Bloomington, Indiana 47405
Phone: 812-855-7384
Fax: 812-855-6705
Email: milynch@indiana.edu
Birth: 6 December 1951, Auburn, New York
Undergraduate education: St. Bonaventure University, Biology - B.S., 1973.
Graduate education: University of Minnesota, Ecology and Behavioral Biology - Ph.D., 1977.
Areas of Interest and Research: The integration of cell biology, development, genetics, ecology, and evolution; quantitative genetics; molecular, genomic, and phenotypic evolution.
Professional Activities:
Distinguished Professor, Indiana University, 2005 – present.
IU Center for Genomics and Bioinformatics Associated Investigator, 2007 – present.
Professor; Biology, Indiana University, 2001 – 2004.
Senior Fellow and Member of Advisory Board, Indiana Molecular Biology Institute, 2001 – present.
Professor; Biology, University of Oregon, 1989 – 2001.
Director, Ecology and Evolution Program, Univ. of Oregon, 1989 – 1993, 1996 – 2000.
Asst., Assoc., Full Professor; Ecology, Ethology, and Evolution; University of Illinois, 1977 – 1989.
Co-director, NSF IGERT Training Grant in Evolution, Development, and Genomics, 1999 – 2004.
Director, NSF Genetic Mechanisms of Evolution Training Grant, 1990 – 2000.
President, Society for Molecular Biology and Evolution, 2009.
President, American Genetic Association, 2007.
President, Society for the Study of Evolution, 2000.
Vice-president, Society for the Study of Evolution, 1994.
Council Member, Society for the Study of Evolution, 1991 – 1993.
Council Member, Society of Molecular Biology and Evolution, 2005 – 2007.
Board of Scientific Counselors, National Center for Biotechnology Information (NCBI), 2008 – 2012.
Associate Editor, Genome Biology and Evolution, 2008 – present.
Associate Editor, Genetics, 1992 – 1996.
Associate Editor, Conservation Genetics, 1999 – present.
Associate Editor, Molecular Ecology, 1991 – 1997.
Associate Editor, Evolution, 1988 – 1990.
Member, NRC/NAS Ecosystems Panel, 1997.
Member, NRC/NAS Committee on Scientific Issues in the Endangered Species Act, 1993 – 1995.
Member, Advisory Board for Extended Workshop, Evolutionary Perspectives on Mechanisms of Cellular
Organization, Kavli Institute for Theoretical Physics, 2010.
Member, Organizing Committee, FASEB Ciliate Molecular Genetics Meeting, 2009.
NESCent Working Group on Human Evolution, 2007 – present.
Member, Oversight Committee for Sequencing of the Daphnia pulex Genome, 2003 – present.
Member, Genetics Advisory Team, Oregon Department of Fish and Wildlife, 1990 – 2001.
Organizer, Symposium on Quantitative Genetics of Natural Populations, Raleigh, NC, 1987.
Instructor, Itasca Field Station, University of Minnesota, Ecological Genetics course, 1987.
Co-founder, Midwest Population Biology Conference (with J. Emlen); Chair, 1979, 1983 meetings.
Chair, NIH Genetic Variation and Evolution Study Section, 2009 – 2010.
Panel Member, NIH Genetic Variation and Evolution Study Section, 2004 – present.
Panel Member, NIH Genome Study Section, 1999.
Panel Member, NIH Quantitative Genetics Study Section, 1998.
Ad hoc Panel Member, NIH Genetics Study Section, 1990, 1997 – 2002.
Panel Member, NSF Eukaryotic Genetics / Genes and Genomes Panel, 2001 – present.
Panel Member, NSF Frontiers for Integrative Research, 2003.
Panel Member, NSF IGERT Program, 2000, 2001.
Advisory Panel Member, NSF Division of Environmental Biology, 1999.
Panel Member, NSF Population Biology Panel, 1987 – 1988, 1998.
Panel Member, NSF Research Training Group Program, BBS, 1990.
Panel Member, NSF Program on Conservation Biology, 1990.
Professional Societies:
American Association for the Advancement of Science
American Genetic Association
Genetics Society of America
Society for Molecular Biology and Evolution
Society for the Study of Evolution
Recognition:
Fellow, US National Academy of Sciences – 2009.
Fellow, American Academy of Arts and Sciences – 2002.
Fellow, American Association for the Advancement of Science – 1998.
Fellow, Max Planck Institut für Limnologie, Plön, West Germany – 1982, 1984, 1985.
Beckman Fellow, Center for Advanced Study, Univ. of Illinois – 1981.
List of Excellent Instructors, Univ. of Illinois – Limnology, 1978, 1982; Population Biology, 1988.
Univ. of Illinois Faculty Summer Fellowship, 1978.
Current Support:
National Institutes of Health, R01GM036827, 2006-2010, The Rate and Molecular Spectrum of Spontaneous Mutations, $2,704,000 (with W. Kelley Thomas, University of New Hampshire).
National Science Foundation, EF-0827411, 2008-2011, The Evolution of Gene and Genome Architecture, $830,000.
National Science Foundation, EF-0328516, 2003-2008, FIBR Grant: The Causes and Consequences of Recombination, $5,000,000 (with eight other coPIs) (in no-cost extension).
National Science Foundation, MCB-0342431, 2004-2007, The Evolution of Spliceosomal Introns, $531,000 (in no-cost extension).
Publications:
Lynch, M. 1974. The phytoplankton of the Allegheny Reservoir from May 1972 to September 1973. Science Studies (St. Bonaventure University) 30: 5-29.
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.
Lynch, M. 1977. Zooplankton competition and plankton community structure. Limnology and Oceanography 22: 775-777.
Lynch, M. 1977. Fitness and optimal body size in zooplankton populations. Ecology 58: 763-774.
Lynch, M. 1978. Complex interactions between natural coexploiters - Daphnia and Ceriodaphnia. Ecology 59: 552-564.
Lynch, M. 1979. Predation, competition, and zooplankton community structure: An experimental study. Limnology and Oceanography 24: 253-272.
Lynch, M. 1980. The evolution of cladoceran life histories. Quarterly Review of Biology 55: 23-42.
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.
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.
Lynch, M. 1981. Predation, enrichment, and phytoplankton community structure. Limnology and Oceanography 26: 86-102.
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.
Lynch, M. 1982. How well does the Edmondson-Paloheimo model approximate instantaneous birth rates? Ecology 63: 12-18.
Lynch, M. 1983. Ecological genetics of Daphnia pulex. Evolution 37: 358-374.
Weis, A., P. Price, and M. Lynch. 1983. Selection for clutch size in the gall-maker Asteromyia carbonifera. Ecology 64: 688-695.
Lynch, M. 1983. Estimation of size-specific mortality rates in zooplankton populations by periodic sampling. Limnology and Oceanography 28: 533-545.
Lynch, M., and R. Ennis. 1983. Resource availability, maternal effects, and longevity. Exper. Gerontology 18: 147-165.
Lynch, M., and W. Gabriel. 1983. Phenotypic evolution and parthenogenesis. American Naturalist 122: 745-764.
Lynch, M. 1984. The genetic structure of a cyclical parthenogen. Evolution 38: 186-203.
Lynch, M. 1984. The limits to life history evolution in Daphnia. Evolution 38: 465-482.
Lynch, M. 1984. Destabilizing hybridization, general-purpose genotypes, and geographic parthenogenesis. Quarterly Review of Biology 59: 257-290.
Lynch, M. 1984. The selective value of alleles underlying polygenic traits. Genetics 108: 1021-1033.
Lynch, M. 1985. Elements of a mechanistic theory for the life history consequences of food limitation. Ergeb. Limnol. 21: 351-362.
Lynch, M. 1985. Speciation in the Cladocera. Verh. Internat. Verein. Limnol. 22: 3116-3123.
Lynch, M. 1985. Spontaneous mutations for life history characters in an obligate parthenogen. Evolution 39: 804-818.
Lynch, M., L. Weider, and W. Lampert. 1986. Measurement of the carbon balance in Daphnia. Limnology and Oceanography 31: 17-33.
Lynch, M. 1986. Random drift, uniform selection, and the degree of population differentiation. Evolution 40: 640-643.
Lynch, M., and W. G. Hill. 1986. Phenotypic evolution by neutral mutation. Evolution 40: 915-935.
Lynch, M. 1987. The consequences of fluctuating selection for isozyme polymorphisms in Daphnia. Genetics 115: 657-669.
Lynch, M., and W. Gabriel. 1987. Environmental tolerance. American Naturalist 129: 283-303.
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.
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.
Lynch, M. 1987. The evolution of intrafamilial interactions. Proc. Natl. Acad. Sci. USA 84: 8507-8511.
Lynch, M. 1988. The rate of polygenic mutation. Genetical Research 51: 137-148.
Lynch, M. 1988. The divergence of neutral quantitative characters among partially isolated populations. Evolution 42: 455-466.
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.
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.
Lynch, M. 1988. Estimation of relatedness by DNA fingerprinting. Mol. Biol. Evol. 5: 584-599.
Lynch, M. 1988. Design and analysis of experiments on random drift and inbreeding. Genetics 120: 791-807.
Lynch, M. 1989. Phylogenetic hypotheses under the assumption of neutral quantitative genetic variation. Evolution 43: 1-17.
Lynch, M., K. Spitze, and T. Crease. 1989. The distribution of life history variation in Daphnia pulex. Evolution 43: 1724-1736.
Lynch, M. 1989. The life history consequences of resource depression in Daphnia pulex. Ecology 70: 246-256.
Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. American Naturalist 136: 727-741.
Lynch, M., and T. Crease. 1990. The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol. 7: 377-394.
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.
Lynch, M. 1990. The similarity index and DNA fingerprinting. Mol. Biol. Evol. 7: 478-484.
Lynch, M., and W. Gabriel. 1990. Mutation load and the survival of small populations. Evolution 44: 1725-1737.
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.
Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45: 1065-1080.
Lynch, M. 1991. The genetic interpretation of inbreeding depression and outbreeding depression. Evolution 45: 622-629.
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.
Crease, T. J., and M. Lynch. 1991. Ribosomal DNA variation in Daphnia pulex. Mol. Biol. Evol. 8: 620-640.
Spitze, K., J. Burnson, and M. Lynch. 1991. The covariance structure of life history characters in Daphnia pulex. Evolution 45: 1081-1090.
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.
Cohen, J. E., M. Lynch, and C. E. Taylor. 1991. Forensic DNA tests and Hardy-Weinberg equilibrium. Science 253: 1037.
Lynch, M. 1992. The life history consequences of resource depression in Ceriodaphnia quadrangula and Daphnia ambigua. Ecology 73: 1620-1629.
Gabriel, W., and M. Lynch. 1992. The selective advantage of reaction norms for environmental tolerance. J. Evol. Biol. 5: 41-59.
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.
Lynch, R. Bürger, D. Butcher, and W. Gabriel. 1993. Mutational meltdowns in asexual populations. J. Heredity 84: 339-344.
Lynch, M., and P. Jerrol. 1993. A method for calibrating molecular clocks and its application to animal mitochondrial DNA. Genetics 135: 1197-1208.
Lynch, M., and K. Spitze. 1994. Evolutionary genetics of Daphnia, pp. 109-128. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press.
Lynch, M. 1994. The neutral theory of phenotypic evolution, pp. 86-108. In L. Real (ed.) Ecological Genetics. Princeton Univ. Press.
Gabriel, W., M. Lynch, and R. Bürger. 1994. Muller's ratchet and mutational meltdowns. Evolution 47: 1744-1757.
Lynch, M., and B. Milligan. 1994. Analysis of population-genetic structure using RAPD markers. Molecular Ecology 3: 91-99.
Bürger, R., and M. Lynch. 1994. Evolution and extinction in a changing environment: a quantitative-genetic analysis. Evolution 49: 151-163.
Lynch, M., and H. W. Deng. 1994. Genetic slippage in response to sex. American Naturalist 144: 242-261.
Toline, C. A., and M. Lynch. 1994. Mutational divergence of life-history traits in an obligate parthenogen. Genome 37: 33-35.
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.
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.
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.
Lynch, M., J. Conery, and R. Bürger. 1995. Mutational meltdowns in sexual populations. Evolution 49: 1067-1080.
Lynch, M., J. Conery, and R. Bürger. 1995. Mutation accumulation and the extinction of small populations. American Naturalist 146: 489-518.
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.
Lynch, M. 1996. Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes. Mol. Biol. Evol. 13: 209-220.
Deng, H.-W., and M. Lynch. 1996. Change of genetic architecture in response to sex. Genetics 143: 203-212.
Deng, H.-W., and M. Lynch. 1996. Estimation of deleterious-mutation parameters in natural populations. Genetics 144: 349-360.
Houle, D., R. Morikawa, and M. Lynch. 1996. Comparing mutational variabilities. Genetics 143: 1467-1483.
Kibota, T., and M. Lynch. 1996. Estimate of the genomic mutation rate deleterious to overall fitness in Escherichia coli. Nature 381: 694-696.
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.
Deng, H.-W., and M. Lynch. 1997. Inbreeding depression and inferred deleterious mutation parameters in Daphnia. Genetics 147: 147-155.
Lynch, M. 1997. Mutation accumulation in nuclear, organelle, and prokaryotic genomes: transfer RNA genes. Mol. Biol. Evol. 14: 914-925.
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.
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.
Lynch, M., and J. Blanchard. 1998. Deleterious mutation accumulation in organelle genomes. Genetica 102/103: 29-39.
Deng, H.-W., Y.-X. Fu, and Lynch, M. 1998. Inferring the major genomic mode of dominance and overdominance. Genetica 102/103: 559-567.
Lynch, M., and R. Lande. 1998. The critical effective size for a genetically secure population. Anim. Cons. 1: 70-72.
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.
Vassilieva, L., and M. Lynch. 1999. Accumulation of spontaneous mutations in Caenorhabditis elegans. Genetics 151: 119-129.
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.
Lynch, M., and K. Ritland. 1999. Estimation of relatedness with molecular markers. Genetics 152: 1753-1766.
Lynch, M. 1999. The age and relationships of the major animal phyla. Evolution 53: 319-325.
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.
Lynch, M., J. Blanchard, D. Houle, T. Kibota, S. Schultz, L. Vassilieva, and J. Willis. 1999. Spontaneous deleterious mutation. Evolution 53: 645-663.
Conery, J. S., and M. Lynch. 1999. Genetic simulation library. Bioinformatics 15: 85-86.
Lynch, M. 1999. Estimation of genetic correlations in natural populations. Genetical Research 74: 255-264.
Schultz, S. T., M. Lynch, and J. H. Willis. 1999. Spontaneous deleterious mutation in Arabidopsis. Proc. Natl. Acad. Sci. USA 96: 11393-11398.
Lynch, M., and A. Force. 2000. The probability of duplicate-gene preservation by subfunctionalization. Genetics 154: 459-473.
Vassilieva, L., A. M. Hook, and M. Lynch. 2000. The fitness effects of spontaneous mutations in Caenorhabditis elegans. Evolution 54: 1234-1246.
Blanchard, J., and M. Lynch. 2000. Why do mitochondrial genes end up in the nuclear genome? Trends in Genetics 16: 315-320.
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.
Pfrender, M. E., and M. Lynch. 2000. Quantitative genetic variation in Daphnia: temporal changes in genetic architecture. Evolution 54: 1502-1509.
Lynch, M., and A. Force. 2000. Gene duplication and the origin of interspecific genomic incompatibility. American Naturalist 156: 590-605.
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.
Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1154.
Lynch, M. 2000. The limits to knowledge in quantitative genetics. Evol. Biol. 32: 225-237.
Lynch, M., and J. S. Conery. 2001. Gene duplication and evolution: response to Long and Thornton and Zhang et al. Science 293: 1551a.
Higgins, K., and M. Lynch. 2001. Metapopulation extinction due to mutation accumulation. Proc. Natl. Acad. Sci. USA 98: 2928-2933.
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.
Lynch, M. 2001. The molecular natural history of the human genome. Trends in Ecology and Evolution 16: 420-422.
Lynch, M., and M. O’Hely. 2001. Supplementation and the genetic fitness of natural populations. Conservation Genetics 2: 363-378.
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.
Lynch, M. 2002. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. USA 99: 6118-6123.
Lynch, M., and A. Richardson. 2002. The evolution of spliceosomal introns. Curr. Opin. Gen. Devel. 12: 701-710.
Lynch, M. 2002. Chromosomal repatterning by gene duplication. Science 297: 945-947.
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.
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.
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.
Keightley, P. D., and M. Lynch. 2003. Towards a realistic model of mutations affecting fitness. Evolution 57: 683-685.
Lynch, M., and A. Kewalramani. 2003. Messenger RNA processing and the evolutionary proliferation of introns. Mol. Biol. Evol. 20: 563-571.
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.
Estes, S., and M. Lynch. 2003. Rapid recovery of mutation-accumulation lines by compensatory mutation. Evolution 57: 1022-1030.
Housworth, E., E. Martins, and M. Lynch. 2003. The phylogenetic mixed model. American Naturalist 163: 84-96.
Lynch, M., and J. S. Conery. 2003. The origins of genome complexity. Science 302: 1401-1404.
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.
Denver, D. R., S. L. Swenson, and M. Lynch. 2003. An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases. Molecular Biology and Evolution 20: 1603-1611.
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.
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.
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.
Lynch, M., and V. Katju. 2004. The altered evolutionary trajectories of gene duplicates. Trends in Genetics 20: 544-549.
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.
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.
Dudycha, J. L., and M. Lynch. 2005. Ontogeny and allometry of resource allocation in animals with indeterminate growth. Evolution 59: 565-576.
Lynch, M., D. G. Scofield, and X. Hong. 2005. The evolution of transcription-initiation sites. Mol. Biol. Evol. 22: 1137-1146.
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.
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.
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.
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.
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.
Paland, S., J. K. Colbourne, and M. Lynch. 2005. Evolutionary history of contagious asexuality in Daphnia pulex. Evolution 59: 800-813.
Ajie, B. C., S. Estes, M. Lynch, and P. C. Phillips. 2005. Behavioral degradation under mutation accumulation. Genetics 170: 655-660.
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.
Lynch, M. 2005. Intelligent design vs. intelligent evolution. Nature 435: 276.
Lynch, M. 2005. Simple evolutionary pathways to complex proteins. Protein Science 14: 2217-2225.
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.
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.
Lynch, M. 2006. The origins of eukaryotic gene structure. Mol. Biol. Evol. 23: 450-468.
Paland, S., and M. Lynch. 2006. Transitions to asexuality result in excess amino-acid substitutions. Science 311: 990-902.
Lynch, M., B. Koskella, and S. Schaack. 2006. Mutation pressure and the evolution of organelle genome architecture. Science 311: 1727-1730.
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.
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.
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.
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.
Snoke, M. S., T. U. Berendonk, D. Barth, and M. Lynch. 2006. Large global effective population sizes in Paramecium. Mol. Biol. Evol. 23: 2474-2479.
Lynch, M. 2006. Streamlining and simplification of microbial genome architecture. Ann. Rev. Microbiol. 60:327-349.
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.
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.
Lynch, M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc. Natl. Acad. Sci. USA 104 (Suppl.): 8597-8604.
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.
Lynch, M. 2007. The evolution of genetic networks by nonadaptive processes. Nature Reviews Genetics 8: 803-813.
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.
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.
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.
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.
Omilian, A. R., D. G. Scofield, and M. Lynch. 2008. Intron presence-absence polymorphisms in Daphnia. Mol. Biol. Evol. 25: 2129-2139.
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.
Lynch, M. 2008. Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects. Mol. Biol. Evol. 25: 2421-2431.
Lynch, M. 2008. The cellular, developmental, and population-genetic determinants of mutation-rate evolution. Genetics 180: 933-943.
Scofield, D. G., and M. Lynch. 2008. Evolutionary diversification of the Sm family of RNA-associated proteins. Mol. Biol. Evol. 25: 2255-2267.
Catania, F., and M. Lynch. 2008. Where do introns come from? PLoS Biology 6: e283.
Catania, F., F. Wurmser, A. A. Potekhin, E. Przybos', and M. Lynch. 2009. Genetic diversity in the Paramecium aurelia complex. Mol. Biol. Evol. 26: 421-431.
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
Omilian, A. R., and M. Lynch. 2009. Patterns of intraspecific DNA variation in the Daphnia nuclear genome. Genetics 182: 325-336.
Lynch, M. 2009. Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics 182: 295-301.
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.
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.
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 (in revision).
Gao, X., and M. Lynch. 2009. Ubiquitous internal gene duplication and intron creation in eukaryotes. Proc. Natl. Acad. Sci. USA (in revision).
Haubold, B., P. Pfaffelhuber, and M. Lynch. 2009. mlDiv – A program for estimating the population mutation and recombination reates from shotgun-sequenced genomes. Submitted to Molecular Ecology.
Eads, B., D. Tsuchiya, M. Lynch, J. Andrews, and M. E. Zolan. 2009. Evolution of REC8 in Daphnia: Duplication, positive selection, and a transposon insertion associated with obligate asexuality. Submitted to Genetics.
Lipinski, K. J., K. A. Fitzpatrick, M. Lynch, V. Katju, and U. Bergrthorsson. 2009. High spontaneous rate of gene duplication in Caenorhabditis elegans. Submitted to Nature.
Ossowski, S., K. Schneeberger, J. Lucas-Lledó, N. Warthmann, R. M. Clark, R. G. Shaw, D. Weigel, and M. Lynch. 2009. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Submitted to Science.
Li, W. A. E. Tucker, W. Sung, W. K. Thomas, M. Lynch. 2009. Extensive, recent intron gains in Daphnia populations. Submitted to Science.
Lynch, M. The rate and molecular spectrum of spontaneous mutations in man. Proc. Natl. Acad. Sci. USA (invited, in prep.)
Lynch, M. The rate and molecular spectrum of spontaneous mutations. Trends in Genetics (invited, in prep.)
Colbourne, J., M. Lynch, and 83 other authors. The genome of Daphnia pulex. Science (invited, in prep.)
Lynch, M. The rate of origin of complex adaptations. (in prep.)
Books:
Lynch, M. 2007. The Origins of Genome Architecture. Sinauer Assocs., Inc., Sunderland, MA.
Lynch, M., and J. B. Walsh. 1998. Genetics and Analysis of Quantitative Traits. Sinauer Assocs., Inc., Sunderland, MA.
With 14 other committee members, for the National Research Council. 1995. Science and the Endangered Species Act. National Academy Press, Washington, DC.
Walsh, J. B., and M. Lynch. Evolution of Quantitative Traits. Sinauer Assocs., Inc., Sunderland, MA (in prep.)
Post-doctoral associates (current and former): Charles Baer, Robert Belsey, Jeffrey Blanchard, Francesco Catania, John Colbourne, Teri Crease, Melania Cristescu, Dee Denver, Thomas Doak, Jeffrey Dudycha, Suzanne Edmands, Allan Force, Michael Fugate, Xiang Gao, Kevin Higgins, Laura Higgins, David Houle, Niles Lehman, Ignasi Lucas, Emilia Martins, Paul McElheny, Phil Morin, Martin O’Hely, Carolina Penalva-Arana, Susan Ratner, Barrie Robison, Stewart Schultz, Douglas Scofield, Ken Spitze, Yoshi Tanaka, Abraham Tucker, Larissa Vassilieva, John Willis.
Visiting associates (current and former): Erika Aguirre, Ricardo Alia, Scott Baird, John Conery, Teri Crease, Reinhard Bürger, Wilfried Gabriel, Thomas Hansen, Elizabeth Housworth, Lawrence Kirkendall, Alex Kondrashov, Peter Larsen, Thomas Little, Thomas Titus, Sara Via, Francois Wurmser, Fumin Zhang.
Ph. D. students (current and former): Desiree Allen, Elizabeth Bohuski, Jennifer Britt, David Butcher, Hong-Wen Deng, Suzanne Estes, Allan Force, Vaishali Katju, Travis Kibota, Britt Koskella, Wenli Li, Casey McGrath, Samuel Miller, Kendall Morgan, Angela Omilian, Susanne Paland, Michael Pfrender, Aaron Richardson, Sarah Schaak, Margaret Snoke, Barry Sullender, Ken Spitze, Michael Vanni, Lawrence Weider.
Masters students (current and former): Deborah Allen, Gary Henderson, Justin Hicks, Xin Hong, Micah Jordan, Scott Kolpak, Leigh Latta, Lisa Nass, Kevin Simonelic, Hui-Hua Sun, Anna Toline.
Recent Speaking Engagements:
1995, National Marine Fisheries Service, Symposium on Genetic Issues in Salmonid Hatcheries.
1995, Pennsylvania State University.
1995, Arizona State University.
1995, Kellogg Biological Station, Eminent Ecologist Lectures.
1995, Duke University.
1995, University of Chicago.
1996, University of Alaska.
1996, North American Forestry Genetics Association.
1996, University of British Columbia.
1996, National Marine Fisheries Service, Symposium on Risk Analysis in Salmonids.
1997, Special Symposium on Inbreeding and Outbreeding in Salmonids, Juneau.
1997, University of Michigan.
1997, University of Arizona.
1997, Environmental Mutagen Society, Symposium Speaker, Minneapolis.
1997, University of Minnesota.
1997, University of Maryland, Symposium on Small Populations.
1997, Society for the Study of Evolution, Symposium on Deleterious Mutation, Boulder.
1997, Genetics Society of Australia, Plenary Speaker, Perth.
1997, University of Queensland, Australia.
1997, LaTrobe University, Australia.
1997, Florida State University.
1998, Sloan Symposium on Limits to Knowledge in Evolution, University of California at Riverside.
1998, Oregon State University.
1998, University of Texas, Distinguished Evolutionary Biologist.
1998, University of Madrid, El Escorial, Conservation of Genetic Resources.
1998, University of Texas Health Science Center, Houston.
1998, Symposium on Evolution of Asexual vs. Sexual Reproduction, La Sage, Switzerland.
1998, Zoological Society of London, Origin and Nature of Biodiversity, Keynote Speaker.
1998, University of Nevada at Reno.
1998, University of California at Davis.
1999, Indiana University.
1999, Washington State University.
1999, New Mexico State University.
1999, North Carolina State University.
1999, European Society of Evolutionary Biology, Barcelona.
1999, University of Helsinki, Finland.
1999, Uppsala University, Norway.
1999, AIBS Presidents’ Summit, Washington, D. C.
1999, University of Oklahoma.
1999, NSF/EC Workshop on the Use of Molecular Tools in the Study of Ecology.
2000, Salmon Research in the Next Millenium, Santa Barbara, CA.
2000, University of Florida.
2000, State University of New York at Stony Brook.
2000, University of Missouri at Kansas City.
2000, Presidential Address, Society for the Study of Evolution, Bloomington, Indiana.
2000, Evolution: From Molecules to Ecosystems, University of Valencia, Spain.
2000, Sloan Symposium on Limits to Knowledge in Science, Columbia University.
2001, Distinguished Speaker Series, Beyond the Human Genome Project, Harvey Mudd College.
2001, Jacques Monod Symposium on Gene Duplication, Aussois, France.
2001, Fred Hutchinson Cancer Research Center, Seattle.
2001, University of Southern California.
2001, Whole Genome Workshop, DIMACS Conference, Rutgers University.
2001, Biophysics and Biochemistry, Oregon State University.
2001, Ecological and Evolutionary Genomics Symposium, University of Lausanne.
2001, Wright State University.
2001, Hatchery Symposium, National Marine Fisheries Service, Seattle.
2001, University of Utah.
2001, Linking Molecular Insights and Ecological Research, Stanford University.
2001, University of Kentucky.
2002, Workshop on the Development of an Evolutionary Synthesis Center, NSF.
2002, University of Illinois.
2002, Stanford University.
2002, Plenary Speaker, European Population Genetics Symposium, University of Leeds.
2002, Symposium on Ecological Genomics, Ecological Society of America.
2002, American Genetics Association, Symposium on Molecular Evolutionary Genetics.
2002, Bioinformatics 2002, Bergen, Norway.
2002, Symposium on Long-term Selection, University of Illinois.
2002, Michigan State University.
2002, Plenary Speaker, Beckman Symposium on Sequenced Genomes, City of Hope Hospital.
2002, Duke University.
2003, Yale University.
2003, University of Wisconsin, Madison.
2003, Plenary Speaker, Stat Day Meeting of Indiana Biostatisticians.
2003, Plenary Speaker, International Congress of Genetics, Melbourne.
2003, Bioinformatics in the Post-genomic Era, Stockholm.
2003, Symposium on Ecological Genetics, Leuven, Belgium.
2003, Symposium Celebrating William Hill’s Honorary Doctorate, North Carolina State University.
2003, Mol. Biol. Evol. Symposium, Functional Evolutionary Genomics of Gene Duplication.
2003, Symposium on the Developmental Basis of Evolutionary Change, University of Chicago.
2003, Mathematical and Statistical Problems in Genome Science, University of Minnesota.
2003, University of Wisconsin, Milwaukee.
2004, Committee on Genetics, University of Chicago.
2004, Center for Gene Research and Biotechnology, Oregon State University.
2004, Gordon Conference on Molecular Evolution.
2004, Evolutionary Genomics Symposium, University of Arizona.
2004, Comparative Genomics of Vertebrates, La Londes Les Maures, France.
2004, Department of Biology, Notre Dame University.
2004, Ecological Genomics Symposium, Kansas State University, Kansas City.
2004, Brown University.
2004, University of Michigan.
2004, Harvard University.
2004, University of Valencia.
2005, Department of Genome Sciences, University of Washington.
2005, Department of Biology, McMaster University.
2005, University of New Mexico.
2005, Lead Speaker, Darwin’s Birthday Celebration, University College, London.
2005, University of Buffalo.
2005, Princeton University.
2005, Department of Biology, University of Pennsylvania.
2005, Plenary Speaker, European Society for Evolutionary Biology, Krakow, Poland.
2005, Max Planck Institute for Developmental Biology, Tübingen.
2005, Symposium on Phenotypic Diversity and Evolution, Wenner-Gren Foundation, Sweden.
2005, NESCent Viral Tree of Life Working Group, Durham, NC.
2005, Symposium on Computational Genomics and Evolutionary Biology, Georgia Tech.
2006, University of Maryland.
2006, University of Massachusetts.
2006, University of Idaho.
2006, University of Iowa.
2006, NAS Sackler Colloquium on Adaptation and Complex Design, Irvine.
2006, Keynote Speaker, Bioinformatics 2006, Aarhus, Denmark.
2006, University of Lausanne.
2006, Pennsylvania State University.
2006, Autonomous University of Barcelona.
2007, University of Rochester.
2007, Evolutionary Genomics Workshop, Instituto Gulbenkian de Ciencia, Lisbon, Portugal.
2007, Keynote Speaker, Symposium on Integration of Genotype and Phenotype, Florida State University.
2007, University of Michigan.
2007, University of Iceland.
2007, Plenary Speaker, Society for Molecular Biology and Evolution, Dalhousie University.
2007, FASEB Ciliate Molecular Genetics Meeting, Tucson.
2007, Keynote Speaker, Gordon Conference on Structural, Functional, and Evolutionary Genomics.
2008, Keynote Speaker, Keystone Symposium on Complex Traits: Biologic and Therapeutic Insights, Sante Fe.
2008, University of Lyon, France.
2008, Portugaliae Genetica Symposium, University of Porto, Portugal.
2008, Keynote Speaker, Cold Spring Harbor Biology of Genomes Symposium.
2008, Advance Talk, Kansas State University.
2008, Genetics Society Symposium on Evolution of Recombination, University of Bath.
2008, Public Lecture on the Genomic Revolution, Sao Paulo, Brazil.
2008, Evolution Symposium, University of Pennsylvania.
2008, Department of Biology, New York University.
2008, Memorial Symposium of the International Prize for Biology 2008, Sendai, Japan.
2008, Marine Biology Laboratory, Woods Hole.
2009, University of Calgary.
2009, University of Lyon.
2009, Dean’s Darwin Symposium, University of California, San Diego.
2009, Conservation Genetics Symposium, University of Chicago.
2009, Evolution Symposium, Max Planck Society.
2009, Plenary Speaker, Evolution of Sex and Recombination Symposium, University of Iowa.
2009, National Academy of Sciences Sackler Colloquium on Evolution in Health and Medicine.
2009, Monterey Bay Aquarium.
2009, Plenary Speaker, European Cytogenetics Conference.
2009, FASEB Ciliate Molecular Biology Meetings.
2009, Biological Evolution Symposium, University of Porto Alegre, Brazil.
2009, Nei Presidential Lecture, Society for Molecular Biology and Evolution.
2009, Evolution Symposium, State University of New York at Stony Brook.
2009, Conference on Next-Generation Sequencing, Barcelona.
2009, IGERT Symposium on Evolution, Genomics, and Development.
2009, Jackson Lab, Bar Harbor, Maine.
2009, Mathematics Institute, University of Tennessee.
2009, Center for Genome Research and Biocomputing, Oregon State University.
2009, Evolution Symposium, University of Valencia.
2010, University of Missouri.
2010, Kavli Institute, Workshop on Bacterial and Viral Evolution.
2010, Kavli Institute, Workshop on Cellular Evolution.
2010, Symposium on Evolution of Form, Konrad Lorenz Institute, Austria.