Michael Pfrender Associate Professor; Director, Genomics Core

Evolutionary and Ecological Genomics
Michael Pfrender

Research Interests:

My lab is interested in a broad range of topics in the area of evolutionary and ecological genomics. Projects include investigation of the molecular genetic basis of adaptive traits and phenotypic plasticity, and the relationship between genetic diversity and ecosystem function. We are particularly interested in the relationship between short-term organismal responses to environmental stresses and long-term adaptive changes in novel environments. Ultimately, we are trying to connect genome structure, quantitative genetic architecture, and patterns of gene expression and gene evolution, with the process of, and limits to, adaptation in changing environments. Anthropogenic influences have created an ecological context of rapidly changing environments. There are many unresolved questions at multiple levels of biological organization that confront the fields of ecology and evolutionary biology. How will populations, species, and communities of organisms respond to novel species introductions and rapidly changing abiotic conditions? Can we predict the probability of adaptations and long-term persistence? Understanding the impacts of alterations in natural ecosystems, and using this knowledge to predict future consequences and preserve biodiversity, is a major challenge for 21st century Biologists with direct relevance to human health and well being.



  • Director, Genomics & Bioinformatics Core Facility, University of Notre Dame 2009-Present
  • Associate Professor, Department of Biological Sciences, University of Notre Dame 2009-Present
  • Adjunct Professor, Department of Biology, Utah State University 2009-Present
  • Associate Professor, Department of Biology, Utah State University 2007-2009
  • Assistant Professor, Utah State University 2001-2007
  • Postdoctoral Research Associate, Oregon State University 1998-2001
  • Instructor, University of Oregon 1997-1998
  • Graduate Teaching Fellow, University of Oregon 1992-1997
  • Graduate Research Fellow, University of Michigan 1990-1992
  • PhD, Department of Biology, University of Oregon, Eugene, Oregon 1998
  • MS, Department of Biological Sciences, University of Michigan, Ann Arbor, Michigan 1992
  • BS, Department of Biological Sciences, University of Michigan, Ann Arbor, Michigan 1988


Recent Papers:


  • Deiner, K, E Machler, M Seymour, HM Bik, A Lacoursiere-Roussel, F Altermatt, S Creer, I Bista, DM Lodge, N de Vere, ME Pfrender, and L Bernatchez. 2017. Must you see to believe? Environmental DNA metabarcoding of animal and plant communities. Molecular Ecology. (In Press)
  • Dowle, EJ, R Bracewell, ME Pfrender, K Mock, B Bentz, and G Ragland. Reproductive isolation and environmental adaptation shape the phylogeography of Mountain Pine Beetle (Dendroctonus ponderosae). Molecular Ecology. (In Press)
  • Li Y, Z Rui, S Liu, A Donath, RS Peters, J Ware, B Misof, O Niehuis, ME Pfrender, and X Zhou. The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera. BMC Evolutionary Biology. (In Press)
  • Ryan, S, MC Fontaine, JM Scriber, ME Pfrender, ST O’Neil, and J Hellmann. 2017. Patterns of differentiation and divergence across the geographic and genomic landscape of a butterfly hybrid zone: a tension zone trapped in a climatic gradient? Molecular Ecology. DOI: 10.1111/mec.14236
  • Asselman, J, DIM De Connick, E Beert, CR Janssen, L Orsini, ME Pfrender, E Decaestecker, and KAC De Schamphelaere. 2017. Bisulfite sequencing with Daphnia highlights a role for epigenetics in regulating stress responses to Microcystis through preferential differential methylation of serine and threonine amino acids. Environmental Science & Technology 51:924-931. DOI:10.1021/acs.est.6b03870.
  • DeinerE, K, MA Renshaw, Y Li, BP Olds, DM Lodge, and ME Pfrender. 2017 Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA. Methods in Ecology and Evolution. 00:1-11. DOI:10.111/2041-210X.12836.
  • Evans, N, Y Li, MA Renshaw, BP Olds, K Deiner, CR Turner, CR Jerde, DM Lodge, GA Lamberti, and ME Pfrender. 2017. Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatics filtering. Canadian Journal of Fisheries and Aquatic Sciences 74:1362-1374. DOI:10.1139/cjfas-2016-0306.
  • Orsini L, JB Brown, OS Solari, D Li, S He, R Podicheti, MH Stoiber, KI Spanier, D Gilbert, M Jansen, D Rusch, ME Pfrender, JK Colbourne, MJ Frilander, J Kvist, E Decaestecker, KAC De Schamphelaere, and L De Meester. 2017. Early transcriptional responses pathways in Daphnia magna are coordinated in networks of crustacean specific genes. Molecular Ecology DOI: 10.1111/mec.14261.
  • Ye, Z, S Xu, K Spitze, J Asselman, X Jiang, MS Ackerman, J Lopez, B Harker, RT Raborn, WK Thomas, J Ramsdell, ME Pfrender, and M Lynch. 2017. A new reference genome assembly for the microcrustacean Daphnia pulex. Genes|Genomes|Genetics 7:1405-1416 DOI:10.1534/g3.116.038638
  • Asselman, J, DIM De Coninck, CR Janssen, ME Pfrender, and KAC De Schamphelaere. 2016. Gene body methylation patterns in Daphnia are associated with gene family size. Genome Biology and Evolution 8:1185-1196 DOI:10.1093/gbe/evw069.
  • Evans, N, B Olds, M Renshaw, C Turner, Y Li, C Jerde, A Mahon, ME Pfrender, G Lamberti, and D Lodge. 2016. Quantification of mesocosm fish and amphibian species richness via environmental DNA-based metagenetic analysis. Molecular Ecology Resources 16:29-41 DOI:10.1111/1755-0998.12433.
  • Feldman, CR, AM Durso, CT Hanifin, ME Pfrender, PK Ducey, AN Stokes, KE Barnett, ED Brodie III, ED Brodie Jr. 2016. Is there more than one way to skin a newt? Convergent toxin resistance in snakes is not due to common genetic mechanisms. Heredity 116:84-91 DOI:10.1038/hdy.2015.73.
  • McGlothlin, JW, M Kobiela, CR Feldman, TA Castoe, FJ Vonk, MK Richardson, ED Brodie Jr, ME Pfrender, and ED Brodie III. 2016. Historical contingency in a multigene family facilitates adaptive evolution of toxin resistance. Current Biology 26:1616-1621 DOI:10.1016/j.cub.2016.04.056.
  • Olds, BP, CL Jerde, MA Renshaw, Y Li, NT Evans, CR Turner, K Deiner, AR Mahon, MA Brueske, PD Shirley, ME Pfrender, DM Lodge, and GA Lamberti. 2016. Estimating species richness using environmental DNA. Ecology & Evolution 6:4214-4226 DOI:10.1002/ece3.2186.
  • Orsini, L, D Gilbert, P Ram, M Jansen, JB Brown, OS Solari, KI Spanier, JK Colbourne, D Rush, E Decaestecker, J Asselman, KAC De Schamphelaere, D Ebert, C Haag, J Kvist, C Laforsch, A Petrusek, A Beckerman, T Little, ME PfrenderG, L De MeesterG, and MJ FrilanderG. 2016. Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Scientific Data 3:160030 DOI:10.1038/sdata.2016.30.
  • Orsini, L, H Marshall, M Cuenca Cambronero, A Chaturvedi, WK Thomas, ME Pfrender, K Spanier, and L De Meester. Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure. Molecular Ecology 25:6024-6038. DOI:10.1111/mec.13907.
  • Rund, SC, B Yoo, C Alam, T. Green, MT Stephens, E. Zeng, GF George, AD Sheppard, GE Duffield, T Milenkovic, and ME Pfrender. 2016. Genome-wide profiling of 24 hr diel rhythmicity in the water fleas, Daphnia pulex: Network analysis reveals rhythmic gene expression and enhances functional gene annotation. BMC Genomics 17:653 DOI:10.1186/s12864-016-2998-2.
  • Vacchina, P, B Norris-Mullins, M.A. Abengozar, J Sarro, MT Stephens, ME Pfrender, L Rivas, and MA Morales. 2016. Multifactorial basis for in vitro acquisition of miltefosine resistance in Leishmania donovani: a genomic appraisal. Antimicrobial Agents & Chemotherapy 60:4089-100 DOI:10.1128/AAc.00478-16.