Epidermal Growth Factor Receptor and Transforming Growth Factor-β Signaling Contributes to Variation for Wing Shape in Drosophila melanogaster
TL;DR: In this article, 50 insertional mutations, representing 43 loci in the RTK, Hedgehog, TGF-β pathways, and their genetically interacting factors were used to study the role of these networks on wing shape.
Abstract: Wing development in Drosophila is a common model system for the dissection of genetic networks and their roles during development. In particular, the RTK and TGF-β regulatory networks appear to be involved with numerous aspects of wing development, including patterning, cell determination, growth, proliferation, and survival in the developing imaginal wing disc. However, little is known as to how subtle changes in the function of these genes may contribute to quantitative variation for wing shape, per se. In this study 50 insertional mutations, representing 43 loci in the RTK, Hedgehog, TGF-β pathways, and their genetically interacting factors were used to study the role of these networks on wing shape. To concurrently examine how genetic background modulates the effects of the mutation, each insertion was introgressed into two wild-type genetic backgrounds. Using geometric morphometric methods, it is shown that the majority of these mutations have profound effects on shape but not size of the wing when measured as heterozygotes. To examine the relationships between how each mutation affects wing shape hierarchical clustering was used. Unlike previous observations of environmental canalization, these mutations did not generally increase within-line variation relative to their wild-type counterparts. These results provide an entry point into the genetics of wing shape and are discussed within the framework of the dissection of complex phenotypes.
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1,091 citations
26 Mar 2010
TL;DR: In the six decades since the publication of Huxley's Evolution: The Modern Synthesis, the spectacular empirical advances in the biological sciences have been accompanied by equally significant developments within the core theoretical framework of the discipline.
Abstract: In the six decades since the publication of Julian Huxley's Evolution: The Modern Synthesis, the spectacular empirical advances in the biological sciences have been accompanied by equally significant developments within the core theoretical framework of the discipline. As a result, evolutionary theory today includes concepts and even entire new fields that were not part of the foundational structure of the Modern Synthesis. In this volume, sixteen leading evolutionary biologists and philosophers of science survey the conceptual changes that have emerged since Huxley's landmark publication, not only in such traditional domains of evolutionary biology as quantitative genetics and paleontology but also in such new fields of research as genomics and EvoDevo. Most of the contributors to Evolution, the Extended Synthesis accept many of the tenets of the classical framework but want to relax some of its assumptions and introduce significant conceptual augmentations of the basic Modern Synthesis structure -- just as the architects of the Modern Synthesis themselves expanded and modulated previous versions of Darwinism. This continuing revision of a theoretical edifice the foundations of which were laid in the middle of the nineteenth century--the reexamination of old ideas, proposals of new ones, and the synthesis of the most suitable -- shows us how science works, and how scientists have painstakingly built a solid set of explanations for what Darwin called the "grandeur" of life. Contributors: John Beatty, Werner Callebaut, Jeremy Draghi, Chrisantha Fernando, Sergey Gavrilets, John C. Gerhart, Eva Jablonka, David Jablonski, Marc W. Kirschner, Marion J. Lamb, Alan C. Love, Gerd B. Muller, Stuart A. Newman, John Odling-Smee, Massimo Pigliucci, Michael Purugganan, Eors Szathmary, Gunter P. Wagner, David Sloan Wilson, Gregory A. Wray.
764 citations
TL;DR: Quantitative studies of shape can characterize developmental and genetic effects and discover their relative importance, which integrate evo-devo and related disciplines into a coherent understanding of evolutionary processes from populations to large-scale evolutionary radiations.
Abstract: Morphological traits have long been a focus of evolutionary developmental biology ('evo-devo'), but new methods for quantifying shape variation are opening unprecedented possibilities for investigating the developmental basis of evolutionary change. Morphometric analyses are revealing that development mediates complex interactions between genetic and environmental factors affecting shape. Evolution results from changes in those interactions, as natural selection favours shapes that more effectively perform some fitness-related functions. Quantitative studies of shape can characterize developmental and genetic effects and discover their relative importance. They integrate evo-devo and related disciplines into a coherent understanding of evolutionary processes from populations to large-scale evolutionary radiations.
581 citations
TL;DR: Escoufier's RV coefficient and the multi‐set RV coefficient are introduced as measures of the correlation between two or more subsets of landmarks and a criterion for spatial contiguity for sets of landmarks using an adjacency graph is proposed.
Abstract: Identifying the modular components of a configuration of landmarks is an important task of morphometric analyses in evolutionary developmental biology Modules are integrated internally by many interactions among their component parts, but are linked to one another only by few or weak interactions Accordingly, traits within modules are tightly correlated with each other, but relatively independent of traits in other modules Hypotheses concerning the boundaries of modules in a landmark configuration can therefore be tested by comparing the strength of covariation among alternative partitions of the configuration into subsets of landmarks If a subdivision coincides with the true boundaries between modules, the correlations among subsets should be minimal This article introduces Escoufier's RV coefficient and the multi-set RV coefficient as measures of the correlation between two or more subsets of landmarks These measures can be compared between alternative partitions of the configuration into subsets Because developmental interactions are tissue bound, it is sensible to require that modules should be spatially contiguous I propose a criterion for spatial contiguity for sets of landmarks using an adjacency graph The new methods are demonstrated with data on shape of the wing in Drosophila melanogaster and the mandible of the house mouse
455 citations
Cites background or methods from "Epidermal Growth Factor Receptor an..."
...…based on separate Procrustes fits have reported low phenotypic and genetic correlations and differences in the genetic architecture of principal components of shape for different subsets of landmarks (Birdsall et al. 2000; Zimmerman et al. 2000; Palsson and Gibson 2004; Dworkin and Gibson 2006)....
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...Whereas analyses based on joint Procrustes fits have underscored the integration across the Drosophila wing (Klingenberg and Zaklan 2000), studies based on separate Procrustes fits have reported low phenotypic and genetic correlations and differences in the genetic architecture of principal components of shape for different subsets of landmarks (Birdsall et al. 2000; Zimmerman et al. 2000; Palsson and Gibson 2004; Dworkin and Gibson 2006)....
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TL;DR: Canonical variate analysis (CVA), the generalization of LDA for multiple groups, is often used in the exploratory style of an ordination technique (a low-dimensional representation of the data) and can be a simple alternative to LDA.
Abstract: Linear discriminant analysis (LDA) is a multivariate classification technique frequently applied to morphometric data in various biomedical disciplines. Canonical variate analysis (CVA), the generalization of LDA for multiple groups, is often used in the exploratory style of an ordination technique (a low-dimensional representation of the data). In the rare case when all groups have the same covariance matrix, maximum likelihood classification can be based on these linear functions. Both LDA and CVA require full-rank covariance matrices, which is usually not the case in modern morphometrics. When the number of variables is close to the number of individuals, groups appear separated in a CVA plot even if they are samples from the same population. Hence, reliable classification and assessment of group separation require many more organisms than variables. A simple alternative to CVA is the projection of the data onto the principal components of the group averages (between-group PCA). In contrast to CVA, these axes are orthogonal and can be computed even when the data are not of full rank, such as for Procrustes shape coordinates arising in samples of any size, and when covariance matrices are heterogeneous. In evolutionary quantitative genetics, the selection gradient is identical to the coefficient vector of a linear discriminant function between the populations before vs. after selection. When the measured variables are Procrustes shape coordinates, discriminant functions and selection gradients are vectors in shape space and can be visualized as shape deformations. Except for applications in quantitative genetics and in classification, however, discriminant functions typically offer no interpretation as biological factors.
419 citations
Cites background from "Epidermal Growth Factor Receptor an..."
...…and visualized the corresponding vector of regression coefficients, which is the vector ða0X0XaÞ 1ðXaÞ0X; ð5Þ where a is the discriminant function or CV axis (e.g., Rohlf et al. 1996; Adams and Funk 1997; Harvati 2003; Klingenberg and Monteiro 2005; Dworkin and Gibson 2006; Leinonen et al. 2006)....
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...Klingenberg and Monteiro noticed that this leads to a visualization of the scaled selection differential s....
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...Klingenberg and Monteiro (2005) claimed that selection gradients for Procrustes shape coordinates are not vectors in shape space and should not be visualized directly, but instead by a regression of shape on the scores along the selection gradient, such as in (5)....
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...Similarly, instead of a direct visualization of selection gradients, Klingenberg and Monteiro (2005) suggested visualizing the multivariate regression of shape on the scores along the selection gradient b....
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...Instead, several authors regressed the shape variables on the canonical variate scores and visualized the corresponding vector of regression coefficients, which is the vector ða0X0XaÞ 1ðXaÞ0X; ð5Þ where a is the discriminant function or CV axis (e.g., Rohlf et al. 1996; Adams and Funk 1997; Harvati 2003; Klingenberg and Monteiro 2005; Dworkin and Gibson 2006; Leinonen et al. 2006)....
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References
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TL;DR: In this article, the authors discuss their experience designing and implementing a statistical computing language, which combines what they felt were useful features from two existing computer languages, and they feel that the new language provides advantages in the areas of portability, computational efficiency, memory management, and scope.
Abstract: In this article we discuss our experience designing and implementing a statistical computing language. In developing this new language, we sought to combine what we felt were useful features from two existing computer languages. We feel that the new language provides advantages in the areas of portability, computational efficiency, memory management, and scoping.
9,446 citations
TL;DR: In this paper, a new method is presented that generalizes Siegel and Benson's (1982) resistant-fit theta-rho analysis so that more than two objects can be compared at the same time.
Abstract: Superimposition methods for comparing configurations of landmarks in two or more specimens are reviewed. These methods show differences in shape among specimens as residuals after rotation, translation, and scaling them so that they align as well as possible. A new method is presented that generalizes Siegel and Benson's (1982) resistant-fit theta-rho analysis so that more than two objects can be compared at the same time. Both least-squares and resistant-fit approaches are generalized to allow for affine transformations (uniform shape change). The methods are compared, using artificial data and data on 18 landmarks on the wings of 127 species of North American mosquitoes. Graphical techniques .are also presented to help sum- marize the patterns of differences in shape among the objects being compared. (Morphometrics; resistant-fit; least-squares; theta-rho analysis; rotational fit; affine transformations.) An important problem in morphomet- is now easy to display a transformation grid rics is that of comparing configurations of that maps the configuration of landmarks landmarks in two or more specimens. of one organism exactly into those of Thompson (1917) suggested an elegant ap- another. proach, using "transformation grids," that An alternative approach to fitting a mod- depicts the overall form of one organism el that completely describes the differences as a distortion in the shape of a reference between two organisms is to fit a very sim- organism. The basic idea was to place a ple model that only takes into consider- Cartesian coordinate grid over the refer- ation global parameters such as differences ence organism and then distort the image in rotation, translation, and scale. Geo- of the organism (including the grid) in var- metrically, this corresponds to superim- ious ways until the form of the second or- posing one organism on top of another so ganism was achieved. The differences in that its landmarks align as well as possible shapes of the two organisms are shown by (in some sense) with the positions of the the deviations of the fitted grid (usually corresponding landmarks on the second. bent and stretched in various ways) from Differences in shape are then shown by the original simple square grid. Thompson differences in positions of corresponding (1917) sketched the grids subjectively landmarks. Shape differences between two without an explicit specification of which organisms are found by studying these re- landmarks were used. Not all landmarks siduals. These methods are the subject of shown in pairs of drawings are located ex- the present paper. actly where the superimposed grids would Sneath (1967) investigated the problem imply they should be. This means that the of finding the optimal translation, rota- grids should be more complex than those tion, and size change of one object in order shown in Thompson (1917) in order to ac- for it to be superimposed on another. The curately show the differences between two two objects were represented as sets of x,y- organisms. Bookstein (1978) developed the coordinates of landmarks. A least-squares method of biorthogonal grid analysis criterion was used to measure the goodness which quantifies Thompson's approach and of fit of one object to another. Gower (1971) makes it objective. But it is complex and further developed Sneath's (1967) method has not been applied very often. A recent and expressed the operations in terms of b~ak-through (Bookstein, 1989) is the use matrix algebra. Siegel and Benson (1982) of methods based on thin-plate splines. It made the important observation that a
3,621 citations
"Epidermal Growth Factor Receptor an..." refers background in this paper
...This can result in the ‘‘Pinocchio’’ effect where after superimposition the effects are transferred across all the landmarks and not just the ones showing displacement (Rohlf and Slice 1990; Walker 2000; Zelditch et al. 2004)....
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TL;DR: In this article, the principal axes of shape change for triangles and features of shape comparison are discussed. But the authors do not discuss the relationship between landmarks and shape coordinates of triangles.
Abstract: 1. Introduction 2. Preliminaries 3. Landmarks 4. Distance measures 5. Shape coordinates 6. Principal axes of shape change for triangles 7. Features of shape comparison 8. Retrospect and prospect.
3,131 citations
Book•
01 Jan 2004
TL;DR: The second edition of "Geometric Morphometrics for Biologists" represents the current state of the art and adds new examples and summarizes recent literature, as well as provides an overview of new software and step-by-step guidance through details of carrying out the analyses.
Abstract: The first edition of "Geometric Morphometrics for Biologists" has been the primary resource for teaching modern geometric methods of shape analysis to biologists who have a stronger background in biology than in multivariate statistics and matrix algebra. These geometric methods are appealing to biologists who approach the study of shape from a variety of perspectives, from clinical to evolutionary, because they incorporate the geometry of organisms throughout the data analysis. The second edition of this book retains the emphasis on accessible explanations, and the copious illustrations and examples of the first, updating the treatment of both theory and practice. The second edition represents the current state-of-the-art and adds new examples and summarizes recent literature, as well as provides an overview of new software and step-by-step guidance through details of carrying out the analyses. This title contains updated coverage of methods, especially for sampling complex curves and 3D forms and a new chapter on applications of geometric morphometrics to forensics. It offers a reorganization of chapters to streamline learning basic concepts. It presents detailed instructions for conducting analyses with freely available, easy to use software. It provides numerous illustrations, including graphical presentations of important theoretical concepts and demonstrations of alternative approaches to presenting results.
2,733 citations
"Epidermal Growth Factor Receptor an..." refers background or methods in this paper
...For an introduction to these methods please refer to Zelditch et al. (2004)....
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...To account for the large replicate effects observed (Table 2), probabilities from each replicate measure were combined using Fisher’s method 2 P ln Pi , combined over both replicates and evaluated assuming a x[2k]2 -distribution (Sokal and Rohlf 1995), where k ¼ number of tests (one for each…...
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...While there is a wealth of information with respect to the role of these genes during the development of the wing, little is known about the genetic modification of wing shape....
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...Analysis: Procrustes superimposition of landmarks: In a mathematical framework, shape is defined as the residual variation in landmark displacement once position, isometric scale, and rotation are accounted for (Bookstein 1991; Zelditch et al. 2004)....
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...Geometric morphometric methods, a recent development in the analysis of shape (Bookstein 1991; Zelditch et al. 2004), allow for sensitive discrimination between groups or treatments (Klingenberg 2002;Houle et al. 2003)....
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TL;DR: In this paper, the authors suggest that recent views on the nature of the developmental process make it easier to understand how the genotypes of evolving organisms can respond to the environment in a more co-ordinated fashion.
Abstract: THE battle, which raged for so long between the theories of evolution supported by geneticists on one hand and by naturalists on the other, has in recent years gone strongly in favour of the former. Few biologists now doubt that genetical investigation has revealed at any rate the most important categories of hereditary variation ; and the classical 'naturalist' theory-the inheritance of acquired characters-has been very generally relegated to the background because, in the forms in which it has been put forward, it has required a type of hereditary variation for the existence of which there was no adequate evidence. The long popularity of the theory was based, not on any positive evidence for it, but on its usefulness in accounting for some of the most striking of the results of evolution. Naturalists cannot fail to be continually and deeply impressed by the adaptation of an organism to its surroundings and of the parts of the organism to each other. These adaptive characters are inherited and some explanation of this must be provided. If we are deprived of the hypothesis of the inheritance of the effects of use and disuse, we seem thrown back on an exclusive reliance on the natural selection of merely chance mutations. It is doubtful, however, whether even the most statistically minded geneticists are entirely satisfied that nothing more is involved than the sorting out of random mutations by the natural selective filter. It is the purpose of this short communication to suggest that recent views on the nature of the developmental process make it easier to understand how the genotypes of evolving organisms can respond to the environment in a more co-ordinated fashion.
2,644 citations