Evolution and Selection of Quantitative Traits

Lynch, M., and J. B. Walsh. 2018.
Evolution and Selection of Quantitative Traits


The Origins of Genome Architecture

Lynch, M. 2007.
The Origins of Genome Architecture


Genetics and Analysis of Quantitative Traits

Lynch, M., and J. B. Walsh. 1998.
Genetics and Analysis of Quantitative Traits

Open access to ‘The Origins of Cellular Architecture’

We have taken on one of the last uncharted fields in evolution: integrating evolutionary biology with cell biology. This sequel to The Origins of Genome Architecture brings evolutionary theory to bear on a diversity of observations on the functional and structural features of cells.

Surprisingly, the details of many cellular traits seem not to be simple products of natural selection, and in some cases can only be explained by an ability of selection to universally make certain kinds of refinements. The chapters provided are freely available for use in evolutionary cell biology courses as well as for more general subject review.

Please feel free to send comments, corrections and suggestions to



1.   Evolutionary Cell Biology

2.   The Origin of Cells

3.   The Major Lines of Descent

The Genetic Mechanisms of Evolution

4.   The Population-genetic Environment

5.   Evolution as a Population-genetic Process

6.   Evolution of Cellular Complexity

Basic Cellular Features

7.   The Cellular Environment

8.   Evolutionary Scaling Laws in Cell Biology

9.   Cell Growth and Division

10. The Cell Life Cycle

11. Cellular Senescence

Structural Evolution

12. The Protein World

13. Multimerization 

14. Protein Management

15. Lipid and Membranes

16. Cytoskeleton, Cell Shape, and Motility

Energetics and Metabolism 

17. The Costs of Cellular Features

18. Resource Acquisition and Homeostasis

19. Enzymes and Metabolic Pathways

Information Processing 

20. Intracellular Errors

21. Intracellular Communication: Transcription

22. Environmental Sensing and Extracellular Communication

Organismal Complexity 

23. Endosymbiosis

24. Origins of Organismal Complexity



  1. Lynch, M., Z. Ye, and T. Maruki. 2021. The recombinational landscape in Daphnia pulex. bioRxiv. PDF

  2. Maruki, T., Z. Ye, and M. Lynch. 2021. The population genomics of a subdivided species. bioRxiv.

  3. 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

  4. 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.

  5. 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).

  6. 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).

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

  8. 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).

  9. 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).

  10. Johri, P., B. Charlesworth, E. Howell, M. Lynch, and J. Jensen. 2021. Revisiting the notion of deleterious sweeps. Genetics (submitted). PDF

  11. 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


  1. 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).

  2. 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

  3. 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

  4. 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. PDF

  5. 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

  6. 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 lippage mutations in the sequence repeat-rich genome of Dictyostelium discoideum. G3 (Bethesda) 10: 3445-3452. PDF

  7. 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

  8. 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

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

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

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

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

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

  14. 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


  1. 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

  2. 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

  3. 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

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

  5. 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


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

  2. 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. 

  3. 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. 

  4. 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. 

  5. 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. 

  6. 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. 

  7.  ​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. 

  8. 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. 

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

  10. 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. 

  11. 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. 


  1. Lynch, M., and G. K. Marinov. 2017. Membranes, energetics, and evolution across the prokaryote-eukaryote divide. ELife 6: e20437. 
  2. 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. 
  3. 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. 
  4. 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. 
  5. Lynch, M., M. Ackerman, K. Spitze, Z. Ye, and T. Maruki. 2017. Population genomics of Daphnia pulex. Genetics 206: 315-332. 
  6. 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. 
  7. Maruki, T., and M. Lynch. 2017. Genotype calling from population-genomic sequencing data. G3: Genes|Genomes|Genetics 7: 1393-1404. 
  8. 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.
  9. 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. 
  10. 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. 
  11. 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. 
  12. 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. 
  13. 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. 
  14. 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. 
  15. 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. 


  1. 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. 
  2. Lynch, M. 2016. Mutation, eugenics, and the boundaries of science. Genetics 204: 825-827. 
  3. 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. 
  4. 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. 
  5. 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. 
  6. 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. 
  7. 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. 
  8. Marinov, G. K., and M. Lynch. 2016. Conservation and divergence of the histone code in nucleomorphs. Biol. Direct 11: 18. 
  9. Lynch, M. 2016. Mutation and human exceptionalism: our future genetic load. Genetics 202: 869-875. 
  10. 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. 
  11. 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. 


  1. Marinov, G. K., and M. Lynch. 2015. Diversity and divergence of dinoflagellate histone proteins. G3: Genes|Genomes|Genetics 6: 397-422. 
  2. Lynch, M., and G. K. Marinov. 2015. The bioenergetic costs of a gene. Proc. Natl. Acad. Sci. USA 112: 15690-15695. 
  3. 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. 
  4. 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. 
  5. 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. 
  6. 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. 
  7. Maruki, T., and M. Lynch. 2015. Genotype-frequency estimation from high-throughput sequencing data. Genetics 201: 473-486. 
  8. 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. 
  9. 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. 
  10. Lynch, M. 2015. Feedforward loop for diversity. Nature 523: 414-416. 
  11. Gout, J. F., and M. Lynch. 2015. Maintenance and loss of duplicated genes by dosage subfunctionalization. Mol. Bio. Evol. 32: 2141-2148. 
  12. 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. 
  13. 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. 


  1. Lynch, M., and K. Hagner. 2014. Evolutionary meandering of intermolecular interactions along the drift barrier. Proc. Natl. Acad. Sci. USA 112: E30-E38. 
  2. Sazer, S., M. Lynch, and D. Needleman. 2014. Deciphering the evolutionary history of open and closed mitosis. Curr. Biol. 24: R1099-R1103. 
  3. 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. 
  4. 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. 
  5. Lynch, M., S. Xu, T. Maruki, P. Pfaffelhuber, and B. Haubold. 2014. Genome-wide linkage-disequilibrium profiles from single individuals. Genetics 198: 269-281. 
  6. 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. 
  7. 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. 
  8. Lynch, M., D. Bost, S. Wilson, and T. Maruki. 2014. Population-genetic inference from pooled-sequencing data. Genome Biol. Evol. 6: 1210-1218. 


  1. Maruki, T., and M. Lynch. 2013. Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data. Genetics 197: 1303-1313. 
  2. 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. 
  3. 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. 
  4. 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. 
  5. 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. 
  6. Schrider, D., D. Houle, M. Lynch, and M. Hahn. 2013. Genetic variation in the mutation rate in Drosophila melanogaster. Genetics 194: 937-954. 
  7. 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. 
  8. 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. 
  9. Lynch, M. 2013. Evolutionary diversification of the multimeric states of proteins. Proc. Natl. Acad. Sci. USA 110: E2821-E2828. 
  10. 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. 
  11. 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. 
  12. 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. 
  13. 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. 
  14. 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. 


  1. Lynch, M. 2012. Evolutionary layering and the limits to cellular perfection. Proc. Natl. Acad. Sci. USA 109: 18851-18856. 
  2. 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. 
  3. 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. 
  4. 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. 
  5. Lynch, M. 2012. The evolution of multimeric protein assemblages. Mol. Biol. Evol. 29: 1353-1366. 
  6. 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. 
  7. 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. 


  1. Lynch, M. 2011. The lower bound to the evolution of mutation rates. Genome Biol. Evol. 3: 1107-1118. 
  2. 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. 
  3. Lynch, M. 2011. Statistical inference on the mechanisms of genome evolution. PLoS Genetics 7(6): e1001389. 
  4. Lucas-Lledó, J. I., R. Maddamsetti, and M. Lynch. 2011. Phylogenomic analysis of the uracil-DNA glycosylase superfamily. Mol. Biol. Evol. 28: 1307-1317.
  5. Colbourne, J., et al. 2011. The ecoresponsive genome of Daphnia pulex. Science 331: 555-561. 
  6. 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. 


  1. 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. 
  2. Lynch, M. 2010. Scaling expectations for the time to establishment of complex adaptations. Proc. Natl. Acad. Sci. USA 107: 16577-16582. 
  3. 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. 
  4. 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. 
  5. 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. 
  6. Lynch, M. 2010. Evolution of the mutation rate. Trends in Genetics 26: 345-352. 
  7. Lynch, M., and A. Abegg. 2010. The rate of origin of complex adaptations. Mol. Biol. Evol. 27: 1404-1414. 
  8. Gleick, P. H., et al. 2010. Climate change and the integrity of science. Science 328: 689-690. 
  9. 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. 
  10. 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. 
  11. 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


  1. Lynch, M. 2009. Rate, molecular spectrum, and consequences of spontaneous mutations in man. Proc. Natl. Acad. Sci. USA 107: 961-968. 
  2. 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. 
  3. Gao, X., and M. Lynch. 2009. Ubiquitous internal gene duplication and intron creation in eukaryotes. Proc. Natl. Acad. Sci. USA 106: 20818-20823. 
  4. 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. 
  5. 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. 
  6. 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. 
  7. Lynch, M. 2009. Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics 182: 295-301. 
  8. Omilian, A. R., and M. Lynch. 2009. Patterns of intraspecific DNA variation in the Daphnia nuclear genome. Genetics 182: 325-336. 
  9. 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. 
  10. 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. 


  1. Catania, F., and M. Lynch. 2008. Where do introns come from? PLoS Biology 6: e283. 
  2. Scofield, D. G., and M. Lynch. 2008. Evolutionary diversification of the Sm family of RNA-associated proteins. Mol. Biol. Evol. 25: 2255-2267. 
  3. Lynch, M. 2008. The cellular, developmental, and population-genetic determinants of mutation-rate evolution. Genetics 180: 933-943. 
  4. Lynch, M. 2008. Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects. Mol. Biol. Evol. 25: 2421-2431. 
  5. 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. 
  6. Omilian, A. R., D. G. Scofield, and M. Lynch. 2008. Intron presence-absence polymorphisms in Daphnia. Mol. Biol. Evol. 25: 2129-2139. 
  7. 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. 
  8. 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. 
  9. 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. 
  10. 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. 


  1. Lynch, M. 2007. The evolution of genetic networks by nonadaptive processes. Nature Reviews Genetics 8: 803-813. 
  2. 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. 
  3. Lynch, M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc. Natl. Acad. Sci. USA 104 Suppl.: 8597-8604. 
  4. 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. 


  1. 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. 
  2. Lynch, M. 2006. Streamlining and simplification of microbial genome architecture. Ann. Rev. Microbiol. 60: 327-349. 
  3. 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. 
  4. 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. 
  5. 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. 
  6. 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. 
  7. 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. 
  8. Lynch, M., B. Koskella, and S. Schaack. 2006. Mutation pressure and the evolution of organelle genome architecture. Science 311: 1727-1730. 
  9. Paland, S., and M. Lynch. 2006. Transitions to asexuality result in excess amino-acid substitutions. Science 311: 990-902. 
  10. Lynch, M. 2006. The origins of eukaryotic gene structure. Mol. Biol. Evol. 23: 450-468.
  11. 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. 
  12. 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. 


  1. Lynch, M. 2005. Simple evolutionary pathways to complex proteins. Protein Science 14: 2217-2225. 
  2. Lynch, M. 2005. Intelligent design vs. intelligent evolution. Nature 435: 276. 
  3. 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. 
  4. Ajie, B. C., S. Estes, M. Lynch, and P. C. Phillips. 2005. Behavioral degradation under mutation accumulation. Genetics 170: 655-660. 
  5. Paland, S., J. K. Colbourne, and M. Lynch. 2005. Evolutionary history of contagious asexuality in Daphnia pulex. Evolution 59: 800-813. 
  6. 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. 
  7. 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. 
  8. 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. P
  9. 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
  10. 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
  11. Lynch, M., D. G. Scofield, and X. Hong. 2005. The evolution of transcription-initiation sites. Mol. Biol. Evol. 22: 1137-1146. 
  12. Dudycha, J. L., and M. Lynch. 2005. Ontogeny and allometry of resource allocation in animals with indeterminate growth. Evolution 59: 565-576. 


  1. 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
  2. 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. 
  3. Lynch, M., and V. Katju. 2004. The altered evolutionary trajectories of gene duplicates. Trends in Genetics 20: 544-549. 
  4. 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. 
  5. 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. 
  6. 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. 


  1. 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. 
  2. 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. 
  3. Lynch, M., and J. S. Conery. 2003. The origins of genome complexity. Science 302: 1401-1404. 
  4. Housworth, E., E. Martins, and M. Lynch. 2003. The phylogenetic mixed model. American Naturalist 163: 84-96. 
  5. Estes, S., and M. Lynch. 2003. Rapid recovery of mutation-accumulation lines by compensatory mutation. Evolution 57: 1022-1030. 
  6. 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. 
  7. Lynch, M., and A. Kewalramani. 2003. Messenger RNA processing and the evolutionary proliferation of introns. Mol. Biol. Evol. 20: 563-571. 
  8. Keightley, P. D., and M. Lynch. 2003. Towards a realistic model of mutations affecting fitness. Evolution 57: 683-685. 
  9. 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. 


  1. 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
  2. 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
  3. Lynch, M. 2002. Chromosomal repatterning by gene duplication. Science 297: 945-947. PDF
  4. Lynch, M., and A. Richardson. 2002. The evolution of spliceosomal introns. Curr. Opin. Gen. Devel. 12: 701-710. PDF
  5. Lynch, M. 2002. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. USA 99: 6118-6123. PDF


  1. 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
  2. Lynch, M., and M. O'Hely. 2001. Supplementation and the genetic fitness of natural populations. Conservation Genetics 2: 363-378. PDF
  3. Lynch, M. 2001. The molecular natural history of the human genome. Trends in Ecology and Evolution 16: 420-422. PDF
  4. 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
  5. Higgins, K., and M. Lynch. 2001. Metapopulation extinction due to mutation accumulation. Proc. Natl. Acad. Sci. USA 98: 2928-2933. PDF
  6. Lynch, M., and J. S. Conery. 2001. Gene duplication and evolution: response to Long and Thornton and Zhang et al. Science 293: 1551a. PDF


  1. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1154. PDF
  2. Lynch, M. 2000. The limits to knowledge in quantitative genetics. Evol. Biol. 32: 225-237. PDF
  3. 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
  4. Lynch, M., and A. Force. 2000. Gene duplication and the origin of interspecific genomic incompatibility. American Naturalist 156: 590-605. PDF
  5. Pfrender, M. E., and M. Lynch. 2000. Quantitative genetic variation in Daphnia: temporal changes in genetic architecture. Evolution 54: 1502-1509. PDF
  6. 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
  7. Blanchard, J., and M. Lynch. 2000. Why do mitochondrial genes end up in the nuclear genome? Trends in Genetics 16: 315-320. PDF
  8. Vassilieva, L., A. M. Hook, and M. Lynch. 2000. The fitness effects of spontaneous mutations in Caenorhabditis elegans. Evolution 54: 1234-1246. PDF
  9. Lynch, M., and A. Force. 2000. The probability of duplicate-gene preservation by subfunctionalization. Genetics 154: 459-473. PDF

Before 2000

  1. Schultz, S. T., M. Lynch, and J. H. Willis. 1999. Spontaneous deleterious mutation in Arabidopsis. Proc. Natl. Acad. Sci. USA 96: 11393-11398. PDF
  2. Lynch, M. 1999. Estimation of genetic correlations in natural populations. Genetical Research 74: 255-264. PDF
  3. Conery, J. S., and M. Lynch. 1999. Genetic simulation library. Bioinformatics 15: 85-86. PDF
  4. Lynch, M., J. Blanchard, D. Houle, T. Kibota, S. Schultz, L. Vassilieva, and J. Willis. 1999. Spontaneous deleterious mutation. Evolution 53: 645-663. PDF
  5. 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
  6. Lynch, M. 1999. The age and relationships of the major animal phyla. Evolution 53: 319-325. PDF
  7. Lynch, M., and K. Ritland. 1999. Estimation of relatedness with molecular markers. Genetics 152: 1753-1766. PDF
  8. 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
  9. Vassilieva, L., and M. Lynch. 1999. Accumulation of spontaneous mutations in Caenorhabditis elegans. Genetics 151: 119-129. PDF
  10. 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
  11. Lynch, M., and R. Lande. 1998. The critical effective size for a genetically secure population. Anim. Cons. 1: 70-72. PDF
  12. 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
  13. Lynch, M., and J. Blanchard. 1998. Deleterious mutation accumulation in organelle genomes. Genetica 102/103: 29-39. PDF
  14. 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 
  15. 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
  16. Lynch, M. 1997. Mutation accumulation in nuclear, organelle, and prokaryotic genomes: transfer RNA genes. Mol. Biol. Evol. 14: 914-925. PDF
  17. Deng, H.-W., and M. Lynch. 1997. Inbreeding depression and inferred deleterious mutation parameters in Daphnia. Genetics 147: 147-155. PDF
  18. 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
  19. Kibota, T., and M. Lynch. 1996. Estimate of the genomic mutation rate deleterious to overall fitness in Escherichia coli. Nature 381: 694-696. PDF
  20. Houle, D., R. Morikawa, and M. Lynch. 1996. Comparing mutational variabilities. Genetics 143: 1467-1483. PDF
  21. Deng, H.-W., and M. Lynch. 1996. Estimation of deleterious-mutation parameters in natural populations. Genetics 144: 349-360. PDF
  22. Deng, H.-W., and M. Lynch. 1996. Change of genetic architecture in response to sex. Genetics 143: 203-212. PDF
  23. Lynch, M. 1996. Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes. Mol. Biol. Evol. 13: 209-220. PDF
  24. 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
  25. Lynch, M., J. Conery, and R. Bürger. 1995. Mutation accumulation and the extinction of small populations. American Naturalist 146: 489-518. PDF
  26. Lynch, M., J. Conery, and R. Bürger. 1995. Mutational meltdowns in sexual populations. Evolution 49: 1067-1080. PDF
  27. 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
  28. 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
  29. 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
  30. Toline, C. A., and M. Lynch. 1994. Mutational divergence of life-history traits in an obligate parthenogen. Genome 37: 33-35. PDF
  31. Lynch, M., and H. W. Deng. 1994. Genetic slippage in response to sex. American Naturalist 144: 242-261. PDF
  32. Bürger, R., and M. Lynch. 1994. Evolution and extinction in a changing environment: a quantitative-genetic analysis. Evolution 49: 151-163. PDF
  33. Lynch, M., and B. Milligan. 1994. Analysis of population-genetic structure using RAPD markers. Molecular Ecology 3: 91-99. PDF
  34. Gabriel, W., M. Lynch, and R. Bürger. 1993. Muller's ratchet and mutational meltdowns. Evolution 47: 1744-1757. PDF
  35. Lynch, M. 1994. The neutral theory of phenotypic evolution, pp. 86-108. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press. PDF
  36. Lynch, M., and K. Spitze. 1994. Evolutionary genetics of Daphnia, pp. 109-128. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press. PDF
  37. Lynch, M., and P. Jerrol. 1993. A method for calibrating molecular clocks and its application to animal mitochondrial DNA. Genetics 135: 1197-1208. PDF
  38. Lynch, R. Bürger, D. Butcher, and W. Gabriel. 1993. Mutational meltdowns in asexual populations. J. Heredity 84: 339-344. PDF
  39. 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
  40. Gabriel, W., and M. Lynch. 1992. The selective advantage of reaction norms for environmental tolerance. J. Evol. Biol. 5: 41-59. PDF
  41. Lynch, M. 1992. The life history consequences of resource depression in Ceriodaphnia quadrangula and Daphnia ambigua. Ecology 73: 1620-1629. PDF
  42. Cohen, J. E., M. Lynch, and C. E. Taylor. 1991. Forensic DNA tests and Hardy-Weinberg equilibrium. Science 253: 1037. PDF
  43. 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
  44. Spitze, K., J. Burnson, and M. Lynch. 1991. The covariance structure of life history characters in Daphnia pulex. Evolution 45: 1081-1090. PDF
  45. Crease, T. J., and M. Lynch. 1991. Ribosomal DNA variation in Daphnia pulex. Mol. Biol. Evol. 8: 620-640. PDF
  46. 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
  47. Lynch, M. 1991. The genetic interpretation of inbreeding depression and outbreeding depression. Evolution 45: 622-629. PDF
  48. Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45: 1065-1080. PDF
  49. 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
  50. Lynch, M., and W. Gabriel. 1990. Mutation load and the survival of small populations. Evolution 44: 1725-1737. PDF
  51. Lynch, M. 1990. The similarity index and DNA fingerprinting. Mol. Biol. Evol. 7: 478-484. PDF
  52. 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
  53. Lynch, M., and T. Crease. 1990. The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol. 7: 377-394. PDF
  54. Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. American Naturalist 136: 727-741. PDF
  55. Lynch, M. 1989. The life history consequences of resource depression in Daphnia pulex. Ecology 70: 246-256. PDF
  56. Lynch, M., K. Spitze, and T. Crease. 1989. The distribution of life history variation in Daphnia pulex. Evolution 43: 1724-1736. PDF
  57. Lynch, M. 1989. Phylogenetic hypotheses under the assumption of neutral quantitative genetic variation. Evolution 43: 1-17. PDF
  58. Lynch, M. 1988. Design and analysis of experiments on random drift and inbreeding. Genetics 120: 791-807. PDF
  59. Lynch, M. 1988. Estimation of relatedness by DNA fingerprinting. Mol. Biol. Evol. 5: 584-599. PDF
  60. 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
  61. 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
  62. Lynch, M. 1988. The divergence of neutral quantitative characters among partially isolated populations. Evolution 42: 455-466. PDF
  63. Lynch, M. 1988. The rate of polygenic mutation. Genetical Research 51: 137-148. PDF
  64. Lynch, M. 1987. The evolution of intrafamilial interactions. Proc. Natl. Acad. Sci. USA 84: 8507-8511. PDF
  65. 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
  66. 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
  67. Lynch, M., and W. Gabriel. 1987. Environmental tolerance. American Naturalist 129: 283-303. PDF
  68. Lynch, M. 1987. The consequences of fluctuating selection for isozyme polymorphisms in Daphnia. Genetics 115: 657-669. PDF
  69. Lynch, M., and W. G. Hill. 1986. Phenotypic evolution by neutral mutation. Evolution 40: 915-935. PDF
  70. Lynch, M. 1986. Random drift, uniform selection, and the degree of population differentiation. Evolution 40: 640-643. PDF
  71. Lynch, M., L. Weider, and W. Lampert. 1986. Measurement of the carbon balance in Daphnia. Limnol. Oceanogr. 31: 17-33. PDF
  72. Lynch, M. 1985. Spontaneous mutations for life history characters in an obligate parthenogen. Evolution 39: 804-818. PDF
  73. Lynch, M. 1985. Speciation in the Cladocera. Verh. Internat. Verein. Limnol. 22: 3116-3123. PDF
  74. Lynch, M. 1985. Elements of a mechanistic theory for the life history consequences of food limitation. Ergeb. Limnol. 21: 351-362. PDF
  75. Lynch, M. 1984. The selective value of alleles underlying polygenic traits. Genetics 108: 1021-1033. PDF
  76. Lynch, M. 1984. Destabilizing hybridization, general-purpose genotypes, and geographic parthenogenesis. Quarterly Review of Biology 59: 257-290. PDF
  77. Lynch, M. 1984. The limits to life history evolution in Daphnia. Evolution 38: 465-482. PDF
  78. Lynch, M. 1984. The genetic structure of a cyclical parthenogen. Evolution 38: 186-203. PDF
  79. Lynch, M., and W. Gabriel. 1983. Phenotypic evolution and parthenogenesis. American Naturalist 122: 745-764. PDF
  80. Lynch, M., and R. Ennis. 1983. Resource availability, maternal effects, and longevity. Experimental Gerontology 18: 147-165. PDF
  81. Lynch, M. 1983. Estimation of size-specific mortality rates in zooplankton populations by periodic sampling. Limnol. Oceanogr. 28: 533-545. PDF
  82. Weis, A., P. Price, and M. Lynch. 1983. Selection for clutch size in the gall-maker Asteromyia carbonifera. Ecology 64: 688-695. PDF
  83. Lynch, M. 1983. Ecological genetics of Daphnia pulex. Evolution 37: 358-374. PDF
  84. Lynch, M. 1982. How well does the Edmondson-Paloheimo model approximate instantaneous birth rates? Ecology 63: 12-18. PDF
  85. 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
  86. Lynch, M. and J. Shapiro. 1981. Predation, enrichment, and phytoplankton community structure. Limnol. Oceanogr. 26: 86-102. PDF
  87. 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
  88. 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 Zooplankton Communities. American Society of Limnology and Oceanography Special Symposium No. 3: 367-376. PDF
  89. Lynch, M. 1980. The evolution of cladoceran life histories. Quarterly Review of Biology 55: 23-42. PDF
  90. Lynch, M. 1979. Predation, competition, and zooplankton community structure: an experimental study. Limnol. Oceanogr. 24: 253-272. PDF
  91. Lynch, M. 1978. Complex interactions between natural coexploiters - Daphnia and Ceriodaphnia. Ecology 59: 552-564. PDF
  92. Lynch, M. 1977. Fitness and optimal body size in zooplankton populations. Ecology 58: 763-774. PDF
  93. Lynch, M. 1977. Zooplankton competition and plankton community structure. Limnol. Oceanogr. 22: 775-777. PDF
  94. 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
  95. Lynch, M. 1974. The phytoplankton of the Allegheny Reservoir from May 1972 to September 1973. Science Studies (St. Bonaventure University) 30: 5-29. PDF