PUBLICATIONS
2021
Lynch, M., Z. Ye, and T. Maruki. 2021. The recombinational landscape in Daphnia pulex. bioRxiv. PDF DOI
Maruki, T., Z. Ye, and M. Lynch. 2021. The population genomics of a subdivided species. bioRxiv.
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. 2021 Universal trends of post-duplication evolution revealed by the genomes of 14 Paramecium species sharing an ancestral whole-genome duplication. bioRxiv. PDF DOI
Behringer, M. G., W.-C. Ho, S. Miller, J. Meraz, G. Boyer, and M. Lynch. 2021. Distinct phenotypic and genotypic responses to long-term fluctuations in resource availability. Mol. Biol. Evol. (submitted).
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. mBio (submitted).
Mahmoudabadi, G., R. Phillips, M. Lynch, and R. Milo. 2021. Defining the energetic costs of cellular structures. Curr. Biol. (submitted). PDF DOI
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 over 1,123 generations. Genome Research (in revision).
Lynch, M., W.-C. Ho, and C. P. Kempes. 2021. Evolutionary scaling of maximum growth rates with the drift barrier. Nature Ecol. Evol. (in revision).
Johri, P., B. Charlesworth, E. Howell, M. Lynch, and J. Jensen. 2021. Revisiting the notion of deleterious sweeps. Genetics (submitted). PDF DOI
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. (in press). PDF DOI
2020
Zheng, W., C. Wang, M. Lynch, and S. Gao. 2020. The compact macronuclear genome of the ciliate Halteria grandinella: a transcriptome-like genome with 29,000 nanochromosomes. mBio (in press).
Jensen, J. D., R. A. Stikeleather, T. F. Kowalik, and M. Lynch. 2020. Imposed mutational meltdown as an antiviral strategy. Evolution (in press). PDF DOI
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 (in press). PDF DOI
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. doi.org/10.1007/s42995-020-00060-0. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
Li, W., and M. Lynch. 2020. Universally high transcript error rates in bacteria. Elife 9: e54898. PDF DOI
Lynch, M. 2020. The evolutionary scaling of cellular traits imposed by the drift barrier. Proc. Natl. Acad. Sci. USA 117: 10435-10444. PDF DOI
Jensen, J. D., and M. Lynch. 2020. Considering mutational meltdown as a potential SARS-CoV-2 treatment strategy. Heredity 124: 619-620. PDF DOI
Lynch, M., and W.-C. Ho. 2020. The limits to estimating population-genetic parameters with temporal data. Genome Biol. Evol. 12: 443-455. PDF DOI
Lynch, M., and B. Trickovic. 2020. A theoretical framework for evolutionary cell biology. J. Mol. Biol.432: 1861-1879. PDF DOI
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. PDF DOI
2019
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. PDF DOI
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. PDF DOI
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. PDF DOI
Lynch, M. 2019. Joseph Shapiro, an icon of applied limnology. Limnol. Oceanogr. 28: 35-37. PDF DOI
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. PDF DOI
2018
Hagner, K., S. Setayeshgar, and M. Lynch. 2018. Stochastic protein multimerization, activity, and fitness. Phys. Rev. E 98: 062401. PDF DOI
Lynch, M., and G. K. Marinov. 2018. Response to Martin and colleagues: mitochondria do not boost the bioenergetic capacity of eukaryotic cells. Biology Direct 13: 26. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
Lynch, M. 2018. Phylogenetic diversification of cell biological features. Elife 7: e34820. PDF DOI
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. PDF DOI
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. PDF DOI
2017
Lynch, M., and G. K. Marinov. 2017. Membranes, energetics, and evolution across the prokaryote-eukaryote divide. ELife 6: e20437. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
Lynch, M., M. Ackerman, K. Spitze, Z. Ye, and T. Maruki. 2017. Population genomics of Daphnia pulex. Genetics 206: 315-332. PDF DOI
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. PDF DOI
Maruki, T., and M. Lynch. 2017. Genotype calling from population-genomic sequencing data. G3: Genes|Genomes|Genetics 7: 1393-1404. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
2016
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. PDF DOI
Lynch, M. 2016. Mutation, eugenics, and the boundaries of science. Genetics 204: 825-827. PDF DOI
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. PDF DOI
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. PDF DOI
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. PDF DOI
Long, H., S. F. Miller, C. Strauss, C. Zhao, L. Cheng, Z. Ye, K. Griffin, R. Te, H. Lee, C. C. Chen, and M. Lynch. 2016. Antibiotic treatment enhances the genome-wide mutation rate of target cells. Proc. Natl. Acad. Sci. USA 113: E2498-E2505. PDF DOI
Oughton, D., C. Mays, L. W. Barnthouse, J. C. Beasley, A. Bonisoli-Alquati, C. Bradshaw, J. Brown, S. Dray, S. Geras'kin, T. Glenn, K. Higley, K. Ishida, L. A Kapustka, W. Kuhne, M. Lynch, T. Mappes, S. Mihok, A. P. Møller, C. Mothersill, T. A Mousseau, J. Otaki, E. Pryakhin, O. E Rhodes, Jr., B. Salbu, and P. Strand. 2016. Addressing ecological effects of radiation on populations and ecosystems to improve protection of the environment against radiation: Agreed statements from a consensus symposium. J. Environ. Radioactivity 158/159: 21-29. PDF DOI
Marinov, G. K., and M. Lynch. 2016. Conservation and divergence of the histone code in nucleomorphs. Biol. Direct 11: 18. PDF DOI
Lynch, M. 2016. Mutation and human exceptionalism: our future genetic load. Genetics 202: 869-875. PDF DOI
Lynch, M., and G. K. Marinov. 2016. Reply to Lane and Martin: Mitochondria do not boost the bioenergetic capacity of eukaryotic cells. Proc. Natl. Acad. Sci. USA 113: E667-E668. PDF DOI
Keith, N., A. E. Tucker, C. E. Jackson, W. Sung, J. I. Lucas-Lledó, D. Schrider, S. Schaack, J. L. Dudycha, and M. Lynch. 2016. High mutational rates of large-scale duplication and deletion in Daphnia pulex. Genome Res. 26: 60-69. PDF DOI
2015
Marinov, G. K., and M. Lynch. 2015. Diversity and divergence of dinoflagellate histone proteins. G3: Genes|Genomes|Genetics 6: 397-422. PDF DOI
Lynch, M., and G. K. Marinov. 2015. The bioenergetic costs of a gene. Proc. Natl. Acad. Sci. USA 112: 15690-15695. PDF DOI
Suzuki, H., A. Dapper, C. Jackson, H. Lee, V. Pejaver, T. Doak, M. Lynch, and J. Preer, Jr. 2015. Draft genome sequence of Caedibacter varicaedens, a Kappa killer endosymbiont bacterium of the ciliate Paramecium biaurelia. Genome Announcements 3: 1-2. PDF DOI
Xu, S., K. Spitze, M. Ackerman, Z. Ye, L. Bright, R. Keith, C. Jackson, J. Shaw, and M. Lynch. 2015. Hybridization and the origin of contagious asexuality in Daphnia pulex. Mol. Biol. Evol. 32: 3215-3225. PDF DOI
Farlow, A., H. Long, S. Arnoux, W. Sung, T. G. Doak, C. Schlötterer, M. Nordborg, and M. Lynch. 2015. The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe. Genetics 201: 737-744. PDF DOI
Xu, S., M. S. Ackerman, H. Long, L. Bright, K. Spitze, J. S. Ramsdell, W. K. Thomas, and M. Lynch. 2015. A male-specific genetic map of the microcrustacean Daphnia pulex based on single sperm whole-genome sequencing. Genetics 201: 31-38. PDF DOI
Maruki, T., and M. Lynch. 2015. Genotype-frequency estimation from high-throughput sequencing data. Genetics 201: 473-486. PDF DOI
Long, H., S. Kucukyildirim, W. Sung, E. Williams, M. Ackerman, T. G. Doak, and M. Lynch. 2015. Background mutational features of the radiation-resistant bacterium Deinococcus radiodurans. Mol. Biol. Evol. 32: 2383-2392. PDF DOI
Dillon, M. M., W. Sung, M. Lynch, and V. S. Cooper. 2015. The rate and molecular spectrum of spontaneous mutations in the GC-rich multi-chromosome genome of Burkholderia cenocepacia. Genetics 200: 935-946. PDF DOI
Long, H., W. Sung, S. F. Miller, M. S. Ackerman, T. G. Doak, and M. Lynch. 2015. Mutation rate, spectrum, topology and context-dependency in the DNA mismatch repair (MMR) deficient isolate Pseudomonas fluorescens Migula ATCC948. Genome Biol. Evol. 7: 262-271. PDF DOI
2014
Lynch, M., and K. Hagner. 2014. Evolutionary meandering of intermolecular interactions along the drift barrier. Proc. Natl. Acad. Sci. USA 112: E30-E38. PDF DOI
Sazer, S., M. Lynch, and D. Needleman. 2014. Deciphering the evolutionary history of open and closed mitosis. Curr. Biol. 24: R1099-R1103. PDF DOI
Lynch, M., M. C. Field, H. Goodson, H. S. Malik, J. B. Pereira-Leal, D. S. Roos, A. Turkewitz, and S. Sazer. 2014. Evolutionary cell biology: two origins, one objective. Proc. Natl. Acad. Sci. USA 111: 16990-16994. PDF DOI
Li, W., R. Kuzoff, K. W. Chen, A. Tucker, and M. Lynch. 2014. Characterization of newly gained introns in Daphnia populations. Genome Biol. Evol. 6: 2218-2234. PDF DOI
Lynch, M., S. Xu, T. Maruki, P. Pfaffelhuber, and B. Haubold. 2014. Genome-wide linkage-disequilibrium profiles from single individuals. Genetics 198: 269-281. PDF DOI
McGrath, C. L., J. F. Gout, P. Johri, T. G. Doak, and M. Lynch. 2014. Differential retention and divergent resolution of duplicate genes following whole-genome duplication. Genome Research 24: 1665-1675. PDF DOI
McGrath, C. L., J. F. Gout, T. G. Doak, A. Yanagi, and M. Lynch. 2014. Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. Genetics 197: 1417-1428. PDF DOI
Lynch, M., D. Bost, S. Wilson, and T. Maruki. 2014. Population-genetic inference from pooled-sequencing data. Genome Biol. Evol. 6: 1210-1218. PDF DOI
2013
Maruki, T., and M. Lynch. 2013. Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data. Genetics 197: 1303-1313. PDF DOI
Boscaro, V., M. Felletti, C. Vannini, M. S. Ackerman, P. S. G. Chain, S. Malfatti, L. M. Vergez, M. Shin, T. G. Doak, M. Lynch, and G. Petroni. 2013. Polynucleobacter necessarius, a new model for genome reduction in both free-living and symbiotic bacteria. Proc. Natl. Acad. Sci. USA 110: 18590-18595. PDF DOI
Gout, J. F., W. K. Thomas, Z. Smith, K. Okamoto, and M. Lynch. 2013. Large-scale detection of in vivo transcription errors. Proc. Natl. Acad. Sci. USA. PDF DOI
Tucker, A., M. Ackerman, B. Eads, S. Xu, and M. Lynch. 2013. Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex. Proc. Natl. Acad. Sci. USA 110: 15740-15745. PDF DOI
Xu, S., D. J. Innes, M. Lynch, and M. E. Cristescu. 2013. The role of hybridization in the origin and spread of asexuality in Daphnia. Mol. Ecol. 22: 4549-4561. PDF DOI
Schrider, D., D. Houle, M. Lynch, and M. Hahn. 2013. Genetic variation in the mutation rate in Drosophila melanogaster. Genetics 194: 937-954. PDF DOI
Raymann, K., L. M. Bobay, T. G. Doak, M. Lynch, and S. Gribaldo. 2013. A genomic survey of Reb homologs suggests widespread occurrence of R-bodies in proteobacteria. G3 (Bethesda) 3: 505-516. PDF DOI
Catania, F., and M. Lynch. 2013. A simple model to explain evolutionary trends of eukaryotic gene architecture and expression: how competition between splicing and leavage/polyadenylation factors may affect gene expression and splice-site recognition in eukaryotes. Bioessays 35: 561-570. PDF DOI
Lynch, M. 2013. Evolutionary diversification of the multimeric states of proteins. Proc. Natl. Acad. Sci. USA 110: E2821-E2828. PDF DOI
Sung, W., M. S. Ackerman, S. F. Miller, T. G. Doak, and M. Lynch. 2013. Reply to Massey: Drift does influence mutation-rate evolution. Proc. Natl. Acad. Sci. USA 110: E860. PDF DOI
Ibarra-Laclette, E., E. Lyons, G. Hernández-Guzmán, C. A. Pérez-Torres, L. Carretero-Paulet, T. H. Chang, T. Lan, A. J. Welch, M. J. Juárez, J. Simpson, A. Fernández-Cortés, M. Arteaga-Vázquez, E. Góngora-Castillo, G. Acevedo-Hernández, S. C. Schuster, H. Himmelbauer, A. E. Minoche, S. Xu, M. Lynch, A. Oropeza-Aburto, S. A. Cervantes-Pérez, M. de Jesús Ortega-Estrada, J. I. Cervantes-Luevano, T. P. Michael, T. Mockler, D. Bryant, A. Herrera-Estrella, V. A. Albert, and L. Herrera-Estrella. 2013. Architecture and evolution of a minute plant genome. Nature 498: 94-98. PDF DOI
Catania, F., C. L. McGrath, T. G. Doak, and M. Lynch. 2013. Spliced DNA sequences in the Paramecium germline: their properties and evolutionary potential. Genome Biol. Evol. 5: 1200-1211. PDF DOI
Schaack, S., D. E. Allen, L. C. Latta, K. K. Morgan, and M. Lynch. 2013. The effect of spontaneous mutations on competitive ability. J. Evol. Biol. 26: 451-456. PDF DOI
Latta, L. C., K. K. Morgan, C. S. Weaver, D. Allen, S. Schaack, and M. Lynch. 2013. Genomic background and generation time influence deleterious mutation rates in Daphnia. Genetics 193: 539-544. PDF DOI
2012
Lynch, M. 2012. Evolutionary layering and the limits to cellular perfection. Proc. Natl. Acad. Sci. USA 109: 18851-18856. PDF DOI
Sung, W., M. S. Ackerman, S. F. Miller, T. G. Doak, and M. Lynch. 2012. The drift-barrier hypothesis and mutation-rate evolution. Proc. Natl. Acad. Sci. USA 109: 18488-18492. PDF DOI
Sung, W., A. Tucker, T. G. Doak, J. Choi, W. K. Thomas, and M. Lynch. 2012. Extraordinary genome stability in the ciliate Paramecium tetraurelia. Proc. Natl. Acad. Sci. USA 109: 19339-19344. PDF DOI
Allen, D. E., and M. Lynch. 2012. The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen. Evolution 66: 919-926. PDF DOI
Lynch, M. 2012. The evolution of multimeric protein assemblages. Mol. Biol. Evol. 29: 1353-1366. PDF DOI
2011
2010
Sung, W., A. Tucker, R. D. Bergeron, M. Lynch, and W. K. Thomas. 2010. Simple sequence repeat variation in the Daphnia pulex genome. BMC Genomics 11: 691. PDF DOI
Lynch, M. 2010. Scaling expectations for the time to establishment of complex adaptations. Proc. Natl. Acad. Sci. USA 107: 16577-16582. PDF DOI
Schaack, S., E. J. Pritham, A. Wolf, and M. Lynch. 2010. DNA transposon dynamics in populations of Daphnia pulex with and without sex. Proc. R. Soc. Lond. B 277: 2381-2387. PDF DOI
Rho, M., S. Schaack, X. Gao, S. Kim, M. Lynch, and H. Tang. 2010. LTR retroelements in the genome of Daphnia pulex. BMC Genomics 11: 425. PDF DOI
Catania, F., and M. Lynch. 2010. Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium. BMC Evol. Biol. 10: 129. PDF DOI
Lynch, M. 2010. Evolution of the mutation rate. Trends in Genetics 26: 345-352. PDF DOI
Gleick, P. H., et al. 2010. Climate change and the integrity of science. Science 328: 689-690. PDF DOI
Haubold, B., P. Pfaffelhuber, and M. Lynch. 2010. mlDiv - A program for estimating the population mutation and recombination rates from shotgun-sequenced genomes. Molecular Ecology 19, Suppl. 1: 277-284. PDF DOI
Schaack, S., E. Choi, M. Lynch, and E. J Pritham. 2010. DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex. Genome Biology 11: R46. PDF DOI
Ossowski, S., K. Schneeberger, J. Lucas-Lledó, N. Warthmann, R. M. Clark, R. G. Shaw, D. Weigel, and M. Lynch. 2010. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94. PDF DOI
2009
Gao, X., and M. Lynch. 2009. Ubiquitous internal gene duplication and intron creation in eukaryotes. Proc. Natl. Acad. Sci. USA 106: 20818-20823. PDF DOI
Denver, D. D., P. C. Dolan, L. J. Wilhelm, W. Sung, J. I. Lucas-Lledó, D. K. Howe, S. C. Lewis, K. Okamoto, M. Lynch, W. K. Thomas, and C. F. Baer. 2009. A genome-wide view of Caenorhabditis elegans base-substitution mutation processes. Proc. Natl. Acad. Sci. USA 106: 16310-16314. PDF DOI
Rho, M., M. Zhou, X. Gao, S. Kim, H. Tang, and M. Lynch. 2009. Parallel mammalian genome contractions following the KT boundary. Genome Biology and Evolution 2009: 2-12. PDF DOI
Lynch, M. 2009. Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics 182: 295-301. PDF DOI
Omilian, A. R., and M. Lynch. 2009. Patterns of intraspecific DNA variation in the Daphnia nuclear genome. Genetics 182: 325-336. PDF DOI
Penalva-Arana, D. C., M. Lynch, and H. M. Robertson. 2009. The chemoreceptor genes of the waterflea Daphnia pulex: many Grs but no Ors. BMC Evol. Biol. 9:79. PDF DOI
Catania, F., F. Wurmser, A. A. Potekhin, E. Przybo, and M. Lynch. 2009. Genetic diversity in the Paramecium aurelia complex. Mol. Biol. Evol. 26: 421-431. PDF DOI
2008
Lynch, M. 2008. The cellular, developmental, and population-genetic determinants of mutation-rate evolution. Genetics 180: 933-943. PDF DOI
Lynch, M. 2008. Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects. Mol. Biol. Evol. 25: 2421-2431. PDF DOI
Lynch, M., A. Seyfert, B. Eads, and E. Williams. 2008. Localization of the genetic determinants of meiosis suppression in Daphnia pulex. Genetics 180: 317-327. PDF DOI
Omilian, A. R., D. G. Scofield, and M. Lynch. 2008. Intron presence-absence polymorphisms in Daphnia. Mol. Biol. Evol. 25: 2129-2139. PDF DOI
Haag-Liautard, C., N. Coffey, D. Houle, M. Lynch, B. Charlesworth, and P. D. Keightley. 2008. Direct estimation of the mitochondrial DNA mutation rate in D. melanogaster. PLoS Biology 6: 1706-1714. PDF DOI
Allen, D. E., and M. Lynch. 2008. Both costs and benefits of sex correlate with relative frequency of asexual reproduction in cyclically parthenogenic Daphnia pulicaria populations. Genetics 179: 1497-1502. PDF DOI
Seyfert, A. L., M. E.A. Cristescu, L. Frisse, S. Schaack, W. K. Thomas, and M. Lynch. 2008. The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics 178: 2113-2121. PDF DOI
Lynch, M., W. Sung, K. Morris, N. Crown, C. R. Landry, E. B. Dopman, W. J. Dickinson, K. Okamoto, S. Kulkarni, D. L. Hartl, and W. K. Thomas. 2008. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc. Natl. Acad. Sci. USA 105: 9272-9277. PDF DOI
2007
Rho, M., J. H. Choi, S. Kim, M. Lynch, and H. Tang. 2007. De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics 8: 90. PDF DOI
Lynch, M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc. Natl. Acad. Sci. USA 104 Suppl.: 8597-8604. PDF DOI
Scofield, D. G., X. Hong, and M. Lynch. 2007. Position of the final intron in full-length transcripts: determined by NMD? Mol. Biol. Evol. 24: 896-899. PDF DOI
2006
Denver, D. R., S. Feinberg, C. Steding, M. Durbin, and M. Lynch. 2006. The relative roles of three DNA repair pathways in preventing Caenorhabditis elegans mutation accumulation. Genetics 174: 57-65. PDF DOI
Cristescu, M. E., J. K. Colbourne, J. Radivojac, and M. Lynch. 2006. A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: on the prospect of crustacean genomics. Genomics 88: 415-430. PDF DOI
Lynch, M., X. Hong, and D. G. Scofield. 2006. Nonsense-mediated decay and the evolution of eukaryotic gene structure, pp. 197-211. In L. E. Maquat (ed.) Nonsense-mediated mRNA Decay. Landes Bioscience, Georgetown, TX. PDF
2005
Lynch, M. 2005. Simple evolutionary pathways to complex proteins. Protein Science 14: 2217-2225. PDF DOI
Lynch, M. 2005. Intelligent design vs. intelligent evolution. Nature 435: 276. PDF DOI
Estes, S., Ajie, B. C., M. Lynch, and P. C. Phillips. 2005. Spontaneous mutational correlations for life-history, morphological, and behavioral characters in Caenorhabditis elegans. Genetics 170: 645-653. PDF DOI
Ajie, B. C., S. Estes, M. Lynch, and P. C. Phillips. 2005. Behavioral degradation under mutation accumulation. Genetics 170: 655-660. PDF DOI
Paland, S., J. K. Colbourne, and M. Lynch. 2005. Evolutionary history of contagious asexuality in Daphnia pulex. Evolution 59: 800-813. PDF DOI
Force, A., W. Cresko, F. B. Pickett, S. Proulx, C. Amemiya, and M. Lynch. 2005. The origin of gene subfunctions and modular gene regulation. Genetics 170: 433-446. PDF DOI
Colbourne, J. K., B. Robison, K. Bogart, and M. Lynch. 2005. Five hundred and twenty eight microsatellite markers for ecological genomic investigations using Daphnia. Mol. Ecol. Notes 4: 485-490. PDF DOI
Baer, C. F., F. Shaw, C. Steding, M. Baumgartner, A. Hawkins, A. Houppert, N. Mason, M. Reed, F. Shaw, K. Simonelic, W. Woodward, and M. Lynch. 2005. Comparative evolutionary genetics of spontaneous mutations affecting fitness in rhabditid nematodes. Proc. Natl. Acad. Sci. USA 102: 5785-5790. PDF DOI
Denver, D. R., S. Feinberg, S. Estes, W. K. Thomas, and M. Lynch. 2005. Mutation rates, spectra and hotspots in mismatch repair-deficient Caenorhabditis elegans. Genetics 170: 107-113. PDF DOI
Denver, D. R., K. Morris, J. T. Streelman, S. K. Kim, M. Lynch, and W. K. Thomas. 2005. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nature Genetics 37: 544-548. PDF DOI
2004
Estes, S., P. C. Phillips, D. R. Denver, W. K. Thomas, and M. Lynch. 2004. Mutation accumulation in populations of varying size: The distribution of mutational effects for fitness correlates in Caenorhabditis elegans. Genetics 166: 1269-1279. PDF DOI
Lynch, M. 2004. Gene duplication and evolution, pp. 33-47. In A. Moya and E. Font (eds.), Evolution: From Molecules to Ecosystems. Oxford University Press, New York, NY. PDF
2003
Estes, S., and M. Lynch. 2003. Rapid recovery of mutation-accumulation lines by compensatory mutation. Evolution 57: 1022-1030. PDF DOI
Baer, C. F., and M. Lynch. 2003. Correlated evolution of life-history with size at maturity in Daphnia pulicaria: patterns within and between populations. Genetical Research 81: 123-132. PDF DOI
Lynch, M., and A. Kewalramani. 2003. Messenger RNA processing and the evolutionary proliferation of introns. Mol. Biol. Evol. 20: 563-571. PDF DOI
Keightley, P. D., and M. Lynch. 2003. Towards a realistic model of mutations affecting fitness. Evolution 57: 683-685. PDF DOI
Lynch, M., and J. S. Conery. 2003. The evolutionary demography of duplicate genes, pp. 35-44. In A. Meyer and Y. Van de Peer (eds.), Genome Evolution. Kluwer Academic Publishers, Dordrecht. PDF DOI
2002
Azevedo, R. B. R., P. D. Keightley, C. Lauren-Maatta, L. L. Vassilieva, M. Lynch, and A. M. Leroi. 2002. Spontaneous mutational variation for body size in Caenorhabditis elegans. Genetics 162: 755-765. PDF DOI
Jackson, R. B., C. R. Linder, M. Lynch, M. Purugannan, and S. Somerville. 2002. Linking molecular insights and ecological research. Trends in Ecology and Evolution 17: 409-414. PDF DOI
2001
Morgan, K. K., J. Hicks, K. Spitze, L. Latta, M. Pfrender, C. Ottone, and M. Lynch. 2001. Patterns of genetic architecture for life-history traits and molecular markers in a subdivided species. Evolution 55: 1753-1761. PDF DOI
Higgins, K., and M. Lynch. 2001. Metapopulation extinction due to mutation accumulation. Proc. Natl. Acad. Sci. USA 98: 2928-2933. PDF DOI
Lynch, M., and J. S. Conery. 2001. Gene duplication and evolution: response to Long and Thornton and Zhang et al. Science 293: 1551a. PDF DOI
2000
Pfrender, M. E., and M. Lynch. 2000. Quantitative genetic variation in Daphnia: temporal changes in genetic architecture. Evolution 54: 1502-1509. PDF DOI
Denver, D., K. Morris, M. Lynch, L. L. Vassilieva, and W. K. Thomas. 2000. High direct estimate of the mutation rate in the mitochondrial genome of C. elegans. Science 289: 2342-2344. PDF DOI
1999
Schultz, S. T., M. Lynch, and J. H. Willis. 1999. Spontaneous deleterious mutation in Arabidopsis. Proc. Natl. Acad. Sci. USA 96: 11393-11398. PDF DOI
Lynch, M. 1999. Estimation of genetic correlations in natural populations. Genetical Research 74: 255-264. PDF DOI
Conery, J. S., and M. Lynch. 1999. Genetic simulation library. Bioinformatics 15: 85-86. PDF DOI
Lynch, M., J. Blanchard, D. Houle, T. Kibota, S. Schultz, L. Vassilieva, and J. Willis. 1999. Spontaneous deleterious mutation. Evolution 53: 645-663. PDF DOI
Force, A., M. Lynch, B. Pickett, A. Amores, Y.-L. Yan, and J. Postlethwait. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545. PDF DOI
Lynch, M. 1999. The age and relationships of the major animal phyla. Evolution 53: 319-325. PDF DOI
Lynch, M., and K. Ritland. 1999. Estimation of relatedness with molecular markers. Genetics 152: 1753-1766. PDF DOI
Lynch, M., M. Pfrender, K. Spitze, N. Lehman, D. Allen, J. Hicks, L. Latta, M. Ottene, F. Bogue, and J. Colbourne. 1999. The quantitative and molecular genetic architecture of subdivided species. Evolution 53: 100-110. PDF DOI
Vassilieva, L., and M. Lynch. 1999. Accumulation of spontaneous mutations in Caenorhabditis elegans. Genetics 151: 119-129. PDF DOI
1998
Lynch, M., L. Latta, J. Hicks, and M. Giorgianni. 1998. Mutation, selection, and the maintenance of life-history variation in a natural population. Evolution 52: 727-733. PDF DOI
Lynch, M., and R. Lande. 1998. The critical effective size for a genetically secure population. Anim. Cons. 1: 70-72. PDF DOI
Deng, H.-W., Y.-X. Fu, and Lynch, M. 1998. Inferring the major genomic mode of dominance and overdominance. Genetica 102/103: 559-567. PDF DOI
1997
Schultz, S. T., and M. Lynch. 1997. Deleterious mutation and extinction: effects of variable mutational effects, synergistic epistasis, beneficial mutations, and degree of outcrossing. Evolution 51: 1363-1371. PDF DOI
Lynch, M. 1997. Mutation accumulation in nuclear, organelle, and prokaryotic genomes: transfer RNA genes. Mol. Biol. Evol. 14: 914-925. PDF DOI
Deng, H.-W., and M. Lynch. 1997. Inbreeding depression and inferred deleterious mutation parameters in Daphnia. Genetics 147: 147-155. PDF DOI
Crease, T., S. K. Sung, S. L. Sung, N. Lehman, K. Spitze, and M. Lynch. 1997. Allozyme and mitochondrial DNA variation in populations of the Daphnia pulex complex from both sides of the Rocky Mountains. Heredity 79: 242-251. PDF DOI
1996
Houle, D., R. Morikawa, and M. Lynch. 1996. Comparing mutational variabilities. Genetics 143: 1467-1483. PDF DOI
Deng, H.-W., and M. Lynch. 1996. Estimation of deleterious-mutation parameters in natural populations. Genetics 144: 349-360. PDF DOI
Deng, H.-W., and M. Lynch. 1996. Change of genetic architecture in response to sex. Genetics 143: 203-212. PDF DOI
Lynch, M. 1996. Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes. Mol. Biol. Evol. 13: 209-220. PDF DOI
Lynch, M. 1996. A quantitative-genetic perspective on conservation issues, pp. 471-501. In J. Avise and J. Hamrick (eds.) Conservation Genetics: Case Histories from Nature. Chapman and Hall, New York. PDF
1995
Avise, J. C., S. M. Haig, O. A. Ryder, M. Lynch, and C. J. Geyer. 1995. Descriptive genetic studies: applications in population management and conservation biology, pp. 183-244. In J. D. Ballou, M. Gilpin, and T. J. Foose (eds.) Population Management for Survival and Recovery. Columbia Univ. Press, New York. PDF
1994
Lynch, M., and K. Spitze. 1994. Evolutionary genetics of Daphnia, pp. 109-128. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press. PDF
1993
Lynch, M., and R. Lande. 1993. Evolution and extinction in response to environmental change, pp. 234-250. In P. Kareiva, J. Kingsolver, and R. Huey (eds.) Biotic Interactions and Global Change. Sinauer Assocs., Inc. Sunderland, MA. PDF
1992
1991
Cohen, J. E., M. Lynch, and C. E. Taylor. 1991. Forensic DNA tests and Hardy-Weinberg equilibrium. Science 253: 1037. PDF DOI
Lynch, M., W. Gabriel, and A. M. Wood. 1991. The adaptive and demographic response of plankton populations to environmental change. Limnol. Oceanogr. 36: 1301-1312. PDF DOI
Spitze, K., J. Burnson, and M. Lynch. 1991. The covariance structure of life history characters in Daphnia pulex. Evolution 45: 1081-1090. PDF DOI
Crease, T. J., and M. Lynch. 1991. Ribosomal DNA variation in Daphnia pulex. Mol. Biol. Evol. 8: 620-640. PDF DOI
Lynch, M. 1991. Analysis of population genetic structure by DNA fingerprinting, pp. 113-126. In T. Burke, G. Dolf, A. J. Jeffreys, and R. Wolff (eds.) DNA Fingerprinting: Approaches and Applications. Birkhäuser Verlag, Basel. PDF
Lynch, M. 1991. The genetic interpretation of inbreeding depression and outbreeding depression. Evolution 45: 622-629. PDF DOI
Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45: 1065-1080. PDF DOI
Gabriel, W., R. Bürger, and M. Lynch. 1991. Population extinction by mutational load and demographic stochasticity, pp. 49-59. In A. Seitz, and V. Loeschcke (eds.) Species Conservation: a Population Biological Approach. Birkhäuser Verlag, Basel. PDF
1990
1989
1988
Lynch, M., and S. J. Arnold. 1988. Measurement of selection on size and growth, pp. 47-59. In L. Persson and B. Ebenman (eds.) The Dynamics of Size-structured Populations. Springer-Verlag. PDF
Lynch, M. 1988. Path analysis of ontogenetic data, pp. 29-46. In L. Persson and B. Ebenman (eds.) The Dynamics of Size-structured Populations. Springer-Verlag. PDF
1987
Lynch, M. 1987. The evolution of intrafamilial interactions. Proc. Natl. Acad. Sci. USA 84: 8507-8511. PDF DOI
Kerfoot, W. C., and M. Lynch. 1987. Branchiopod communities: associations with planktivorous fish in space and time, pp. 367-378. In W. C. Kerfoot and A. Sih (eds.) Predation. Univ. Press New England, Hanover, NH. PDF
Lynch, M., and W. Gabriel. 1987. Evolution of breadth of biochemical adaptation, pp. 67-83. In P. Calow (ed.) Evolutionary Physiological Ecology. Cambridge Univ. Press, Cambridge, UK. PDF
1986
Lynch, M., and W. G. Hill. 1986. Phenotypic evolution by neutral mutation. Evolution 40: 915-935. PDF DOI
Lynch, M. 1986. Random drift, uniform selection, and the degree of population differentiation. Evolution 40: 640-643. PDF DOI
Lynch, M., L. Weider, and W. Lampert. 1986. Measurement of the carbon balance in Daphnia. Limnol. Oceanogr. 31: 17-33. PDF DOI
1985
Lynch, M. 1985. Elements of a mechanistic theory for the life history consequences of food limitation. Ergeb. Limnol. 21: 351-362. PDF
1984
Lynch, M. 1984. The selective value of alleles underlying polygenic traits. Genetics 108: 1021-1033. PDF
Lynch, M. 1984. Destabilizing hybridization, general-purpose genotypes, and geographic parthenogenesis. Quarterly Review of Biology 59: 257-290. PDF
1983
Lynch, M., and W. Gabriel. 1983. Phenotypic evolution and parthenogenesis. American Naturalist 122: 745-764. PDF
Lynch, M. 1983. Estimation of size-specific mortality rates in zooplankton populations by periodic sampling. Limnol. Oceanogr. 28: 533-545. PDF
1982
1981
1980
Lynch, M. 1980. Aphanizomenon blooms: Alternate control and cultivation by Daphnia pulex. In W. C. Kerfoot (ed.) The Evolution and Ecology of Zooplankton Communities. American Society of Limnology and Oceanography Special Symposium No. 3: 299-304. PDF
Lynch, M. 1980. Predation, enrichment, and the evolution of cladoceran life histories: A theoretical approach. In W. C. Kerfoot (ed.) The Evolution and Ecology of Zoplankton Communities. American Society of Limnology and Oceanography Special Symposium No. 3: 367-376. PDF
Lynch, M. 1980. The evolution of cladoceran life histories. Quarterly Review of Biology 55: 23-42. PDF
1979
1978
1977
1975
Shapiro, J., V. Lamarra, and Lynch, M. 1975. Biomanipulation: An ecosystem approach to lake restoration, pp. 85-96. In P. L. Brezonik and J. L. Fox (eds.) Water Quality Management Through Biological Control. Proc. Symp. Univ. Florida. PDF
1974
Lynch, M. 1974. The phytoplankton of the Allegheny Reservoir from May 1972 to September 1973. Science Studies (St. Bonaventure University) 30: 5. PDF