Vincent J Lynch

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06551, USA
    Proc Biol Sci 271:2201-7. 2004
  2. ncbi The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts
    Karen D Crow
    Department of Ecology and Evolutionary Biology, Yale University, USA
    Mol Biol Evol 23:121-36. 2006
  3. pmc Adaptive evolution of Hox-gene homeodomains after cluster duplications
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, Connecticut 06551, USA
    BMC Evol Biol 6:86. 2006
  4. pmc Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
    BMC Evol Biol 7:2. 2007
  5. doi Resurrecting the role of transcription factor change in developmental evolution
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Evolution 62:2131-54. 2008
  6. doi Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB
    Vincent J Lynch
    Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Nature 480:383-6. 2011
  7. doi Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology and Yale Systems Biology Institute, Yale University, New Haven, Connecticut, USA
    Nat Genet 43:1154-9. 2011
  8. doi Revisiting a classic example of transcription factor functional equivalence: are Eyeless and Pax6 functionally equivalent or divergent?
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology and Yale Institute for Systems Biology, Yale University, New Haven, Connecticut 06511, USA
    J Exp Zool B Mol Dev Evol 316:93-8. 2011
  9. pmc HoxA-11 and FOXO1A cooperate to regulate decidual prolactin expression: towards inferring the core transcriptional regulators of decidual genes
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 4:e6845. 2009
  10. pmc Use with caution: developmental systems divergence and potential pitfalls of animal models
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    Yale J Biol Med 82:53-66. 2009

Detail Information

Publications22

  1. pmc Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06551, USA
    Proc Biol Sci 271:2201-7. 2004
    ..These results support the idea that adaptive evolution of transcription factors can be an integral part in the evolution of novel structures...
  2. ncbi The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts
    Karen D Crow
    Department of Ecology and Evolutionary Biology, Yale University, USA
    Mol Biol Evol 23:121-36. 2006
    ..Taken together, these results support the notion that the duplicated Hox genes of teleosts were causally relevant to adaptive evolution during the initial teleost radiation...
  3. pmc Adaptive evolution of Hox-gene homeodomains after cluster duplications
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, Connecticut 06551, USA
    BMC Evol Biol 6:86. 2006
    ..But for Hox genes the mechanisms of paralog divergence is unknown, leaving open the role of Hox gene duplication in morphological evolution...
  4. pmc Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
    BMC Evol Biol 7:2. 2007
    ..Snake venom phospholipase A2 genes are members of large multigene families with many diverse functions, thus they are excellent models to study the emergence of novel functions after gene duplications...
  5. doi Resurrecting the role of transcription factor change in developmental evolution
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Evolution 62:2131-54. 2008
    ..Finally, we present an argument that the evolution of proteins may play a more substantial, but thus far underestimated, role in developmental evolution...
  6. doi Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB
    Vincent J Lynch
    Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Nature 480:383-6. 2011
    ..We conclude that changing the response of transcription factors to signalling pathways can be an important mechanism of gene regulatory evolution...
  7. doi Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology and Yale Systems Biology Institute, Yale University, New Haven, Connecticut, USA
    Nat Genet 43:1154-9. 2011
    ....
  8. doi Revisiting a classic example of transcription factor functional equivalence: are Eyeless and Pax6 functionally equivalent or divergent?
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology and Yale Institute for Systems Biology, Yale University, New Haven, Connecticut 06511, USA
    J Exp Zool B Mol Dev Evol 316:93-8. 2011
    ..Thus, we conclude that Pax6 genes are both functionally equivalent and divergent between species...
  9. pmc HoxA-11 and FOXO1A cooperate to regulate decidual prolactin expression: towards inferring the core transcriptional regulators of decidual genes
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 4:e6845. 2009
    ..In addition, the functional non-equivalence of HoxA-11 and HoxA-10 with respect to PRL regulation suggests that these transcription factors regulate distinct sets of target genes during decidualization...
  10. pmc Use with caution: developmental systems divergence and potential pitfalls of animal models
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    Yale J Biol Med 82:53-66. 2009
    ..Therefore, animal models of gene function and human disease may not provide appropriate information, particularly for rapidly evolving genes and systems...
  11. pmc Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS Genet 5:e1000349. 2009
    ....
  12. pmc Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 105:14928-33. 2008
    ..These results demonstrate that the evolution of novel gene expression domains is not only mediated by the evolution of cis-regulatory elements but can also require evolutionary changes of transcription factor proteins themselves...
  13. doi Clitoral and penile size variability are not significantly different: lack of evidence for the byproduct theory of the female orgasm
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
    Evol Dev 10:396-7. 2008
  14. pmc Evolution of a derived protein-protein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation
    Kathryn J Brayer
    Department of Ecology and Evolutionary Biology and Yale Systems Biology Institute, Yale University, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 108:E414-20. 2011
    ..We speculate that evolutionary changes of intramolecular regulation have limited pleiotropic effects compared with changes to interaction domains themselves...
  15. doi Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements
    Deena Emera
    Department of Ecology and Evolutionary Biology and Yale Systems Biology Institute, Yale University, USA
    Mol Biol Evol 29:239-47. 2012
    ....
  16. ncbi Molecular evolution of evolutionary novelties: the vagina and uterus of therian mammals
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    J Exp Zool B Mol Dev Evol 304:580-92. 2005
    ..We conclude that a careful analysis of sequence variation in developmental genes can aid in testing which developmental changes were instrumental in the origin of novel morphological characters...
  17. doi A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13
    Tiana Kohlsdorf
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
    J Mol Evol 67:581-93. 2008
    ....
  18. doi The gene regulatory logic of transcription factor evolution
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
    Trends Ecol Evol 23:377-85. 2008
    ..We conclude that changes in the function of proteins are likely directly contributing to developmental evolution...
  19. doi Live-birth in vipers (Viperidae) is a key innovation and adaptation to global cooling during the Cenozoic
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Evolution 63:2457-65. 2009
    ....
  20. doi Evolutionary novelties
    Gunter P Wagner
    Yale University, New Haven, CT 06511, USA
    Curr Biol 20:R48-52. 2010
    ..molecular and genomic tools are being brought to bear on this question that we are finally in a position to answer Mivart's challenge and explain one of the most fundamental questions of biology: how does novelty arise in evolution?..
  21. doi Did egg-laying boas break Dollo's law? Phylogenetic evidence for reversal to oviparity in sand boas (Eryx: Boidae)
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06551
    Evolution 64:207-16. 2010
    ..Remarkably, like other viviparous boas hatchlings of oviparous Eryx lack an egg-tooth providing independent evidence that oviparity is a derived state in these species...
  22. doi Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale Systems Biology Institute, Yale University, 300 Heffernan Drive, West Haven, CT 06516, USA
    Theory Biosci 131:281-5. 2012
    ..We propose a slight modification of RPKM that eliminates this inconsistency and call it TPM for transcripts per million. TPM respects the average invariance and eliminates statistical biases inherent in the RPKM measure...