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Genomes and Genes | Gunter P WagnerSummaryAffiliation: Yale University Country: USA Publications
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Publications
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samplesGunter 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...- An evolutionary test of the isoform switching hypothesis of functional progesterone withdrawal for parturition: humans have a weaker repressive effect of PR-A than miceGunter 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... 
What is the promise of developmental evolution? III. The crucible of developmental evolutionGunter 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- Rupert Riedl and the re-synthesis of evolutionary and developmental biology: body plans and evolvabilityGunter 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... - The gene regulatory logic of transcription factor evolutionGunter 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... - Divergence of conserved non-coding sequences: rate estimates and relative rate testsGunter 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... - Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequencesGunter 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... - 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... - Molecular evolution of evolutionary novelties: the vagina and uterus of therian mammalsGunter 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... 
On the nature of thumbsGunter 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...- The developmental evolution of avian digit homology: an updateGunter 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... - The road to modularityGunter 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... - A stochastic model for the evolution of transcription factor binding site abundanceGunter 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... - Evolutionary genetics: the nature of hidden genetic variation unveiledGunter 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 - The developmental genetics of homologyGunter 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... - 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... - Modeling the evolution of genetic architecture: A continuum of alleles model with pairwise AxA epistasisG 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... - The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organismsGunter 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... - The measurement theory of fitnessGunter 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... - Evolutionary noveltiesGunter 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?.. - 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 - Molecular evolution of the HoxA cluster in the three major gnathostome lineagesChi 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... - The "fish-specific" Hox cluster duplication is coincident with the origin of teleostsKaren 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... - Evolution of digit identity in the three-toed Italian skink Chalcides chalcides: a new case of digit identity frame shiftRebecca 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... - Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammalsVincent 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... 
Adaptive evolution of Hox-gene homeodomains after cluster duplicationsVincent 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...- HoxA-11 and FOXO1A cooperate to regulate decidual prolactin expression: towards inferring the core transcriptional regulators of decidual genesVincent 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... - Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elementsDeena Emera
Department of Ecology and Evolutionary Biology and Yale Systems Biology Institute, Yale University, USA
Mol Biol Evol 29:239-47. 2012.... - A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13Tiana Kohlsdorf
Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
J Mol Evol 67:581-93. 2008.... - Frame-shifts of digit identity in bird evolution and Cyclopamine-treated wingsAlexander 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... - Transposable element recruitments in the mammalian placenta: impacts and mechanismsDeena 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'... - Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomesVincent J Lynch
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
PLoS Genet 5:e1000349. 2009.... - The evolution of HoxD-11 expression in the bird wing: insights from Alligator mississippiensisAlexander 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... - Evolution of a derived protein-protein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulationKathryn 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... - Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birdsZhe Wang
Yale Systems Biology Institute, and Department of Ecology and Evolutionary Biology, Yale University, West Haven, Connecticut 06516, USA
Nature 477:583-6. 2011.... - Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPBVincent 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... - 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... - Resurrecting the role of transcription factor change in developmental evolutionVincent 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... - Transformation of a transposon into a derived prolactin promoter with function during human pregnancyDeena 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... - Quasi-independence, homology and the unity of type: a topological theory of charactersGunter 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... - The origin of conserved protein domains and amino acid repeats via adaptive competition for control over amino acid residuesMary 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... - Tinkering with transcription factor proteins: the role of transcription factor adaptation in developmental evolutionGunter 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... - Evolution of evolvability in a developmental modelJeremy 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... - Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammalsVincent 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... - Finding the frame shift: digit loss, developmental variability, and the origin of the avian handGabe 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... - 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... - Why ontogenetic homology criteria can be misleading: lessons from digit identity transformationsRebecca 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.... - Inhibition of Sonic hedgehog signaling leads to posterior digit loss in Ambystoma mexicanum: parallels to natural digit reduction in urodelesGeffrey 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... - Modeling genetic architecture: a multilinear theory of gene interactionT 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... - Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanismsMatthew 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... - Identity of the avian wing digits: problems resolved and unsolvedRebecca 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... - Pentadactyl ground state of the avian wingHans 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... - 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 geneC 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... - The tetrapod limb: a hypothesis on its originG 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... - Genetic measurement of theory of epistatic effectsG 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... - Evolution of Hoxa-11 in lineages phylogenetically positioned along the fin-limb transitionC 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... - Of chicken wings and frog legs: a smorgasbord of evolutionary variation in mechanisms of tetrapod limb developmentGeffrey F Stopper
Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
Dev Biol 288:21-39. 2005.... - Epistasis in polygenic traits and the evolution of genetic architecture under stabilizing selectionJoachim 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... - Protein structural modularity and robustness are associated with evolvabilityMary 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... - 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... - 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... - Simon-Ando decomposability and fitness landscapesMax 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... - PCR-survey of Hox-genes of the zebrafish: new sequence information and evolutionary implicationsB 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... - Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammalsVincent 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.... - Aggregation of variables and system decomposition: Applications to fitness landscape analysisMax 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... - Epistasis and the mutation load: a measurement-theoretical approachT 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...