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

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. Bio. Evol. 32: 1672-1683. PDF DOI

Lynch, M. 2015. Feedforward loop for diversity. Nature 523: 414-416. PDF DOI

Gout, J. F., and M. Lynch. 2015. Maintenance and loss of duplicated genes by dosage subfunctionalization. Mol. Bio. Evol. 32: 2141-2148. 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

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 DOI

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 DOI

2011

Lynch, M. 2011. The lower bound to the evolution of mutation rates. Genome Biol. Evol. 3: 1107-1118. PDF DOI

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 DOI

Lynch, M. 2011. Statistical inference on the mechanisms of genome evolution. PLoS Genetics 7(6): e1001389. PDF DOI

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 DOI

Colbourne, J., et al. 2011. The ecoresponsive genome of Daphnia pulex. Science 331: 555-561. PDF DOI

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 DOI

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

Lynch, M., and A. Abegg. 2010. The rate of origin of complex adaptations. Mol. Biol. Evol. 27: 1404-1414. 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

Lynch, M. 2009. Rate, molecular spectrum, and consequences of spontaneous mutations in man. Proc. Natl. Acad. Sci. USA 107: 961-968. PDF DOI

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 DOI

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

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 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

Catania, F., and M. Lynch. 2008. Where do introns come from? PLoS Biology 6: e283. PDF DOI

Scofield, D. G., and M. Lynch. 2008. Evolutionary diversification of the Sm family of RNA-associated proteins. Mol. Biol. Evol. 25: 2255-2267. PDF DOI

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

Lynch, M. 2007. The evolution of genetic networks by nonadaptive processes. Nature Reviews Genetics 8: 803-813. PDF DOI

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

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 DOI

Lynch, M. 2006. Streamlining and simplification of microbial genome architecture. Ann. Rev. Microbiol. 60: 327-349. PDF DOI

Snoke, M. S., T. U. Berendonk, D. Barth, and M. Lynch. 2006. Elevated effective population sizes in unicellular eukaryotes. Mol. Biol. Evol. 23: 2474-2479. PDF DOI

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 DOI

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

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 DOI

Lynch, M., B. Koskella, and S. Schaack. 2006. Mutation pressure and the evolution of organelle genome architecture. Science 311: 1727-1730. PDF DOI

Paland, S., and M. Lynch. 2006. Transitions to asexuality result in excess amino-acid substitutions. Science 311: 990-902. PDF DOI

Lynch, M. 2006. The origins of eukaryotic gene structure. Mol. Biol. Evol. 23: 450-468. PDF DOI

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 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

Lynch, M., D. G. Scofield, and X. Hong. 2005. The evolution of transcription-initiation sites. Mol. Biol. Evol. 22: 1137-1146. PDF DOI

Dudycha, J. L., and M. Lynch. 2005. Ontogeny and allometry of resource allocation in animals with indeterminate growth. Evolution 59: 565-576. PDF DOI

2004

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 DOI

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 DOI

Lynch, M., and V. Katju. 2004. The altered evolutionary trajectories of gene duplicates. Trends in Genetics 20: 544-549. PDF DOI

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 DOI

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

Denver, D. R., S. L. Swenson, and M. Lynch. 2003. An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases. Mol. Biol. Evol. 20: 1603-1611. PDF DOI

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 DOI

Lynch, M., and J. S. Conery. 2003. The origins of genome complexity. Science 302: 1401-1404. PDF DOI

Housworth, E., E. Martins, and M. Lynch. 2003. The phylogenetic mixed model. American Naturalist 163: 84-96. PDF DOI

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

Lynch, M. 2002. Chromosomal repatterning by gene duplication. Science 297: 945-947. PDF DOI

Lynch, M., and A. Richardson. 2002. The evolution of spliceosomal introns. Curr. Opin. Gen. Devel. 12: 701-710. PDF DOI

Lynch, M. 2002. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. USA 99: 6118-6123. PDF DOI

2001

Lynch, M., M. O'Hely, B. Walsh, and A. Force. 2001. The probability of fixation of a newly arisen gene duplicate. Genetics 159: 1789-1804. PDF DOI

Lynch, M., and M. O'Hely. 2001. Supplementation and the genetic fitness of natural populations. Conservation Genetics 2: 363-378. PDF DOI

Lynch, M. 2001. The molecular natural history of the human genome. Trends in Ecology and Evolution 16: 420-422. PDF DOI

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

Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1154. PDF DOI

Lynch, M. 2000. The limits to knowledge in quantitative genetics. Evol. Biol. 32: 225-237. PDF DOI

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 DOI

Lynch, M., and A. Force. 2000. Gene duplication and the origin of interspecific genomic incompatibility. American Naturalist 156: 590-605. PDF DOI

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

Blanchard, J., and M. Lynch. 2000. Why do mitochondrial genes end up in the nuclear genome? Trends in Genetics 16: 315-320. PDF DOI

Vassilieva, L., A. M. Hook, and M. Lynch. 2000. The fitness effects of spontaneous mutations in Caenorhabditis elegans. Evolution 54: 1234-1246. PDF DOI

Lynch, M., and A. Force. 2000. The probability of duplicate-gene preservation by subfunctionalization. Genetics 154: 459-473. 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

Lynch, M., and J. Blanchard. 1998. Deleterious mutation accumulation in organelle genomes. Genetica 102/103: 29-39. PDF DOI

1997

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 DOI

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

Kibota, T., and M. Lynch. 1996. Estimate of the genomic mutation rate deleterious to overall fitness in Escherichia coli. Nature 381: 694-696. PDF DOI

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

Lynch, M., J. Conery, and R. Bürger. 1995. Mutation accumulation and the extinction of small populations. American Naturalist 146: 489-518. PDF DOI

Lynch, M., J. Conery, and R. Bürger. 1995. Mutational meltdowns in sexual populations. Evolution 49: 1067-1080. PDF DOI

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 DOI

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 DOI

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

Toline, C. A., and M. Lynch. 1994. Mutational divergence of life-history traits in an obligate parthenogen. Genome 37: 33-35. PDF DOI

Lynch, M., and H. W. Deng. 1994. Genetic slippage in response to sex. American Naturalist 144: 242-261. PDF DOI

Bürger, R., and M. Lynch. 1994. Evolution and extinction in a changing environment: a quantitative-genetic analysis. Evolution 49: 151-163. PDF DOI

Lynch, M., and B. Milligan. 1994. Analysis of population-genetic structure using RAPD markers. Molecular Ecology 3: 91-99. PDF DOI

Gabriel, W., M. Lynch, and R. Bürger. 1993. Muller's ratchet and mutational meltdowns. Evolution 47: 1744-1757. PDF DOI

Lynch, M. 1994. The neutral theory of phenotypic evolution, pp. 86-108. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press. PDF

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 P. Jerrol. 1993. A method for calibrating molecular clocks and its application to animal mitochondrial DNA. Genetics 135: 1197-1208. PDF DOI

Lynch, R. Bürger, D. Butcher, and W. Gabriel. 1993. Mutational meltdowns in asexual populations. J. Heredity 84: 339-344. PDF DOI

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

Gabriel, W., and M. Lynch. 1992. The selective advantage of reaction norms for environmental tolerance. J. Evol. Biol. 5: 41-59. PDF DOI

Lynch, M. 1992. The life history consequences of resource depression in Ceriodaphnia quadrangula and Daphnia ambigua. Ecology 73: 1620-1629. PDF DOI

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

Lynch, M., and W. Gabriel. 1990. Mutation load and the survival of small populations. Evolution 44: 1725-1737. PDF DOI

Lynch, M. 1990. The similarity index and DNA fingerprinting. Mol. Biol. Evol. 7: 478-484. PDF DOI

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 DOI

Lynch, M., and T. Crease. 1990. The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol. 7: 377-394. PDF DOI

Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. American Naturalist 136: 727-741. PDF DOI

1989

Lynch, M. 1989. The life history consequences of resource depression in Daphnia pulex. Ecology 70: 246-256. PDF DOI

Lynch, M., K. Spitze, and T. Crease. 1989. The distribution of life history variation in Daphnia pulex. Evolution 43: 1724-1736. PDF DOI

Lynch, M. 1989. Phylogenetic hypotheses under the assumption of neutral quantitative genetic variation. Evolution 43: 1-17. PDF DOI

1988

Lynch, M. 1988. Design and analysis of experiments on random drift and inbreeding. Genetics 120: 791-807. PDF DOI

Lynch, M. 1988. Estimation of relatedness by DNA fingerprinting. Mol. Biol. Evol. 5: 584-599. PDF DOI

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

Lynch, M. 1988. The divergence of neutral quantitative characters among partially isolated populations. Evolution 42: 455-466. PDF DOI

Lynch, M. 1988. The rate of polygenic mutation. Genetical Research 51: 137-148. PDF DOI

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

Lynch, M., and W. Gabriel. 1987. Environmental tolerance. American Naturalist 129: 283-303. PDF DOI

Lynch, M. 1987. The consequences of fluctuating selection for isozyme polymorphisms in Daphnia. Genetics 115: 657-669. PDF DOI

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. Spontaneous mutations for life history characters in an obligate parthenogen. Evolution 39: 804-818. PDF DOI

Lynch, M. 1985. Speciation in the Cladocera. Verh. Internat. Verein. Limnol. 22: 3116-3123. PDF

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

Lynch, M. 1984. The limits to life history evolution in Daphnia. Evolution 38: 465-482. PDF DOI

Lynch, M. 1984. The genetic structure of a cyclical parthenogen. Evolution 38: 186-203. PDF DOI

1983

Lynch, M., and W. Gabriel. 1983. Phenotypic evolution and parthenogenesis. American Naturalist 122: 745-764. PDF

Lynch, M., and R. Ennis. 1983. Resource availability, maternal effects, and longevity. Experimental Gerontology 18: 147-165. PDF DOI

Lynch, M. 1983. Estimation of size-specific mortality rates in zooplankton populations by periodic sampling. Limnol. Oceanogr. 28: 533-545. PDF

Weis, A., P. Price, and M. Lynch. 1983. Selection for clutch size in the gall-maker Asteromyia carbonifera. Ecology 64: 688-695. DOI

Lynch, M. 1983. Ecological genetics of Daphnia pulex. Evolution 37: 358-374. PDF DOI

1982

Lynch, M. 1982. How well does the Edmondson-Paloheimo model approximate instantaneous birth rates? Ecology 63: 12-18. PDF DOI

1981

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 DOI

Lynch, M. and J. Shapiro. 1981. Predation, enrichment, and phytoplankton community structure. Limnol. Oceanogr. 26: 86-102. PDF DOI

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

Lynch, M. 1979. Predation, competition, and zooplankton community structure: an experimental study. Limnol. Oceanogr. 24: 253-272. PDF DOI

1978

Lynch, M. 1978. Complex interactions between natural coexploiters - Daphnia and Ceriodaphnia. Ecology 59: 552-564. PDF DOI

1977

Lynch, M. 1977. Fitness and optimal body size in zooplankton populations. Ecology 58: 763-774. PDF DOI

Lynch, M. 1977. Zooplankton competition and plankton community structure. Limnol. Oceanogr. 22: 775-777. PDF DOI

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