Search

The Modern Synthesis has received criticism for its purported gene-centrism. That criticism relies on a concept of the gene as a unit of instructional information. In this paper I discuss information concepts and endorse one, developed from Floridi, that sees information as a functional relationship between data and context. I use this concept to inspect developmental criticisms of the Modern Synthesis and argue that the instructional gene arose as an idealization practice when evolutionary biologists made comment on development. However, a closer inspection of key claims shows that at least some associated with the Modern Synthesis were in fact adopting the data led definition I favour and made clear arguments for the role of developmental processes beyond genetic input. There was no instructional gene., (© 2023. The Author(s).)

The celebrated 1917 work "On Growth and Form" of D'Arcy W. Thompson has established a landmark for mathematical biology, introducing new perspectives of study and research in biology, providing mathematical methods to morphology of biological systems. In this brief historical essay, we recall the novelties and relevance of the work from a retrospective stance, above all pointing out the crucial role played by it in the dawning of epigenetic standpoint. The role of underlying epigenetic processes in generation of biological forms via similarity transformations is analyzed within the framework of D'Arcy Thompson. The significance of D'Arcy Thompson as a predecessor of the relational biology and of the epigenetic concepts of evolution is discussed., (Copyright © 2020 Elsevier B.V. All rights reserved.)

In this article I critically evaluate the thesis that DNA is an ontologically distinctive developmental cause. I shall critically analyse different versions of the latter thesis by taking into consideration concrete developmental cases. I shall argue that DNA is neither a developmental determinant nor an ontologically distinctive developmental cause. Instead, I shall argue that mechanistic analysis shows that DNA's causal role in development depends on the higher robustness of the developmental processes in which it exerts its causal capacities. The focus on process and developmental system implies a metaphysical shift: rather than attributing to DNA molecules biochemically unique properties, I suggest that it might be better to think about DNA's causal role in development in terms of the causal capacities that DNA molecules manifest in a rich developmental milieu. I shall also suggest that my position is distinct both from the view advocating the instrumental primacy of DNA-centric biology and developmental constructionism. It is different from the former because it provides a substantial answer to the question of what makes DNA causally central in developmental processes. Finally, I argue that evolutionary considerations pose an important challenge to developmental constructionism., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Canalization, or robustness to genetic or environmental perturbations, is fundamental to complex organisms. While there is strong evidence for canalization as an evolved property that varies among genotypes, the developmental and genetic mechanisms that produce this phenomenon are very poorly understood. For evolutionary biology, understanding how canalization arises is important because, by modulating the phenotypic variation that arises in response to genetic differences, canalization is a determinant of evolvability. For genetics of disease in humans and for economically important traits in agriculture, this subject is important because canalization is a potentially significant cause of missing heritability that confounds genomic prediction of phenotypes. We review the major lines of thought on the developmental-genetic basis for canalization. These fall into two groups. One proposes specific evolved molecular mechanisms while the other deals with robustness or canalization as a more general feature of development. These explanations for canalization are not mutually exclusive and they overlap in several ways. General explanations for canalization are more likely to involve emergent features of development than specific molecular mechanisms. Disentangling these explanations is also complicated by differences in perspectives between genetics and developmental biology. Understanding canalization at a mechanistic level will require conceptual and methodological approaches that integrate quantitative genetics and developmental biology., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to 'extend' the Modern Synthesis-derived 'standard evolutionary theory' (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES-published by Laland and collaborators in 2015-in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework.

In biological classification, a character is a property of a taxon that can distinguish it from other taxa. Characters are not independent, and the relations between characters can arise from structural constraints, developmental pathways or functional constraints. That has lead to famous controversies in the history of biology. In addition, a character as a tool of data analysis has some subjective aspects. In this contribution, I develop algebraic and geometric schemes to address these issues in a mathematical framework.

Background: Various groups of flowering plants reveal profound ('saltational') changes of their bauplans (architectural rules) as compared with related taxa. These plants are known as morphological misfits that appear as rather large morphological deviations from the norm. Some of them emerged as morphological key innovations (perhaps 'hopeful monsters') that gave rise to new evolutionary lines of organisms, based on (major) genetic changes., Scope: This pictorial report places emphasis on released bauplans as typical for bladderworts (Utricularia, approx. 230 secies, Lentibulariaceae) and river-weeds (Podostemaceae, three subfamilies, approx. 54 genera, approx. 310 species). Bladderworts (Utricularia) are carnivorous, possessing sucking traps. They live as submerged aquatics (except for their flowers), as humid terrestrials or as epiphytes. Most Podostemaceae are restricted to rocks in tropical river-rapids and waterfalls. They survive as submerged haptophytes in these extreme habitats during the rainy season, emerging with their flowers afterwards. The recent scientific progress in developmental biology and evolutionary history of both Lentibulariaceae and Podostemaceae is summarized., Conclusions: Lentibulariaceae and Podostemaceae follow structural rules that are different from but related to those of more typical flowering plants. The roots, stems and leaves - as still distinguishable in related flowering plants - are blurred ('fuzzy'). However, both families have stable floral bauplans. The developmental switches to unusual vegetative morphologies facilitated rather than prevented the evolution of species diversity in both families. The lack of one-to-one correspondence between structural categories and gene expression may have arisen from the re-use of existing genetic resources in novel contexts. Understanding what developmental patterns are followed in Lentibulariaceae and Podostemaceae is a necessary prerequisite to discover the genetic alterations that led to the evolution of these atypical plants. Future molecular genetic work on morphological misfits such as bladderworts and river-weeds will provide insight into developmental and evolutionary aspects of more typical vascular plants., (© The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company.)

Background: The origin of new species and of new forms is one of the fundamental characteristics of evolution. However, the mechanisms that govern the diversity and disparity of lineages remain poorly understood. Particularly unclear are the reasons why some taxa are vastly more species-rich than others and the manner in which species diversity and morphological disparity are interrelated., Scope and Conclusions: Evolutionary innovations and ecological opportunities are usually cited as among the major factors promoting the evolution of species diversity. In many cases it is likely that these factors are positively reinforcing, with evolutionary innovations creating ecological opportunities that in turn foster the origin of new innovations. However, we propose that a third factor, developmental robustness, is very often essential for this reinforcement to be effective. Evolutionary innovations need to be stably and robustly integrated into the developmental genetic programme of an organism to be a suitable substrate for selection to 'explore' ecological opportunities and morphological 'design' space (morphospace). In particular, we propose that developmental robustness of the bauplan is often a prerequisite for the exploration of morphospace and to enable the evolution of further novelties built upon this bauplan Thus, while robustness may reduce the morphological disparity at one level, it may be the basis for increased morphological disparity and for evolutionary innovations at another level, thus fostering species diversity., (© The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

We introduce a new subfield of the recently created field of Evolutionary-Developmental-Anthropology (Evo-Devo-Anth): Evolutionary-Developmental-Pathology-and-Anthropology (Evo-Devo-P'Anth). This subfield combines experimental and developmental studies of nonhuman model organisms, biological anthropology, chordate comparative anatomy and evolution, and the study of normal and pathological human development. Instead of focusing on other organisms to try to better understand human development, evolution, anatomy, and pathology, it places humans as the central case study, i.e., as truly model organism themselves. We summarize the results of our recent Evo-Devo-P'Anth studies and discuss long-standing questions in each of the broader biological fields combined in this subfield, paying special attention to the links between: (1) Human anomalies and variations, nonpentadactyly, homeotic transformations, and "nearest neighbor" vs. "find and seek" muscle-skeleton associations in limb+facial muscles vs. other head muscles; (2) Developmental constraints, the notion of "phylotypic stage," internalism vs. externalism, and the "logic of monsters" vs. "lack of homeostasis" views about human birth defects; (3) Human evolution, reversions, atavisms, paedomorphosis, and peromorphosis; (4) Scala naturae, Haeckelian recapitulation, von Baer's laws, and parallelism between phylogeny and development, here formally defined as "Phylo-Devo parallelism"; and (5) Patau, Edwards, and Down syndrome (trisomies 13, 18, 21), atavisms, apoptosis, heart malformations, and medical implications., (© 2015 Wiley Periodicals, Inc.)

The integration of research from developmental biology and ecology into evolutionary theory has given rise to a relatively new field, ecological evolutionary developmental biology (Eco-Evo-Devo). This field integrates and organizes concepts such as developmental symbiosis, developmental plasticity, genetic accommodation, extragenic inheritance and niche construction. This Review highlights the roles that developmental symbiosis and developmental plasticity have in evolution. Developmental symbiosis can generate particular organs, can produce selectable genetic variation for the entire animal, can provide mechanisms for reproductive isolation, and may have facilitated evolutionary transitions. Developmental plasticity is crucial for generating novel phenotypes, facilitating evolutionary transitions and altered ecosystem dynamics, and promoting adaptive variation through genetic accommodation and niche construction. In emphasizing such non-genomic mechanisms of selectable and heritable variation, Eco-Evo-Devo presents a new layer of evolutionary synthesis.

The ideas and techniques developed in [12,3] are extended to a basic stage structured model. Each strategy consists of two stages: a Juvenile (L for larvae), and Adult (A). A general model of this basic stage structure is formulated as a dynamical system on the state space of finite signed measures. Nonnegativity, well-posedness and uniform eventual boundedness are established under biologically natural conditions on the rates. Similar to [12] we also have the unifying of discrete and continuous systems and the containment of the classic nonlinearities.

As understood historically, typological thinking has no place in evolutionary biology since its conceptual framework is viewed as incompatible with population thinking. In this article, I propose that what I describe as dynamic typological thinking has been confused with, and has been overshadowed by, a static form of typological thinking. This conflation results from an inability to grasp dynamic typological thinking due to the overlooked requirement to engage our cognitive activity in an unfamiliar way. Thus, analytical thinking alone is unsuited to comprehend the nature of dynamic typological thinking. Over 200 years ago, J. W. von Goethe, in his Metamorphosis of Plants (1790) and other writings, introduced a dynamic form of typological thinking that has been traditionally misunderstood and misrepresented. I describe in detail Goethe's phenomenological methodology and its contemporary value in understanding morphological patterns in living organisms. Furthermore, contrary to the implications of static typological thinking, dynamic typological thinking is perfectly compatible with evolutionary dynamics and, if rightly understood, can contribute significantly to the still emerging field of evolutionary developmental biology (evo-devo)., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

The emergence of evo-devo has had profound effects on how we study evolution. However, evo-devo research has tended to involve two general approaches, one being mechanistic and typological with a focus on simple, bimodal phenotypes, and the other being quantitative and focusing on multidimensional phenotypes without an understanding of underlying genetic mechanisms. Here, we suggest that, given recent technological advances in genomics, molecular biology, and morphometrics, evo-devo is poised for a reconciliation through which the field will realize far greater explanatory potential with respect to the patterns and processes that underlie adaptive phenotypic divergence. With this in mind, we review the recent literature and put forward a generalized evo-devo approach that is suitable for studies of quantitative traits in a range of taxa., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Evolutionary developmental biology (or evo-devo) is the scientific connectivity that allowed a more comprehensive and practical completeness in the contemporary conceptualisation of evolution. The links between genetics, developmental mechanics and evolution led to a better understanding of evolutionary mechanisms. An analysis of evolutionary concepts such as homology, homeoses, constraints, novelties, modularity, and selection is given through the recurring example of the variations identified in the modular repartition of the cervical vertebrae in extant and fossil penguins. The inclusion of this study about penguins in the evolutionary system also involves a reflection on the current state and the future of evo-devo. Three principles of assessment and method, applicable to many natural and conceptual scales, are introduced to define a "survival strategy" for evo-devo. The above-mentioned principles are intended to strengthen and continue the connectivity induced de facto. These current and future investigation challenges are discussed and connected to three main naturalist names related directly to the conceptualisation of evolution: Charles Darwin, Étienne Geoffroy Saint-Hilaire, and Lamarck.

Spiders belong to the chelicerates, which is an arthropod group that branches basally from myriapods, crustaceans and insects. Spiders are thus useful models with which to investigate whether aspects of development are ancestral or derived with respect to the arthropod common ancestor. Moreover, they serve as an important reference point for comparison with the development of other metazoans. Therefore, studies of spider development have made a major contribution to advancing our understanding of the evolution of development. Much of this knowledge has come from studies of the common house spider, Parasteatoda tepidariorum. Here, we describe how the growing number of experimental tools and resources available to study Parasteatoda development have provided novel insights into the evolution of developmental regulation and have furthered our understanding of metazoan body plan evolution.

This essay has three parts. First, I posit that much research in contemporary evodevo remains steeped in a traditional framework that views traits and trait differences as being caused by genes and genetic variation, and the environment as providing an external context in which development and evolution unfold. Second, I discuss three attributes of organismal development and evolution, broadly applicable to all organisms and traits that call into question the usefulness of gene- and genome-centric views of development and evolution. I then focus on the third and main aim of this essay and ask: what conceptual and empirical opportunities exist that would permit evodevo research to transcend the traditional boundaries inherited from its parent disciplines and to move toward the development of a more comprehensive and realistic theory of developmental evolution? Here, I focus on three conceptual frameworks, the theory of facilitated variation, the theory of evolution by genetic accommodation, and the theory of niche construction. I conclude that combined they provide a rich, interlocking framework within which to revise existing and develop novel empirical approaches toward a better understanding of the nature of developmental evolution. Examples of such approaches are highlighted, and the consequences of expanding existing frameworks are discussed.

Shapes change during development because tissues, organs, and various anatomical features differ in onset, rate, and duration of growth. Allometry is the study of the consequences of differences in the growth of body parts on morphology, although the field of allometry has been surprisingly little concerned with understanding the causes of differential growth. The power-law equation y = ax(b), commonly used to describe allometries, is fundamentally an empirical equation whose biological foundation has been little studied. Huxley showed that the power-law equation can be derived if one assumes that body parts grow with exponential kinetics, for exactly the same amount of time. In life, however, the growth of body parts is almost always sigmoidal, and few, if any, grow for exactly the same amount of time during ontogeny. Here, we explore the shapes of allometries that result from real growth patterns and analyze them with new allometric equations derived from sigmoidal growth kinetics. We use an extensive ontogenetic dataset of the growth of internal organs in the rat from birth to adulthood, and show that they grow with Gompertz sigmoid kinetics. Gompertz growth parameters of body and internal organs accurately predict the shapes of their allometries, and that nonlinear regression on allometric data can accurately estimate the underlying kinetics of growth. We also use these data to discuss the developmental relationship between static and ontogenetic allometries. We show that small changes in growth kinetics can produce large and apparently qualitatively different allometries. Large evolutionary changes in allometry can be produced by small and simple changes in growth kinetics, and we show how understanding the development of traits can greatly simplify the interpretation of how they evolved.

It is increasingly recognized that current established model systems are not sufficient to understand the evolution of biodiversity. The main limitation in developing additional model systems is the difficulty or inability to perform functional studies of target genes. Evolutionary developmental (evo-devo) biologists have adopted a transient transgenic technique, developed over the last decade for agricultural applications, which is allowing functional studies in the most disparate plant lineages. From monocots to dicots and from herbs to trees, virus-induced gene silencing (VIGS) has opened up a world of opportunities in plant evo-devo., (Copyright © 2011 WILEY Periodicals, Inc.)

The recent Keystone Symposium on Evolutionary Developmental Biology at Tahoe City in February 2011 provided an opportunity to take stock of where the past three decades have brought this interdisciplinary field. It revealed maturation on several fronts, including increased experimental rigor, the softening of dichotomies that were crucial to its founding and growth, and its growing relevance to both basic and biomedical biology.

Embryos of the echinoderms, especially those of sea urchins and sea stars, have been studied as model organisms for over 100 years. The simplicity of their early development, and the ease of experimentally perturbing this development, provides an excellent platform for mechanistic studies of cell specification and morphogenesis. As a result, echinoderms have contributed significantly to our understanding of many developmental mechanisms, including those that govern the structure and design of gene regulatory networks, those that direct cell lineage specification, and those that regulate the dynamic morphogenetic events that shape the early embryo.

This review paper is devoted to present a personal perspective, based on a critical analysis of the existing literature, about the conceptual difficulties that mathematics meets when attempting to describe the complexity of living matter focusing on the challenging goal of developing a mathematical theory for living systems. The authors propose a personal path, starting from the identification of a number of common features of living systems that can be viewed as sources of complexity, firstly in general, and subsequently focusing specifically on evolution problems. Further, three key questions are posed addressing to a mathematical theory. Finally, the tools of the kinetic theory of active particles are critically analyzed to understand how far this approach still is from the achievement of the afore said ambitious objective., (Copyright © 2010 Elsevier B.V. All rights reserved.)

Contributions from the emerging fields of molecular genetics and evo-devo (evolutionary developmental biology) are greatly benefiting the field of evolutionary computation, initiating a promise of renewal in the traditional methodology. While direct encoding has constituted a dominant paradigm, indirect ways to encode the solutions have been reported, yet little attention has been paid to the benefits of the proposed methods to real problems. In this work, we study the biological properties that emerge by means of using indirect encodings in the context of form-finding problems. A novel indirect encoding model for artificial development has been defined and applied to an engineering structural-design problem, specifically to the discovery of tensegrity structures. This model has been compared with a direct encoding scheme. While the direct encoding performs similarly well to the proposed method, indirect-based results typically outperform the direct-based results in aspects not directly linked to the nature of the problem itself, but to the emergence of properties found in biological organisms, like organicity, generalization capacity, or modularity aspects which are highly valuable in engineering., (Copyright 2010 Elsevier Ireland Ltd. All rights reserved.)

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.

Gilbert and Epel present a new approach to developmental biology: embryogenesis must be understood within the full context of the organism's environment. Instead of an insular embryo following a genetic blueprint, this revised program maintains that embryogenesis is subject to inputs from the environment that generate novel genetic variation with dynamic consequences for development. Beyond allelic variation of structural genes and of regulatory loci, plasticity-derived epigenetic variation completes the triad of the major types of variation required for evolution. Developmental biology and ecology, disciplines that have previously been regarded as distinct, are presented here as fully integrated under the rubric of "eco-devo," and from this perspective, which highlights how the environment not only selects variation, it helps construct it, another synthesis with evolutionary biology must also be made, "eco-evo-devo." This second integration has enormous implications for expanding evolution theory, inasmuch as the Modern Synthesis (Provine 1971), which combined classical genetics and Darwinism in the mid-20th century, did not account for the role of development in evolution. The eco-evo-devo synthesis thus portends a major theoretical inflection in evolutionary biology. Following a description of these scientific developments, comment is offered as to how this new integrated approach might be understood within the larger shifts in contemporary biology.

As a result of the integration of molecular and morphological approaches for the reconstruction of phylogenies, and of the intertwining of developmental and evolutionary biology, further prospects are open for a fruitful interaction between these two fields in what we may call a phylo-evo-devo approach.Wiegmann et al.'s molecular phylogeny of the holometabolous insect orders, recently published in BMC Biology, offers a good opportunity to revisit the inverted positions of wings and halteres in the Diptera and the Strepsiptera in terms of a putative homeotic mutation in the Hox gene Ultrabithorax. The main finding of this paper is that Strepsiptera are closely related to the Coleoptera rather than Diptera, as recently claimed. Through this exemplary case, the paper demonstrates the value of the reciprocal illumination we can expect from the integration of a good phylogeny and a sound knowledge of the evolvability of developmental mechanisms.

Evolutionary theory is undergoing an intense period of discussion and reevaluation. This, contrary to the misleading claims of creationists and other pseudoscientists, is no harbinger of a crisis but rather the opposite: the field is expanding dramatically in terms of both empirical discoveries and new ideas. In this essay I briefly trace the conceptual history of evolutionary theory from Darwinism to neo-Darwinism, and from the Modern Synthesis to what I refer to as the Extended Synthesis, a more inclusive conceptual framework containing among others evo-devo, an expanded theory of heredity, elements of complexity theory, ideas about evolvability, and a reevaluation of levels of selection. I argue that evolutionary biology has never seen a paradigm shift, in the philosophical sense of the term, except when it moved from natural theology to empirical science in the middle of the 19th century. The Extended Synthesis, accordingly, is an expansion of the Modern Synthesis of the 1930s and 1940s, and one that--like its predecessor--will probably take decades to complete.

Because little is known about embryonic developmental stages in any haplochromine cichlid, we describe here a series of normal stages of the Lake Victoria cichlid Haplochromis piceatus. We collected 273 embryos and scored them for 47 morphological characters. The result was an illustrated series of 12 stages from embryonic shield until hatching based on live, fixed, and histological material. We defined each stage according to a single "key" character that applied to all embryos of that stage. Other characters forming part of the stage descriptions were not necessarily present in all embryos of a stage. We compare our findings with published studies of other freshwater teleosts and find wide variation in staging systems. Our data will form a baseline for further research on cichlid development., ((c) 2009 Wiley-Liss, Inc.)

Lampreys are one of the most basal animals in which many of the true vertebrate characteristics (e.g., neural crest, placodes, segmented brain, skull, paired sensory organs, pharyngeal skeleton) are present. Studying the molecular and developmental mechanisms responsible for the formation of these structures in lamprey and higher vertebrates can provide insight into how these vertebrate characteristics evolved. The relative ease of obtaining mature adults and embryos makes this animal an ideal model for investigations into early vertebrate evolution. In addition, studies of features that are unique to lampreys can provide insights into mechanisms of parallel evolution. This protocol describes how to produce lamprey embryos by collecting sperm and eggs from mature lampreys, performing fertilization, and culturing the embryos through to the desired developmental stage.

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype-phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles.

Cavefish and their conspecific surface-dwelling ancestors (Astyanax mexicanus) are emerging as a model system to study the microevolution of development. Here we describe attributes that make this system highly promising for such studies. We review how the Astyanax system is being used to understand evolutionary forces underlying loss of eyes and pigmentation in cavefish. Pigment regression is probably explained by neutral mutations, whereas natural selection is a likely mechanism for loss of eyes. Finally, we discuss several research frontiers in which Astyanax is poised to make significant contributions in the future: evolution of constructive traits, the craniofacial skeleton, the central nervous system, and behavior.

Most animals evolved from a common ancestor, Urbilateria, which already had in place the developmental genetic networks for shaping body plans. Comparative genomics has revealed rather unexpectedly that many of the genes present in bilaterian animal ancestors were lost by individual phyla during evolution. Reconstruction of the archetypal developmental genomic tool-kit present in Urbilateria will help to elucidate the contribution of gene loss and developmental constraints to the evolution of animal body plans.

Proteins involved in reproduction often evolve rapidly, raising the possibility that changes in these proteins contribute to reproductive isolation between species. We review the evidence for rapid and adaptive change in reproductive proteins in animals, focusing on studies in recently diverged vertebrates. We identify common patterns and point out promising directions for future research. In particular, we highlight the ways that integrating the different but complementary approaches of evolutionary and developmental biology will provide new insights into fertilization processes.

The chorioallantoic placenta is an organ of gaseous exchange that exhibits a high degree of structural diversity. One factor determining oxygen transfer across the placenta, the diffusion distance, is in part dependent on the number of cell layers separating maternal from fetal blood. This interhaemal barrier occurs in three principal variants. The focus of this review is on determining how the barrier evolved in placental mammals. The analysis was based on current knowledge of placental structure, as far as possible using ultrastructural data, and on current views about the evolution of placental mammals, derived from molecular phylogenetics. We show that epitheliochorial placentation, the least invasive type, is a derived state and discuss factors that may have determined its evolution with reference to conflict theory, as applied to the allocation of resources between mother and fetus. It is not yet possible to determine which of the two more invasive types of placentation occurred in the last common ancestor of crown placentals. Depending on tree topology and taxon sampling, the result achieved is either endotheliochorial, haemochorial or unresolved. Finally we discuss other factors important to placental gas exchange and point to physiological variables that might become amenable to phylogenetic analysis.

The shark and its embryology have recently returned to the spotlight as a model animal in the quest to determine the origins of paired appendages during vertebrate evolution. As the most basal living gnathostomes, sharks and other extant chondrichthyans are ideal models to elucidate the developmental mechanisms utilised in mesoderm-derived primitive fin morphologies. Chondrichthyans occupy a phylogenetic position and possess morphological structures that can answer major questions on the origin of the body plan of vertebrates. This review will outline the past, present, and future use of shark species as a model system with particular emphasis on the recent studies that have utilised comparative molecular embryology of chondrichthyan species to examine the question of the origin of the paired fins. We will also examine the problems and pitfalls of utilising chondrichthyans and the barriers that remain to their utilisation in the modern era of developmental biology., ((c) 2007 Wiley-Liss, Inc.)

Evolution of transcriptional regulation is often seen as being driven by the origin of transcription factor binding sites in cis-regulatory DNA. But there is strong evidence that transcriptional specificity of transcription factor proteins is determined by protein-protein interaction with other transcription factors. 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.

Although flourishing, I argue that evo-devo is not yet a mature scientific discipline. Its philosophical foundation exhibits an internal inconsistency that results from a metaphysical confusion. In modern evolutionary biology, species and other taxa are most commonly considered as individuals. I accept this thesis to be the best available foundation for modern evolutionary biology. However, evo-devo is characterized by a remarkable degree of typological thinking, which instead treats taxa as classes. This metaphysical incompatibility causes much distorted thinking. In this paper, I will discuss the logical implications of accepting the individuality thesis for evo-devo. First, I will illustrate the degree to which typological thinking pervades evo-devo. This ranges from the relatively innocent use of typologically tainted language to the more serious misuse of differences between taxa as evidence against homology and monophyly, and the logically flawed concept of partial homology. Second, I will illustrate how, in a context of typological thinking, evo-devo's harmless preoccupation with distant ancestors has become transformed into a pernicious problem afflicting the choice of model organisms. I will expose the logical flaws underlying the common assumption that model organisms can be expected to represent the clades they are a part of in an unambiguous way. I will expose the logical flaws underlying the general assumption that basal taxa are the best available stand-ins for ancestors and that they best represent the clade of which they are a part, while also allowing for optimal extrapolation of results.

Developmental data have the potential to give novel insights into morphological evolution. Because developmental data are time-consuming to obtain, support for hypotheses often rests on data from only a few distantly related species. Similarities between these distantly related species are parsimoniously inferred to represent ancestral aspects of development. However, with limited taxon sampling, ancestral similarities in developmental patterning can be difficult to distinguish from similarities that result from convergent co-option of developmental networks, which appears to be common in developmental evolution. Using a case study from insect wings, we discuss how these competing explanations for similarity can be evaluated. Two kinds of developmental data have recently been used to support the hypothesis that insect wings evolved by modification of limb branches that were present in ancestral arthropods. This support rests on the assumption that aspects of wing development in Drosophila, including similarities to crustacean epipod patterning, are ancestral for winged insects. Testing this assumption requires comparisons of wing development in Drosophila and other winged insects. Here we review data that bear on this assumption, including new data on the functions of wingless and decapentaplegic during appendage allocation in the red flour beetle Tribolium castaneum.

Developmental processes shape plant morphologies, which constitute important adaptive traits selected for during evolution. Identifying the genes that act in developmental pathways and determining how they are modified during evolution is the focus of the field of evolutionary developmental biology, or evo-devo. Knowledge of genetic pathways in the plant model Arabidopsis serves as the starting point for investigating how the toolkit of developmental pathways has been used and reused to form different plant body plans. One productive approach is to identify genes in other species that are orthologous to genes known to control developmental pathways in Arabidopsis and then determine what changes have occurred in the protein coding sequence or in the gene's expression to produce an altered morphology. A second approach relies on natural variation among wild populations or crop plants. Natural variation can be exploited to identify quantitative trait loci that underlie important developmental traits and, thus, define those genes that are responsible for adaptive changes. The possibility of applying comparative genomics approaches to Arabidopsis and related species promises profound new insights into the interplay of evolution and development.