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publications.html

@@ -72,17 +72,23 @@
             <li><strong>2025</strong></li>
             <li>
 
+				<p>Larson, D.A., M.W. Itgen, R.D. Denton, and M.W. Hahn (in press) Reconsidering cytonuclear discordance in the genomic age. <em>Evolution</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>Hahn, M.W. and S.R. Mishra (<em>in press</em>) Estimating recombination using only the allele frequency spectrum. <em>Genetics</em>. </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 (<em>in press</em>) The Tree of Sex consortium: A global initiative for studying the evolution of reproduction in eukaryotes. <em>Journal of Evolutionary Biology</em>.</p>
+				<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 (<em>in press</em>) Repeated behavioral evolution is associated with convergence of gene expression in cavity-nesting songbirds. <em>Nature Ecology & Evolution</em>. </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 (<em>in press</em>) Genome-wide adaptation to a complex environmental gradient in a keystone phytoplankton species. <em>Molecular Ecology</em>. </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  (2024) 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>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>
 
@@ -356,7 +362,7 @@
                     <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> <a href="Publications/Rockman_etal2005/PDYN.html">Supplementary Materials</a></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>

research.html

@@ -58,13 +58,13 @@
         <div class="eleven columns offset-by-one">
         <p>Our work focuses broadly on asking questions about organismal function  and evolution using genomic data. The huge amount of data currently  being produced allows us to ask and answer questions on a genomic scale  that have never been possible before. Our questions largely revolve  around the relative roles of natural selection and genetic drift in  shaping nucleotide, gene family, and gene expression variation both  within and between species. Although most of the empirical work has been  on systems such as humans, flies,&nbsp; mosquitoes,&nbsp;and tomatoes, members of the lab can work  on topics and organisms that appeal to them. This page covers several major topics currently being studied.
         <h3>The evolution of gene gain and loss</h3>
-        <p>Comparison of whole genomes has revealed large and frequent changes in  the size of gene families, the result of gene duplication and loss. Comparative genomic analyses allow us to  identify large-scale patterns of change and to make  inferences regarding the role of natural selection in gene gain and  loss. To make these analyses possible, we have developed a stochastic  birth-and-death model for gene family evolution, applied in the software package, CAFE.  Application of this method to data from multiple whole  genomes of  many groups is revealing remarkable patterns of  gene gain and loss.
-        Other approaches to studying this question have involved the analysis of gene movement among chromosomes (especially sex chromosomes), the discovery of polymorphic copy-number variants under local selection, and even new methods for carrying out genome assembly to more accurately estimate gene number.<h3>Population genomics</h3>
-        <p>Selective, demographic, and random processes all determine the frequency  of alleles in a population and differences between species.  One of the  major goals of population genetics has been to uncover which of these  processes is acting in natural populations through a combination of  directed empirical studies and theoretical models that provide  expectations under a variety of conditions.  While most of the work in  the field has involved single loci or limited multiple locus studies and  models, the availability of genomic-scale data will begin to require  new genomic-scale approaches. We have been pursuing these questions in a wide variety  of studies, largely focused on humans and flies (where the best data have always been). The work has presented new methods for distinguishing demography from selection, distinguishing different forms of positive selection, and more recently, using clinal variation to uncover local adaptation.</p>
+        <p>Comparison of whole genomes has revealed large and frequent changes in  the size of gene families, the result of gene duplication and loss. Comparative genomic analyses allow us to  identify large-scale patterns of change and to make  inferences regarding the role of natural selection in gene gain and  loss. To make these analyses possible, we have developed multiple models and methods for inferring gene gain and loss. These methods include a stochastic  birth-and-death model for gene family evolution, applied in the software package, CAFE, and multiple reconciliation methods for use with gene trees (implemented in the software packages GRAMPA and reconcILS).  Application of this method to data from multiple whole  genomes of  many groups is revealing remarkable patterns of  gene gain and loss.
+        <h3>Population genomics</h3>
+        <p>Selective, demographic, and random processes all determine the frequency  of alleles in a population and differences between species.  One of the  major goals of population genetics has been to uncover which of these  processes is acting in natural populations through a combination of  directed empirical studies and theoretical models that provide  expectations under a variety of conditions.  While classical work in  the field involved single loci or limited multiple locus studies and  models, the availability of genomic-scale data requires genomic-scale approaches. We have pursued these questions in a wide variety  of systems, using a wide variety of computational and statistical approaches. The work has resulted in new methods for distinguishing demography from selection, distinguishing different forms of positive selection, and more recently, using and analyzing machine learning approaches to population genetic inference.</p>
         <h3>Speciation genomics</h3>
-        <p>Population genomic data are being applied in new and creative ways to recently diverged lineages. One of the goals of the new field of speciation genomics is to understand how the patterns of divergence uncovered by such studies are related to mechanisms of reproductive isolation. Focusing on divergence within the <em>Anopheles gambiae</em> species complex, we have been interested in the roles of introgression and selection in shaping heterogeneous patterns of divergence. This work has built on much of our more general research into population genomics, but  also now encompasses new approaches to detecting introgression and to distinguishing differences in introgression among loci from differences in selection among loci.</p>
+        <p>Population genomic data are being applied in new and creative ways to recently diverged lineages. One of the goals of the field of speciation genomics is to understand how the patterns of divergence uncovered by such studies are related to mechanisms of reproductive isolation. We have been particularly interested in the roles of introgression and selection in shaping heterogeneous patterns of divergence between closely related species. This work has built on much of our more general research into population genomics, but also encompasses the development of many new approaches for detecting introgression.</p>
         <h3>The evolution of mutation rates</h3>
-        <p>Parents leave many mutations to their offspring, but this number differs among species and between the sexes. Using pedigree-based studies of mutation rates across mammals, our work has focused on explaining the evolution of this complex trait. We have found that variation in the mutation rate among species is largely driven by generation time: longer-lived organisms pass on more mutations. Our newer on the difference between the sexes attempts to determine the developmental and molecular mechanisms underlying male-mutation bias.</p>
+        <p>Parents leave many mutations to their offspring, but this number differs among species and between the sexes. Using pedigree-based studies of mutation rates across mammals, our work has focused on explaining the evolution of this complex trait. We have found that variation in the mutation rate among species is largely driven by generation time: longer-lived organisms pass on more mutations. Our newer work on  differences between the sexes attempts to determine the developmental and molecular mechanisms underlying male-mutation bias.</p>
         <p>&nbsp;</p>
         <p>&nbsp;</p>
 </div>
@@ -85,9 +85,7 @@ <h3>The evolution of mutation rates</h3>
         <p>&nbsp;</p><p>&nbsp;</p>
     <img src="lib/img/research/Figure3.jpg" width="216" height="173" alt="A diagram showing varying levels of nucleotide diversity along a chromosome."	>
      <p>&nbsp;</p>
-        <p>&nbsp;</p>
-        <p>&nbsp;</p><p>&nbsp;</p>
-    <img src="lib/img/research/Figure1_revised.jpg" width="155" height="196" alt="A climatic map of Cameroon with pie charts overlaid."	>
+<img src="lib/img/research/Figure1_revised.jpg" width="155" height="196" alt="A climatic map of Cameroon with pie charts overlaid."	>
      <p>&nbsp;</p>
         <p>&nbsp;</p>
     <img src="lib/img/research/muts.jpg" width="200" height="133" alt="Differences in generation time between male and female humans across the last 10,000 generations."	>