MICHAEL R LYNCH

Summary

Affiliation: Indiana University
Country: USA

Publications

  1. pmc Population-genetic inference from pooled-sequencing data
    Michael Lynch
    Department of Biology, Indiana University, Bloomington
    Genome Biol Evol 6:1210-8. 2014
  2. pmc Independent Mammalian Genome Contractions Following the KT Boundary
    Mina Rho
    School of Informatics, Indiana University, Bloomington
    Genome Biol Evol 2009:2-12. 2009
  3. pmc Evolutionary diversification of the multimeric states of proteins
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 110:E2821-8. 2013
  4. pmc Evolutionary layering and the limits to cellular perfection
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 109:18851-6. 2012
  5. pmc The evolution of multimeric protein assemblages
    Michael Lynch
    Department of Biology, Indiana University, IN, USA
    Mol Biol Evol 29:1353-66. 2012
  6. pmc DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex
    Sarah Schaack
    Department of Biology, University of Texas Arlington, 501 S, Nedderman Drive, Arlington, TX 76019, USA
    Genome Biol 11:R46. 2010
  7. pmc Simple sequence repeat variation in the Daphnia pulex genome
    Way Sung
    Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
    BMC Genomics 11:691. 2010
  8. pmc LTR retroelements in the genome of Daphnia pulex
    Mina Rho
    School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
    BMC Genomics 11:425. 2010
  9. pmc De novo identification of LTR retrotransposons in eukaryotic genomes
    Mina Rho
    Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
    BMC Genomics 8:90. 2007
  10. pmc The chemoreceptor genes of the waterflea Daphnia pulex: many Grs but no Ors
    D Carolina Peñalva-Arana
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    BMC Evol Biol 9:79. 2009

Detail Information

Publications67

  1. pmc Population-genetic inference from pooled-sequencing data
    Michael Lynch
    Department of Biology, Indiana University, Bloomington
    Genome Biol Evol 6:1210-8. 2014
    ..The power to detect significant allele-frequency differences between two populations is very limited unless both the number of sampled individuals and depth of sequencing coverage exceed 100. ..
  2. pmc Independent Mammalian Genome Contractions Following the KT Boundary
    Mina Rho
    School of Informatics, Indiana University, Bloomington
    Genome Biol Evol 2009:2-12. 2009
    ....
  3. pmc Evolutionary diversification of the multimeric states of proteins
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 110:E2821-8. 2013
    ..Under the proposed hypothesis, on a long evolutionary timescale, the numbers of transitions from monomers to dimers should approximate the numbers in the opposite direction and similarly for transitions between higher-order structures. ..
  4. pmc Evolutionary layering and the limits to cellular perfection
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 109:18851-6. 2012
    ..As a consequence of such changes, increased molecular/cellular complexity can arise by Darwinian processes, while yielding no long-term increase in adaptation and imposing increased energetic and mutational costs...
  5. pmc The evolution of multimeric protein assemblages
    Michael Lynch
    Department of Biology, Indiana University, IN, USA
    Mol Biol Evol 29:1353-66. 2012
    ..Nonetheless, it is equally clear that further advancements in this area will require comparative studies on the fitness consequences of alternative monomeric and dimeric proteins...
  6. pmc DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex
    Sarah Schaack
    Department of Biology, University of Texas Arlington, 501 S, Nedderman Drive, Arlington, TX 76019, USA
    Genome Biol 11:R46. 2010
    ....
  7. pmc Simple sequence repeat variation in the Daphnia pulex genome
    Way Sung
    Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
    BMC Genomics 11:691. 2010
    ..The recently sequenced Daphnia pulex genome provides us with a valuable data set to study the mode and tempo of SSR evolution, without the inherent biases that accompany marker selection...
  8. pmc LTR retroelements in the genome of Daphnia pulex
    Mina Rho
    School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
    BMC Genomics 11:425. 2010
    ....
  9. pmc De novo identification of LTR retrotransposons in eukaryotic genomes
    Mina Rho
    Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
    BMC Genomics 8:90. 2007
    ..Currently, LTR retrotransposons are annotated in eukaryotic genomes mainly through the conventional homology searching approach. Hence, it is limited to annotating known elements...
  10. pmc The chemoreceptor genes of the waterflea Daphnia pulex: many Grs but no Ors
    D Carolina Peñalva-Arana
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    BMC Evol Biol 9:79. 2009
    ..This has allowed us the initial investigation of chemoreceptor genes in an aquatic invertebrate, and to begin the study of chemoreceptor evolution across the arthropod phylum...
  11. pmc Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium
    Francesco Catania
    Department of Biology, Indiana University, 1001E 3rd Street, Bloomington, IN 47405, USA
    BMC Evol Biol 10:129. 2010
    ..Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue...
  12. ncbi request reprint The evolution of genetic networks by non-adaptive processes
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Nat Rev Genet 8:803-13. 2007
    ..The widespread reliance on computational procedures that are devoid of population-genetic details to generate hypotheses for the evolution of network configurations seems to be unjustified...
  13. pmc A genome-wide view of the spectrum of spontaneous mutations in yeast
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 105:9272-7. 2008
    ....
  14. pmc Localization of the genetic determinants of meiosis suppression in Daphnia pulex
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 180:317-27. 2008
    ..With the enormous set of genomic tools now available for D. pulex, these results set the stage for the determination of the functional underpinnings of the conversion of meiosis to a mitotic-like mode of inheritance...
  15. pmc The frailty of adaptive hypotheses for the origins of organismal complexity
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 104:8597-604. 2007
    ....
  16. pmc Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects
    Michael Lynch
    Department of Biology, Indiana University, Bloomington Indiana, USA
    Mol Biol Evol 25:2409-19. 2008
    ..These methods provide a general platform for the efficient utilization of data from population-genomic surveys, while also providing guidance for the optimal design of such studies...
  17. pmc Estimation of allele frequencies from high-coverage genome-sequencing projects
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 182:295-301. 2009
    ....
  18. pmc Rate, molecular spectrum, and consequences of human mutation
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 107:961-8. 2010
    ....
  19. pmc The rate of establishment of complex adaptations
    Michael Lynch
    Department of Biology, Indiana University, USA
    Mol Biol Evol 27:1404-14. 2010
    ....
  20. pmc Evolution of the mutation rate
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Trends Genet 26:345-52. 2010
    ....
  21. pmc Scaling expectations for the time to establishment of complex adaptations
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 107:16577-82. 2010
    ..These general results provide insight into a number of ongoing controversies regarding the molecular basis of adaptation, including the adaptive utility of recombination and the role of drift in the passage through adaptive valleys...
  22. doi request reprint The repatterning of eukaryotic genomes by random genetic drift
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, Indiana 47408, USA
    Annu Rev Genomics Hum Genet 12:347-66. 2011
    ....
  23. pmc The lower bound to the evolution of mutation rates
    Michael Lynch
    Department of Biology, Indiana University, USA
    Genome Biol Evol 3:1107-18. 2011
    ....
  24. ncbi request reprint Streamlining and simplification of microbial genome architecture
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Annu Rev Microbiol 60:327-49. 2006
    ....
  25. pmc The cellular, developmental and population-genetic determinants of mutation-rate evolution
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 180:933-43. 2008
    ....
  26. ncbi request reprint Mutation pressure and the evolution of organelle genomic architecture
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Science 311:1727-30. 2006
    ..These observations provide support for the hypothesis that the fundamental features of genome evolution are largely defined by the relative power of two nonadaptive forces: random genetic drift and mutation pressure...
  27. ncbi request reprint The origins of eukaryotic gene structure
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, USA
    Mol Biol Evol 23:450-68. 2006
    ..Under this hypothesis, arguments based on molecular, cellular, and/or physiological constraints are insufficient to explain the disparities in gene, genomic, and phenotypic complexity between prokaryotes and eukaryotes...
  28. ncbi request reprint On the formation of novel genes by duplication in the Caenorhabditis elegans genome
    Vaishali Katju
    Department of Biology, Indiana University, USA
    Mol Biol Evol 23:1056-67. 2006
    ..Finally, both intron loss and gain contribute to the differential distribution of introns between two copies...
  29. pmc Intron presence-absence polymorphisms in Daphnia
    Angela R Omilian
    Department of Biology, Indiana University, USA
    Mol Biol Evol 25:2129-39. 2008
    ....
  30. pmc Extensive, recent intron gains in Daphnia populations
    Wenli Li
    Biology Department, Indiana University, Bloomington, IN 47405, USA
    Science 326:1260-2. 2009
    ....
  31. pmc Patterns of intraspecific DNA variation in the Daphnia nuclear genome
    Angela R Omilian
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 182:325-36. 2009
    ..5255 for species of the Daphnia genus. Lastly, a divergence population-genetics approach was used to investigate gene flow and divergence between D. pulex and D. pulicaria...
  32. ncbi request reprint Large global effective population sizes in Paramecium
    Margaret S Snoke
    Department of Biology, Indiana University, IN, USA
    Mol Biol Evol 23:2474-9. 2006
    ..Drawing from observations on well-defined species within the genus Paramecium, we report exceptionally high levels of silent-site polymorphism, which appear to be a reflection of large N(e)...
  33. ncbi request reprint Biogeographic patterns and current distribution of molecular-genetic variation among populations of speckled dace, Rhinichthys osculus (Girard)
    Michael E Pfrender
    Department of Biology, Utah State University, 5305 Old Main Hill Road, Logan, UT 84322 5305, USA
    Mol Phylogenet Evol 30:490-502. 2004
    ..We recommend that major basins be regarded as distinct ESUs based on high levels of subdivision, deep divergences, and reciprocal monophyly among basins...
  34. ncbi request reprint The evolution of transcription-initiation sites
    Michael Lynch
    Department of Biology, Indiana University, USA
    Mol Biol Evol 22:1137-46. 2005
    ..These results provide a further example of how an increase in the power of random genetic drift can passively promote the evolution of forms of gene architecture that ultimately facilitate the evolution of organismal complexity...
  35. ncbi request reprint The altered evolutionary trajectories of gene duplicates
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Trends Genet 20:544-9. 2004
    ....
  36. ncbi request reprint High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome
    Dee R Denver
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Nature 430:679-82. 2004
    ....
  37. ncbi request reprint Abundance, distribution, and mutation rates of homopolymeric nucleotide runs in the genome of Caenorhabditis elegans
    Dee R Denver
    Department of Biology, Indiana University, 327 Jordan Hall, 1001 East Third Street, 47405, Bloomington, IN, USA
    J Mol Evol 58:584-95. 2004
    ..This integrative approach yields a total nuclear genome-wide homopolymer mutation rate estimate of approximately 1.6 mutations per genome per generation...
  38. ncbi request reprint The phylogenetic mixed model
    Elizabeth A Housworth
    Department of Mathematics, Indiana University, Bloomington, Indiana, 47405, USA
    Am Nat 163:84-96. 2004
    ....
  39. pmc The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome
    Vaishali Katju
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 165:1793-803. 2003
    ..We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms...
  40. ncbi request reprint Correlated evolution of life-history with size at maturity in Daphnia pulicaria: patterns within and between populations
    Charles F Baer
    Department of Biology, Jordan Hall, Indiana University, Bloomington, IN 47405, USA
    Genet Res 81:123-32. 2003
    ..One trait, offspring size, appears to have evolved in a way different from that expected from the within-population genetic architecture and may be under stabilizing selection...
  41. ncbi request reprint Genomics. Gene duplication and evolution
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Science 297:945-7. 2002
  42. ncbi request reprint The origins of genome complexity
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Science 302:1401-4. 2003
    ..The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies...
  43. pmc The ecoresponsive genome of Daphnia pulex
    John K Colbourne
    Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
    Science 331:555-61. 2011
    ..Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges...
  44. pmc Intron evolution as a population-genetic process
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 99:6118-23. 2002
    ....
  45. ncbi request reprint An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases
    Dee R Denver
    Department of Biology, Indiana University, USA
    Mol Biol Evol 20:1603-11. 2003
    ....
  46. ncbi request reprint Messenger RNA surveillance and the evolutionary proliferation of introns
    Michael Lynch
    Department of Biology, Indiana University
    Mol Biol Evol 20:563-71. 2003
    ..The spatial distribution of introns, as revealed by whole-genome analysis, is consistent with expectations for a model in which maximum protective coverage of a gene stochastically evolves over time...
  47. ncbi request reprint The evolution of spliceosomal introns
    Michael Lynch
    Department of Biology Indiana University Bloomington, Indiana 47405, USA
    Curr Opin Genet Dev 12:701-10. 2002
    ....
  48. pmc Ubiquitous internal gene duplication and intron creation in eukaryotes
    Xiang Gao
    Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 106:20818-23. 2009
    ..These results strongly suggest a major evolutionary role for internal gene duplications in the origin of genomic novelties, particularly as a mechanism for intron gain...
  49. ncbi request reprint Transitions to asexuality result in excess amino acid substitutions
    Susanne Paland
    Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405, USA
    Science 311:990-2. 2006
    ..These results support the hypothesis that sexual reproduction plays a prominent role in reducing the mutational burden in populations...
  50. ncbi request reprint Evolutionary history of contagious asexuality in Daphnia pulex
    Susanne Paland
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Evolution 59:800-13. 2005
    ..If environment-mediated selective asymmetries play no significant role in determining the outcome of competitive interactions between sexuals and asexuals, regions of contact may be setting the stage for continued asexual conquests...
  51. ncbi request reprint Conserved ontogeny and allometric scaling of resource acquisition and allocation in the Daphniidae
    Jeffry L Dudycha
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Evolution 59:565-76. 2005
    ..Using this approach, a wide range of interspecific variation in life-history features can be related to a single underlying trait, the size at first reproductive investment...
  52. ncbi request reprint A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomics
    Melania E A Cristescu
    Department of Biology, Indiana University at Bloomington, Bloomington, IN 47405, USA
    Genomics 88:415-30. 2006
    ..By mapping 342 tentative orthologous gene pairs (Daphnia/Drosophila) into the Daphnia linkage map, we facilitate future comparative projects...
  53. pmc Genetic diversity in the Paramecium aurelia species complex
    Francesco Catania
    Department of Biology, Indiana University, USA
    Mol Biol Evol 26:421-31. 2009
    ..aurelia strains and their multilocus genetic profile, a controversial finding that has major consequences for both the current methods of species assignment and the species problem in the P. aurelia complex...
  54. pmc Simple evolutionary pathways to complex proteins
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Protein Sci 14:2217-25; discussion 2226-7. 2005
    ..Thus, the classical evolutionary trajectory of descent with modification is adequate to explain the diversification of protein functions...
  55. pmc Evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family
    José Ignacio Lucas-Lledó
    Department of Biology, Indiana University, Bloomington, Indiana, USA
    Mol Biol Evol 26:1143-53. 2009
    ..In contrast, the loss of photolyase genes in prokaryotes may not cause an increase in the mutation rate and be neutral in most cases...
  56. pmc Ameiotic recombination in asexual lineages of Daphnia
    Angela R Omilian
    Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 103:18638-43. 2006
    ....
  57. pmc Mutation rates, spectra and hotspots in mismatch repair-deficient Caenorhabditis elegans
    Dee R Denver
    Department of Biology, Indiana University, Bloomington, 47405, USA
    Genetics 170:107-13. 2005
    ..elegans MA lines. This, along with the apparent absence of a Saccharomyces cerevisiae MSH3 ortholog in the C. elegans genome, suggests that C. elegans MMR surveillance is carried out by a single Msh-2/Msh-6 heterodimer...
  58. pmc The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex
    Amanda L Seyfert
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 178:2113-21. 2008
    ..Contrary to the expectations under the stepwise mutation model, most microsatellite mutations in C. elegans and D. pulex involve changes of multiple repeat units, with expansions being much more common than contractions...
  59. pmc Both costs and benefits of sex correlate with relative frequency of asexual reproduction in cyclically parthenogenic Daphnia pulicaria populations
    Desiree E Allen
    Department of Ecology and Evolution, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 179:1497-502. 2008
    ..We show that both the costs and benefits of sex, as measured by changes in means and variances in life-history traits, increase substantially with decreasing frequency of sex...
  60. pmc The relative roles of three DNA repair pathways in preventing Caenorhabditis elegans mutation accumulation
    Dee R Denver
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 174:57-65. 2006
    ..elegans mutation accumulation and provides evidence for the presence of pathway-specific DNA repair territories in the C. elegans genome...
  61. pmc Evolutionary diversification of the Sm family of RNA-associated proteins
    Douglas G Scofield
    Department of Biology, Indiana University, USA
    Mol Biol Evol 25:2255-67. 2008
    ....
  62. pmc DNA transposon dynamics in populations of Daphnia pulex with and without sex
    Sarah Schaack
    Department of Biology, University of Texas Arlington, 501 S Nedderman Drive, Arlington, TX 76019, USA
    Proc Biol Sci 277:2381-7. 2010
    ..Our multi-element survey reveals that the impact of sex on TE proliferation is consistent among different Class II TE families and we discuss the genomic consequences of different reproductive strategies over long time periods...
  63. ncbi request reprint The evolutionary demography of duplicate genes
    Michael Lynch
    Dept of Biology, Indiana University, Bloomington, Indiana 47405, USA
    J Struct Funct Genomics 3:35-44. 2003
    ....
  64. ncbi request reprint Rapid fitness recovery in mutationally degraded lines of Caenorhabditis elegans
    Suzanne Estes
    Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
    Evolution 57:1022-30. 2003
    ..This surprising result has broad implications for the influence of the mutational process on many issues in evolutionary and conservation biology...
  65. ncbi request reprint The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans
    Dee R Denver
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Nat Genet 37:544-8. 2005
    ..elegans expressed sequences...
  66. ncbi request reprint Intron size, abundance, and distribution within untranslated regions of genes
    Xin Hong
    Department of Biology, Indiana University, IN, USA
    Mol Biol Evol 23:2392-404. 2006
    ..thaliana and D. melanogaster, which may lack intron-dependent NMD. Our findings have several implications for theories of intron evolution and genome evolution in general...

Research Grants10

  1. The Rate and Molecular Spectrum of Spontaneous Mutations
    Michael Lynch; Fiscal Year: 2009
    ....
  2. The Rate and Molecular Spectrum of Spontaneous Mutations
    Michael Lynch; Fiscal Year: 2007
    ..abstract_text> ..
  3. The Rate and Molecular Spectrum of Spontaneous Mutations
    Michael Lynch; Fiscal Year: 2007
    ....
  4. The Rate and Molecular Spectrum of Spontaneous Mutations
    Michael Lynch; Fiscal Year: 2006
    ....
  5. The Rate and Molecular Spectrum of Spontaneous Mutations
    Michael Lynch; Fiscal Year: 2009
    ....