hahn (2012) Inferring the history of interchromosomal gene transposition in <em>Drosophila</em> using <em>n</em>-dimensional parsimony. <em>Genetics</em>. 190:813-825. <a href="Publications/HanHahn2012.pdf">PDF</a></li>
<li>Hahn, M.W., B.J. White, C.D. Muir, and N.J. Besansky (2012) No evidence for biased co-transmission of speciation islands in <em>Anopheles gambiae</em>. <em>Philosophical Transactions of the Royal Society B: Biological Sciences.</em> 367:374-384. <a href="Publications/Hahn_etal2012.pdf">PDF</a></li>
<li><strong>2011</strong></li>
<li>Schrider, D.R., K.A. Stevens, C.M. Cardeno, C.H. Langley, and M.W. Hahn (2011) Genome-wide analysis of retrogene polymorphisms in <em>Drosophila melanogaster. Genome Research</em>. 21:2087-2095. <a href="Publications/Schrider_etal2011c.pdf">PDF</a></li>
<li>Toups, M.A., J.B. Pease, and M.W. Hahn (2011) No excess gene movement is detected off the avian or lepidopteran Z chromosome. <em>Genome Biology and Evolution</em>. 3:1381-1390. <a href="Publications/Toups_etal2011.pdf">PDF</a></li>
<li>Schrider, D.R., J.-F. Gout, and M.W. Hahn (2011) Very few RNA and DNA sequence differences in the human transcriptome. <em>PLoS ONE.</em> 6:e25842. <a href="Publications/Schrider_etal2011b.pdf">PDF</a></li>
<li>Nehrt, N.L., W.T. Clark, P. Radivojac, and M.W. Hahn (2011) Testing the ortholog conjecture with comparative functional genomic data from mammals. <em>PLoS Computational Biology</em>. 7:e1002073. <a href="Publications/Nehrt_etal2011.pdf">PDF</a></li>
<li>Schrider, D.R., J.N. Hourmozdi, and M.W. Hahn (2011) Pervasive multinucleotide mutational events in eukaryotes. <em>Current Biology</em>. 21:1051-1054. <a href="Publications/Schrider_etal2011_combined.pdf">PDF (includes Supplementary Materials)</a> </li>
<li>Cassone, B.J., M.J. Molloy, C. Cheng, J.C. Tan, M.W. Hahn, and N.J.Besansky (2011) Divergent transcriptional response to thermal stress by<em> Anopheles gambiae</em> larvae carrying alternative arrangements of inversion 2La. <em>Molecular Ecology</em>. 20:2567-2580. <a href="Publications/Cassone_etal2011.pdf">PDF</a></li>
<li>Bentley, R.A. and M.W. Hahn (2011) Is there a "Neutral Theory of Anthropology"?<em> Current Anthropology.</em> 52:117-118. <a href="Publications/BentleyHahn2011.pdf">PDF</a></li>
<li>Locke, D.P....C. Casola, D.R. Schrider, M.W. Hahn...et al. (2011) Comparative and demographic analysis of orang-utan genomes.<em> Nature</em>. 469:529-533. <a href="Publications/Locke_etal2011.pdf">PDF</a></li>
<li><strong>2010</strong></li>
<li>Toups, M.A. and M.W. Hahn (2010) Retrogenes reveal the direction of sex-chromosome evolution in mosquitoes. <em>Genetics</em>. 186:763-766. <a href="Publications/ToupsHahn2010.pdf">PDF</a></li>
<li>Schrider, D.R. and M.W. Hahn (2010) Gene copy-number polymorphism in nature. <em>Proceedings of the Royal Society B: Biological Sciences</em>. 277:3213-3221. <a href="Publications/SchriderHahn2010b.pdf">PDF</a></li>
<li>Kostka, D., M.W. Hahn, and K.S. Pollard (2010) Non-coding sequences near duplicated genes evolve rapidly. <em>Genome Biology and Evolution. </em>2:518-533 <a href="Publications/Kostka_etal2010.pdf">PDF</a></li>
<li>Moyle, L.C., C.D. Muir, M.V. Han, and M.W. Hahn (2010) The contribution of gene movement to the "Two Rules of Speciation". <em>Evolution</em>. 64:1541-1557. <a href="Publications/Moyle_etal2010.pdf">PDF</a></li>
<li>Casola, C., C.L. Ganote, and M.W. Hahn (2010) Nonallelic gene conversion in the genus <em>Drosophila</em>. <em>Genetics</em>. 185:95-103. <a href="Publications/Casola_etal2010.pdf">PDF</a></li>
<li>Turner, T.L. and M.W. Hahn (2010) Genomic islands <em>of</em> speciation or genomic islands <em>and</em> speciation? <em>Molecular Ecology</em>. 19:848-850. <a href="Publications/TurnerHahn2010.pdf">PDF</a></li>
<li>Nuzhdin, S.V., A. Rachkova, and M.W. Hahn (2010) The strength of transcription-factor binding modulates co-variation in transcriptional networks. <em>Trends in Genetics</em>. 26:51-53. <a href="Publications/Nuzhdin_etal2010.pdf">PDF</a></li>
<li>Schrider, D.R. and M.W. Hahn (2010) Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications. <em>Molecular Biology and Evolution.</em> 27:103-111. <a href="Publications/SchriderHahn2010.pdf">PDF</a></li>
<li><strong>2009</strong></li>
<li>Schrider, D.R., J.C. Costello, and M.W. Hahn (2009) All human-specific gene losses are present in the genome as pseudogenes. <em>Journal of Computational Biology</em>. 16:1419-1427. <a href="Publications/Schrider_etal2009.pdf">PDF</a></li>
<li>Hahn, M.W. (2009) Distinguishing among evolutionary models for the maintenance of gene duplicates. <em>Journal of Heredity</em>. 100:605-617. <a href="Publications/Hahn2009.pdf">PDF</a> <a href="JHedCorrection.html">Correction</a></li>
<li>Meisel, R.P., M.V. Han, and M.W. Hahn (2009) A complex suite of forces drives gene traffic from <em>Drosophila </em>X chromosomes. <em>Genome Biology and Evolution.</em> 1:176-188. <a href="Publications/Meisel_etal2009.pdf">PDF</a></li>
<li>McGrath, C.L., C. Casola, and M.W. Hahn (2009) Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes. <em>Genetics</em>. 182:615-622. <a href="Publications/McGrath_etal2009.pdf">PDF (includes Supplementary Materials)</a></li>
<li>Casola, C. and M.W. Hahn (2009) Gene conversion among paralogs results in moderate false detection of positive selection using likelihood methods. <em>Journal of Molecular Evolution</em>. 68:679-687. <a href="Publications/CasolaHahn2009.pdf">PDF</a></li>
<li>Han, M.V., J.P. Demuth, C.L. McGrath, C. Casola, and M.W. Hahn (2009) Adaptive evolution of young gene duplicates in mammals. <em>Genome Research. </em>19:859-867. <a href="Publications/Han_etal2009.pdf">PDF</a></li>
<li>Demuth, J.P. and M.W. Hahn (2009) The life and death of gene families. <em>BioEssays</em>. 31:29-39. <a href="Publications/DemuthHahn2009.pdf">PDF</a></li>
<li>Han, M.V. and M.W. Hahn (2009) Identifying parent-daughter relationships among duplicated genes. <em>Pacific Symposium on Biocomputing</em>. 14:114-125. <a href="Publications/HanHahn2009.pdf">PDF</a></li>
<li><strong>2008</strong></li>
<li>Li, Y., J.C. Costello, A.K. Holloway, and M.W. Hahn (2008) "Reverse ecology" and the power of population genomics. <em>Evolution</em>. 62:2984-2994. <a href="Publications/Li_etal2008.pdf">PDF</a></li>
<li>Nuzhdin, S.V., D.M. Tufts, and M.W. Hahn (2008) Abundant genetic variation in transcript level during early Drosophila development. <em>Evolution & Development</em>. 10:683-689. <a href="Publications/Nuzhdin_etal2008.pdf">PDF</a></li>
<li>Costello, J.C., M.V. Han, and M.W. Hahn (2008) Limitations of pseudogenes in identifying gene losses. <em>Sixth Annual RECOMB Satellite Workshop on Comparative Genomics</em>. pp. 14-25. <a href="Publications/Costello_etal2008.pdf">PDF</a></li>
<li>Radivojac, P., P.H. Baenziger, M.G. Kann, M. Mort, M.W. Hahn, and S.D. Mooney (2008) Gain and loss of phosphorylation sites in human cancer. <em>Bioinformatics. </em>24:i241-i247. <a href="Publications/Radivojac_etal2008.pdf">PDF</a></li>
<li>Cassone, B.J., K. Mouline, M.W. Hahn, B.J. White, M. Pombi, F. Simard, C. Costantini, and N.J. Besansky (2008) Differential gene expression in incipient species of <em>Anopheles gambiae</em>. <em>Molecular Ecology</em>. 17:2491-2504. <a href="Publications/Cassone_etal2008.pdf">PDF</a></li>
<li>Hahn, M.W. (2008) Toward a selection theory of molecular evolution. <em>Evolution</em>. 62:255-265. <a href="Publications/Hahn2008.pdf">PDF</a></li>
<li><strong>2007</strong></li>
<li>White, B.J., M.W. Hahn, M. Pombi, B.J. Cassone, N.F. Lobo, F. Simard, and N.J. Besansky (2007) Localization of candidate regions maintaining a common polymorphic inversion (2La) in <em>Anopheles gambiae</em>. <em>PLoS Genetics</em>. 3:e197. <a href="Publications/White_etal2007.pdf">PDF</a></li>
<li>Hahn, M.W., J.P. Demuth, and S.-G. Han (2007) Accelerated rate of gene gain and loss in primates. <em>Genetics</em>. 177:1941-1949. <a href="Publications/Hahn_etal2007_Genetics.pdf">PDF</a></li>
<li>Hahn, M.W., M.V. Han, and S.-G. Han (2007) Gene family evolution across 12 <em>Drosophila</em> genomes. <em>PLoS Genetics</em>. 3:e197. <a href="Publications/Hahn_etal2007_PLoSG.pdf">PDF</a></li>
<li>Begun, D.J., A.K. Holloway, K. Stephens, L.W. Hillier, Y.-P. Poh, M.W. Hahn, P.M. Nista, C.D. Jones, A.D. Kern, C. Dewey, L. Pachter, E. Myers, and C.H. Langley (2007) Population genomics: whole-genome analysis of polymorphism and divergence in <em>Drosophila simulans</em>. <em>PLoS Biology</em>. 5:e310. <a href="Publications/Begun_etal2007.pdf">PDF</a></li>
<li><em>Drosophila</em> Comparative Genome Sequencing and Analysis Consortium (2007) Evolution of genes and genomes in the context of the <em>Drosophila </em>phylogeny. <em>Nature. </em>450:203-218. <a href="Publications/Clark_etal2007.pdf">PDF</a></li>
<li>Stark, A., M.F. Lin, P. Kheradpour, J.S. Pedersen, L. Parts, J.W. Carlson, M.A. Crosby, M.D. Rasmussen, S. Roy, A.N. Deoras, J.G. Ruby, J. Brennecke, Harvard FlyBase curators, Berkeley Drosophila Genome Project, E. Hodges, A.S. Hinrichs, A. Caspi, B. Paten, S.-W. Park, M.V. Han, M.L. Maeder, B.J. Polansky, B.E. Robson, S. Aerts, J. van Helden, B. Hassan, D.G. Gilbert, D.A. Eastman, M. Rice, M. Weir, M.W. Hahn, Y. Park, C.N. Dewey, L. Pachter, W.J. Kent, D. Haussler, E.C. Lai, D.P. Bartel, G.J. Hannon, T.C. Kaufman, M.B. Eisen, A.G. Clark, D. Smith, S.E. Celniker, W.M. Gelbart, and M. Kellis (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. <em>Nature</em>. 450:219-232. <a href="Publications/Stark_etal2007.pdf">PDF</a></li>
<li>Turner, T.L. and M.W. Hahn (2007) Locus- and population-specific selection and differentiation between incipient species of <em>Anopheles gambiae</em>. <em>Molecular Biology and Evolution</em>. 24:2132-2138. <a href="Publications/TurnerHahn2007.pdf">PDF</a></li>
<li>Hahn, M.W. (2007) Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. <em>Genome Biology</em>. 8:R141 <a href="Publications/Hahn2007_GB.pdf">PDF</a></li>
<li>Rhesus Macaque Genome Sequencing and Analysis Consortium (2007) Evolutionary and biomedical insights from the Rhesus Macaque genome sequence. <em>Science</em>. 316:222-234. <a href="Publications/Gibbs_etal2007.pdf">PDF</a> <a href="Publications/Gibbs_etal2007_SOM.pdf">Supplementary Materials</a></li>
<li>Bentley, R.A., C.P. Lipo, H.A. Herzog, and M.W. Hahn (2007) Regular rates of popular culture change reflect random copying. <em>Evolution and Human Behavior</em>. 28:151-158. <a href="Publications/Bentley_etal2007.pdf">PDF</a></li>
<li>Hahn, M.W. (2007) Detecting natural selection on <em>cis</em>-regulatory DNA. <em>Genetica</em>. 129:7-18. <a href="Publications/Hahn2007.pdf">PDF</a></li>
<li><strong>2006</strong></li>
<li>Demuth, J.P., T. De Bie, J.E. Stajich, N. Cristianini, and M.W. Hahn (2006) The evolution of mammalian gene families. <em>PLoS ONE</em>. 1:e85. <u><a href="Publications/Demuth_etal2006.pdf">PDF</a></u> <u><a href="http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000085">PLoS ONE</a></u></li>
<li>Hahn, M.W. (2006) Accurate inference and estimation in population genomics. <em>Molecular Biology and Evolution. </em>23:911-918. <a href="Publications/Hahn2006.pdf">PDF</a></li>
<li id="anchor">De Bie, T., N. Cristianini, J.P. Demuth, and M.W. Hahn (2006) CAFE: a computational tool for the study of gene family evolution. <em>Bioinformatics</em>. 22:1269-1271. <a href="Publications/DeBie_etal2006.pdf">PDF</a></li>
<li><strong>2005</strong></li>
<li>Rockman, M.V., M.W. Hahn, N. Soranzo, F. Zimprich, D.B. Goldstein, and G.A. Wray (2005) Ancient and recent positive selection transformed opioid <em>cis</em>-regulation in humans. <em>PLoS Biology</em>. 3:e387. <a href="Publications/Rockman_etal2005.pdf">PDF</a></li>
<li id="BirthDeath">Hahn, M.W., T. De Bie, J.E. Stajich, C. Nguyen, and N. Cristianini (2005) Estimating the tempo and mode of gene family evolution from comparative genomic data.<em> Genome Research</em>. 15:1153-1160. <a href="Publications/Hahn_etal_bd2005.pdf">PDF</a> <a href="Publications/Hahn_bd2005_supp.pdf">Supplementary Materials</a></li>
<li>Turner, T.L., M.W. Hahn, and S.V. Nuzhdin (2005) Genomic islands of speciation in <em>Anopheles gambiae. PLoS Biology. </em>3:e285. <a href="Publications/Turner_etal2005.pdf">PDF</a> <a href="Publications/Turner_etal_SuppMaterials.xls">Supplementary Materials</a></li>
<li>Hahn, M.W. and G.C. Lanzaro (2005) Female-biased gene expression in the malaria mosquito <em>Anopheles gambiae</em>. <em>Current Biology. </em>15:192-193. <a href="Publications/HahnLanzaro2005.pdf">PDF (includes Supplementary data)</a></li>
<li>Hahn, M.W. and A.D. Kern (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. <em>Molecular Biology and Evolution</em>. 22:803-806. <a href="Publications/HahnKern2005.pdf">PDF</a> <a href="Publications/HK2005_Supp.pdf">Supplementary Materials</a></li>
<li>Hahn, M.W., J.G. Mezey, D.J. Begun, J.H. Gillespie, A.D. Kern, C.H. Langley, and L.C. Moyle (2005) Codon bias and selection on single genomes. <em>Nature</em>. 433:E5-E6. <a href="Publications/Hahn_etal2005.pdf">PDF</a></li>
<li id="Perlymorphism">Stajich, J.E. and M.W. Hahn (2005) Disentangling the effects of demography and selection in human history. <em>Molecular Biology and Evolution.</em> 22:63-73. <a href="Publications/StajichHahn2005.pdf">PDF</a></li>
<li><strong>2004</strong></li>
<li>Rockman, M.V., M.W. Hahn, D. Loisel, N. Soranzo, D.B. Goldstein, and G.A. Wray (2004) Positive selection on <em>MMP3</em> regulation has shaped heart disease risk. <em>Current Biology.</em> 14:1531-1539. <a href="Publications/Rockman_etal2004.pdf">PDF</a></li>
<li>Hahn, M.W., M.V. Rockman, N. Soranzo, D.B. Goldstein, and G.A. Wray (2004) Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the <em>Factor VII</em> locus in humans. <em>Genetics.</em> 167:867-877. <a href="Publications/Hahn_etal2004.pdf">PDF</a></li>
<li>Bentley, R.A., M.W. Hahn, and S.J. Shennan (2004) Random drift and culture change. <em>Proceedings of the Royal Society London B</em>. 271:1443-1450. <a href="Publications/Bentley_etal2004.pdf">PDF</a></li>
<li>Hahn, M.W. and S.V. Nuzhdin (2004) The fixation of malaria refractoriness in mosquitoes. <em>Current Biology</em>. 14:264-265. <a href="Publications/HahnNuzhdin2004.pdf">PDF (includes Supplementary data)</a></li>
<li>Herzog, H.A., R.A. Bentley, and M.W. Hahn (2004) Random drift and large shifts in the popularity of dog breeds. <em>Proceedings of the Royal Society London B, Biology Letters</em>. 271:S353-S356. <a href="Publications/Herzog_etal2004.pdf">PDF</a></li>
<li>Hahn, M.W., G. Conant, and A. Wagner (2004) Molecular evolution in large genetic networks: Does connectivity equal constraint? <em>Journal of Molecular Evolution.</em> 58:203-211. <a href="Publications/HahnConantWagner2004.pdf">PDF</a></li>
<li><strong>2003</strong></li>
<li>Rockman, M.V., M.W. Hahn, N. Soranzo, D.B. Goldstein, and G.A. Wray (2003) Positive selection on a human-specific transcription factor binding site regulating <em>IL4 </em>expression. <em>Current Biology</em> 13:2118-2123. <a href="Publications/Rockman_etal2003.pdf">PDF</a></li>
<li>Hahn, M.W. and R.A. Bentley (2003) Drift as a mechanism for cultural change: An example from baby names. <em>Proceedings of the Royal Society London B, Biology Letters</em>, 270:S120-S123. <a href="Publications/HahnBentley2003.pdf">PDF</a></li>
<li>Wray, G. A., M.W. Hahn, E. Abouheif, J. P. Balhoff, M. Pizer, M. V. Rockman, and L. Romano (2003). The evolution of transcriptional regulation in eukaryotes. <em>Molecular Biology and Evolution.</em> 20:1377-1419<em>. </em><a href="Publications/Wray_etal2003.pdf">PDF</a></li>
<li id="CGRmotif">Hahn, M.W., J.E. Stajich, and G.A. Wray (2003) The effects of selection against spurious transcription factor binding sites. <em>Molecular Biology and Evolution</em>. 20:901-906. <a href="Publications/Hahn_etal2003.pdf">PDF</a></li>
<li><strong>2002</strong></li>
<li>Hahn, M.W. and G.A. Wray (2002) The G-value paradox. <em>Evolution and Development</em>. 4:73-75. <a href="Publications/HahnWray2002.pdf">PDF</a></li>
<li>Tiffin, P. and M.W. Hahn (2002) Coding sequence divergence between two closely related plant species: <em>Arabidopsis thaliana</em> and <em>Brassica rapa</em> ssp. <em>pekinensis</em>. <em>Journal of Molecular Evolution.</em> 54:746-753. <a href="Publications/TiffinHahn2002.pdf">PDF</a></li>
<li id="Heterogeneity">Hahn, M.W., M.D. Rausher, and C.W. Cunningham (2002) Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7. <em>Genetics.</em> 161:11-20. <a href="Publications/Hahn_etal2002.pdf">PDF</a></li>
</ul>
<br>
</div>
<p> </p>
<div class="fourteen columns bluebox" >
<p id="spub" class="half-bottom"><strong>Post-doc and Student Publications</strong></p>
</div>
<div class="fourteen columns">
<ul class="publist">
<li>
<p>Sharma, P., <u>S. MISHRA</u>, H. Kurban, and M. Dalkilic (2025) <em>p</em>-clustval: a novel <em>p</em>-adic approach for enhanced clustering of high-dimensional single-cell RNASeq data. <em>International Journal of Data Science and Analytics</em> 20:4051-4066.</p>
<p>Tyszka, A.S., <u>D.A. LARSON</u>, and J.F. Walker (2025) Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life. <em>Trends in Plant Science</em> 30:705-711.</p>
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</ul>
<p> </p>
</div>
<div id="books" class="fourteen columns remove-bottom bluebox" >
<p class="half-bottom"><strong>Books</strong></p>
</div>
<div class="fourteen columns">
<ul class="publist">
<li>Cristianini, N. and M.W. Hahn (2007) <em>Introduction to Computational Genomics</em>. Cambridge University Press. <a href="http://www.computational-genomics.net">Website</a></li>
<li>Hahn, M.W. (2018) <em>Molecular Population Genetics.</em> Sinauer Associates/Oxford University Press.
<a href="Book/All_chapters.enlx">EndNote library</a> <a href="Book/All_chapters.bib">Bibtex library</a></li>
</ul>
<p> </p>
<p> </p>
</div>
<p> </p>
</div>
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