Modularity: genes, development and evolution.

Modularity has emerged as a central concept for evolutionary biology, providing the field with a theory of organismal structure and variation. This theory has reframed long standing questions and serves as a unified conceptual framework for genetics, developmental biology and multivariate evolution. Research programs in systems biology and quantitative genetics are bridging the gap between these fields. While this synthesis is ongoing, some major themes have emerged and empirical evidence for modularity has become abundant. In this review, we look at modularity from an historical perspective, highlighting its meaning at different levels of biological organization and the different methods that can be used to detect it. We then explore the relationship between quantitative genetic approaches to modularity and developmental genetic studies. We conclude by investigating the dynamic relationship between modularity and the adaptive landscape and how this potentially shapes evolution and can help bridge the gap between micro- and macroevolution.

[1]  J. Finarelli,et al.  EMMLi: A maximum likelihood approach to the analysis of modularity , 2016, Evolution; international journal of organic evolution.

[2]  U. Schliewen,et al.  Rugged adaptive landscapes shape a complex, sympatric radiation , 2016, Proceedings of the Royal Society B: Biological Sciences.

[3]  M. Pavlicev,et al.  Constraints Evolve: Context Dependency of Gene Effects Allows Evolution of Pleiotropy , 2015 .

[4]  T. F. Hansen,et al.  Complex constraints on allometry revealed by artificial selection on the wing of Drosophila melanogaster , 2015, Proceedings of the National Academy of Sciences.

[5]  K. Meyer,et al.  Estimating sampling error of evolutionary statistics based on genetic covariance matrices using maximum likelihood , 2015, Journal of evolutionary biology.

[6]  Julie Messier,et al.  Fitness of multidimensional phenotypes in dynamic adaptive landscapes. , 2015, Trends in ecology & evolution.

[7]  Clayton E Cressler,et al.  Detecting Adaptive Evolution in Phylogenetic Comparative Analysis Using the Ornstein-Uhlenbeck Model. , 2015, Systematic biology.

[8]  J. Cheverud,et al.  Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation , 2015, Journal of evolutionary biology.

[9]  Diogo Melo,et al.  Directional selection can drive the evolution of modularity in complex traits , 2014, Proceedings of the National Academy of Sciences.

[10]  Benjamin L de Bivort,et al.  Behavioral idiosyncrasy reveals genetic control of phenotypic variability , 2014, Proceedings of the National Academy of Sciences.

[11]  T. F. Hansen,et al.  Genetic constraints predict evolutionary divergence in Dalechampia blossoms , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[12]  R. Cerqueira,et al.  Quantitative Genetics and Modularity in Cranial and Mandibular Morphology of Calomys expulsus , 2014, bioRxiv.

[13]  S. J. Arnold,et al.  Epistasis and Natural Selection Shape the Mutational Architecture of Complex Traits , 2014, Nature Communications.

[14]  G. Wagner,et al.  THE EVOLUTION OF PHENOTYPIC CORRELATIONS AND “DEVELOPMENTAL MEMORY” , 2014, Evolution; international journal of organic evolution.

[15]  S. J. Arnold Phenotypic Evolution: The Ongoing Synthesis , 2014, The American Naturalist.

[16]  T. F. Hansen WHY EPISTASIS IS IMPORTANT FOR SELECTION AND ADAPTATION , 2013, Evolution; international journal of organic evolution.

[17]  D. Garlaschelli,et al.  Community detection for correlation matrices , 2013, 1311.1924.

[18]  A. Porto,et al.  SIZE VARIATION, GROWTH STRATEGIES, AND THE EVOLUTION OF MODULARITY IN THE MAMMALIAN SKULL , 2013, Evolution; international journal of organic evolution.

[19]  Taylor J. Maxwell,et al.  APOE Modulates the Correlation Between Triglycerides, Cholesterol, and CHD Through Pleiotropy, and Gene-by-Gene Interactions , 2013, Genetics.

[20]  O. Ovaskainen,et al.  driftsel: an R package for detecting signals of natural selection in quantitative traits , 2013, Molecular ecology resources.

[21]  Dean C. Adams,et al.  A field comes of age: geometric morphometrics in the 21 st century , 2013 .

[22]  Annalise B. Paaby,et al.  The many faces of pleiotropy. , 2013, Trends in Genetics.

[23]  P. Wainwright,et al.  Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild , 2013, Science.

[24]  L. Gustafsson,et al.  Rapid and unpredictable changes of the G‐matrix in a natural bird population over 25 years , 2013, Journal of evolutionary biology.

[25]  T. F. Hansen,et al.  A phylogenetic comparative method for studying multivariate adaptation. , 2012, Journal of theoretical biology.

[26]  S. J. Arnold,et al.  The effects of stochastic and episodic movement of the optimum on the evolution of the G‐matrix and the response of the trait mean to selection , 2012, Journal of evolutionary biology.

[27]  J. Conner QUANTITATIVE GENETIC APPROACHES TO EVOLUTIONARY CONSTRAINT: HOW USEFUL? , 2012, Evolution; international journal of organic evolution.

[28]  R. Woods,et al.  The Measurement of Local Variation in Shape , 2012, Evolutionary Biology.

[29]  Nathan M. Young,et al.  The generation of variation and the developmental basis for evolutionary novelty. , 2012, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[30]  Joel G. Kingsolver,et al.  Synthetic analyses of phenotypic selection in natural populations: lessons, limitations and future directions , 2012, Evolutionary Ecology.

[31]  Gabriel Marroig,et al.  MODULARITY, NOISE, AND NATURAL SELECTION , 2011, Evolution; international journal of organic evolution.

[32]  Christopher R. Herlihy,et al.  ELIMINATION OF A GENETIC CORRELATION BETWEEN THE SEXES VIA ARTIFICIAL CORRELATIONAL SELECTION , 2011, Evolution; international journal of organic evolution.

[33]  T. F. Hansen,et al.  Genotype-Phenotype Maps Maximizing Evolvability: Modularity Revisited , 2011, Evolutionary Biology.

[34]  A. Hendry,et al.  Quantitative genetic inheritance of morphological divergence in a lake–stream stickleback ecotype pair: implications for reproductive isolation , 2011, Journal of evolutionary biology.

[35]  M. Pavlicev,et al.  Evolution of pleiotropy: epistatic interaction pattern supports a mechanistic model underlying variation in genotype-phenotype map. , 2011, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[36]  G. Wagner,et al.  Evolution of adaptive phenotypic variation patterns by direct selection for evolvability , 2011, Proceedings of the Royal Society B: Biological Sciences.

[37]  F. Eroukhmanoff,et al.  Evolution and stability of the G‐matrix during the colonization of a novel environment , 2011, Journal of evolutionary biology.

[38]  D. Berner Size correction in biology: how reliable are approaches based on (common) principal component analysis? , 2011, Oecologia.

[39]  Frank W. Stearns One Hundred Years of Pleiotropy: A Retrospective , 2010, Genetics.

[40]  Jianzhi Zhang,et al.  Genomic patterns of pleiotropy and the evolution of complexity , 2010, Proceedings of the National Academy of Sciences.

[41]  C. Geyer,et al.  INFERRING FITNESS LANDSCAPES , 2010, Evolution; international journal of organic evolution.

[42]  William E. Stutz,et al.  FORAGING TRAIT (CO)VARIANCES IN STICKLEBACK EVOLVE DETERMINISTICALLY AND DO NOT PREDICT TRAJECTORIES OF ADAPTIVE DIVERSIFICATION , 2010, Evolution; international journal of organic evolution.

[43]  J. Cheverud,et al.  SIZE AS A LINE OF LEAST RESISTANCE II: DIRECT SELECTION ON SIZE OR CORRELATED RESPONSE DUE TO CONSTRAINTS? , 2010, Evolution; international journal of organic evolution.

[44]  Isaac Salazar-Ciudad,et al.  A computational model of teeth and the developmental origins of morphological variation , 2010, Nature.

[45]  H. Rundle,et al.  The Contribution of Selection and Genetic Constraints to Phenotypic Divergence , 2010, The American Naturalist.

[46]  Philipp Mitteroecker,et al.  The Developmental Basis of Variational Modularity: Insights from Quantitative Genetics, Morphometrics, and Developmental Biology , 2009, Evolutionary Biology.

[47]  Trish E. Parsons,et al.  Deciphering the Palimpsest: Studying the Relationship Between Morphological Integration and Phenotypic Covariation , 2009, Evolutionary Biology.

[48]  C. Goodnight,et al.  Empirical Comparison of G Matrix Test Statistics: Finding Biologically Relevant Change , 2009, Evolution; international journal of organic evolution.

[49]  E. Stone,et al.  The genetics of quantitative traits: challenges and prospects , 2009, Nature Reviews Genetics.

[50]  Christian Peter Klingenberg,et al.  Morphometric integration and modularity in configurations of landmarks: tools for evaluating a priori hypotheses , 2009, Evolution & development.

[51]  David Houle,et al.  Inferring the Nature of Allometry from Geometric Data , 2009, Evolutionary Biology.

[52]  A. Porto,et al.  The Evolution of Modularity in the Mammalian Skull I: Morphological Integration Patterns and Magnitudes , 2009, Evolutionary Biology.

[53]  E. Stone,et al.  Systems Genetics of Complex Traits in Drosophila melanogaster , 2009, Nature Genetics.

[54]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[55]  Reinhard Bürger,et al.  Understanding The Evolution And Stability Of The G-Matrix , 2008, Evolution; international journal of organic evolution.

[56]  E. Márquez,et al.  A Statistical Framework for Testing Modularity in Multidimensional Data , 2008, Evolution; international journal of organic evolution.

[57]  D. Houle,et al.  Measuring and comparing evolvability and constraint in multivariate characters , 2008, Journal of evolutionary biology.

[58]  P. D. Polly Developmental Dynamics and G-Matrices: Can Morphometric Spaces be Used to Model Phenotypic Evolution? , 2008, Evolutionary Biology.

[59]  S. J. Arnold,et al.  MIPoD: A Hypothesis‐Testing Framework for Microevolutionary Inference from Patterns of Divergence , 2008, The American Naturalist.

[60]  G. Wagner,et al.  The road to modularity , 2007, Nature Reviews Genetics.

[61]  F. Bookstein,et al.  The conceptual and statistical relationship between modularity and morphological integration. , 2007, Systematic biology.

[62]  James M. Cheverud,et al.  GENETIC VARIATION IN PLEIOTROPY: DIFFERENTIAL EPISTASIS AS A SOURCE OF VARIATION IN THE ALLOMETRIC RELATIONSHIP BETWEEN LONG BONE LENGTHS AND BODY WEIGHT , 2007, Evolution; international journal of organic evolution.

[63]  G. Wagner The developmental genetics of homology , 2007, Nature Reviews Genetics.

[64]  J. Cheverud,et al.  Research Article Comparing covariance matrices: random skewers method compared to the common principal components model , 2007 .

[65]  J. Auffray,et al.  CONSERVED PHENOTYPIC VARIATION PATTERNS, EVOLUTION ALONG LINES OF LEAST RESISTANCE, AND DEPARTURE DUE TO SELECTION IN FOSSIL RODENTS , 2006, Evolution; international journal of organic evolution.

[66]  Joachim Hermisson,et al.  EVOLUTION OF GENETIC ARCHITECTURE UNDER DIRECTIONAL SELECTION , 2006, Evolution; international journal of organic evolution.

[67]  K. Pepin,et al.  Variable Pleiotropic Effects From Mutations at the Same Locus Hamper Prediction of Fitness From a Fitness Component , 2006, Genetics.

[68]  J. Reichardt,et al.  Statistical mechanics of community detection. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[69]  Nathan M. Young,et al.  SERIAL HOMOLOGY AND THE EVOLUTION OF MAMMALIAN LIMB COVARIATION STRUCTURE , 2005, Evolution; international journal of organic evolution.

[70]  K. Strimmer,et al.  Statistical Applications in Genetics and Molecular Biology A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics , 2011 .

[71]  J. Cheverud,et al.  Epistatic Pleiotropy and the Genetic Architecture of Covariation Within Early and Late-Developing Skull Trait Complexes in Mice , 2005, Genetics.

[72]  Ary A. Hoffmann,et al.  A reassessment of genetic limits to evolutionary change , 2005 .

[73]  J. Micol,et al.  Quantitative trait loci mapping of floral and leaf morphology traits in Arabidopsis thaliana: evidence for modular genetic architecture , 2005, Evolution & development.

[74]  J. Cheverud,et al.  SIZE AS A LINE OF LEAST EVOLUTIONARY RESISTANCE: DIET AND ADAPTIVE MORPHOLOGICAL RADIATION IN NEW WORLD MONKEYS , 2005, Evolution; international journal of organic evolution.

[75]  J. Cheverud,et al.  Detecting genetic drift versus selection in human evolution , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[76]  A. King,et al.  Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution , 2004, The American Naturalist.

[77]  S. J. Arnold,et al.  EVOLUTION AND STABILITY OF THE G-MATRIX ON A LANDSCAPE WITH A MOVING OPTIMUM , 2004, Evolution; international journal of organic evolution.

[78]  J. Cheverud,et al.  Cranial evolution in sakis (Pithecia, Platyrrhini) II: evolutionary processes and morphological integration , 2003, Journal of evolutionary biology.

[79]  S. J. Arnold,et al.  STABILITY OF THE G‐MATRIX IN A POPULATION EXPERIENCING PLEIOTROPIC MUTATION, STABILIZING SELECTION, AND GENETIC DRIFT , 2003, Evolution; international journal of organic evolution.

[80]  C. Pélabon,et al.  Evolvability and genetic constraint in Dalechampia blossoms: components of variance and measures of evolvability , 2003, Journal of evolutionary biology.

[81]  T. F. Hansen Is modularity necessary for evolvability? Remarks on the relationship between pleiotropy and evolvability. , 2003, Bio Systems.

[82]  P. Brakefield,et al.  Modularity, individuality, and evo-devo in butterfly wings , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[83]  M. Whitlock,et al.  PERSISTENCE OF CHANGES IN THE GENETIC COVARIANCE MATRIX AFTER A BOTTLENECK , 2002, Evolution; international journal of organic evolution.

[84]  Yaniv Ziv,et al.  Revealing modular organization in the yeast transcriptional network , 2002, Nature Genetics.

[85]  P. Phillips,et al.  Comparative quantitative genetics : evolution of the G matrix , 2002 .

[86]  Isaac Salazar-Ciudad,et al.  A gene network model accounting for development and evolution of mammalian teeth , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[87]  P. Brakefield,et al.  The genetics and evo–devo of butterfly wing patterns , 2002, Nature Reviews Genetics.

[88]  J. Cheverud,et al.  A COMPARISON OF PHENOTYPIC VARIATION AND COVARIATION PATTERNS AND THE ROLE OF PHYLOGENY, ECOLOGY, AND ONTOGENY DURING CRANIAL EVOLUTION OF NEW WORLD MONKEYS , 2001, Evolution; international journal of organic evolution.

[89]  R. Cerqueira,et al.  Evolutionary rates and stabilizing selection in large‐bodied opossum skulls (Didelphimorphia: Didelphidae) , 2001 .

[90]  Paul M. Magwene,et al.  NEW TOOLS FOR STUDYING INTEGRATION AND MODULARITY , 2001, Evolution; international journal of organic evolution.

[91]  M. Whitlock,et al.  Inbreeding changes the shape of the genetic covariance matrix in Drosophila melanogaster. , 2001, Genetics.

[92]  J. M. Hoekstra,et al.  The Strength of Phenotypic Selection in Natural Populations , 2001, The American Naturalist.

[93]  F. Bookstein,et al.  Morphometric Tools for Landmark Data: Geometry and Biology , 1999 .

[94]  T. F. Hansen STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION , 1997, Evolution; international journal of organic evolution.

[95]  Dolph Schluter,et al.  ADAPTIVE RADIATION ALONG GENETIC LINES OF LEAST RESISTANCE , 1996, Evolution; international journal of organic evolution.

[96]  L. Altenberg,et al.  PERSPECTIVE: COMPLEX ADAPTATIONS AND THE EVOLUTION OF EVOLVABILITY , 1996, Evolution; international journal of organic evolution.

[97]  J. Cheverud Developmental Integration and the Evolution of Pleiotropy , 1996 .

[98]  B. Grant,et al.  PREDICTING MICROEVOLUTIONARY RESPONSES TO DIRECTIONAL SELECTION ON HERITABLE VARIATION , 1995, Evolution; international journal of organic evolution.

[99]  A. Templeton,et al.  The molecular through ecological genetics of abnormal abdomen in Drosophila mercatorum. V. Female phenotypic expression on natural genetic backgrounds and in natural environments. , 1993, Genetics.

[100]  S. Lele,et al.  Euclidean distance matrix analysis: a coordinate-free approach for comparing biological shapes using landmark data. , 1991, American journal of physical anthropology.

[101]  J. Cheverud A COMPARATIVE ANALYSIS OF MORPHOLOGICAL VARIATION PATTERNS IN THE PAPIONINS , 1989, Evolution; international journal of organic evolution.

[102]  M. Turelli PHENOTYPIC EVOLUTION, CONSTANT COVARIANCES, AND THE MAINTENANCE OF ADDITIVE VARIANCE , 1988, Evolution; international journal of organic evolution.

[103]  Z. Zeng LONG‐TERM CORRELATED RESPONSE, INTERPOPULATION COVARIATION, AND INTERSPECIFIC ALLOMETRY , 1988, Evolution; international journal of organic evolution.

[104]  S. Kauffman,et al.  Towards a general theory of adaptive walks on rugged landscapes. , 1987, Journal of theoretical biology.

[105]  Joan T. Richtsmeier,et al.  Finite-Element Scaling Applied to Sexual Dimorphism in Rhesus Macaque (Macaca Mulatta) Facial Growth , 1986 .

[106]  A. Templeton,et al.  The molecular through ecological genetics of abnormal abdomen in Drosophila mercatorum. I. Basic genetics. , 1985, Genetics.

[107]  J. Cheverud,et al.  Quantitative genetics and developmental constraints on evolution by selection. , 1984, Journal of theoretical biology.

[108]  D. Kendall SHAPE MANIFOLDS, PROCRUSTEAN METRICS, AND COMPLEX PROJECTIVE SPACES , 1984 .

[109]  S. J. Arnold,et al.  THE MEASUREMENT OF SELECTION ON CORRELATED CHARACTERS , 1983, Evolution; international journal of organic evolution.

[110]  J. Cheverud PHENOTYPIC, GENETIC, AND ENVIRONMENTAL MORPHOLOGICAL INTEGRATION IN THE CRANIUM , 1982, Evolution; international journal of organic evolution.

[111]  R. Lande QUANTITATIVE GENETIC ANALYSIS OF MULTIVARIATE EVOLUTION, APPLIED TO BRAIN:BODY SIZE ALLOMETRY , 1979, Evolution; international journal of organic evolution.

[112]  R. Lande NATURAL SELECTION AND RANDOM GENETIC DRIFT IN PHENOTYPIC EVOLUTION , 1976, Evolution; international journal of organic evolution.

[113]  M. Bulmer,et al.  The Effect of Selection on Genetic Variability , 1971, The American Naturalist.

[114]  G. Simpson The Study of Evolution: Methods and Present Status of Theory , 1962 .

[115]  L. N. Hazel The Genetic Basis for Constructing Selection Indexes. , 1943, Genetics.

[116]  M. S. Almén,et al.  Making quantitative morphological variation from basic developmental processes : Where are we ? The case of the Drosophila wing , 2015 .

[117]  P. Alberch From genes to phenotype: dynamical systems and evolvability , 2004, Genetica.

[118]  T. F. Hansen,et al.  Floral integration, modularity, and accuracy: distinguishing complex adaptations from genetic constraints , 2004 .

[119]  S. J. Arnold,et al.  The adaptive landscape as a conceptual bridge between micro- and macroevolution , 2004, Genetica.

[120]  S. J. Arnold,et al.  EVOLUTION AND STABILITY OF THE G-MATRIX ON A LANDSCAPE WITH A MOVING OPTIMUM , 2004 .

[121]  J. Felsenstein Phylogenies and quantitative characters , 1988 .

[122]  G. A. Horridge,et al.  Animal species and evolution. , 1964 .

[123]  K. Pearson Mathematical Contributions to the Theory of Evolution. III. Regression, Heredity, and Panmixia , 1896 .