Gunter P Wagner

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies
    Wolfgang Otto
    , , , Leipzig, Germany
    Genome Biol Evol 2009:85-98. 2009
  2. doi request reprint A model based criterion for gene expression calls using RNA-seq data
    Gunter P Wagner
    Yale Systems Biology Institute, 300 Heffernan Drive, West Haven, CT 06516, USA
    Theory Biosci 132:159-64. 2013
  3. doi request reprint 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
  4. doi request reprint An evolutionary test of the isoform switching hypothesis of functional progesterone withdrawal for parturition: humans have a weaker repressive effect of PR-A than mice
    Gunter P Wagner
    Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
    J Perinat Med 40:345-51. 2012
  5. ncbi request reprint Divergence of conserved non-coding sequences: rate estimates and relative rate tests
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology Yale University, New Haven, Connecticut, USA
    Mol Biol Evol 21:2116-21. 2004
  6. ncbi request reprint What is the promise of developmental evolution? III. The crucible of developmental evolution
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    J Exp Zool B Mol Dev Evol 300:1-4. 2003
  7. ncbi request reprint Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
    J Mol Evol 60:665-76. 2005
  8. doi request reprint 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
  9. ncbi request reprint 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
  10. doi request reprint Pleiotropic scaling of gene effects and the 'cost of complexity'
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    Nature 452:470-2. 2008

Detail Information

Publications70

  1. pmc Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies
    Wolfgang Otto
    , , , Leipzig, Germany
    Genome Biol Evol 2009:85-98. 2009
    ..The analysis tool, called CRETO (Cis-Regulatory Element Turn-Over) can be downloaded from http://www.bioinf.uni-leipzig.de/Software/creto/...
  2. doi request reprint A model based criterion for gene expression calls using RNA-seq data
    Gunter P Wagner
    Yale Systems Biology Institute, 300 Heffernan Drive, West Haven, CT 06516, USA
    Theory Biosci 132:159-64. 2013
    ....
  3. doi request reprint 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...
  4. doi request reprint An evolutionary test of the isoform switching hypothesis of functional progesterone withdrawal for parturition: humans have a weaker repressive effect of PR-A than mice
    Gunter P Wagner
    Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
    J Perinat Med 40:345-51. 2012
    ..One attractive hypothesis is the isoform switching hypothesis (ISH). ISH is supported by in vitro evidence that progesterone receptor isoform A (PR-A) inhibits PR-B and that the PR-A/PR-B ratio increases towards term...
  5. ncbi request reprint Divergence of conserved non-coding sequences: rate estimates and relative rate tests
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology Yale University, New Haven, Connecticut, USA
    Mol Biol Evol 21:2116-21. 2004
    ..We conclude that the proposed methods can be used for testing hypotheses about the rate and pattern of evolution of putative cis-regulatory elements...
  6. ncbi request reprint What is the promise of developmental evolution? III. The crucible of developmental evolution
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    J Exp Zool B Mol Dev Evol 300:1-4. 2003
  7. ncbi request reprint Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
    J Mol Evol 60:665-76. 2005
    ..e., putative cis-regulatory elements. These results suggest that the 5' HoxA genes in the same cluster belong to a co-evolutionary unit in which genes have a tendency to diverge together...
  8. doi request reprint 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...
  9. ncbi request reprint 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...
  10. doi request reprint Pleiotropic scaling of gene effects and the 'cost of complexity'
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    Nature 452:470-2. 2008
    ..This suggests that evolution of higher organisms does not suffer a 'cost of complexity' because most mutations affect few traits and the size of the effects does not decrease with pleiotropy...
  11. ncbi request reprint The developmental evolution of avian digit homology: an update
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 208106, New Haven, CT 06520 8106, USA
    Theory Biosci 124:165-83. 2005
    ..This evidence suggests that the evolution of digits in tetrapods can proceed at least on two distinct levels of integration, the level of digit condensations and that of adult digits...
  12. pmc On the nature of thumbs
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, Prospect Street, New Haven, CT 06520 8106, USA
    Genome Biol 9:213. 2008
    ..This asymmetric expression correlates with independent morphological evolutionary variation of digit 1...
  13. ncbi request reprint A stochastic model for the evolution of transcription factor binding site abundance
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
    J Theor Biol 247:544-53. 2007
    ..3 x 10(-8)/year and a rate of origination of lambda approximately 1.6 x 10(-7)/year. We conclude that the model can be used to estimate the rate of binding site turnover from comparative genomic data...
  14. ncbi request reprint The developmental genetics of homology
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, POB 208106, New Haven, Connecticut 06520 8106, USA
    Nat Rev Genet 8:473-9. 2007
    ..These networks, here referred to as 'character identity networks', enable the execution of a character-specific developmental programme...
  15. doi request reprint The measurement theory of fitness
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Evolution 64:1358-76. 2010
    ..For instance, this theory identifies the correct scale for measuring gene interaction with respect to fitness and shows that different scales may lead to wrong conclusions...
  16. ncbi request reprint Evolutionary genetics: the nature of hidden genetic variation unveiled
    Gunter P Wagner
    Department of Ecology Evolutionary Biology, Osborn Memorial Labs, Yale University, 165 Prospect Street, New Haven, CT 06520 8106, USA
    Curr Biol 13:R958-60. 2003
  17. ncbi request reprint Is Hsp90 a regulator of evolvability?
    G P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    J Exp Zool 285:116-8. 1999
    ..We conclude that Hsp90 holds promise as a molecular model system for the evolution of evolvability. J. Exp. Zool. ( Mol. Dev. Evol. ) 285:116-118, 1999...
  18. ncbi request reprint Modeling the evolution of genetic architecture: A continuum of alleles model with pairwise AxA epistasis
    G P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
    J Theor Biol 203:163-75. 2000
    ..A consequence of this result is that, in this model, the genetic architecture of a set of characters is always evolvable i.e. no hard constraints can evolve...
  19. ncbi request reprint Rupert Riedl and the re-synthesis of evolutionary and developmental biology: body plans and evolvability
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    J Exp Zool B Mol Dev Evol 302:92-102. 2004
    ..In Riedl's view development is the most important factor besides natural selection in shaping the pattern and processes of morphological evolution...
  20. doi request reprint The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms
    Gunter P Wagner
    Yale Systems Biology Institute, and Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, POB 208106 New Haven, Connecticut 06405 8106, USA
    Nat Rev Genet 12:204-13. 2011
    ..This finding has major implications for the evolvability of complex organisms and the mapping of disease-causing mutations...
  21. ncbi request reprint Evolutionary innovations overcome ancestral constraints: a re-examination of character evolution in male sepsid flies (Diptera: Sepsidae)
    Gunter P Wagner
    Yale University, New Haven, CT 06520 8106, USA
    Evol Dev 4:1-6; discussion 7-8. 2002
  22. doi request reprint 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?..
  23. ncbi request reprint The road to modularity
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    Nat Rev Genet 8:921-31. 2007
    ..Although there is an emerging agreement that organisms have a modular organization, the main open problem is the question of whether modules arise through the action of natural selection or because of biased mutational mechanisms...
  24. pmc Molecular evolution of the HoxA cluster in the three major gnathostome lineages
    Chi hua Chiu
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 99:5492-7. 2002
    ..Such genomic revolutions may contribute significantly to the evolutionary process...
  25. ncbi request reprint 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...
  26. doi request reprint Evolution of digit identity in the three-toed Italian skink Chalcides chalcides: a new case of digit identity frame shift
    Rebecca L Young
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Evol Dev 11:647-58. 2009
    ..This result suggests that changes in of digit identity might be a more frequent consequence of digit reduction than previously assumed...
  27. 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...
  28. 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...
  29. doi request reprint Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds
    Zhe Wang
    Yale Systems Biology Institute, and Department of Ecology and Evolutionary Biology, Yale University, West Haven, Connecticut 06516, USA
    Nature 477:583-6. 2011
    ....
  30. 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...
  31. 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...
  32. doi request reprint 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
    ....
  33. doi request reprint Frame-shifts of digit identity in bird evolution and Cyclopamine-treated wings
    Alexander O Vargas
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
    Evol Dev 11:163-9. 2009
    ..The serial shift of digit identity toward posterior confirms a mechanistic possibility that was previously inferred from the evolutionary history of birds...
  34. doi request reprint 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
    ....
  35. doi request reprint Transposable element recruitments in the mammalian placenta: impacts and mechanisms
    Deena Emera
    Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
    Brief Funct Genomics 11:267-76. 2012
    ..We discuss the process by which one TE was transformed into a promoter for prolactin expression in the endometrium, describing a model for TE domestication called 'epistatic capture'...
  36. pmc The evolution of HoxD-11 expression in the bird wing: insights from Alligator mississippiensis
    Alexander O Vargas
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
    PLoS ONE 3:e3325. 2008
    ..If this is the case, we can expect closer relatives of birds to show no HoxD-11 expression only in digit 1. To test this prediction we investigate HoxD-11 expression in crocodilians, the closest living relatives of birds...
  37. 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
    ....
  38. ncbi request reprint Evolution of evolvability in a developmental model
    Jeremy Draghi
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
    Evolution 62:301-15. 2008
    ..We also show that this result is robust to the presence or absence of recombination, and explore how nonrandom environmental change can select for a modular pattern of variability...
  39. doi request reprint 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...
  40. ncbi request reprint Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. What is the role of genome duplication in the evolution of complexity and diversity?
    Karen D Crow
    Department of Ecology and Evolutionary Biology, Yale University, CT, USA
    Mol Biol Evol 23:887-92. 2006
    ..In this paper, we will develop the idea that genome duplication could contribute to species diversity through reduced probability of extinction...
  41. doi request reprint 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...
  42. 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...
  43. pmc Transformation of a transposon into a derived prolactin promoter with function during human pregnancy
    Deena Emera
    Department of Ecology and Evolutionary Biology and Yale Systems Biology Institute, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 109:11246-51. 2012
    ..Because prolactin communicates with immune cells during pregnancy, which regulate fetal invasion into maternal tissues, we speculate that ape dPRL promoter activity evolved in response to increased invasiveness of ape fetal tissue...
  44. pmc The origin of conserved protein domains and amino acid repeats via adaptive competition for control over amino acid residues
    Mary M Rorick
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
    J Mol Evol 70:29-43. 2010
    ..We conclude that the COAA model can explain two widely recognized features of transcription factor proteins: conserved domains and a tendency to accumulate homopeptides...
  45. ncbi request reprint Tinkering with transcription factor proteins: the role of transcription factor adaptation in developmental evolution
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, Howard Hughes Medical Institute, New Haven, CT 06520 8106, USA
    Novartis Found Symp 284:116-25; discussion 125-9, 158-63. 2007
    ..Here we summarize the evidence that transcription factor protein function itself is evolving and suggest that this might play an integral if not leading role in the evolution of gene regulation...
  46. ncbi request reprint Quasi-independence, homology and the unity of type: a topological theory of characters
    Gunter P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
    J Theor Biol 220:505-27. 2003
    ..In other words types have a statistical tendency of retaining evolutionary trajectories within their interior and thus add to the evolutionary persistence of types...
  47. doi request reprint Finding the frame shift: digit loss, developmental variability, and the origin of the avian hand
    Gabe S Bever
    Department of Geology and Geophysics, Yale University, New Haven, CT 06511, USA
    Evol Dev 13:269-79. 2011
    ..This model provides a new conceptual framework for the role of developmental variability in communicating broad evolutionary patterns on a taxonomically inclusive phylogenetic tree...
  48. ncbi request reprint Inhibition of Sonic hedgehog signaling leads to posterior digit loss in Ambystoma mexicanum: parallels to natural digit reduction in urodeles
    Geffrey F Stopper
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
    Dev Dyn 236:321-31. 2007
    ..This pattern of digit loss mimics the order of digit loss in natural variation. We suggest that variation in Shh expression and/or signal transmission may explain natural variation in digit number in urodeles...
  49. doi request reprint 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...
  50. doi request reprint Why ontogenetic homology criteria can be misleading: lessons from digit identity transformations
    Rebecca L Young
    Yale Systems Biology Institute, Department of Ecology and Evolutionary Biology, Yale University, West Haven, Connecticut 06516, USA
    J Exp Zool B Mol Dev Evol 316:165-70. 2011
    ....
  51. ncbi request reprint Modeling genetic architecture: a multilinear theory of gene interaction
    T F Hansen
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    Theor Popul Biol 59:61-86. 2001
    ..It is shown how the model can be used to estimate the strength of "functional" epistasis from a variety of genetic experiments...
  52. pmc Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model
    Ashley J R Carter
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
    Proc Biol Sci 269:953-60. 2002
    ..We propose that the different degree of conservation seen in vertebrate and Drosophila enhancers may be explained solely by differences in their population sizes and generation times...
  53. pmc Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms
    Matthew C Brandley
    Department of Ecology and Evolutionary Biology, Yale University, USA
    Genome Biol Evol 4:394-411. 2012
    ..ocellatus pregnancy are likely a result of regulation of genes continually expressed in the uterus rather than the initiation of expression of unique genes...
  54. doi request reprint Identity of the avian wing digits: problems resolved and unsolved
    Rebecca L Young
    Yale Systems Biology Institute, Department of Ecology and Evolutionary Biology, Yale University, West Haven, Connecticut, USA
    Dev Dyn 240:1042-53. 2011
    ..There is considerable uncertainty about these issues and we identify exciting new research directions to resolve them...
  55. ncbi request reprint Pentadactyl ground state of the avian wing
    Hans C E Larsson
    Department of Zoology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
    J Exp Zool 294:146-51. 2002
    ..Such a vestige suggests that strong constraints are maintaining a pentadactyl ground state in amniotes...
  56. ncbi request reprint Evolution of Hoxa-11 in lineages phylogenetically positioned along the fin-limb transition
    C H Chiu
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    Mol Phylogenet Evol 17:305-16. 2000
    ..Using electrophoretic mobility shift assays, a 35-bp intron sequence, which is 100% conserved in all Hoxa-11 loci except for the zebrafish Hoxa-11a paralog, was found to bind protein(s) in HeLa and chick whole-cell extracts...
  57. ncbi request reprint A recombinogenic targeting method to modify large-inserts for cis-regulatory analysis in transgenic mice: construction and expression of a 100-kb, zebrafish Hoxa-11b-lacZ reporter gene
    C H Chiu
    Department of Ecology and Evolutionary Biology, Osborn Memorial Laboratory 327, Yale University, P O Box 208106, New Haven, CT 06520 8106, USA
    Dev Genes Evol 210:105-9. 2000
    ..These findings demonstrate the utility of recombinogenic targeting for the modification and expression of large inserts captured from P1/PAC clones...
  58. ncbi request reprint The tetrapod limb: a hypothesis on its origin
    G P Wagner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    J Exp Zool 291:226-40. 2001
    ..We propose that the evolution of the derived expression patterns of Hoxa-11 and Hoxa-13 may be causally involved in the origin of the tetrapod limb...
  59. ncbi request reprint Genetic measurement of theory of epistatic effects
    G P Wagner
    Center for Computational Ecology, Yale University, New Haven, CT 06520 8106, USA
    Genetica 102:569-80. 1998
    ..e., it will tend to have a negative (canalizing) interaction with a subsequent gene substitution. This is confirmed in a preliminary analysis of QTL-data for adult body weight in mice...
  60. ncbi request reprint Epistasis in polygenic traits and the evolution of genetic architecture under stabilizing selection
    Joachim Hermisson
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 208106, New Haven, Connecticut 06520 8106, USA
    Am Nat 161:708-34. 2003
    ..Here, primarily genes with a high mutation rate are buffered, often at the cost of decanalization of other genes. An intuitive interpretation of this view is given in the discussion...
  61. ncbi request reprint Of chicken wings and frog legs: a smorgasbord of evolutionary variation in mechanisms of tetrapod limb development
    Geffrey F Stopper
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
    Dev Biol 288:21-39. 2005
    ....
  62. ncbi request reprint Simon-Ando decomposability and fitness landscapes
    Max Shpak
    Department of Ecology and Evolutionary Biology, University of Tennessee, 37996, Knoxville, TN, USA
    Theory Biosci 123:139-80. 2004
    ..For these reasons, the Simon-Ando formalism does not appear to be applicable to other forms of decomposition and aggregation of variables that are important in evolutionary systems...
  63. ncbi request reprint Evidence for the reversibility of digit loss: a phylogenetic study of limb evolution in Bachia (Gymnophthalmidae: Squamata)
    Tiana Kohlsdorf
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, Connecticut 06520, USA
    Evolution 60:1896-912. 2006
    ..We conclude that there are a limited number of cases with strong evidence for the reevolution of lost morphological structures, raising questions about the mechanisms that retain the genetic information for a latent character...
  64. pmc Protein structural modularity and robustness are associated with evolvability
    Mary M Rorick
    Department of Genetics, Yale University, New Haven, Connecticut, USA
    Genome Biol Evol 3:456-75. 2011
    ..We interpret these associations to be the result of reduced constraints on amino acid substitutions in highly modular and robust protein structures, which results in faster adaptation through natural selection...
  65. doi request reprint 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...
  66. ncbi request reprint PCR-survey of Hox-genes of the zebrafish: new sequence information and evolutionary implications
    B Y Misof
    Department of Biology, Yale University, New Haven, Connecticut 06520 8104, USA
    J Exp Zool 274:193-206. 1996
    ..In contrast, the Hox gene complement appears to be highly conserved among all tetrapods...
  67. ncbi request reprint Aggregation of variables and system decomposition: Applications to fitness landscape analysis
    Max Shpak
    Department of Ecology and Evolutionary Biology, University of Tennessee, 37996 1610, Knoxville, TN, USA
    Theory Biosci 123:33-68. 2004
    ..We propose that the aggregate variable descriptions of mutation-selection systems offer a potential formal definition of units of selection and evolution...
  68. doi request reprint 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
    ....
  69. pmc Epistasis and the mutation load: a measurement-theoretical approach
    T F Hansen
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
    Genetics 158:477-85. 2001
    ..We derive a simple criterion for the strength of epistasis that is necessary to overcome the twofold disadvantage of sex...