植物进化发育生物学的形成与研究进展

植物进化发育生物学是最近十几年来才兴起的一门学科, 它是进化发育生物学的主要分支之一。进化发育生物学的产生经历了进化生物学与胚胎学、遗传学和发育生物学的三次大的综合, 其历史可追溯到19世纪初冯.贝尔所创立的比较胚胎学。相关研究曾沉寂了近一个世纪, 直到20世纪80年代早期, 动物中homeobox基因被发现, 90年代初花发育的 ABC模型被提出, 加之对发育相关基因研究的不断深入, 才使基因型与表型联系了起来, 进而促进了进化发育生物学的飞速发展。目前进化发育生物学已成为21世纪生命科学领域的研究热点之一。本文详细阐述了进化发育生物学产生和发展的历程, 综述了最近十几年来植物进化发育生物学的主要研究进展。文中重点介绍了与植物发育密切相关的MADS-box基因在植物各大类群中的研究现状, 讨论了植物进化发育生物学领域的研究成果对花被演化、花对称性以及叶的进化等重要问题的启示。     

植物进化发育生物学的形成与研究进展

植物进化发育生物学是最近十几年来才兴起的一门学科,它是进化发育生物学的主要分支之一。进化发育生物学的产生经历了进化生物学与胚胎学、遗传学和发育生物学的三次大的综合,其历史可追溯到19世纪初冯.贝尔所创立的比较胚胎学。相关研究曾沉寂了近一个世纪,直到20世纪80年代早期,动物中homeobox基因被发现,90年代初花发育的ABC模型被提出,加之对发育相关基因研究的不断深入,才使基因型与表型联系了起来,进而促进了进化发育生物学的飞速发展。目前进化发育生物学已成为21世纪生命科学领域的研究热点之一。本文详细阐述了进化发育生物学产生和发展的历程,综述了最近十几年来植物进化发育生物学的主要研究进展。文中重点介绍了与植物发育密切相关的MADS-box基因在植物各大类群中的研究现状,讨论了植物进化发育生物学领域的研究成果对花被演化、花对称性以及叶的进化等重要问题的启示。     

How developmental is evolutionary developmental biology?

Evolutionary developmental biology (evo-devo) offers both an account of developmental processes and also new integrative frameworks for analyzing interactions between development and evolution. Biologists and philosophers are keen on evo-devo in part because it appears to offer a comfort zone between, on the one hand, what some take to be the relative inability of mainstream evolutionary biology to integrate a developmental perspective; and, on the other hand, what some take to be more intractable syntheses of development and evolution. In this article, I outline core concerns of evo-devo, distinguish theoretical and practical variants, and counter Sterelny's recent argument that evo-devo's attention to development, while important, offers no significant challenge to evolutionary theory as we know it. This revised version was published online in July 2006 with corrections to the Cover Date.     

Morphology and behaviour: functional links in development and evolution

Development and evolution of animal behaviour and morphology are frequently addressed independently, as reflected in the dichotomy of disciplines dedicated to their study distinguishing object of study (morphology versus behaviour) and perspective (ultimate versus proximate). Although traits are known to develop and evolve semi-independently, they are matched together in development and evolution to produce a unique functional phenotype. Here I highlight similarities shared by both traits, such as the decisive role played by the environment for their ontogeny. Considering the widespread developmental and functional entanglement between both traits, many cases of adaptive evolution are better understood when proximate and ultimate explanations are integrated. A field integrating these perspectives is evolutionary developmental biology (evo-devo), which studies the developmental basis of phenotypic diversity. Ultimate aspects in evo-devo studies--which have mostly focused on morphological traits--could become more apparent when behaviour, 'the integrator of form and function', is integrated into the same framework of analysis. Integrating a trait such as behaviour at a different level in the biological hierarchy will help to better understand not only how behavioural diversity is produced, but also how levels are connected to produce functional phenotypes and how these evolve. A possible framework to accommodate and compare form and function at different levels of the biological hierarchy is outlined. At the end, some methodological issues are discussed.     

Evo-devo and the search for homology (“sameness”) in biological systems

Developmental biology and evolutionary studies have merged into evolutionary developmental biology (“evo-devo”). This synthesis already influenced and still continues to change the conceptual framework of structural biology. One of the cornerstones of structural biology is the concept of homology. But the search for homology (“sameness”) of biological structures depends on our favourite perspectives (axioms, paradigms). Five levels of homology (“sameness”) can be identified in the literature, although they overlap to some degree: (i) serial homology (homonomy) within modular organisms, (ii) historical homology (synapomorphy), which is taken as the only acceptable homology by many biologists, (iii) underlying homology (i.e., parallelism) in closely related taxa, (iv) deep evolutionary homology due to the “same” master genes in distantly related phyla, and (v) molecular homology exclusively at gene level. The following essay gives emphasis on the heuristic advantages of seemingly opposing perspectives in structural biology, with examples mainly from comparative plant morphology. The organization of the plant body in the majority of angiosperms led to the recognition of the classical root–shoot model. In some lineages bauplan rules were transcended during evolution and development. This resulted in morphological misfits such as the Podostemaceae, peculiar eudicots adapted to submerged river rocks. Their transformed “roots” and “shoots” fit only to a limited degree into the classical model which is based on either–or thinking. It has to be widened into a continuum model by taking over elements of fuzzy logic and fractal geometry to accommodate for lineages such as the Podostemaceae.     

The Body Plan Concept and Its Centrality in Evo-Devo

A body plan is a suite of characters shared by a group of phylogenetically related animals at some point during their development. The concept of bauplane, or body plans, has played and continues to play a central role in the study of evolutionary developmental biology (evo-devo). Despite the importance of the body plan concept in evo-devo, many researchers may not be familiar with the progression of ideas that have led to our current understanding of body plans, and/or current research on the origin and maintenance of body plans. This lack of familiarity, as well as former ties between the body plan concept and metaphysical ideology is likely responsible for our underappreciation of the body plan concept in its own right, as well as its role in evo-devo. My aim in this review is to outline how we have arrived at our modern definition of body plan, the controversies associated with the concept, its role in evo-devo, and how current research is informing us on body plans. To this end, I integrate concepts such as the nature of phyla, the Cambrian explosion, constraint, evolvability, and results from recent research on gene regulatory networks with the much older concept of the body plan.     

Emerging model systems in evo-devo: horned beetles and the origins of diversity

Horned beetles and beetle horns are emerging as a model system suited to address fundamental questions in evolutionary developmental biology. Here we briefly review the biology of horned beetles and highlight the unusual opportunities they provide for evo-devo research. We then summarize recent advances in the development of new approaches and techniques that are now available to scientists interested in working with these organisms. We end by discussing ways to implement and combine these new approaches to explore new frontiers in evo-devo research previously unavailable to reseachers working outside traditional model organisms.     

Phylogeny,fossils, and model systems in the study of evolutionary developmental biology

The emerging field of evolutionary developmental biology (evo-devo) continues to operate largely under a single paradigm. In this paradigm developmental regulatory genes and processes are compared among a collection of "model organisms" selected primarily on the basis of their historical utility in the study of development. This approach has proven to be extremely informative, revealing an unexpected deep evolutionary conservation among developmental genes and genetic systems. Despite its success, concern has been expressed regarding its limitations. We discuss the "model organism" paradigm in evo-devo research. Based on our interpretation of its limitations, we propose a separate but complementary approach that is centered on "model groups." These groups are selected on the basis of their taxonomic affinity and their relevance to questions of interest to evo-devo biologists. We further discuss the Tetraodontiformes (Teleostei, Pisces) as an example of a "model group" for the evo-devo study of vertebrate skeletal elements.     

Evolvability as the proper focus of evolutionary developmental biology

SUMMARY Research conducted under the label of evolutionary developmental biology has tended to revolve around a few central issues such as modularity, integration, and canalization. Yet, as the field has grown, it has become increasingly difficult to define in terms of its central question and relation to broader evolutionary concerns. We argue that these central issues of evo-devo gain their currency from connections to a central question that defines the field, and we propose that this central question is about the nature of evolvability. However, not all research currently carried out under the label of "evo-devo" speaks to this focal concern. The aim of this article is therefore to argue for a precise formulation of evolutionary developmental biology's core question.     

Evo-devo of non-bilaterian animals

The non-bilaterian animals comprise organisms in the phyla Porifera, Cnidaria, Ctenophora and Placozoa. These early-diverging phyla are pivotal to understanding the evolution of bilaterian animals. After the exponential increase in research in evolutionary development (evo-devo) in the last two decades, these organisms are again in the spotlight of evolutionary biology. In this work, I briefly review some aspects of the developmental biology of nonbilaterians that contribute to understanding the evolution of development and of the metazoans. The evolution of the developmental genetic toolkit, embryonic polarization, the origin of gastrulation and mesodermal cells, and the origin of neural cells are discussed. The possibility that germline and stem cell lineages have the same origin is also examined. Although a considerable number of non-bilaterian species are already being investigated, the use of species belonging to different branches of non-bilaterian lineages and functional experimentation with gene manipulation in the majority of the non-bilaterian lineages will be necessary for further progress in this field.     

Evolutionary concepts meet the neck of penguins (Aves: Sphenisciformes), towards a “survival strategy” for evo-devo

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.     

Reversing opinions on Dollo's Law

Dollo's Law, the idea that the loss of complex features in evolution is irreversible, is a popular concept in evolutionary biology. Here we review how application of recent phylogenetic methods, genomics and evo-devo approaches is changing our view of Dollo's Law and its underlying mechanisms. Phylogenetic studies have recently demonstrated cases where seemingly complex features such as digits and wings have been reacquired. Meanwhile, large genomics databases and evo-devo studies are showing how the underlying developmental pathways and genetic architecture can be retained after the loss of a character. With dwindling evidence for the law-like nature of Dollo's Law, we anticipate a return to Dollo's original focus on irreversibility of all kinds of changes, not exclusively losses.     

Functional evolutionary developmental biology (evo-devo) of morphological novelties in plants

The origin of morphological and ecological novelties is a long-standing problem in evolutionary biology.Understanding these processes requires investigation from both the development and evolution standpoints,which promotes a new research field called evolutionary developmental biology (evo-devo).The fundamental mechanism for the origin of a novel structure may involve heterotopy,heterochrony,ectopic expression,or loss of an existing regulatory factor.Accordingly,the morphological and ecological traits cont...     

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

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.     

Modern evolutional developmental biology: Mechanical and molecular genetic or phenotypic approaches?

Heightened interest in the evolutionary problems of developmental biology in the 1980s was due to the success of molecular genetics and disappointment in the synthetic theory of evolution, where the chapters of embryology and developmental biology seem to have been left out. Modern evo-devo, which turned out to be antipodean to the methodology of the synthetic theory of evolution, propagandized in the development of evolutionary problems only the mechanical and molecular genetic approach to the evolution of ontogenesis, based on cellular and intercellular interactions. The phonotypical approach to the evaluation of evolutionary occurrences in ontogenesis, which aids in the joining of the genetic and epigenetic levels of research, the theory of natural selection, the nomogenetic conception, and the problem of the wholeness of the organism in onto- and phylogenesis may be against this. The phenotypic approach to ontogenesis is methodologically the most perspective for evolutionary developmental biology.     

Evolutionary Developmental Biology: the Interaction of Developmental Biology,Evolutionary Biology,Paleontology, and Genomics

Paleontological Journal - Evolutionary developmental biology (evo-devo) formed due to the interactions of evolutionary biology, paleontology, and comparative genomics, analyzes the interrelations...     

A hypothesis on the role of transposons

Genomic transposable elements, or transposons, are sequences of DNA that can move to different positions in the genome; in the process, they can cause chromosomal rearrengements and changes in gene expression. Despite their prevalence in the genomes of many species, their function is largely unknown: for this reason, they have been labelled “junk” DNA. “Epigenetic Tracking” is a model of development that, combined with a standard evolutionary algorithm, become an evo-devo method able to generate arbitrary shapes of any kind and complexity (in terms of number of cells, number of colours, etc.). The model of development has been also shown to be able to produce the artificial version of key biological phenomena such as the phenomenon of ageing, and the process of carcinogenesis. In this paper the evo-devo core of the method is explored and the result is a novel hypothesis on the biological role of transposons, according to which transposition in somatic cells during development drives cellular differentiation and transposition in germ cells is an indispensable tool to boost evolution. Thus, transposable elements, far from being “junk”, have one of the most important roles in multicellular biology.     

Evo-devo and the evolution of social behavior

The integration of evolutionary biology with developmental genetics into the hybrid field of 'evo-devo' resulted in major advances in understanding multicellular development and morphological evolution. Here we show how insights from evo-devo can be applied to study the evolution of social behavior. We develop this idea by reviewing studies that suggest that molecular pathways controlling feeding behavior and reproduction in solitary insects are part of a 'genetic toolkit' underlying the evolution of a particularly complex form of social behavior, division of labor among workers in honeybee colonies. The evo-devo approach, coupled with advances in genomics for non-model genetic organisms, including the recent sequencing of the honeybee genome, promises to advance our understanding of the evolution of social behavior.     

The road to modularity

A network of interactions is called modular if it is subdivided into relatively autonomous, internally highly connected components. Modularity has emerged as a rallying point for research in developmental and evolutionary biology (and specifically evo-devo), as well as in molecular systems biology. Here we review the evidence for modularity and models about its origin. 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.     

Unburdening evo-devo: ancestral attractions, model organisms, and basal baloney

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.