M Lynch

Summary

Affiliation: Indiana University
Country: USA

Publications

  1. pmc The probability of preservation of a newly arisen gene duplicate
    M Lynch
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 159:1789-804. 2001
  2. 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
  3. 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
  4. 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
  5. 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
  6. ncbi request reprint The origins of genome complexity
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Science 302:1401-4. 2003
  7. 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
  8. ncbi request reprint The evolution of transcription-initiation sites
    Michael Lynch
    Department of Biology, Indiana University, USA
    Mol Biol Evol 22:1137-46. 2005
  9. ncbi request reprint Genomics. Gene duplication and evolution
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Science 297:945-7. 2002
  10. 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

Detail Information

Publications89

  1. pmc The probability of preservation of a newly arisen gene duplicate
    M Lynch
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 159:1789-804. 2001
    ..Tight linkage also influences the probability of duplicate-gene preservation, increasing the probability of subfunctionalization but decreasing the probability of neofunctionalization...
  2. 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
    ....
  3. 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...
  4. 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
    ....
  5. 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...
  6. 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...
  7. 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
    ....
  8. 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...
  9. ncbi request reprint Genomics. Gene duplication and evolution
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Science 297:945-7. 2002
  10. 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...
  11. ncbi request reprint The evolutionary fate and consequences of duplicate genes
    M Lynch
    Department of Biology, University of Oregon, Eugene, OR 97403, USA
    Science 290:1151-5. 2000
    ..Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species...
  12. pmc Change of genetic architecture in response to sex
    H W Deng
    Department of Biology, University of Oregon, Eugene 97403, USA
    Genetics 143:203-12. 1996
    ..The data are also used to infer the effects of natural selection on the mean and the genetic variance of the population...
  13. pmc Intron presence-absence polymorphisms in Daphnia
    Angela R Omilian
    Department of Biology, Indiana University, USA
    Mol Biol Evol 25:2129-39. 2008
    ....
  14. doi request reprint Extensive, recent intron gains in Daphnia populations
    Wenli Li
    Biology Department, Indiana University, Bloomington, IN 47405, USA
    Science 326:1260-2. 2009
    ....
  15. 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...
  16. pmc The probability of duplicate gene preservation by subfunctionalization
    M Lynch
    Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
    Genetics 154:459-73. 2000
    ....
  17. pmc Preservation of duplicate genes by complementary, degenerative mutations
    A Force
    Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
    Genetics 151:1531-45. 1999
    ..Cooke et al. 1997 (p. 362)..
  18. ncbi request reprint The fitness effects of spontaneous mutations in Caenorhabditis elegans
    L L Vassilieva
    Department of Biology, University of Oregon, Eugene 97403, USA
    Evolution 54:1234-46. 2000
    ....
  19. 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...
  20. 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)...
  21. ncbi request reprint Quantitative genetic variation in Daphnia: temporal changes in genetic architecture
    M E Pfrender
    Department of Biology, University of Oregon, Eugene 97403, USA
    Evolution 54:1502-9. 2000
    ..The results of this study highlight the complexity of natural selection operating on populations that undergo alternating phases of sexual and asexual reproduction...
  22. 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...
  23. 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
    ....
  24. 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
    ....
  25. 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...
  26. 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
    ....
  27. 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
    ....
  28. 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...
  29. 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...
  30. 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...
  31. 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...
  32. 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...
  33. 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...
  34. pmc The rate of establishment of complex adaptations
    Michael Lynch
    Department of Biology, Indiana University, USA
    Mol Biol Evol 27:1404-14. 2010
    ....
  35. pmc Evolution of the mutation rate
    Michael Lynch
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Trends Genet 26:345-52. 2010
    ....
  36. 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...
  37. 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...
  38. 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
    ....
  39. 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...
  40. 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
    ....
  41. 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...
  42. 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...
  43. doi request reprint 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...
  44. 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
    ....
  45. 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
    ....
  46. 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...
  47. 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...
  48. 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
    ....
  49. 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...
  50. 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...
  51. 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
    ....
  52. 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...
  53. 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
    ....
  54. 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...
  55. 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...
  56. 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...
  57. ncbi request reprint Estimating genetic correlations in natural populations
    M Lynch
    Department of Biology, University of Oregon, Eugene 97403, USA
    Genet Res 74:255-64. 1999
    ....
  58. ncbi request reprint Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes
    M Lynch
    Department of Biology, University of Oregon, Eugene 97403, USA
    Mol Biol Evol 14:914-25. 1997
    ....
  59. pmc Estimation of deleterious-mutation parameters in natural populations
    H W Deng
    Department of Biology, University of Oregon, Eugene 97403, USA
    Genetics 144:349-60. 1996
    ....
  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 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...
  62. doi request reprint 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
    ....
  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. 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...
  65. pmc The effect of spontaneous mutations on competitive ability
    S Schaack
    Department of Biology, Reed College, Portland, OR 97202, USA
    J Evol Biol 26:451-6. 2013
    ..In addition, in some assays, MA lines outperform controls providing insight into the frequency of beneficial mutations...
  66. 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...
  67. 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
    ....
  68. 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...
  69. pmc Inbreeding depression and inferred deleterious-mutation parameters in Daphnia
    H W Deng
    Department of Biology, University of Oregon, Eugene 97403, USA
    Genetics 147:147-55. 1997
    ..04) is discussed. It is shown that different reproductive modes do not affect gene frequency at mutation-selection equilibrium if mutational effects on fitness are multiplicative and not completely recessive...
  70. pmc Spontaneous deleterious mutation in Arabidopsis thaliana
    S T Schultz
    Department of Biology, University of Miami, Coral Gables, FL 33124, USA
    Proc Natl Acad Sci U S A 96:11393-8. 1999
    ....
  71. ncbi request reprint Patterns of genetic architecture for life-history traits and molecular markers in a subdivided species
    K K Morgan
    Department of Biology, University of Oregon, Eugene 97403, USA
    Evolution 55:1753-61. 2001
    ..These data are compared to an identical dataset for 17 populations of the temporary-pond species, D. pulex...
  72. pmc Metapopulation extinction caused by mutation accumulation
    K Higgins
    Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR 97403, USA
    Proc Natl Acad Sci U S A 98:2928-33. 2001
    ..Because of mutation accumulation, viable metapopulations may need to be far larger and better connected than would be required under just stochastic demography...
  73. 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...
  74. pmc Spontaneous mutational correlations for life-history, morphological and behavioral characters in Caenorhabditis elegans
    Suzanne Estes
    Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, 97403, USA
    Genetics 170:645-53. 2005
    ..Observed mutational correlations are shown to be higher than those produced by the chance accumulation of nonpleiotropic mutations in the same lines...
  75. pmc Behavioral degradation under mutation accumulation in Caenorhabditis elegans
    Beverly C Ajie
    Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, 97503 5289, USA
    Genetics 170:655-60. 2005
    ..These results have important implications for the maintenance of genetic variation for behavior in natural populations as well as for expectations for behavioral change within endangered species and captive populations...
  76. pmc Mutation accumulation in populations of varying size: the distribution of mutational effects for fitness correlates in Caenorhabditis elegans
    Suzanne Estes
    Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403, USA
    Genetics 166:1269-79. 2004
    ....
  77. pmc Spontaneous mutational variation for body size in Caenorhabditis elegans
    Ricardo B R Azevedo
    Department of Biology, Imperial College, Berks SL5 7PY, United Kingdom
    Genetics 162:755-65. 2002
    ..We observed a strongly asymmetrical response to selection of a magnitude consistent with the input of mutational variance observed in the MA experiment...
  78. ncbi request reprint Toward a realistic model of mutations affecting fitness
    Peter D Keightley
    University of Edinburgh, Institute of Cell, Animal and Population Biology, West Mains Road, Edinburgh EH9 3JT, United Kingdom
    Evolution 57:683-5; discussion 686-9. 2003
    ..We evaluate this in the light of data from other MA experiments, along with molecular evidence, that suggest the vast majority of new mutations are deleterious...
  79. ncbi request reprint Position of the final intron in full-length transcripts: determined by NMD?
    Douglas G Scofield
    Mol Biol Evol 24:896-9. 2007
    ..This mechanism may also help to explain the roughly 3 times greater length of 3' UTRs in comparison to 5' UTRs...
  80. pmc The origin of subfunctions and modular gene regulation
    Allan Force
    Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA
    Genetics 170:433-46. 2005
    ..Many aspects of gene complexity in multicellular eukaryotes may have arisen passively as population size reductions accompanied increases in organism size, with the adaptive exploitation of such complexity occurring secondarily...
  81. ncbi request reprint Structural and mutational analysis of antiquitin as a candidate gene for Menière disease
    Michael Lynch
    Am J Med Genet 110:397-9. 2002
  82. doi request reprint Segmentation of the left ventricle of the heart in 3-D+t MRI data using an optimized nonrigid temporal model
    Michael Lynch
    Siemens AG, 91058 Erlangen, Germany
    IEEE Trans Med Imaging 27:195-203. 2008
    ..The expectation step deforms the level-set function while the maximization step updates the prior temporal model parameters to perform the segmentation in a nonrigid sense...
  83. pmc Comparative evolutionary genetics of spontaneous mutations affecting fitness in rhabditid nematodes
    Charles F Baer
    Department of Zoology, University of Florida, P O Box 118525, Gainesville, FL 32611 8525, USA
    Proc Natl Acad Sci U S A 102:5785-90. 2005
    ....
  84. pmc Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster
    Cathy Haag-Liautard
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Biol 6:e204. 2008
    ..Strand-asymmetric mutation bias, coupled with selection to maintain specific nonsynonymous bases, therefore provides an explanation for the extreme base composition of the mitochondrial genome of Drosophila...
  85. ncbi request reprint God's signature: DNA profiling, the new gold standard in forensic science
    Michael Lynch
    Department of Science and Technology Studies, Cornell University, 302 Rockefeller Hall, Ithaca, NY 14853 2401, USA
    Endeavour 27:93-7. 2003
    ..This article discusses the socio-legal and socio-technical issues that led to the inversion of credibility that characterized the intertwined history of the two techniques...
  86. ncbi request reprint Intelligent design or intellectual laziness?
    Michael Lynch
    Nature 435:276. 2005
  87. ncbi request reprint MRI diffusion-based filtering: a note on performance characterisation
    Ovidiu Ghita
    Vision Systems Group, School of Electronic Engineering, Dublin City University, Glasnevin, Dublin 9, Ireland
    Comput Med Imaging Graph 29:267-77. 2005
    ..In this paper we detail the implementation of a number of 3D diffusion-based filtering techniques and we analyse their performance when they are applied to a large collection of MR datasets of varying type and quality...
  88. ncbi request reprint Functional protein nanoarrays for biomarker profiling
    Michael Lynch
    BioForce Nanosciences, Ames, Iowa 50010, USA
    Proteomics 4:1695-702. 2004
    ....
  89. ncbi request reprint Viral transgenesis of embryonic cell cultures from the freshwater microcrustacean Daphnia
    Christy D Robinson
    Department Tropical Medicine, Tulane University, New Orleans, Louisiana 70112, USA
    J Exp Zoolog A Comp Exp Biol 305:62-7. 2006
    ..VSV was found to replicate in the cells with no apparent cytopathic effect. Here we report the first evidence of gene transfer and foreign gene expression in cultures of Daphnia embryonic cells using a recombinant viral vector...