Articles:
2024
Behringer, M. G., W.-C. Ho, S. F. Miller, S. B. Worthan, Z. Cen, R. Stikeleather, and M. Lynch. 2024. Trade-offs, trade-ups, and high mutational parallelism underly microbial adaptation to extreme feast/famine. Curr. Biol. 4: 1403-1413.e5. PDF
Zhang, Y., H. Li, Y. Wang, M. Nie, K. Zhang, J. Pan, Y. Zhang, Z. Ye, R. Zufall, M. Lynch, and H. Long. 2024. Mitogenomic architecture and evolution of the soil ciliates Colpoda. Msystems 9: e01161-23.. PDF
Li, H., K. Wu, Y. Feng, C. Gao, Y. Wang, Y. Zhang, J. Pan, X. Shen, R. Zufall, W. Zhang, J. Sun, Y. Zhang, Z. Ye, W. Li, M. Lynch, and H. Long. 2024. Integrative analyses on the ciliated protozoa Colpoda illuminate the life history evolution of soil microorganisms. Msystems e01379-23. PDF
Jiang, W., T. Lin, J. Pan, C. Rivera, C. Tincher, Y. Wang, Y. Zhang, X. Gao, Y. Wang, H. C. T. Tsui, M. E. Winkler, M. Lynch, and H. Long. 2024. Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39. Marine Life Science & Technology, 6: 198-211. PDF
Lynch, M., W. Wei, Z. Ye, and M. Pfrender. 2024. The genome-wide signature of short-term temporal selection. Proc. Nat. Acad. Sci. USA 121: e2307107121. PDF
Li, W., S. Baehr, M. Marasco, L. Reyes, D. Brister, C. S. Pikaard, J.-F. Gout, M. Vermulst, and M. Lynch. 2024. A narrow range of transcript-error rates across the Tree of Life. Nature Comm. (in revision).
Trickovic, B., and M. Lynch. 2024. Resource allocation to cell envelopes and the scaling of bacterial growth rate. (in revision for Physical Biology).
Zheng, W., C. Li, Z. Zhou, X. Chen, M. Lynch, and Y. Yan. 2024. Unveiling an ancient whole-genome duplication event in Stentor, the model unicellular eukaryote. (submitted).
Yu, M., T. Lin, J. Zhang, S. Diao; J. Yan, K. Zhangm, J. Cao, J. Huang, Y. Wang, Z. Lv, S. K. B. Sy, M. Lynch, and H. Long. 2024. The molecular mechanisms and resistance mutagenesis in the synergistic action of aztreonam and clavulanate against multidrug-resistant Escherichia coli. (submitted).
2023
Lynch, M., B. Trickovic, and C. P. Kempes. 2023. Evolutionary scaling of maximum growth rates with organism size. Scientific Reports 12: 22586. PDF
Kucukyildirim, S. H. Ozdemirel, and M. Lynch. 2023. Similar mutation rates but different mutation spectra in moderate and extremely halophilic archaea. G3 13: jkac303. PDF
Chung, C. B. M. Verheijen, X. Zhang, B. Huang, A. Coakley, E. McGann, E. Wade, O. Dinep-Schneider, J. LaGosh, M. Anagnostou, S. Simpson, K. Thomas, J. M. Ernst, A. Rattray, M. Lynch, M. Kashlev, B. A. Benayoun, Z. Li, J. Strathern, J-F. Gout, and M. Vermulst. 2023. The fidelity of transcription in human cells. Proc. Natl. Acad. Sci. USA 120: e2210038120. PDF
Wu, K., H. Li, Y. Wang, D. Liu, H. Li, Y. Zhang, M. Lynch, and H. Long. 2023. Silver nanoparticles elevate mutagenesis of eukaryotic genomes. G3 13: jkad008. PDF
Ye, Z., T. Bishop, Y. Wang, R. Shahriari, and M. Lynch. 2023. Evolution of sex determination in crustaceans. Marine Life Science & Technology 5: 1-11. PDF
Gout, J.-F., Y. Hao, P. Johri, O. Arnaiz, T. G. Doak, S. Bhullar, A. Couloux, F. Guérin, S. Malinsky, A. Potekhin, N. Sawka, L. Sperling, K. Labadie, E. Meyer, S. Duharcourt, and M. Lynch. 2023. Dynamics of gene loss following ancient whole-genome duplication in the cryptic Paramecium complex. Mol. Biol. Evol. 40: msad107. PDF
Long, H., P. Johri, J.-F. Gout, J. Ni, Y. Hao, T. Licknack, Y. Wang, J. Pan, B. Jimenez Marin, and M. Lynch. 2023. Paramecium genetics, genomics, and evolution. Ann. Rev. Genetics 57: 391-410. PDF
Devi, A., G. Speyer, and M. Lynch. 2023. The divergence of mean phenotypes under persistent directional selection. Genetics 224: iyad091. PDF
Ni, J., J. Pan, Y. Wang, T. Chen, X. Feng, Y. Li, T. Lin, M. Lynch, H. Long, and W. Li. 2023. An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data. Marine Life Science & Technology 1-9. PDF
Lynch, M. 2023. Mutation pressure, drift, and the tempo of molecular coevolution. Proc. Natl. Acad. Sci. USA 120: e2306741120. PDF
Suvorov, V., D. Saakian, and M. Lynch. 2023. The solution of the Crow-Kimura evolution model on fluctuating fitness landscape. Europhysics Letters 142: 57003. PDF
Moger-Reischer, R. Z., J. I. Glass, K. S. Wise, L. Sun, D. M. C. Bittencourt, B. K. Lehmkuhl, M. Lynch, and J. T. Lennon. 2023. Evolution of a minimal cell. Nature 620: 122-127. PDF
Lynch, M. 2023. Masatoshi Nei (1931-2023): founder of molecular evolutionary genetics. Proc. Natl. Acad. Sci. USA 120: e2312259120. PDF
Lynch, M., F. Ali, T. Lin, Y. Wang, J. Ni, and H. Long. 2023. The divergence of mutation rates across the Tree of Life. EMBO Reports 24: e57561. PDF
Hoelzel, A. R., and M. Lynch. 2023. The raw material of evolution. Science 381: 942-943. PDF
Lin, T., J. Pan, C. Gregory, J. Ni, C. Tincher, C. Rivera, M. Lynch, H. Long, and Y. Zhang. 2023. Contribution of the SOS response and the DNA repair systems to antibiotic induced mutations. Marine Life Science & Technology 5: 538-550. PDF
Ye, Z. W. Wei, M. Pfrender, and M. Lynch. 2023. Evolutionary insights from a large-scale survey of population-genomic variation. Mol. Biol. Evol. 40: msad233. PDF
Ye, Z., W. Wei, M. Pfrender, and M. Lynch. 2023. Population genomics of sister species differing in levels of nucleotide diversity and recombination rates. Genome Biol. Evol. 15: evad202. PDF
2022
Wei, W., W. C. Ho, M. Behringer, S. Miller, G. Bcharah, and M. Lynch. Rapid evolution of mutation rate and spectrum in response to environmental and population-genetic challenges. Nature Communications. 13: 4752. PDF
Maruki, T., Z. Ye, and M. Lynch. 2022. The population genomics of a subdivided species. Mol. Biol. Evol 39(8): msac152. https://doi.org/10.1093/molbev/msac152.
Schavemaker, P. E., and M. Lynch. 2022. Flagellar energy costs across the tree of life. eLife 11: e77266. PDF
Lynch, M., P. Schavemaker, T. Licknack, Y. Hao, and A. Pezzano. 2022. Evolutionary bioenergetics of ciliates. J. Euk. Microbiol 69(5): e12934. PDF
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 39(6): msac118. PDF
Johri, P., C. F. Aquadro, M. Beaumont, B. Charlesworth, L. Excoffier, A. Eyre-Walker, P. D. Keightley, M. Lynch, G. McVean, B. A. Payseur, S. P. Pfeifer, W. Stephan, and J. D. Jensen. 2022. Recommendations for improving statistical inference in population genomics. PLoS Biology 20: e3001669. PDF
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. mBio 13(3): e03467-21. PDF
Pan, P., W. Li, J. Ni, K. Wu, I. Konigsberg, C. Patterson, C. Tincher, C. Gregory, X. Zhou, T. G. Doak, H. Lee, Y. Wang, X. Gao, M. Lynch, and H. Long. 2022. Rates of mutations and transcript errors in the foodborne pathogen Salmonella enterica subsp. enterica. Mol. Biol. Evol 39(4): msac081. PDF
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 39(4): msac059. PDF
Wu, K., H. Li, X. Cui, R. Feng, W. Chen, Y. Jiang, C. Tang, Y. Wang, Y. Wang, X. Shen, Y. Liu, M. Lynch, and H. Long. 2022. Mutagenesis and resistance development of bacteria challenged by silver nano-particles. Antimicrobial Agents Chemotherapy 66: e0062822. PDF
Harrison, J. F., A. Biewener, J. R. Bernhardt, J. R Burger, J. H. Brown, Z. N. Coto, M. E. Duell, M. Lynch, E. R. Moffett, T. Norin, A. K. Pettersen, F. A. Smith, U. Somjee, J. F. A. Traniello, and T. M. Williams. 2022. White Paper: an integrated perspective on the causes of hypometric metabolic scaling in animals. Integrative and Comparative Biology 62: 1395-1418. PDF
Lynch, M., Z. Ye, T. Maruki, and X. Wang. 2022. The linkage-disequilibrium and recombinational landscape in Daphnia pulex. Genome Biol. Evol. 14: evac145. PDF
2021
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. PDF
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. PDF
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. 13: evab243. PDF
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. PDF
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. PDF
Johri, P., B. Charlesworth, E. Howell, M. Lynch, and J. Jensen. 2021. Revisiting the notion of deleterious sweeps. Genetics 219: iyab094. PDF
Pan, J., E. Williams, W. Sung, M. Lynch, H. Long. 2021. The insect-killing bacterium has the lowest mutation rate among bacteria. Marine Life Science & Technology. 3: 20-27. PDF
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. PDF
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. PDF
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. PDF
2020
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
Lynch, M., and B. Trickovic. 2020. A theoretical framework for evolutionary cell biology. J. Mol. Biol. 432: 1861-1879. PDF
Lynch, M., and W.-C. Ho. 2020. The limits to estimating population-genetic parameters with temporal data. Genome Biol. Evol. 12: 443-455. PDF
Jensen, J. D., and M. Lynch. 2020. Considering mutational meltdown as a potential SARS-CoV-2 treatment strategy. Heredity 124: 619-620. PDF
Lynch, M. 2020. The evolutionary scaling of cellular traits imposed by the drift barrier. Proc. Natl. Acad. Sci. USA 117: 10435-10444. PDF
Li, W., and M. Lynch. 2020. Universally high transcript error rates in bacteria. eLife 9: e54898. PDF
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
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
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
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
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. PDF
Jensen, J. D., R. A. Stikeleather, T. F. Kowalik, and M. Lynch. 2020. Imposed mutational meltdown as an antiviral strategy. Evolution 12: 2549-2559. PDF
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. PDF
2010-2019
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
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
Haubold, B., P. Pfaffelhuber, and M. Lynch. 2010. mlRho – A program for estimating the population mutation and recombination rates from shotgun-sequenced genomes. Molecular Ecology 19, Suppl. 1: 277-284. PDF
Gleick, P. H., et al. 2010. Climate change and the integrity of science. Science 328: 689-690. PDF
Lynch, M., and A. Abegg. 2010. The rate of origin of complex adaptations. Mol. Biol. Evol. 27: 1404-1414. PDF
Lynch, M. 2010. Evolution of the mutation rate. Trends in Genetics 26: 345-352. PDF
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
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
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
Lynch, M. 2010. Scaling expectations for the time to establishment of complex adaptations. Proc. Natl. Acad. Sci. USA 107: 16577-16582. PDF
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
Lipinski, K. J., K. A. Fitzpatrick, M. Lynch, V. Katju, and U. Bergthorsson. 2011. High spontaneous rate of gene duplication in Caenorhabditis elegans. Curr. Biol. 21: 306-310. PDF
Colbourne, J., et al. 2011. The ecoresponsive genome of Daphnia pulex. Science 331: 555-561. PDF
Lucas-Lledó, J. I., R. Maddamsetti, and M. Lynch. 2011. Phylogenomic analysis of the uracil-DNA glycosylase superfamily. Mol. Biol. Evol. 28: 1307-1317. PDF
Lynch, M. 2011. Statistical inference on the mechanisms of genome evolution. PLoS Genetics 7(6): e1001389. PDF
Lynch, M., L.-M. Bobay, F. Catania, J.-F. Gout, and M. Rho. 2011. The repatterning of eukaryotic genomes by random genetic drift. Ann. Rev. Genomics Hum. Genet. 12: 347-366. PDF
Lynch, M. 2011. The lower bound to the evolution of mutation rates. Genome Biol. Evol. 3: 1107-1118. PDF
Eads, B., D. Tsuchiya, M. Lynch, J. Andrews, and M. E. Zolan. 2012. Evolution of REC8 in Daphnia: the spread of a transposon insertion associated with obligate asexuality. Proc. Natl. Acad. Sci. USA 109: 858-863. PDF
Xu, S., S. Schaack, A. Seyfert, E. Choi, M. Lynch, and M. E. Cristescu. 2012. High mutation rates in the mitochondrial genomes of Daphnia pulex. Mol. Biol. Evol. 29: 763-769. PDF
Lynch, M. 2012. The evolution of multimeric protein assemblages. Mol. Biol. Evol. 29: 1353-1366. PDF
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
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
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
Lynch, M. 2012. Evolutionary layering and the limits to cellular perfection. Proc. Natl. Acad. Sci. USA 109: 18851-18856. PDF
McGrath, C. L., and M. Lynch. 2012. Evolutionary significance of whole-genome duplication, p. 1-20. In P. S. Soltis and D. E. Soltis (eds.) Polyploidy and Genome Evolution. Springer-Verlag, New York, NY.
Latta, L. C. 4th, 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
Schaack, S., D. E. Allen, L. C. Latta 4th, K. K. Morgan, and M. Lynch. 2013. The effect of spontaneous mutations on competitive ability. J. Evol. Biol. 26: 451-456. PDF
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
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
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
Lynch, M. 2013. Evolutionary diversification of the multimeric states of proteins. Proc. Natl. Acad. Sci. USA 110: E2821-E2828. PDF
Catania, F., and M. Lynch. 2013. A simple model to explain evolutionary trends of eukaryotic gene architecture and expression: how competition between splicing and cleavage/polyadenylation factors may affect gene expression and splice-site recognition in eukaryotes. Bioessays 35: 561-570. PDF
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
Schrider, D., D. Houle, M. Lynch, and M. Hahn. 2013. Genetic variation in the mutation rate in Drosophila melanogaster. Genetics 194: 937-954. PDF
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
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
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 110: 18584-18589. PDF
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
Lynch, M., D. Bost, S. Wilson, and T. Maruki. 2014. Population-genetic inference from pooled-sequencing data. Genome Biol. Evol. 6: 1210-1218. PDF
Maruki, T., and M. Lynch. 2014. Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data. Genetics 197: 1303-1313. PDF
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
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
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
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
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
Sazer, S., M. Lynch, and D. Needleman. 2014. Deciphering the evolutionary history of open and closed mitosis. Curr. Biol. 24: R1099-R1103. PDF
Lynch, M., and K. Hagner. 2014. Evolutionary meandering of intermolecular interactions along the drift barrier. Proc. Natl. Acad. Sci. USA 112: E30-E38. PDF
Long, H., W. Sung, S. F. Miller, M. S. Ackerman, T. G. Doak, and M. Lynch. 2014. 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
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
Gout, J. F., and M. Lynch. 2015. Maintenance and loss of duplicated genes by dosage subfunctionalization. Mol. Bio. Evol. 32: 2141-2148. PDF
Lynch, M. 2015. Feedforward loop for diversity. Nature 523: 414-416. PDF
Sung, W., M. S. Ackerman, J. F. Gout, S. F. Miller, P. Foster, and M. Lynch. 2015. Asymmetric context-dependent mutation patterns revealed through mutation-accumulation experiments. Mol. Biol. Evol. 32: 1672-1683. PDF
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
Maruki, T., and M. Lynch. 2015. Genotype-frequency estimation from high-throughput sequencing data. Genetics 201: 473-486. PDF
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
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
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
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
Lynch, M., and G. K. Marinov. 2015. The bioenergetic costs of a gene. Proc. Natl. Acad. Sci. USA 112: 15690-15695. PDF
Marinov, G. K., and M. Lynch. 2015. Diversity and divergence of dinoflagellate histone proteins. G3: Genes|Genomes|Genetics 6: 397-422. PDF
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
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
Lynch, M. 2016. Mutation and human exceptionalism: our future genetic load. Genetics 202: 869-875. PDF
Marinov, G. K., and M. Lynch. 2016. Conservation and divergence of the histone code in nucleomorphs. Biol. Direct 11: 18. PDF
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
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
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
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
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
Lynch, M. 2016. Mutation, eugenics, and the boundaries of science. Genetics 204: 825-827. PDF
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
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. PDF
Lynch, M., and G. K. Marinov. 2017. Membranes, energetics, and evolution across the prokaryote-eukaryote divide. eLife 6: e20437. PDF
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
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
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
Lynch, M., M. Ackerman, K. Spitze, Z. Ye, and T. Maruki. 2017. Population genomics of Daphnia pulex. Genetics 206: 315-332. PDF
Ackerman, M. S., P. Johri, K. Spitze, S. Xu, T. Doak, K. Young, and M. Lynch. 2017. Estimating seven coefficients of pairwise relatedness using population-genomic data. Genetics 206: 105-118. PDF
Maruki, T., and M. Lynch. 2017. Genotype calling from population-genomic sequencing data. G3: Genes|Genomes|Genetics 7: 1393-1404. PDF
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
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
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
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
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
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
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
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
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
Lynch, M. 2018. Phylogenetic diversification of cell biological features. eLife 7: e34820. PDF
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
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
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. PDF
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
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
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
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. PDF
Hagner, K., S. Setayeshgar, and M. Lynch. 2018. Stochastic protein multimerization, activity, and fitness. Phys. Rev. E 98: 062401. PDF
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
Lynch, M. 2019. Joseph Shapiro, an icon of applied limnology. Limnol. Oceanogr. 28: 35-37. PDF
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
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
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
2000-2009
Lynch, M., and A. Force. 2000. The probability of duplicate-gene preservation by subfunctionalization. Genetics 154: 459-473. PDF
Vassilieva, L., A. M. Hook, and M. Lynch. 2000. The fitness effects of spontaneous mutations in Caenorhabditis elegans. Evolution 54: 1234-1246. PDF
Blanchard, J., and M. Lynch. 2000. Why do mitochondrial genes end up in the nuclear genome? Trends in Genetics 16: 315-320. PDF
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
Pfrender, M. E., and M. Lynch. 2000. Quantitative genetic variation in Daphnia: temporal changes in genetic architecture. Evolution 54: 1502-1509. PDF
Lynch, M., and A. Force. 2000. Gene duplication and the origin of interspecific genomic incompatibility. American Naturalist 156: 590-605. PDF
Pfrender, M. E., 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. PDF
Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1154. PDF
Lynch, M. 2000. The limits to knowledge in quantitative genetics. Evol. Biol. 32: 225-237. PDF
Lynch, M., and J. S. Conery. 2001. Gene duplication and evolution: response to Long and Thornton and Zhang et al. Science 293: 1551a.
Higgins, K., and M. Lynch. 2001. Metapopulation extinction due to mutation accumulation. Proc. Natl. Acad. Sci. USA 98: 2928-2933. PDF
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
Lynch, M. 2001. The molecular natural history of the human genome. Trends in Ecology and Evolution 16: 420-422. PDF
Lynch, M., and M. O’Hely. 2001. Supplementation and the genetic fitness of natural populations. Conservation Genetics 2: 363-378. PDF
Lynch, M., M. O’Hely, B. Walsh, and A. Force. 2001. The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804. PDF
Lynch, M. 2002. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. USA 99: 6118-6123. PDF
Lynch, M., and A. Richardson. 2002. The evolution of spliceosomal introns. Curr. Opin. Gen. Devel. 12: 701-710. PDF
Lynch, M. 2002. Chromosomal repatterning by gene duplication. Science 297: 945-947. PDF
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
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
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
Keightley, P. D., and M. Lynch. 2003. Towards a realistic model of mutations affecting fitness. Evolution 57: 683-685. PDF
Lynch, M., and A. Kewalramani. 2003. Messenger RNA processing and the evolutionary proliferation of introns. Mol. Biol. Evol. 20: 563-571. PDF
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
Estes, S., and M. Lynch. 2003. Rapid recovery of mutation-accumulation lines by compensatory mutation. Evolution 57: 1022-1030. PDF
Housworth, E., E. Martins, and M. Lynch. 2003. The phylogenetic mixed model. American Naturalist 163: 84-96. PDF
Lynch, M., and J. S. Conery. 2003. The origins of genome complexity. Science 302: 1401-1404. PDF
Katju, V., and M. Lynch. 2003. The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. Genetics 165: 1793-1803. PDF
Denver, D. R., S. L. Swenson, and M. Lynch. 2003. An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases. Molecular Biology and Evolution 20: 1603-1611. PDF
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
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
Denver, D. R., K. Morris, M. Lynch, and W. K. Thomas. 2004. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature 430: 679-682. PDF
Lynch, M., and V. Katju. 2004. The altered evolutionary trajectories of gene duplicates. Trends in Genetics 20: 544-549. PDF
Denver, D. R., K. Morris, A. Kewalramani, K. Harris, A. Chow, S. Randell-Estes, M. Lynch, and W. K. Thomas. 2004. Abundance, distribution and mutation rates of homopolymeric nucleotide runs in the genome of Caenorhabditis elegans. J. Mol. Evol. 58: 584-595. PDF
Pfrender, M. E., J. Hicks, and M. Lynch. 2004. Biogeographic patterns and current distribution of molecular-genetic variation among populations of speckled dace, Rhinichthys osculus (Girard). Mol. Phylogenet. Evol. 30: 490-502. PDF
Dudycha, J. L., and M. Lynch. 2005. Ontogeny and allometry of resource allocation in animals with indeterminate growth. Evolution 59: 565-576. PDF
Lynch, M., D. G. Scofield, and X. Hong. 2005. The evolution of transcription-initiation sites. Mol. Biol. Evol. 22: 1137-1146. PDF
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
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
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
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
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
Paland, S., J. K. Colbourne, and M. Lynch. 2005. Evolutionary history of contagious asexuality in Daphnia pulex. Evolution 59: 800-813. PDF
Ajie, B. C., S. Estes, M. Lynch, and P. C. Phillips. 2005. Behavioral degradation under mutation accumulation. Genetics 170: 655-660. PDF
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
Lynch, M. 2005. Intelligent design vs. intelligent evolution. Nature 434: 276. PDF
Lynch, M. 2005. Simple evolutionary pathways to complex proteins. Protein Science 14: 2217-2225. PDF
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
Robinson, C. D., S. Lourido, S. P. Whelan, J. L. Dudycha, M. Lynch, and S. Isern. 2006. Viral transgenesis of embryonic cell cultures from the freshwater microcrustacean Daphnia. J. Exp. Zool. 305: 62-67. PDF
Lynch, M. 2006. The origins of eukaryotic gene structure. Mol. Biol. Evol. 23: 450-468. PDF
Paland, S., and M. Lynch. 2006. Transitions to asexuality result in excess amino-acid substitutions. Science 311: 990-902. PDF
Lynch, M., B. Koskella, and S. Schaack. 2006. Mutation pressure and the evolution of organelle genome architecture. Science 311: 1727-1730. PDF
Katju, V., and M. Lynch. 2006. On the formation of novel genes by duplication in the Caenorhabditis elegans genome. Mol. Biol. Evol. 23: 1056-1067. PDF
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
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
Hong, X., D. G. Scofield, and M. Lynch. 2006. Intron size, abundance, and distribution within untranslated regions of genes. Mol. Biol. Evol. 23: 2392-2404. PDF
Snoke, M. S., T. U. Berendonk, D. Barth, and M. Lynch. 2006. Large global effective population sizes in Paramecium. Mol. Biol. Evol. 23: 2474-2479. PDF
Lynch, M. 2006. Streamlining and simplification of microbial genome architecture. Ann. Rev. Microbiol. 60:327-349. PDF
Omilian, A. R., M. E. A. Cristescu, J. L. Dudycha, and M. Lynch. 2006. Ameiotic recombination in asexual lineages. Proc. Natl. Acad. Sci. USA 103: 18638-18643. PDF
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
Lynch, M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc. Natl. Acad. Sci. USA 104 (Suppl.): 8597-8604. PDF
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
Lynch, M. 2007. The evolution of genetic networks by nonadaptive processes. Nature Reviews Genetics 8: 803-813. PDF
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
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
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
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
Omilian, A. R., D. G. Scofield, and M. Lynch. 2008. Intron presence-absence polymorphisms in Daphnia. Mol. Biol. Evol. 25: 2129-2139. PDF
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
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
Lynch, M. 2008. The cellular, developmental, and population-genetic determinants of mutation-rate evolution. Genetics 180: 933-943. PDF
Scofield, D. G., and M. Lynch. 2008. Evolutionary diversification of the Sm family of RNA-associated proteins. Mol. Biol. Evol. 25: 2255-2267. PDF
Catania, F., and M. Lynch. 2008. Where do introns come from? PLoS Biology 6: e283. PDF
Catania, F., F. Wurmser, A. A. Potekhin, E. Przyboś, and M. Lynch. 2009. Genetic diversity in the Paramecium aurelia complex. Mol. Biol. Evol. 26: 421-431. PDF
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
Omilian, A. R., and M. Lynch. 2009. Patterns of intraspecific DNA variation in the Daphnia nuclear genome. Genetics 182: 325-336. PDF
Lynch, M. 2009. Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics 182: 295-301. PDF
Lucas-Lledó, J. I., and M. Lynch. 2009. Evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family. Mol. Biol. Evol. 26: 1143-1153. PDF
Rho, M., M. Zhou, X. Gao, S. Kim, H. Tang, and M. Lynch. 2009. Parallel mammalian genome contractions following the KT boundary. Genome Biol. Evol. 1: 2-12. PDF
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
Li, W. A. E. Tucker, W. Sung, W. K. Thomas, and M. Lynch. 2009. Extensive, recent intron gains in Daphnia populations. Science 326: 1260-1262. PDF
Gao, X., and M. Lynch. 2009. Ubiquitous internal gene duplication and intron creation in eukaryotes. Proc. Natl. Acad. Sci. USA 106: 20818-20823. PDF
Lynch, M. 2009. Rate, molecular spectrum, and consequences of spontaneous mutations in man. Proc. Natl. Acad. Sci. USA 107: 961-968. PDF
1974-1999
Lynch, M. 1974. The phytoplankton of the Allegheny Reservoir from May 1972 to September 1973. Science Studies (St. Bonaventure University) 30: 5-29. PDF
Shapiro, J., V. Lamarra, and M. Lynch. 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
Lynch, M. 1977. Zooplankton competition and plankton community structure. Limnology and Oceanography 22: 775-777. PDF
Lynch, M. 1977. Fitness and optimal body size in zooplankton populations. Ecology 58: 763-774. PDF
Lynch, M. 1978. Complex interactions between natural coexploiters - Daphnia and Ceriodaphnia. Ecology 59: 552-564. PDF
Lynch, M. 1979. Predation, competition, and zooplankton community structure: An experimental study. Limnology and Oceanography 24: 253-272. PDF
Lynch, M. 1980. The evolution of cladoceran life histories. Quarterly Review of Biology 55: 23-42. 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. 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., and J. Shapiro. 1981. Predation, enrichment, and phytoplankton community structure. Limnology and Oceanography 26: 86-102. PDF
Lynch, M., B. Monson, M. Sandheinrich, and L. Weider. 1981. Patterns of size-specific mortality in zooplankton populations. Verh. Internat. Verein. Limnol. 21: 363-368. PDF
Lynch, M. 1982. How well does the Edmondson-Paloheimo model approximate instantaneous birth rates? Ecology 63: 12-18. PDF
Lynch, M. 1983. Ecological genetics of Daphnia pulex. Evolution 37: 358-374. PDF
Weis, A., P. Price, and M. Lynch. 1983. Selection for clutch size in the gall-maker Asteromyia carbonifera. Ecology 64: 688-695.
Lynch, M. 1983. Estimation of size-specific mortality rates in zooplankton populations by periodic sampling. Limnology and Oceanography 28: 533-545. PDF
Lynch, M., and R. Ennis. 1983. Resource availability, maternal effects, and longevity. Exper. Gerontology 18: 147-165. PDF
Lynch, M., and W. Gabriel. 1983. Phenotypic evolution and parthenogenesis. American Naturalist 122: 745-764. PDF
Lynch, M. 1984. The genetic structure of a cyclical parthenogen. Evolution 38: 186-203. PDF
Lynch, M. 1984. The limits to life history evolution in Daphnia. Evolution 38: 465-482. PDF
Lynch, M. 1984. Destabilizing hybridization, general-purpose genotypes, and geographic parthenogenesis. Quarterly Review of Biology 59: 257-290. PDF
Lynch, M. 1984. The selective value of alleles underlying polygenic traits. Genetics 108: 1021-1033. PDF
Lynch, M. 1985. Elements of a mechanistic theory for the life history consequences of food limitation. Ergeb. Limnol. 21: 351-362. PDF
Lynch, M. 1985. Speciation in the Cladocera. Verh. Internat. Verein. Limnol. 22: 3116-3123. PDF
Lynch, M. 1985. Spontaneous mutations for life history characters in an obligate parthenogen. Evolution 39: 804-818. PDF
Lynch, M., L. Weider, and W. Lampert. 1986. Measurement of the carbon balance in Daphnia. Limnology and Oceanography 31: 17-33. PDF
Lynch, M. 1986. Random drift, uniform selection, and the degree of population differentiation. Evolution 40: 640-643. PDF
Lynch, M., and W. G. Hill. 1986. Phenotypic evolution by neutral mutation. Evolution 40: 915-935. PDF
Lynch, M. 1987. The consequences of fluctuating selection for isozyme polymorphisms in Daphnia. Genetics 115: 657-669. PDF
Lynch, M., and W. Gabriel. 1987. Environmental tolerance. American Naturalist 129: 283-303. 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
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. 1987. The evolution of intrafamilial interactions. Proc. Natl. Acad. Sci. USA 84: 8507-8511. PDF
Lynch, M. 1988. The rate of polygenic mutation. Genetical Research 51: 137-148. PDF
Lynch, M. 1988. The divergence of neutral quantitative characters among partially isolated populations. Evolution 42: 455-466. 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
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. Estimation of relatedness by DNA fingerprinting. Mol. Biol. Evol. 5: 584-599. PDF
Lynch, M. 1988. Design and analysis of experiments on random drift and inbreeding. Genetics 120: 791-807. PDF
Lynch, M. 1989. Phylogenetic hypotheses under the assumption of neutral quantitative genetic variation. Evolution 43: 1-17. PDF
Lynch, M., K. Spitze, and T. Crease. 1989. The distribution of life history variation in Daphnia pulex. Evolution 43: 1724-1736. PDF
Lynch, M. 1989. The life history consequences of resource depression in Daphnia pulex. Ecology 70: 246-256. PDF
Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. American Naturalist 136: 727-741. PDF
Lynch, M., and T. Crease. 1990. The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol. 7: 377-394. PDF
Crease, T., M. Lynch, and K. Spitze. 1990. A hierarchical analysis of population genetic variation in nuclear and mitochondrial genes in Daphnia. Mol. Biol. Evol. 7: 444-458. PDF
Lynch, M. 1990. The similarity index and DNA fingerprinting. Mol. Biol. Evol. 7: 478-484. PDF
Lynch, M., and W. Gabriel. 1990. Mutation load and the survival of small populations. Evolution 44: 1725-1737. PDF
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
Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45: 1065-1080. PDF
Lynch, M. 1991. The genetic interpretation of inbreeding depression and outbreeding depression. Evolution 45: 622-629. PDF
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
Crease, T. J., and M. Lynch. 1991. Ribosomal DNA variation in Daphnia pulex. Mol. Biol. Evol. 8: 620-640. PDF
Spitze, K., J. Burnson, and M. Lynch. 1991. The covariance structure of life history characters in Daphnia pulex. Evolution 45: 1081-1090. PDF
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
Cohen, J. E., M. Lynch, and C. E. Taylor. 1991. Forensic DNA tests and Hardy-Weinberg equilibrium. Science 253: 1037. PDF
Lynch, M. 1992. The life history consequences of resource depression in Ceriodaphnia quadrangula and Daphnia ambigua. Ecology 73: 1620-1629. PDF
Gabriel, W., and M. Lynch. 1992. The selective advantage of reaction norms for environmental tolerance. J. Evol. Biol. 5: 41-59. PDF
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
Lynch, M., R. Bürger, D. Butcher, and W. Gabriel. 1993. Mutational meltdowns in asexual populations. J. Heredity 84: 339-344. PDF
Lynch, M., and P. Jerrol. 1993. A method for calibrating molecular clocks and its application to animal mitochondrial DNA. Genetics 135: 1197-1208. PDF
Lynch, M., and K. Spitze. 1994. Evolutionary genetics of Daphnia, pp. 109-128. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press. PDF
Lynch, M. 1994. The neutral theory of phenotypic evolution, pp. 86-108. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press. PDF
Gabriel, W., M. Lynch, and R. Bürger. 1994. Muller's ratchet and mutational meltdowns. Evolution 47: 1744-1757. PDF
Lynch, M., and B. Milligan. 1994. Analysis of population-genetic structure using RAPD markers. Molecular Ecology 3: 91-99. PDF
Bürger, R., and M. Lynch. 1994. Evolution and extinction in a changing environment: a quantitative-genetic analysis. Evolution 49: 151-163. PDF
Lynch, M., and H. W. Deng. 1994. Genetic slippage in response to sex. American Naturalist 144: 242-261. PDF
Toline, C. A., and M. Lynch. 1994. Mutational divergence of life-history traits in an obligate parthenogen. Genome 37: 33-35. PDF
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
Conery, J. S., M. Lynch, and T. Hovland. 1995. Irregular computations on SIMD machines: a case study. Proc. 5th Symp. Frontiers of Massively Parallel Computation: 222-230. PDF
Lehman, N., M. E. Pfrender, P. A. Morin, T. J. Crease, and M. Lynch. 1995. A hierarchical molecular phylogeny of the genus Daphnia. Mol. Phylog. Evol. 4: 395-407. PDF
Lynch, M., J. Conery, and R. Bürger. 1995. Mutational meltdowns in sexual populations. Evolution 49: 1067-1080. PDF
Lynch, M., J. Conery, and R. Bürger. 1995. Mutation accumulation and the extinction of small populations. American Naturalist 146: 489-518. PDF
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
Lynch, M. 1996. Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes. Mol. Biol. Evol. 13: 209-220. PDF
Deng, H.-W., and M. Lynch. 1996. Change of genetic architecture in response to sex. Genetics 143: 203-212. PDF
Deng, H.-W., and M. Lynch. 1996. Estimation of deleterious-mutation parameters in natural populations. Genetics 144: 349-360. PDF
Houle, D., R. Morikawa, and M. Lynch. 1996. Comparing mutational variabilities. Genetics 143: 1467-1483. PDF
Kibota, T., and M. Lynch. 1996. Estimate of the genomic mutation rate deleterious to overall fitness in Escherichia coli. Nature 381: 694-696. PDF
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
Deng, H.-W., and M. Lynch. 1997. Inbreeding depression and inferred deleterious mutation parameters in Daphnia. Genetics 147: 147-155. PDF
Lynch, M. 1997. Mutation accumulation in nuclear, organelle, and prokaryotic genomes: transfer RNA genes. Mol. Biol. Evol. 14: 914-925. PDF
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
Bürger, R., and M. Lynch. 1997. Adaptation and extinction in changing environments, pp. 209-240. In R. Bijlsma and V. Loeschcke (eds.) Environmental Stress, Adaptation and Evolution. Birkhäuser Verlag, Basel. PDF
Lynch, M., and J. Blanchard. 1998. Deleterious mutation accumulation in organelle genomes. Genetica 102/103: 29-39. PDF
Deng, H.-W., Y.-X. Fu, and M. Lynch. 1998. Inferring the major genomic mode of dominance and overdominance. Genetica 102/103: 559-567. PDF
Lynch, M., and R. Lande. 1998. The critical effective size for a genetically secure population. Anim. Cons. 1: 70-72. PDF
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
Vassilieva, L., and M. Lynch. 1999. Accumulation of spontaneous mutations in Caenorhabditis elegans. Genetics 151: 119-129. PDF
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
Lynch, M., and K. Ritland. 1999. Estimation of relatedness with molecular markers. Genetics 152: 1753-1766. PDF
Lynch, M. 1999. The age and relationships of the major animal phyla. Evolution 53: 319-325. PDF
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
Lynch, M., J. Blanchard, D. Houle, T. Kibota, S. Schultz, L. Vassilieva, and J. Willis. 1999. Spontaneous deleterious mutation. Evolution 53: 645-663. PDF
Conery, J. S., and M. Lynch. 1999. Genetic simulation library. Bioinformatics 15: 85-86. PDF
Lynch, M. 1999. Estimation of genetic correlations in natural populations. Genetical Research 74: 255-264. PDF
Schultz, S. T., M. Lynch, and J. H. Willis. 1999. Spontaneous deleterious mutation in Arabidopsis. Proc. Natl. Acad. Sci. USA 96: 11393-11398. PDF
Books:
Lynch, M., and J. B. Walsh. 1998. Genetics and Analysis of Quantitative Traits. Sinauer Assocs., Inc., Sunderland, MA.
With 14 other committee members, for the National Research Council. 1995. Science and the Endangered Species Act. National Academy Press, Washington, DC.
Lynch, M. 2007. The Origins of Genome Architecture. Sinauer Assocs., Inc., Sunderland, MA.
Walsh, J. B., and M. Lynch. 2018. Evolution and Selection of Quantitative Traits. Oxford Univ. Press, Oxford, UK.
Lynch, M. Evolutionary Cell Biology: the Origins of Cellular Features. 2024. Oxford Univ. Press, Oxford, UK.