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Asselman, J, ME Pfrender, JA Lopez, JR Shaw, KAC De Schamphelaere. 2018. Linking reproductive effects to anthropogenic and natural stressors through gene co-expression networks. Environmental Science & Technology 52:317-326. DOI:10.1021/acs.est.


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.

Bradshaw, WE, J Burkhart, JK Colbourne, R Borowczak, J Lopez, DL Denlinger, JA Reynolds, ME Pfrender, and CM Holzapfel. 2017. Evolutionary transition from blood feeding to obligate non-biting in a mosquito. PNAS DOI: 10.1073/pnas.1717502115

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. 26:5872-5895. DOI: 10.1111/mec.14350

Deiner, 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.

Dowle, EJ, R Bracewell, ME Pfrender, K Mock, B Bentz, and G Ragland. 2017. Reproductive isolation and environmental adaptation shape the phylogeography of Mountain Pine Beetle (Dendroctonus ponderosae). Molecular Ecology. 26:6071-6084. DOI:10.1111/mec.14342

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.

Li**, Y, Z Rui, S Liu, A Donath, RS Peters, J Ware, B Misof, O Niehuis, ME Pfrender, and X Zhou. 2017. The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera. BMC Evolutionary Biology 17:269 DOI 10.1186/s12862-017-1111-z

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.

Ryan, S, MC Fontaine, JM Scriber, ME Pfrender, ST O’Neil, and J Hellmann. 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. 26:4725-4742. DOI:10.1111/mec.14236

Ye, Z, S Xu, K Spitze, J Asselman, X Jiang, MS Ackerman, J Lopez, B Harker, RT Raborn, W K 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 16:29-41DOI: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 26:1616-1621DOI:10.1016/j.cub.2016.04.056. Cover Photo

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 Pfrender, L De Meester, and MJ Frilander. 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. 2016. Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure. Molecular Ecology 24:6024-6038. 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, M 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.


Asselman, J, ME Pfrender, JA Lopez, DIM De Coninck, CR Janssen, JR Shaw, and KAC De Schamphelaere. 2015. Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia. Molecular Ecology 24:1844-1855 DOI:10.1111/mec.13148.

Mbengue, A, S Bhattacharjee, T Pandharkar, RV Stahelin, G Estiu, K Chotivanich, C Nguon, Y Fedotova, O Wiest, M Ghorbal, J-J Lopez-Rubio, ME Pfrender, S Emrich, N Mohandas, AM Dondorp and K Haldar. 2015. Phosphatidylinositol-3-kinase proteostasis: a central mechanism of artemisininresistance in malaria. Nature 520:683-687 DOI:10.138/nature14412.


McGlothlin, J, J Chuckalovcak, D Janes, S Edwards, C Feldman, ED Brodie Jr., ME Pfrender, and ED Brodie III. 2014. Parallel evolution of tetrodotoxin resistance in three voltage-gated sodium channel genes in the garter snake Thamnophis sirtalis. Molecular Biology and Evolution 31:2836-2846. DOI:10.1093/molbev/msu237. Text Box: Fast Track

Routtu, J, MD Hall, B Albere, C Beisel, RD Bergeron, A Chaturvedi, J-H Choi, J Colbourne, L De Meester, MT Stephens, C-P Stelzer, E Solorzano, WK Thomas, ME Pfrender, and D Ebert. 2014. A SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits. BMC Genomics 15:1033 DOI:10.1186/1471-2164-15-1033.

Stokes**, AN, PK Ducey, L Neuman-Lee**, CT Hanifin, SS French, ME Pfrender, ED Brodie, III, ED Brodie, Jr. 2014. Confirmation and distribution of tetrodotoxin for the first time in terrestrial invertebrates: two terrestrial flatworm species (Bipalium adventitium and Bipalium kewense). PLoS ONE 9:e100718 DOI:10.1371/journal.pone0100718.

Yampolsky, L, E Zeng, J Lopez, P Williams**, K Dick**, JK Colbourne, and ME Pfrender. 2014. Functional Genomics of acclimation and adaptation in response to thermal stress in Daphnia. BMC Genomics 15:859. DOI:10.1186/1471-2164-15-859.


Bracewell, RR, ME Pfrender, KE Mock, and BJ Bentz. 2013. Contrasting geographic patterns of genetic differentiation in body size and development time with reproductive isolation in Dendroctonus ponderosae (Coleoptera: Curculionidae, Scolytinae). Annals of the Entomological Society of America 106:385-391.

i5K Consortium. 2013. The i5K initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. Journal of Heredity 104:595-600. Cover Photo

Miner, BE, JK Colbourne, RA Knapp, and ME Pfrender. 2013. Evolutionary history of alpine and subalpine Daphnia of western North America. Freshwater Biology 58:1512-1522.

Orsini, L, N K Schwenk, L De Meester, JK Colbourne, ME Pfrender, and LJ Weider. 2013. The Evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments. TREE 28:274-282.


Feldman CR, ED Brodie, JR., ED Brodie, III, and ME Pfrender. 2012. Constraint shapes convergence in tetrodotoxin resistant sodium channels of snakes. PNAS 109:4556-4561(Supplemental files)

Latta LC, IV, LJ Weider, JK Colbourne, and ME Pfrender. 2012. The evolution of salinity tolerance in Daphnia: a functional genomics approach. Ecology Letters 15:794-802.

Lodge DM, CR Turner, CL Jerde, MA Barnes, L Chaderton, JL Feder, AR Mahon, ME Pfrender. 2012. Conservation in a cup of water: estimating biodiversity and population abundance with environmental DNA. Molecular Ecology 21:2555-2558.

Miner B, L De Meester, ME Pfrender, W Lampert, and NG Hairston, Jr. 2012. Daphnia is Different: The Expansive Ecological Role of an Emerging Genomic Model. PRSLB 279:1873-1882.

O’Neill EM, KH Beard, and ME Pfrender. 2012. Cast adrift on an island: introduced populations experience an altered balance between selection and drift. Biology Letters doi:10.1098/rsbl.2012.0312

Pfrender ME. 2012. Triangulating the genetic basis of adaptation to multifarious selection. Molecular Ecology 21:2051-2053.


Bentz BJ, RR Bracewell**, KE Mock, and ME Pfrender. 2011. Complex genetic architecture underlies plasticity in development time and adult size of Dendroctonus ponderosae, the Mountain Pine Beetle. Evolutionary Ecology 25:1269-1288.

Bracewell** RR, ME Pfrender, KE Mock, and BJ Bentz. 2011. Cryptic Postzygotic Isolation in an Eruptive Species of Bark Beetle (Dendroctonus ponderosae). Evolution 65:961-975.

Castoe TA, AM Bronikowski, ED Brodie III, SV Edwards, ME Pfrender, MD Shapiro, DD Pollock, and WC Warren. 2011. A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Standards in Genomic Sciences 4:257-270.

Colbourne, JK, ME Pfrender, D Gilbert, WK Thomas, A Tucker, TH Oakley, S Tokishita, A Aerts, GJ Arnold, M Kumar Basu, DJ Bauer, CE Cáceres, L Carmel, C Casola, J-H Choi, C Detter, Q Dong, S Dusheyko, BD Eads, T Fröhlich, KA Geiler-Samerotte, D Gerlach, P Hatcher, S Jogdeo, J Krijgsveld, EV Kriventseva, D Kültz, C Laforsch, E Lindquist, J Lopez, JR Manak, J Muller, J Pangilinan, RP Patwardhan, S Pitluck, EJ Pritham, A Rechtsteiner, M Rho, IB Rogozin, O Sakarya, A Salamov, S Schaack, H Shapiro, Y Shiga, C Skalitzky, Z Smith, A Souvorov, W Sung, Z Tang, D Tsuchiya, H Tu, H Vos, M Wang, YI Wolf, H Yamagata, T Yamada, Y Ye, JR Shaw, J Andrews, TJ Crease, H Tang, SM Lucas, HM Robertson, P Bork, EV Koonin, EM Zdobnov, I Grigoriev, M Lynch and JL Boore. 2011. The ecoresponsive genome of Daphnia pulex. Science 331:555-561. (Supplemental Online Material)(Commentaries by Dieter Ebert and Diethard Tautz)

Hellmann JJ, and ME Pfrender.Future Human Intervention in Ecosystems and the Critical Role for Evolutonary Biology. Conservation Biology 25:1143-1147.

Latta** LC, IV, M Baker, T Crowl, JJ Parnell, B Weimer, D DeWald, and ME Pfrender. 2011. Species and Genotype Diversity Drive Community and Ecosystem Properties in Experimental Microcosms. Evolutionary Ecology 25:107-1125.

Latta** LC, IV, S Frederick*, and ME Pfrender. Diet Restriction and Life History Trade-offs in short- and Long-lived species of Daphnia. Journal of Experimental Zoology Part A ePub 309A.

Neuman-Lee L, S McGaugh, ME Pfrender, FJ Janzen. Using Mitochondrial DNA to Determine the Origin of a Snake Found in Alaska. Journal of Herpetology 45:63-65.

Orsini L, E Decaester, L De Meester, ME Pfrender, and JK Colbourne, 2011. Genomics in the Ecological Arena. Biology Letters 7:2-3.

Parnell JJ, SJ Callister, G Rompato, CD Nicora, L Pasa-Tolic, A Williamson***, and ME Pfrender. 2011. Time-course Analysis of the Shewanella Amazonensis SB2B Proteome in Response to Sodium Chloride Shock. Scientific Reports 1:25.

Parnell JJ, G Rompato, TA Crowl, BC Weimer, and ME Pfrender. 2011.Phylogenetic Distance in Great salt Lake Microbial Communities. Aquatic Microbial Ecology 64:267-273.

Simon J-C, ME Pfrender, R Tollrian, D Tagu, and JK Colbourne. 2011. Genomics of Environmentally-induced Phenotypes in Two Extremely Plastic Organisms. Journal of Heredity 102:512-525.


Feldman** CR, ED Brodie, JR., ED Brodie, III, and ME Pfrender. 2010. Genetic Architecture of a Feeding Adaptation: Garter Snake (Thamnophis) Resistance to Tetrodotoxin Bearing Prey. PRSLB 277:3317-3325.

Latta** LC, IV, DL Fisk**, RA Knapp, and ME Pfrender. 2010. Genetic Resilience of Daphnia Populations Following Experimental Removal of Introduced Fish. Conservation Genetics 11:1737-1745.

Parnell JJ, G Rompato, LC Latta IV, ME Pfrender, J VanNostrand, Z He, J Zhou, G Anderson, P Champine, B Ganesan, and BC Weimer. 2010. Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities. PLoSOne 5:e12919.

Pfrender ME, et al. 2010. Genetic approaches to biodiversity assessment in freshwater ecosystems. Quarterly Review of Biology 85:319-340.

Scoville** AG, and ME Pfrender. 2010. Phenotypic plasticity facilitates rapid parallel adaptation to an introduced predator. PNAS 107:4260-4263.

Spanier KI, F Leese, C Mayer, JK Colbourne, D Gilbert, ME Pfrender, R Tollrian. 2010. Predator-induced defenses in Daphnia pulex: Selection and evaluation of internal reference genes for gene expression studies with real-time PCR. BMC Molecular Biology 11:50.(Supplementary File)


Callister SJ, JJ Parnell, ME Pfrender, and SA Hashsham. 2009. Relating Perturbation Magnitude to Temporal Gene Expression in Biological Systems. BMC Research Notes 2:43.

Feldman** CR, ED Brodie, JR., ED Brodie, III, and ME Pfrender. 2009. Testing the evolutionary origins of beneficial alleles during the repeated adaptation of garter snakes (Thamnophis) to deadly prey. PNAS 106:13415-13420.

Kanaga** MK, LC Latta** IV, KE Mock, RL Lindroth, and ME Pfrender. 2009. Plant genotypic diversity and environmental stress interact to negatively affect arthropod community diversity. Arthropod-Plant Interactions 3:249-258.

Latta** LC, IV, RP O’Donnell**, and ME Pfrender. 2009. Vertical Distribution of Chlamydomonas reinhardtii: Changes in Response to Kairomones Produced by Grazers and Predators. Oikos 118:853-858.

Parnell JJ, TA Crowl, BC Weimer, and ME Pfrender. 2009. Biodiversity in microbial communities: system scale patterns and mechanisms. Molecular Ecology 18:1455-1462.


Homel** K, P Budy, ME Pfrender, TA Whitesel, L Bjerregaard**, and K Mock. 2008. Evaluating genetic structure among resident and migratory forms of bull trout (Salvelinus confluentus) in Northeast Oregon. Ecology of Freshwater Fish 17:465-474.

Kanaga** MK, RJ Ryel, KE Mock, and ME Pfrender. 2008. Quantitative genetic variation within a quaking aspen (Populus tremuloides) population. Can. J. Forestry Research 38:1690-1694.

Shaw JR, ME Pfrender, BD Eads, R Klapper, A Callaghan, RM Sibly, I Colson, B Jansen, D Gilbert, and JK Colbourne. 2008. Daphnia as an emerging model for toxicological genomics. In: Advances in Experimental Biology vol. 2 (eds. C Hogstrand and P Kille). Elsevier Press, London.

Stillman JH, JK Colbourne, C Lee, NH Patel, MR Phillips, DW Towle, BD Eads, GW Gelembiuk, RP Henry, EA Johnson, ME Pfrender, and NB Terwilliger. 2008. Recent Advances in Crustacean Genomics. Integrative and Comparative Biology 48:852-868.


Bushman BS, SR Larson, MD Peel, and ME Pfrender. 2007. Population structure and genetic diversity in North American Hedysarum boreale Nutt. (Hedysarae: Fabaceae). Crop Science 47:1281-1288.

Fisk** D, LC Latta, IV**, RA Knapp, and ME Pfrender. 2007. Rapid evolution in response to introduced predators I: Rates and patterns of morphological and life-history trait divergence. BMC Evolutionary Biology 7:22. (Designated as Highly Accessed)

Latta** LC, IV, J Bakelar*, RA Knapp, and ME Pfrender. 2007. Rapid evolution in response to introduced predators II: The contribution of adaptive plasticity. BMC Evolutionary Biology 7:21. IF 4.373

Mock KE, BJ Bentz, EM O’Neill**, JP Chong**, JT Orwin*, and ME Pfrender. 2007. Landscape-scale genetic variation in a forest outbreak species, the mountain pine beetle (Dendroctonus ponderosae). Molecular Ecology 16:553-568.


Deng H-W, J Li, ME Pfrender, J-L Li, H Deng. 2006. Upper limit of the rate and per generation effects of deleterious genomic mutations. Genetical Research, Camb. 88:57-65.


Mead LS, RS Nauman, D Clayton, DH Olson, and ME Pfrender. 2005. Newly discovered populations of salamanders from Siskiyou County California represent a species distinct from Plethodon stormi. Herpetologica 61:158-177.


Pfrender ME, J Hicks, and M Lynch. 2004. Biogeographic patterns and current distribution of molecular genetic variation among populations of speckled Dace (Rhinichthys osculus). Molecular Phylogenetics and Evolution 30:490-502.

Watts RA, CA Palmer, RC Feldhoff, PW Feldhoff, LD Houck, AG Jones, ME Pfrender, SM Rollmann, and SJ Arnold. 2004. Discordant Modes of Evolution at Different Levels in a Pheromone Signaling System. Molecular Biology and Evolution 21:1032-1041.


Dunham SM, A Kretzer, and ME Pfrender. 2003. Characterization of the extent and distribution of Pacific golden chanterelle (Cantharellus formosus) individuals using co-dominant microsatellite loci. Molecular Ecology 12:1607-1618.


Arnold SJ, ME Pfrender, and AG Jones. 2001. The adaptive landscape as a conceptual bridge between micro- and macroevolution. Genetica 112-113:9-32.

Morgan KK, J Hicks, K Spitze, L Latta, M Pfrender, C Weaver, M Ottone, and M Lynch. 2001. Patterns of genetic architecture for life-history traits and molecular markers in a subdivided species. Evolution 55:1753-1761.


Fernando P, ME Pfrender, S Encalada, and R Lande. 2000. Mitochondrial DNA variation, phylogeography and population structure of the Asian Elephant. Heredity 84:362-372.

Pfrender ME, K Spitze, J Hicks, K Morgan, L Latta, and M Lynch. 2000. Lack of concordance between genetic diversity estimates at the molecular and quantitative-trait levels. Conservation Genetics 1:263-269.

Pfrender ME, and M Lynch. 2000. Quantitative genetic variation in Daphnia: temporal changes in genetic architecture. Evolution 54:1502-1509.

Pfrender ME, K Spitze, and N Lehman. 2000. Multi-locus evidence for rapid ecologically-based speciation in Daphnia. Molecular Ecology 9:1717-1735.


Lynch M, ME Pfrender, K Spitze, N Lehman, D Allen, J Hicks, L Latta, M Ottene, F Bogues, and J Colbourne. 1999. The quantitative and molecular genetic architecture of a subdivided species. Evolution 53:100-110.


Nussbaum RA, and ME Pfrender. 1998. Revision of the African caecilian genus Schistometopum Parker (Amphibia: Gymnophiona: Caeciliidae). Misc. Pub. Mus. Zool. Univ. Mich. 187:1-32.

Pfrender ME, WE Bradshaw, and CA Kleckner. 1998. Patterns in the geographical range sizes of ectotherms in North America. Oecologia 115:439-444.

Pfrender ME, and H-W Deng. 1998. Genetic and environmental control of diapause termination in Daphnia. Arch. Hydrobiol. 52:237-251.


Lehman N, ME Pfrender, PA Morin, TJ Crease, and M Lynch. 1995. A hierarchical molecular phylogeny within the genus Daphnia. Molecular Phylogenetics and Evolution 4:395-407.