1. Lynch, M. 1974. The phytoplankton of the Allegheny Reservoir from May 1972 to September 1973. Science Studies (St. Bonaventure University) 30: 5-29. PDF
2. 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
3. Lynch, M. 1977. Zooplankton competition and plankton community structure. Limnol. Oceanogr. 22: 775-777. PDF
4. Lynch, M. 1977. Fitness and optimal body size in zooplankton populations. Ecology 58: 763-774. PDF
5. Lynch, M. 1978. Complex interactions between natural coexploiters - Daphnia and Ceriodaphnia. Ecology 59: 552-564. PDF
6. Lynch, M. 1979. Predation, competition, and zooplankton community structure: an experimental study. Limnol. Oceanogr. 24: 253-272. PDF
7. Lynch, M. 1980. The evolution of cladoceran life histories. Quarterly Review of Biology 55: 23-42. PDF
8. 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
9. 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
10. Lynch, M. and J. Shapiro. 1981. Predation, enrichment, and phytoplankton community structure. Limnol. Oceanogr. 26: 86-102. PDF
11. 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
12. Lynch, M. 1982. How well does the Edmondson-Paloheimo model approximate instantaneous birth rates? Ecology 63: 12-18. PDF
13. Lynch, M. 1983. Ecological genetics of Daphnia pulex. Evolution 37: 358-374. PDF
14. Weis, A., P. Price, and M. Lynch. 1983. Selection for clutch size in the gall-maker Asteromyia carbonifera. Ecology 64: 688-695.
15. Lynch, M. 1983. Estimation of size-specific mortality rates in zooplankton populations by periodic sampling. Limnol. Oceanogr. 28: 533-545. PDF
16. Lynch, M., and R. Ennis. 1983. Resource availability, maternal effects, and longevity. Experimental Gerontology 18: 147-165. PDF
17. Lynch, M., and W. Gabriel. 1983. Phenotypic evolution and parthenogenesis. American Naturalist 122: 745-764. PDF
18. Lynch, M. 1984. The genetic structure of a cyclical parthenogen. Evolution 38: 186-203. PDF
19. Lynch, M. 1984. The limits to life history evolution in Daphnia. Evolution 38: 465-482. PDF
20. Lynch, M. 1984. Destabilizing hybridization, general-purpose genotypes, and geographic parthenogenesis. Quarterly Review of Biology 59: 257-290. PDF
21. Lynch, M. 1984. The selective value of alleles underlying polygenic traits. Genetics 108: 1021-1033. PDF
22. Lynch, M. 1985. Elements of a mechanistic theory for the life history consequences of food limitation. Ergeb. Limnol. 21: 351-362. PDF
23. Lynch, M. 1985. Speciation in the Cladocera. Verh. Internat. Verein. Limnol. 22: 3116-3123. PDF
24. Lynch, M. 1985. Spontaneous mutations for life history characters in an obligate parthenogen. Evolution 39: 804-818. PDF
25. Lynch, M., L. Weider, and W. Lampert. 1986. Measurement of the carbon balance in Daphnia. Limnol. Oceanogr. 31: 17-33. PDF
26. Lynch, M. 1986. Random drift, uniform selection, and the degree of population differentiation. Evolution 40: 640-643. PDF
27. Lynch, M., and W. G. Hill. 1986. Phenotypic evolution by neutral mutation. Evolution 40: 915-935. PDF
28. Lynch, M. 1987. The consequences of fluctuating selection for isozyme polymorphisms in Daphnia. Genetics 115: 657-669. PDF
29. Lynch, M., and W. Gabriel. 1987. Environmental tolerance. American Naturalist 129: 283-303. PDF
30. 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
31. 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
32. Lynch, M. 1987. The evolution of intrafamilial interactions. Proc. Natl. Acad. Sci. USA 84: 8507-8511. PDF
33. Lynch, M. 1988. The rate of polygenic mutation. Genetical Research 51: 137-148. PDF
34. Lynch, M. 1988. The divergence of neutral quantitative characters among partially isolated populations. Evolution 42: 455-466. PDF
35. 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
36. 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
37. Lynch, M. 1988. Estimation of relatedness by DNA fingerprinting. Mol. Biol. Evol. 5: 584-599. PDF
38. Lynch, M. 1988. Design and analysis of experiments on random drift and inbreeding. Genetics 120: 791-807. PDF
39. Lynch, M. 1989. Phylogenetic hypotheses under the assumption of neutral quantitative genetic variation. Evolution 43: 1-17. PDF
40. Lynch, M., K. Spitze, and T. Crease. 1989. The distribution of life history variation in Daphnia pulex. Evolution 43: 1724-1736. PDF
41. Lynch, M. 1989. The life history consequences of resource depression in Daphnia pulex. Ecology 70: 246-256. PDF
42. Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. American Naturalist 136: 727-741. PDF
43. Lynch, M., and T. Crease. 1990. The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol. 7: 377-394. PDF
44. 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
45. Lynch, M. 1990. The similarity index and DNA fingerprinting. Mol. Biol. Evol. 7: 478-484. PDF
46. Lynch, M., and W. Gabriel. 1990. Mutation load and the survival of small populations. Evolution 44: 1725-1737. PDF
47. 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
48. Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45: 1065-1080. PDF
49. Lynch, M. 1991. The genetic interpretation of inbreeding depression and outbreeding depression. Evolution 45: 622-629. PDF
50. 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
51. Crease, T. J., and M. Lynch. 1991. Ribosomal DNA variation in Daphnia pulex. Mol. Biol. Evol. 8: 620-640. PDF
52. Spitze, K., J. Burnson, and M. Lynch. 1991. The covariance structure of life history characters in Daphnia pulex. Evolution 45: 1081-1090. PDF
53. 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
54. Cohen, J. E., M. Lynch, and C. E. Taylor. 1991. Forensic DNA tests and Hardy-Weinberg equilibrium. Science 253: 1037. PDF
55. Lynch, M. 1992. The life history consequences of resource depression in Ceriodaphnia quadrangula and Daphnia ambigua. Ecology 73: 1620-1629. PDF
56. Gabriel, W., and M. Lynch. 1992. The selective advantage of reaction norms for environmental tolerance. J. Evol. Biol. 5: 41-59. PDF
57. 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
58. Lynch, R. Bürger, D. Butcher, and W. Gabriel. 1993. Mutational meltdowns in asexual populations. J. Heredity 84: 339-344. PDF
59. Lynch, M., and P. Jerrol. 1993. A method for calibrating molecular clocks and its application to animal mitochondrial DNA. Genetics 135: 1197-1208. PDF
60. Lynch, M., and K. Spitze. 1994. Evolutionary genetics of Daphnia, pp. 109-128. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press. PDF
61. Lynch, M. 1994. The neutral theory of phenotypic evolution, pp. 86-108. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press. PDF
62. Gabriel, W., M. Lynch, and R. Bürger. 1993. Muller's ratchet and mutational meltdowns. Evolution 47: 1744-1757. PDF
63. Lynch, M., and B. Milligan. 1994. Analysis of population-genetic structure using RAPD markers. Molecular Ecology 3: 91-99. PDF
64. Bürger, R., and M. Lynch. 1994. Evolution and extinction in a changing environment: a quantitative-genetic analysis. Evolution 49: 151-163. PDF
65. Lynch, M., and H. W. Deng. 1994. Genetic slippage in response to sex. American Naturalist 144: 242-261. PDF
66. Toline, C. A., and M. Lynch. 1994. Mutational divergence of life-history traits in an obligate parthenogen. Genome 37: 33-35. PDF
67. 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
68. 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.
69. 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
70. Lynch, M., J. Conery, and R. Bürger. 1995. Mutational meltdowns in sexual populations. Evolution 49: 1067-1080. PDF
71. Lynch, M., J. Conery, and R. Bürger. 1995. Mutation accumulation and the extinction of small populations. American Naturalist 146: 489-518. PDF
72. 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
73. Lynch, M. 1996. Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes. Mol. Biol. Evol. 13: 209-220. PDF
74. Deng, H.-W., and M. Lynch. 1996. Change of genetic architecture in response to sex. Genetics 143: 203-212. PDF
75. Deng, H.-W., and M. Lynch. 1996. Estimation of deleterious-mutation parameters in natural populations. Genetics 144: 349-360. PDF
76. Houle, D., R. Morikawa, and M. Lynch. 1996. Comparing mutational variabilities. Genetics 143: 1467-1483. PDF
77. Kibota, T., and M. Lynch. 1996. Estimate of the genomic mutation rate deleterious to overall fitness in Escherichia coli. Nature 381: 694-696. PDF
78. 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
79. Deng, H.-W., and M. Lynch. 1997. Inbreeding depression and inferred deleterious mutation parameters in Daphnia. Genetics 147: 147-155. PDF
80. Lynch, M. 1997. Mutation accumulation in nuclear, organelle, and prokaryotic genomes: transfer RNA genes. Mol. Biol. Evol. 14: 914-925. PDF
81. 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
82. 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
83. Lynch, M., and J. Blanchard. 1998. Deleterious mutation accumulation in organelle genomes. Genetica 102/103: 29-39. PDF
84. 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
85. Lynch, M., and R. Lande. 1998. The critical effective size for a genetically secure population. Anim. Cons. 1: 70-72. PDF
86. 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
87. Vassilieva, L., and M. Lynch. 1999. Accumulation of spontaneous mutations in Caenorhabditis elegans. Genetics 151: 119-129. PDF
88. 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
89. Lynch, M., and K. Ritland. 1999. Estimation of relatedness with molecular markers. Genetics 152: 1753-1766. PDF
90. Lynch, M. 1999. The age and relationships of the major animal phyla. Evolution 53: 319-325. PDF
91. 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
92. Lynch, M., J. Blanchard, D. Houle, T. Kibota, S. Schultz, L. Vassilieva, and J. Willis. 1999. Spontaneous deleterious mutation. Evolution 53: 645-663. PDF
93. Conery, J. S., and M. Lynch. 1999. Genetic simulation library. Bioinformatics 15: 85-86. PDF
94. Lynch, M. 1999. Estimation of genetic correlations in natural populations. Genetical Research 74: 255-264. PDF
95. Schultz, S. T., M. Lynch, and J. H. Willis. 1999. Spontaneous deleterious mutation in Arabidopsis. Proc. Natl. Acad. Sci. USA 96: 11393-11398. PDF
96. Lynch, M., and A. Force. 2000. The probability of duplicate-gene preservation by subfunctionalization. Genetics 154: 459-473. PDF
97. Vassilieva, L., A. M. Hook, and M. Lynch. 2000. The fitness effects of spontaneous mutations in Caenorhabditis elegans. Evolution 54: 1234-1246. PDF
98. Blanchard, J., and M. Lynch. 2000. Why do mitochondrial genes end up in the nuclear genome? Trends in Genetics 16: 315-320. PDF
99. 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
100. Pfrender, M. E., and M. Lynch. 2000. Quantitative genetic variation in Daphnia: temporal changes in genetic architecture. Evolution 54: 1502-1509. PDF
101. Lynch, M., and A. Force. 2000. Gene duplication and the origin of interspecific genomic incompatibility. American Naturalist 156: 590-605. PDF
102. 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
103. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1154. PDF
103a. Lynch, M. 2000. The limits to knowledge in quantitative genetics. Evol. Biol. 32: 225-237. PDF
104. Lynch, M., and J. S. Conery. 2001. Gene duplication and evolution: response to Long and Thornton and Zhang et al. Science 293: 1551a.
105. Higgins, K., and M. Lynch. 2001. Metapopulation extinction due to mutation accumulation. Proc. Natl. Acad. Sci. USA 98: 2928-2933. PDF
106. 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
107. Lynch, M. 2001. The molecular natural history of the human genome. Trends in Ecology and Evolution 16: 420-422. PDF
108. Lynch, M., and M. O'Hely. 2001. Supplementation and the genetic fitness of natural populations. Conservation Genetics 2: 363-378. PDF
109. 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
110. Lynch, M. 2002. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. USA 99: 6118-6123. PDF
111. Lynch, M., and A. Richardson. 2002. The evolution of spliceosomal introns. Curr. Opin. Gen. Devel. 12: 701-710. PDF
112. Lynch, M. 2002. Chromosomal repatterning by gene duplication. Science 297: 945-947. PDF
113. 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
114. 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
115. 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
116. Keightley, P. D., and M. Lynch. 2003. Towards a realistic model of mutations affecting fitness. Evolution 57: 683-685. PDF
117. Lynch, M., and A. Kewalramani. 2003. Messenger RNA processing and the evolutionary proliferation of introns. Mol. Biol. Evol. 20: 563-571. PDF
118. 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
119. Estes, S., and M. Lynch. 2003. Rapid recovery of mutation-accumulation lines by compensatory mutation. Evolution 57: 1022-1030. PDF
120. Housworth, E., E. Martins, and M. Lynch. 2003. The phylogenetic mixed model. American Naturalist 163: 84-96. PDF
121. Lynch, M., and J. S. Conery. 2003. The origins of genome complexity. Science 302: 1401-1404. PDF
122. 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
123. 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
124. 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
125. 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
126. 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
127. Lynch, M., and V. Katju. 2004. The altered evolutionary trajectories of gene duplicates. Trends in Genetics 20: 544-549. PDF
128. 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
129. 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
130. Dudycha, J. L., and M. Lynch. 2005. Ontogeny and allometry of resource allocation in animals with indeterminate growth. Evolution 59: 565-576. PDF
131. Lynch, M., D. G. Scofield, and X. Hong. 2005. The evolution of transcription-initiation sites. Mol. Biol. Evol. 22: 1137-1146. PDF
132. 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
133. 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
134. 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
135. 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
136. 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
137. Paland, S., J. K. Colbourne, and M. Lynch. 2005. Evolutionary history of contagious asexuality in Daphnia pulex. Evolution 59: 800-813. PDF
138. Ajie, B. C., S. Estes, M. Lynch, and P. C. Phillips. 2005. Behavioral degradation under mutation accumulation. Genetics 170: 655-660. PDF
139. 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
140. Lynch, M. 2005. Intelligent design vs. intelligent evolution. Nature 435: 276. PDF
141. Lynch, M. 2005. Simple evolutionary pathways to complex proteins. Protein Science 14: 2217-2225. PDF
142. 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
143. 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
144. Lynch, M. 2006. The origins of eukaryotic gene structure. Mol. Biol. Evol. 23: 450-468. PDF
145. Paland, S., and M. Lynch. 2006. Transitions to asexuality result in excess amino-acid substitutions. Science 311: 990-902. PDF
146. Lynch, M., B. Koskella, and S. Schaack. 2006. Mutation pressure and the evolution of organelle genome architecture. Science 311: 1727-1730. PDF
147. 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
148. 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
149. 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
150. 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
151. 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
152. Lynch, M. 2006. Streamlining and simplification of microbial genome architecture. Ann. Rev. Microbiol. 60: 327-349. PDF
153. 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
154. 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
155. Lynch, M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc. Natl. Acad. Sci. USA 104 Suppl.: 8597-8604. PDF
156. 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
157. Lynch, M. 2007. The evolution of genetic networks by nonadaptive processes. Nature Reviews Genetics 8: 803-813. PDF
158. 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
159. 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
160. 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
161. 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
162. Omilian, A. R., D. G. Scofield, and M. Lynch. 2008. Intron presence-absence polymorphisms in Daphnia. Mol. Biol. Evol. 25: 2129-2139. PDF
163. 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
164. 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
165. Lynch, M. 2008. The cellular, developmental, and population-genetic determinants of mutation-rate evolution. Genetics 180: 933-943. PDF
166. Scofield, D. G., and M. Lynch. 2008. Evolutionary diversification of the Sm family of RNA-associated proteins. Mol. Biol. Evol. 25: 2255-2267. PDF
167. Catania, F., and M. Lynch. 2008. Where do introns come from? PLoS Biology 6: e283. PDF
168. 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
169. 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
170. Omilian, A. R., and M. Lynch. 2009. Patterns of intraspecific DNA variation in the Daphnia nuclear genome. Genetics 182: 325-336. PDF
171. Lynch, M. 2009. Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics 182: 295-301. PDF
172. 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
173. 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
174. 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
175. Gao, X., and M. Lynch. 2009. Ubiquitous internal gene duplication and intron creation in eukaryotes. Proc. Natl. Acad. Sci. USA 106: 20818-20823. PDF
176. 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
177. Lynch, M. 2009. Rate, molecular spectrum, and consequences of spontaneous mutations in man. Proc. Natl. Acad. Sci. USA 107: 961-968. PDF
178. 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
179. 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
180. 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
181. Gleick, P. H., et al. 2010. Climate change and the integrity of science. Science 328: 689-690. PDF
182. Lynch, M., and A. Abegg. 2010. The rate of origin of complex adaptations. Mol. Biol. Evol. 27: 1404-1414. PDF
183. Lynch, M. 2010. Evolution of the mutation rate. Trends in Genetics 26: 345-352. PDF
184. 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
185. 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
186. 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
187. Lynch, M. 2010. Scaling expectations for the time to establishment of complex adaptations. Proc. Natl. Acad. Sci. USA 107: 16577-16582. PDF
188. 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
189. 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
190. Colbourne, J., et al. 2011. The ecoresponsive genome of Daphnia pulex. Science 331: 555-561. PDF
191. 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
192. Lynch, M. 2011. Statistical inference on the mechanisms of genome evolution. PLoS Genetics 7(6): e1001389. PDF
193. 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
194. Lynch, M. 2011. The lower bound to the evolution of mutation rates. Genome Biol. Evol. 3: 1107-1118. PDF
195. 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
196. 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
197. Lynch, M. 2012. The evolution of multimeric protein assemblages. Mol. Biol. Evol. 29: 1353-1366. PDF
198. 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
199. 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
200. 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
201. Lynch, M. 2012. Evolutionary layering and the limits to cellular perfection. Proc. Natl. Acad. Sci. USA 109: 18851-18856. PDF
202. 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
203. 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
204. 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
205. 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
206. 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
207. Lynch, M. 2013. Evolutionary diversification of the multimeric states of proteins. Proc. Natl. Acad. Sci. USA 110: E2821-E2828.PDF
208. 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
209. 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
210. Schrider, D., D. Houle, M. Lynch, and M. Hahn. 2013. Genetic variation in the mutation rate in Drosophila melanogaster. Genetics 194: 937-954.PDF
211. 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
212. 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
213. 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
214. 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
215. Maruki, T., and M. Lynch. 2013. Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data. Genetics 197: 1303-1313. PDF
216. Lynch, M., D. Bost, S. Wilson, and T. Maruki. 2014. Population-genetic inference from pooled-sequencing data. Genome Biol. Evol. 6: 1210-1218. PDF
217. 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
218. 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
219. 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
220. 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
221. 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
222. Sazer, S., M. Lynch, and D. Needleman. 2014. Deciphering the evolutionary history of open and closed mitosis. Curr. Biol. 24: R1099-R1103. PDF
223. Lynch, M., and K. Hagner. 2014. Evolutionary meandering of intermolecular interactions along the drift barrier. Proc. Natl. Acad. Sci. USA 112: E30-E38. PDF
224. 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
225. 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
226. Gout, J. F., and M. Lynch. 2015. Maintenance and loss of duplicated genes by dosage subfunctionalization. Mol. Bio. Evol. 32: 2141-2148. PDF
227. Lynch, M. 2015. Feedforward loop for diversity. Nature 523: 414-416. PDF
228. 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
229. 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
230. Maruki, T., and M. Lynch. 2015. Genotype-frequency estimation from high-throughput sequencing data. Genetics 201: 473-486. PDF
231. 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
232. 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
Books:
With 14 other committee members, for the National Research Council. 1995. Science and the Endangered Species Act. National Academy Press, Washington, DC.
Lynch, M., and J. B. Walsh. 1998. Genetics and Analysis of Quantitative Traits. Sinauer Assocs., Inc., Sunderland, MA.
Lynch, M. 2007. The Origins of Genome Architecture. Sinauer Assocs., Inc., Sunderland, MA.
Walsh, J. B., and M. Lynch. Evolution
of Quantitative Traits. Sinauer Assocs., Inc., Sunderland, MA (in prep.)