Integrated Search Menu

Michael Lynch

Profile photo
Professor and Center Director
Faculty w/Admin Appointment, TEMPE Campus, Mailcode 7701
Center Director & Professor
Faculty w/Admin Appointment, TEMPE Campus, Mailcode 7701
Center Director & Professor
Faculty w/Admin Appointment, TEMPE Campus, Mailcode 7701
Biography: 

Michael Lynch is a professor in the School of Life Sciences and director of the Biodesign Center for Mechanisms of Evolution. Professor Lynch has served as President of the Genetics Society of America, the Society for Molecular Biology and Evolution, the Society for the Study of Evolution, and the American Genetic Association. He is a member of the U.S. National Academy of Sciences, and a fellow of the American Academy of Arts and Sciences.

His research is focused on mechanisms of evolution at the gene, genomic, cellular, and phenotypic levels, with special attention being given to the roles of mutation, random genetic drift, and recombination. This work relies on the integration of theory development and computational analysis with empirical work on several model systems, including the microcrustacean Daphnia, the ciliate Paramecium, and numerous microbial species. The overarching mission of the new Biodesign Center for Mechanisms of Evolution is to understand the primary forces of evolution to empower all areas of the life sciences and solve key practical and urgent societal issues such as our understanding of mutation and disease.

Besides many highly acclaimed papers, especially in population genetics, he has written a two volume treatise on quantitative genetics with Bruce Walsh, the first volume (1998) focused on the genetics and analysis of quantitative traits, and the second (forthcoming) on the evolution of quantitative traits. He has been a major force in promoting neutral theories to explain variation in genomic and gene-structural architecture based on the effects of population sizes in different lineages; he presented this point of view comprehensively in his 2007 book "The Origins of Genome Architecture". He is currently extending these ideas to the cellular level in an emerging book on “The Origins of Cellular Features.”

Education: 
  • PhD Ecology, University of Minnesota
  • BS Biology, St. Bonaventure University
Research Interests: 
  • The 5000 Daphnia pulex genome project. The goal is to sequence the genomes of 96 genotypes from each of 50 populations in this model organism for evolutionary and ecological genomics. In addition to developing a resource for the research community, the results are being used to test ideas on the origin of introns, the genetic consequences of loss of recombination, and the genetic consequences of long-term population bottlenecks. This project is also now extending to similar analyses with other species.
  • The genome biology of the Paramecium aurelia complex. The goal is to determine the causes and consequences of the differential retention of duplicate genes following whole-genome duplication in this cryptic species complex. In addition, we are attempting to resolve the regulatory vocabulary in this genus, as well studying the evolution of vesicle transport pathways.
  • Development of methods for the analysis of population-genomic data. We are developing a series of maximum-likelihood methods for ascertaining the population-genetic features using high-throughput genome sequence data. These methods, which take into account uncertainties due to low coverage and error-prone sequences, are being made available to the general public in the former of user-friendly software.
  • Experimental molecular evolution in microbial populations. We are pursuing highly replicated experiments (~500 lines) with multiple bacterial species grown at different population sizes, mutation rates, and nutritional status in an effort to reveal general principles regarding the mechanisms of evolution. The work involves periodic population-level, whole-genome sequencing, transcriptomics, and proteomics
  • Mutation rates. We are utilizing a mutation-accumulation strategy, followed by whole-genome sequencing, to measure the rate and complete molecular spectrum of mutations across the Tree of Life.  This work is focused on testing the drift-barrier hypothesis. Parallel work is being done on the transcription-error rate and on the rate of somatic mutation, and will soon be extended to the issue of translation error rates.
  • In various ways, we are attempting to establish a formal field of evolutionary cell biology, with a goal of integrating ideas from cell biology, evolutionary biology, biophysics, and biochemistry. Specific projects underway include the estimation of the bioenergetic costs of genes and various cellular parts, and the evolution of multimeric protein structure.
Publications: 
  • Kucukyildirim, S., H. Long, W. Sung, S. F. Miller, T. G. Doak, and M. Lynch. 2016. The rate and spectrum of spontaneous mutations in Mycobacterium smegmatis, a bacterium naturally devoid of the post-replicative mismatch repair pathway. G3: Genes|Genomes|Genetics 6: 2157-2163.

     

    Sung, W., M. S. Ackerman, M. Dillon, T. Platt, C. Fuqua, V. Cooper, and M. Lynch. 2016. Evolution of the insertion-deletion mutation rate across the tree of life. G3: Genes|Genomes|Genetics 6: 2583-2591.

     

    Lynch, M., M. Ackerman, J.-F. Gout, H. Long, W. Sung, W. K. Thomas, and P. L. Foster. 2016. Genetic drift, selection, and evolution of the mutation rate. Nature Rev. Genetics 17: 704-714.

     

    Lynch, M. 2016. Mutation, eugenics, and the boundaries of science. Genetics 204: 825-827.

     

    Raborn, R. T., K. Spitze, V. P. Brendel, and M. Lynch. 2016. An atlas of promoters in the Daphnia genome revealed by comprehensive mapping of 5'-mRNA ends. Genetics 204: 593-612.

     

    Long, H., M. G. Behringer, E. Williams, R. Te, and M. Lynch. 2016. Similar mutation rates but highly diverse mutation spectra in ascomycete and basidiomycete yeasts. Genome Biol. Evol. 8: 3815-3821.

     

    Long, H., D. J. Winter, A. Y.-C. Chang, W. Sung, S. H. Wu, M. Balboa, R. B. R. Azevedo, R. A. Cartwright, M. Lynch, and R. A. Zufall. 2016. Low base-substitution mutation rate in the germline genome of the ciliate Tetrahymena thermophila. Genome Biol. Evol. 8: 3629-3639.

     

    Dillon, M. M., W. Sung, M. Lynch, R. Sebra, and V. S. Cooper. 2017. Genome-wide biases in the rate and molecular spectrum of spontaneous mutations in Vibrio cholera and Vibrio fischeri. Mol. Biol. Evol. 34: 93-109.

     

    Lynch, M., and G. K. Marinov. 2017. Membranes, energetics, and evolution across the prokaryote-eukaryote divide. eLife 6: e20437.

     

    Jiang, X., H. Tang, Z. Ye, and M. Lynch. 2017. Insertion polymorphisms of mobile elements in sexual and asexual populations of Daphnia pulex. Genome Biol. Evol. 9: 362-374.

     

    Johri, P., S. Krenek, G. K. Marinov, T. G. Doak, T. Berendonk, and M. Lynch. 2017. Population genomics of Paramecium species. Mol. Biol. Evol. 34: 1194-1216.

     

    Bright, L. J., J.-F. Gout, and M. Lynch. 2017. Early stages of functional diversification in the Rab GTPase gene family revealed by genomic and functional studies in Paramecium species. Mol. Biol. Cell 28: 1101-1110.

     

    Lynch, M., M. Ackerman, K. Spitze, Z. Ye, and T. Maruki. 2017. Population genomics of Daphnia pulex. Genetics 206: 315-332.

     

    Ackerman, M. S., P. Johri, K. Spitze, S. Xu, T. Doak, K. Young, and M. Lynch. 2017. Estimating coefficients of pairwise relatedness using population-genomic data. Genetics 206: 105-118.

     

    Maruki, T., and M. Lynch. 2017. Genotype calling from population-genomic sequencing data. G3: Genes|Genomes|Genetics 7: 1393-1404.

     

    Ye, Z., S. Xu, K. Spitze, J. Asselman, X. Jiang, M. S. Ackerman, J. Lopez, B. Harker, R. T. Raborn, M. E. Pfrender, and M. Lynch. 2017. Comparative genomics of the Daphnia pulex species complex. G3: Genes|Genomes|Genetics 7: 1405-1416.

     

    Sun, Y., K. E. Powell, W. Sung, M. Lynch, M. A. Moran, and H. Luo. 2017. Spontaneous mutations of a model heterotrophic marine bacterium. ISME J. 11: 1713-1718.

     

    Strauss, C., H. Long, C. E. Patterson, R. Te, and M. Lynch. 2017. Genome-wide mutation rate response to pH change in the coral reef pathogen Vibrio shilonii AK1. MBio 8: e01021-17.

     

    Gout, J.-F., W. Li, C. Fritsch, A. Li, S. Haroon, L. Singh, D. Hua, H. Fazelinia, S. Seeholzer, M. Lynch, and M. Vermulst. 2017. The landscape of transcription errors in eukaryotic cells. Science Advances 3: e1701484.

     

    Tincher, C., H. Long, M. G. Behringer, N. Walker, and M. Lynch. 2017. The glyphosate-based herbicide Roundup® does not elevate genome-wide mutagenesis of Escherichia coli. G3: Genes|Genomes|Genetics 7: 3331-3335.

     

    Marasco, M., W. Li, M. Lynch, and C. S. Pikaard. 2017. Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation, and rNTP/dNTP discrimination. Nucleic Acids Res. 45: 11315-11326.

     

    Long, H., W. Sung, S. Kucukyildirim, E. Williams, S., W. Guo, C. Patterson, C. Gregory, C. Strauss, C. Stone, C. Berne, D. Kysela, W. R. Shoemaker, M. Muscarella, H. Luo, J. T. Lennon, Y. V. Brun, and M. Lynch. 2017. Evolutionary determinants of genome-wide nucleotide composition. Nature Ecol. Evol. 2: 237-240.

     

    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. Macias 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. The celibate genome of the Amazon molly, Poecilia formosa. Nature Ecol. Evol. 2: 669-679.

     

    Senra, M. V. X., W. Sung, M. Ackerman, S. F. Miller, V. F. Vizzoni, M. Lynch, and C. A. G. Soares. 2018. An unbiased genome-wide view of the mutation rate and spectrum of the endosymbiotic bacterium Teredinibacter turnerae. Genome Biol. Evol. 10: 723-730.

     

    Lynch, M. 2018. Phylogenetic diversification of cell biological features. eLife 7: e34820.

     

    Bright, L. J., and M. Lynch. 2018. The Rab7 subfamily across Paramecium aurelia species: evidence of high conservation in sequence and function. Small GTPases. Aug 29: 1-9.

     

    Dillon, M., M. Lynch, and V. S. Cooper. 2018. Periodic variation of mutation rates in bacterial genomes associated with replication timing. mBio 9: e01371-18.

     

    Behringer, M. G., B. I. Choi, S. F. Miller, T. G. Doak, J. A. Karty, W. Guo, and M. Lynch. 2018. Escherichia coli cultures maintain stable subpopulation structure during long-term evolution. Proc. Natl. Acad. Sci. USA 115: E4642-E4650.

     

    Long, H., and M. Lynch. 2018. Specificity of the DNA mismatch repair system (MMR) and mutagenesis bias in bacteria. Mol. Biol. Evol. 35: 2414-2421.

     

    Jiang, X., H. Tang, and M. Lynch. 2018. A maximum-likelihood approach to estimating the insertion frequencies of transposable elements from population sequencing data. Mol. Biol. Evol. 35: 2560-2571.

     

    Long, H., T. G. Doak, and M. Lynch. 2018. Limited mutation rate variation within the Paramecium aurelia species complex. G3: Genes|Genomes|Genetics 8: 2523-2526.

     

    McCully, A. L., M. G. Behringer, J. R. Gliessman, E. V. Pilipenko, J. L. Mazny, M. Lynch, D. A. Drummond, J. B. McKinlay. 2018. An Escherichia coli nitrogen starvation response is important for mutualistic coexistence with Rhodopseudomonas palustris. Appl. Environ. Microbiol. 84: e00404-18.

     

    Lynch, M., and G. K. Marinov. 2018. Reply to Martin and colleagues: mitochondria do not boost the bioenergetic capacity of eukaryotic cells.  Biology Direct 13: 26.

     

    Hagner, K., S. Setayeshgar, and M. Lynch. 2018. Stochastic protein multimerization, activity, and fitness. Phys. Rev. E 98: 062401.

     

    Jensen, J. D., B. A. Payseur, W. Stephan, C. F. Aquadro, M. Lynch, D. Charlesworth, and B. Charlesworth. 2019. The importance of the neutral theory in 1968 and 50 years on: a response to Kern & Hahn 2018. Evolution 73: 111-114.

     

    Lynch, M. 2019. Joseph Shapiro, an icon of applied limnology. Limnol. Oceanogr. 28: 35-37.

     

    Zabel, W. J., K. P. Hagner, B. J. Livesey, J. A. Marsh, S. Setayeshgar, M. Lynch, and P. G. Higgs. 2019. Evolution of protein interfaces in multimers and fibrils. J. Chem. Physics 150: 225102.

     

    Johri, P., G. K. Marinov, T. G. Doak, and M. Lynch. 2019. Population genetics of Paramecium mitochondrial genomes: recombination, mutation spectrum, and efficacy of selection. Genome Biol. Evol. 11: 1398-1416.

     

    Ye, Z., C. Molinier, C. Zhao, C. R. Haag, and M. Lynch. 2019. Genetic control of male production in Daphnia pulex Proc. Natl. Acad. Sci. USA 116: 15602-15609.

     

    Lynch, M., B. Haubold, P. Pfaffelhuber, and T. Maruki. 2020. Inference of historical population-size changes with allele-frequency data. G3 (Bethesda) 10: 211-223.

     

    Lynch, M., and B. Trickovic.  2020. A theoretical framework for evolutionary cell biology. J. Mol. Biol. 432: 1861-1879.

     

    Lynch, M., and W.-C. Ho. 2020. The limits to estimating population-genetic parameters with temporal data. Genome Biol. Evol. 12: 443-455.

     

    Jensen, J. D., and M. Lynch. 2020. Considering mutational meltdown as a potential SARS-CoV-2 treatment strategy. Heredity 124: 619-620.

     

    Lynch, M. 2020. The evolutionary scaling of cellular traits imposed by the drift barrier. Proc. Natl. Acad. Sci. USA 117: 10435-10444.

     

    Li, W., and M. Lynch. 2020. Universally high transcript error rates in bacteria. eLife 9: e54898.

     

    Fritts, R. K., J. T. Bird, M. G. Behringer, A. Lipzen, J. Martin, M. Lynch, and J. B. McKinlay. 2020. Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community. ISME J. 14: 2816-2828.

     

    Kucukyildirim, S., M. Behringer, E. M. Williams, T. G. Doak, and M. Lynch. 2020. Estimation of the genome-wide mutation rate and spectrum in the archaeal species Haloferax volcanii. Genetics 215: 1107-1116.

     

    Kucukyildirim, S., W. Sung, M. Behringer, D. A. Brocke, T. G. Doak, H. Mergenb, D. C. Queller, J. E. Strassmann, and M. Lynch. 2020. Low base-substitution mutation rate but high rate of slippage mutations in the sequence repeat-rich genome of Dictyostelium discoideum. G3 (Bethesda) 10: 3445-3452.

     

    Nguyen, D. T., B. Wu, H. Long, N. Zhang, C. Patterson, S. Simpson, K. Morris, W. K. Thomas, M. Lynch, and W. Hao. 2020. Variable spontaneous mutation and loss of heterozygosity among heterozygous genomes in yeast. Mol. Biol. Evol. 37: 3118-3130.

     

    Pan, J., E. Williams, W. Sung, M. Lynch, and H. Long. 2020. The insect-killing bacterium Photorhabdus luminescens has one of the lowest mutation rates among bacteria. Marine Life Sci. Tech. 3: 20-27.

     

    Jensen, J. D., R. A. Stikeleather, T. F. Kowalik, and M. Lynch. 2020. Imposed mutational meltdown as an antiviral strategy. Evolution 12: 2549-2559.

     

    Frisch, C., J.-F. Gout, S. Haroon, A. Towheed, X. Zhang, Y. Song, S. Simpson, D. Wallace, K. Thomas, M. Lynch, and M. Vermulst. 2020. Genome-wide surveillance of transcription errors in response to genotoxic stress. Proc. Natl. Acad. Sci. USA 118: e2004077118.

     

    Zheng, W., C. Wang, M. Lynch, and S. Gao. 2021. The compact macronuclear genome of the ciliate Halteria grandinella: a transcriptome-like genome with 29,000 nanochromosomes. mBio 12: e01964-20.

     

    Yang, X., M. Heinemann, J. Howard, G. Huber, S. Iyer-Biswas, G. Le Treut, M. Lynch, K. L. Montooth, D. J. Needleman, S. Pigolotti, J. Rodenfels, P. Ronceray, S. Shankar, I. Tavassoly, S. Thutupalli, D. V. Titov, J. Wang, and P. J. Foster. 2021. Physical bioenergetics: energy fluxes, budgets, and constraints in cells. Proc. Natl. Acad. Sci. USA 118: e2026786118.

     

    Ye, Z., E. Williams, C. Zhao, C. W. Burns, and M. Lynch. 2021. The rapid, mass invasion of New Zealand by North American Daphnia pulex/pulicaria. Limnol. Oceanogr. 66: 2672-2683.

     

    Kucukyildirim, S., S. F. Miller, and M. Lynch. 2021. Low base-substitution mutation rate and predominance of insertion-deletion events in the acidophilic bacterium Acidobacterium capsulatum. Ecol. Evol. 11: 17609-17614.

     

    Keith, N., C. E. Jackson, K. Young, S. P. Glaholt, M. Lynch, and J. R. Shaw. 2021. Genome-wide analysis of cadmium-induced, germline mutations in a long-term Daphnia pulex mutation-accumulation experiment over 1,123 generations. Env. Health Perspectives 129: 107003.

     

    Johri, P., B. Charlesworth, E. Howell, M. Lynch, and J. Jensen. 2021. Revisiting the notion of deleterious sweeps. Genetics 219: iyab094.

           

    Wu, K., Z.-H. Cheng, E. Williams, N. T. Turner, D. Ran, H. Li, X. Zhou, H. Guo, W. Sung, D.-F. Liu, M. Lynch, and H. Long. 2021. Unexpected discovery of hypermutator phenotype sounds the alarm for quality control strains. Genome Biol. Evol. 13: evab148.

     

    Ye, Z., X. Jiang, M. E. Pfrender, and M. Lynch. 2021. Genome-wide allele-specific expression in obligately asexual Daphnia pulex and the implications for the genetic basis of asexuality. Genome Biol. Evol. (in press).

     

    Ho, W.-C., M. G. Behringer, S. F. Miller, J. Gonzales, A. Nguyen, M. Allahwerdy, G. F. Boyer, and M. Lynch. 2021. Evolutionary dynamics of asexual hypermutators adapting to a novel environment. Genome Biol. Evol. 13: evab243.

     

    Johri, J., J.-F. Gout, T. G. Doak, and M. Lynch. 2022. A population-genetic lens into the process of gene loss following whole-genome duplication. Mol. Biol. Evol. (in press).

     

    Ye, Z., C. Zhao, R. T. Raborn, M. Lin, W. Wei, Y. Hao, and M. Lynch. 2022. Genetic diversity, heteroplasmy, and recombination in mitochondrial genomes in Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Mol. Biol. Evol. (in press).

     

    Lynch, M., P. Schavemaker, T. Licknack, and Y. Hao, and A. Pezzano. 2022. Evolutionary bioenergetics of ciliates. J. Euk. Microbiol. (in review).

     

    Maruki, T., Z. Ye, and M. Lynch. 2022. The population genomics of a subdivided species. Mol. Biol. Evol. (in revision).

     

    Lynch, M., Z. Ye, T. Maruki, and X. Wang. 2022. The linkage-disequilibrium and recombinational landscape in Daphnia pulex. Genome Biol. Evol. (in revision).

     

    Lynch, M. 2022. Molecular coevolutionary drive. (submitted).

     

    Lynch, M., B. Trickovic, and C. P. Kempes. 2022. Evolutionary scaling of maximum growth rates with organism size. (submitted).

     

    Behringer, M. G., W.-C. Ho, S. Miller, J. Meraz, G. Boyer, C. Stone, M. Andersen, and M. Lynch. 2022. Complex ecotype dynamics evolve in response to fluctuating resources. (submitted).

     

    Gout, J.-F., P. Johri, O. Arnaiz, T. G. Doak, A. Couloux, K. Labadie, F. Guérin, S. Duharcourt, S. Malinsky, S. Bhullar, E. Meyer, L. Sperling, and M. Lynch. 2022. Universal trends of post-duplication evolution revealed by the genomes of 14 Paramecium species sharing an ancestral whole-genome duplication. (submitted).

     

    Mahmoudabadi, G., R. Phillips, M. Lynch, and R. Milo. 2021. Defining the energetic costs of cellular structures. (submitted).

Summer 2022
Course NumberCourse Title
BDE 792Research
Spring 2022
Course NumberCourse Title
BIO 494Special Topics
MIC 495Undergraduate Research
MBB 495Undergraduate Research
BIO 495Undergraduate Research
BIO 598Special Topics
BDE 792Research
BDE 795Continuing Registration
BDE 799Dissertation
Fall 2021
Course NumberCourse Title
BIO 492Honors Directed Study
MBB 495Undergraduate Research
BIO 495Undergraduate Research
BDE 792Research
BDE 799Dissertation
Summer 2021
Course NumberCourse Title
BDE 792Research
Spring 2021
Course NumberCourse Title
BIO 495Undergraduate Research
BDE 792Research
BDE 799Dissertation
Fall 2020
Course NumberCourse Title
BIO 492Honors Directed Study
MBB 495Undergraduate Research
BIO 495Undergraduate Research
BDE 792Research
BDE 799Dissertation
Summer 2020
Course NumberCourse Title
BDE 792Research
Spring 2020
Course NumberCourse Title
BIO 493Honors Thesis
BIO 495Undergraduate Research
BDE 792Research
BDE 799Dissertation
Fall 2019
Course NumberCourse Title
BIO 492Honors Directed Study
BIO 493Honors Thesis
BIO 495Undergraduate Research
BDE 792Research
BDE 799Dissertation
Spring 2019
Course NumberCourse Title
BIO 492Honors Directed Study
MBB 495Undergraduate Research
BIO 495Undergraduate Research
BDE 792Research
BDE 799Dissertation
Fall 2018
Course NumberCourse Title
BIO 495Undergraduate Research
Spring 2018
Course NumberCourse Title
BIO 495Undergraduate Research