When is homology not homology?

Ancestral role of Pax6 in chordate brain regionalization

The Pax6 gene is essential for eye and brain development across various animal species. Here, we investigate the function of Pax6 in the development of the anterior central nervous system (CNS) of the invertebrate chordate amphioxus using CRISPR/Cas9-induced genome editing. Specifically, we examined Pax6 mutants featuring a 6 bp deletion encompassing two invariant amino acids in the conserved paired domain, hypothesized to impair Pax6 DNA-binding capacity and gene regulatory functions. Although this mutation did not result in gross morphological changes in amphioxus larvae, it demonstrated a reduced ability to activate Pax6-responsive reporter gene, suggesting a hypomorphic effect. Expression analysis in mutant larvae revealed changes in gene expression within the anterior CNS, supporting the conserved role of Pax6 gene in brain regionalization across chordates. Additionally, our findings lend support to the hypothesis of a zona limitans intrathalamica (ZLI)-like region in amphioxus, suggesting evolutionary continuity in brain patterning mechanisms. ZLI region, found in both hemichordates and vertebrates, functions as a key signaling center and serves as a restrictive boundary between major thalamic regions.

Deep conservation and co-option of programmed cell death facilitates evolution of alternative phenotypes at multiple biological levels

Alternative phenotypes, such as polyphenisms and sexual dimorphisms, are widespread in nature and appear at all levels of biological organization, from genes and cells to morphology and behavior. Yet, our understanding of the mechanisms through which alternative phenotypes develop and how they evolve remains understudied. In this review, we explore the association between alternative phenotypes and programmed cell death, a mechanism responsible for the elimination of superfluous cells during development. We discuss the ancient origins and deep conservation of programmed cell death (its function, forms and underlying core regulatory gene networks), and propose that it was co-opted repeatedly to generate alternative phenotypes at the level of cells, tissues, organs, external morphology, and even individuals. We review several examples from across the tree of life to explore the conditions under which programmed cell death is likely to facilitate the evolution of alternative phenotypes.

My road to the ants: A model clade for eco-evo-devo

This chapter is the story of how I pioneered ants as a system for studying eco-evo-devo, a field that integrates developmental biology with ecology and evolutionary biology. One aim of eco-evo-devo is to understand how the interactions between genes and their environments during development facilitates the origin and evolution of novel phenotypes. In a series of six parts, I review some of the key discoveries from my lab on how novel worker caste systems in ants--soldiers and supersoldiers--originated and evolved. I also discuss some of the ideas that emerged from these discoveries, including the role that polyphenisms, hidden developmental potentials, and rudimentary organs play in facilitating developmental and evolutionary change. As superorganisms, I argue that ants are uniquely positioned to reveal types of variation that are often difficult to observe in nature. In doing so, they have the potential to transform our view of biology and provide new perspectives in medicine, agriculture, and biodiversity conservation. With my story I hope to inspire the next generation of biologists to continue exploring the unknown regions of phenotypic space to solve some of our most pressing societal challenges.

Conserved Mechanisms, Novel Anatomies: The Developmental Basis of Fin Evolution and the Origin of Limbs

The transformation of paired fins into tetrapod limbs is one of the most intensively scrutinized events in animal evolution. Early anatomical and embryological datasets identified distinctive morphological regions within the appendage and posed hypotheses about how the loss, gain, and transformation of these regions could explain the observed patterns of both extant and fossil appendage diversity. These hypotheses have been put to the test by our growing understanding of patterning mechanisms that regulate formation of the appendage axes, comparisons of gene expression data from an array of phylogenetically informative taxa, and increasingly sophisticated and elegant experiments leveraging the latest molecular approaches. Together, these data demonstrate the remarkable conservation of developmental mechanisms, even across phylogenetically and morphologically disparate taxa, as well as raising new questions about the way we view homology, evolutionary novelty, and the often non-linear connection between morphology and gene expression. In this review, we present historical hypotheses regarding paired fin evolution and limb origins, summarize key aspects of central appendage patterning mechanisms in model and non-model species, address how modern comparative developmental data interface with our understanding of appendage anatomy, and highlight new approaches that promise to provide new insight into these well-traveled questions.

Cell Proliferation Pattern and Twist Expression in an Aplacophoran Mollusk Argue Against Segmented Ancestry of Mollusca

The study of aplacophoran mollusks (i.e., Solenogastres or Neomeniomorpha and Caudofoveata or Chaetodermomorpha) has traditionally been regarded as crucial for reconstructing the morphology of the last common ancestor of the Mollusca. Since their proposed close relatives, the Polyplacophora, show a distinct seriality in certain organ systems, the aplacophorans are also in the focus of attention with regard to the question of a potential segmented ancestry of mollusks. To contribute to this question, we investigated cell proliferation patterns and the expression of the twist ortholog during larval development in solenogasters. In advanced to late larvae, during the outgrowth of the trunk, a pair of longitudinal bands of proliferating cells is found subepithelially in a lateral to ventrolateral position. These bands elongate during subsequent development as the trunk grows longer. Likewise, expression of twist occurs in two laterally positioned, subepithelial longitudinal stripes in advanced larvae. Both, the pattern of proliferating cells and the expression domain of twist demonstrate the existence of extensive and long‐lived mesodermal bands in a worm‐shaped aculiferan, a situation which is similar to annelids but in stark contrast to conchiferans, where the mesodermal bands are usually rudimentary and ephemeral. Yet, in contrast to annelids, neither the bands of proliferating cells nor the twist expression domain show a separation into distinct serial subunits, which clearly argues against a segmented ancestry of mollusks. Furthermore, the lack of twist expression during the development of the ventromedian muscle argues against homology of a ventromedian longitudinal muscle in protostomes with the notochord of chordates.

Mirror neurons in the tree of life: mosaic evolution, plasticity and exaptation of sensorimotor matching responses

Considering the properties of mirror neurons (MNs) in terms of development and phylogeny, we offer a novel, unifying, and testable account of their evolution according to the available data and try to unify apparently discordant research, including the plasticity of MNs during development, their adaptive value and their phylogenetic relationships and continuity. We hypothesize that the MN system reflects a set of interrelated traits, each with an independent natural history due to unique selective pressures, and propose that there are at least three evolutionarily significant trends that gave raise to three subtypes: hand visuomotor, mouth visuomotor, and audio-vocal. Specifically, we put forward a mosaic evolution hypothesis, which posits that different types of MNs may have evolved at different rates within and among species. This evolutionary hypothesis represents an alternative to both adaptationist and associative models. Finally, the review offers a strong heuristic potential in predicting the circumstances under which specific variations and properties of MNs are expected. Such predictive value is critical to test new hypotheses about MN activity and its plastic changes, depending on the species, the neuroanatomical substrates, and the ecological niche.

Phenotypic Novelty in EvoDevo: The Distinction Between Continuous and Discontinuous Variation and Its Importance in Evolutionary Theory

The introduction of novel phenotypic structures is one of the most significant aspects of organismal evolution. Yet the concept of evolutionary novelty is used with drastically different connotations in various fields of research, and debate exists about whether novelties represent features that are distinct from standard forms of phenotypic variation. This article contrasts four separate uses for novelty in genetics, population genetics, morphology, and behavioral science, before establishing how novelties are used in evolutionary developmental biology (EvoDevo). In particular, it is detailed how an EvoDevo-specific research approach to novelty produces insight distinct from other fields, gives the concept explanatory power with predictive capacities, and brings new consequences to evolutionary theory. This includes the outlining of research strategies that draw attention to productive areas of inquiry, such as threshold dynamics in development. It is argued that an EvoDevo-based approach to novelty is inherently mechanistic, treats the phenotype as an agent with generative potential, and prompts a distinction between continuous and discontinuous variation in evolutionary theory.

Genomic data do not support comb jellies as the sister group to all other animals

Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the "Ctenophora-sister" hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.

Comparative functional analyses of ultrabithorax reveal multiple steps and paths to diversification of legs in the adaptive radiation of semi-aquatic insects

Invasion of new ecological habitats is often associated with lineage diversification, yet the genetic changes underlying invasions and radiations are poorly understood. Over 200 million years ago, the semi-aquatic insects invaded water surface from a common terrestrial ancestor and diversified to exploit a wide array of niches. Here, we uncover the changes in regulation and function of the gene Ultrabithorax associated with both the invasion of water surface and the subsequent diversification of the group. In the common ancestor of the semi-aquatic insects, a novel deployment of Ubx protein in the mid-legs increased their length, thereby enhancing their role in water surface walking. In derived lineages that specialize in rowing on the open water, additional changes in the timing of Ubx expression further elongated the mid-legs thereby facilitating their function as oars. In addition, Ubx protein function was selectively reversed to shorten specific rear-leg segments, thereby enabling their function as rudders. These changes in Ubx have generated distinct niche-specialized morphologies that account for the remarkable diversification of the semi-aquatic insects. Therefore, changes in the regulation and function of a key developmental gene may facilitate both the morphological change necessary to transition to novel habitats and fuel subsequent morphological diversification.

Eco-evo-devo: the time has come

The major goal of ecological evolutionary developmental biology, also known as "eco-evo-devo," is to uncover the rules that underlie the interactions between an organism's environment, genes, and development and to incorporate these rules into evolutionary theory. In this chapter, we discuss some key and emerging concepts within eco-evo-devo. These concepts show that the environment is a source and inducer of genotypic and phenotypic variation at multiple levels of biological organization, while development acts as a regulator that can mask, release, or create new combinations of variation. Natural selection can subsequently fix this variation, giving rise to novel phenotypes. Combining the approaches of eco-evo-devo and ecological genomics will mutually enrich these fields in a way that will not only enhance our understanding of evolution, but also of the genetic mechanisms underlying the responses of organisms to their natural environments.

Molecular hyperdiversity and evolution in very large populations

The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements.

The wing-patterning network in the wingless castes of Myrmicine and Formicine ant species is a mix of evolutionarily labile and non-labile genes

Wing polyphenism in ants is the ability of a single genome to produce winged or wingless castes in a colony in response to environmental cues. Although wing polyphenism is a universal and homologous feature of ants, the gene network underlying wing polyphenism is conserved in the winged castes, but is labile in the wingless castes, that is, the network is interrupted at different points in the wingless castes of different ant species. Because the expression of all genes sampled so far in this network in the wingless castes is evolutionarily labile across species, an important question is whether all "interruption points" in the network are evolutionarily labile or are there interruption points that are evolutionarily non-labile. Here we show that in the wingless castes, the expression of the gene brinker (brk), which mediates growth, patterning, and apoptosis in the Drosophila wing disc, is non-labile; it is absent in vestigial wing discs of four ants species. In contrast, the expression of engrailed (en), a gene upstream of brk is labile; it is present in some species but absent in others. In the winged castes, both brk and en expression are conserved relative to their expression in Drosophila wing discs. The differential lability of genes in the network in wingless castes may be a general feature of networks underlying polyphenic traits. This raises the possibility that some genes, like brk, may be under stabilizing selection while most others, like en, may be evolving via directional selection or neutral drift.

Importing the homology concept from biology into developmental psychology

To help introduce the idea of homology into developmental psychology, this article presents some of the concepts, distinctions, and guidelines biologists and philosophers of biology have devised to study homology. Some unresolved issues related to this idea are considered as well. Because homology reflects continuity across time, developmental scientists should find this concept to be useful in the study of psychological/behavioral development, just as biologists have found it essential in the study of the evolution and development of morphological and other characteristics.

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.

What is parallelism?

Although parallel and convergent evolution are discussed extensively in technical articles and textbooks, their meaning can be overlapping, imprecise, and contradictory. The meaning of parallel evolution in much of the evolutionary literature grapples with two separate hypotheses in relation to phenotype and genotype, but often these two hypotheses have been inferred from only one hypothesis, and a number of subsidiary but problematic criteria, in relation to the phenotype. However, examples of parallel evolution of genetic traits that underpin or are at least associated with convergent phenotypes are now emerging. Four criteria for distinguishing parallelism from convergence are reviewed. All are found to be incompatible with any single proposition of homoplasy. Therefore, all homoplasy is equivalent to a broad view of convergence. Based on this concept, all phenotypic homoplasy can be described as convergence and all genotypic homoplasy as parallelism, which can be viewed as the equivalent concept of convergence for molecular data. Parallel changes of molecular traits may or may not be associated with convergent phenotypes but if so describe homoplasy at two biological levels-genotype and phenotype. Parallelism is not an alternative to convergence, but rather it entails homoplastic genetics that can be associated with and potentially explain, at the molecular level, how convergent phenotypes evolve.

Involvement of the conserved Hox gene Antennapedia in the development and evolution of a novel trait

BACKGROUND

Hox proteins specify segment identity during embryogenesis and have typical associated expression patterns. Changes in embryonic expression and activity of Hox genes were crucial in the evolution of animal body plans, but their role in the post-embryonic development of lineage-specific traits remains largely unexplored. Here, we focus on the insect Hox genes Ultrabithorax (Ubx) and Antennapedia (Antp), and implicate the latter in the formation and diversification of novel, butterfly-specific wing patterns.

RESULTS

First, we describe a conserved pattern of Ubx expression and a novel pattern of Antp expression in wing discs of Bicyclus anynana butterflies. The discrete, reiterated domains of Antp contrast with the typical expression of Hox genes in single continuous regions in arthropod embryos. Second, we show that this pattern is associated with the establishment of the organizing centres of eyespots. Antp upregulation is the earliest event in organizer development described to date, and in contrast to all genes implicated in eyespot formation, is exclusive to those centres. Third, our comparative analysis of gene expression across nymphalids reveals unexpected differences in organizer determination.

CONCLUSIONS

We show that the Antp's recruitment for the formation of novel traits in butterfly wing discs involved the evolution of new expression domains, and is restricted to a particular lineage. This study contributes novel insights into the evolution of Antp expression, as well as into the genetic mechanisms underlying morphological diversification. Our results also underscore how a wider representation of morphological and phylogenetic diversity is essential in evolutionary developmental biology.

Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria

The similarity in the genetic regulation of arthropod and vertebrate appendage formation has been interpreted as the product of a plesiomorphic gene network that was primitively involved in bilaterian appendage development and co-opted to build appendages (in modern phyla) that are not historically related as structures. Data from lophotrochozoans are needed to clarify the pervasiveness of plesiomorphic appendage-forming mechanisms. We assayed the expression of three arthropod and vertebrate limb gene orthologs, Distal-less (Dll), dachshund (dac), and optomotor blind (omb), in direct-developing juveniles of the polychaete Neanthes arenaceodentata. Parapodial Dll expression marks pre-morphogenetic notopodia and neuropodia, becoming restricted to the bases of notopodial cirri and to ventral portions of neuropodia. In outgrowing cephalic appendages, Dll activity is primarily restricted to proximal domains. Dll expression is also prominent in the brain. dac expression occurs in the brain, nerve cord ganglia, a pair of pharyngeal ganglia, presumed interneurons linking a pair of segmental nerves, and in newly differentiating mesoderm. Domains of omb expression include the brain, nerve cord ganglia, one pair of anterior cirri, presumed precursors of dorsal musculature, and the same pharyngeal ganglia and presumed interneurons that express dac. Contrary to their roles in outgrowing arthropod and vertebrate appendages, Dll, dac, and omb lack comparable expression in Neanthes appendages, implying independent evolution of annelid appendage development. We infer that parapodia and arthropodia are not structurally or mechanistically homologous (but their primordia might be), that Dll's ancestral bilaterian function was in sensory and central nervous system differentiation, and that locomotory appendages possibly evolved from sensory outgrowths.

Evolutionary variation in gene expression is associated with dimorphism in eusocial vespid wasps

Phenotypic diversity is frequently generated by differences in gene expression. In this study, we addressed the relationship between homology in gene expression and phenotype among four species of eusocial wasps. Specifically, we investigated the evolution of caste-specific and sex-specific gene expression patterns associated with caste polyphenisms and sexual dimorphisms. We also identified several genes with functions relevant to their phenotype-specific roles. Our results suggest that gene expression profiles associated with caste polyphenisms may evolve rapidly relative to those associated with sexes. Thus, caste-biased genes may undergo less regulatory constraint or be subject to greater neutral variation in expression than sex-biased genes.

Deep homology: a view from systematics

Over the past decade, it has been discovered that disparate aspects of morphology - often of distantly related groups of organisms - are regulated by the same genetic regulatory mechanisms. Those discoveries provide a new perspective on morphological evolutionary change. A conceptual framework for exploring these research findings is termed 'deep homology'. A comparative framework for morphological relations of homology is provided that distinguishes analogy, homoplasy, plesiomorphy and synapomorphy. Four examples - three from plants and one from animals - demonstrate that homologous developmental mechanisms can regulate a range of morphological relations including analogy, homoplasy and examples of uncertain homology. Deep homology is part of a much wider range of phenomena in which biological (genes, regulatory mechanisms, morphological traits) and phylogenetic levels of homology can both be disassociated. Therefore, to understand homology, precise, comparative, independent statements of both biological and phylogenetic levels of homology are necessary.

Geometric control of tissue morphogenesis

Morphogenesis is the dynamic and regulated change in tissue form that leads to creation of the body plan and development of mature organs. Research over the past several decades has uncovered a multitude of genetic factors required for morphogenesis in animals. The behaviors of individual cells within a developing tissue are determined by combining these genetic signals with information from the surrounding microenvironment. At any point in time, the local microenvironment is influenced by macroscale tissue geometry, which sculpts long range signals by affecting gradients of morphogens and mechanical stresses. The geometry of a tissue thus acts as both a template and instructive cue for further morphogenesis.

Origin of the genetic components of the vomeronasal system in the common ancestor of all extant vertebrates

Comparative genomics provides a valuable tool for inferring the evolutionary history of physiological systems, particularly when this information is difficult to ascertain by morphological traits. One such example is the vomeronasal system (VNS), a vertebrate nasal chemosensory system that is responsible for detecting intraspecific pheromonal cues as well as environmental odorants. The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. To determine when the genetic components of the VNS originated, we searched for the VNS-specific genes in the genomes of two early diverging vertebrate lineages: the sea lamprey from jawless fishes and the elephant shark from cartilaginous fishes. Genes encoding vomeronasal type 1 receptors (V1Rs) and Trpc2, two components of the vomeronasal signaling pathway, are present in the sea lamprey genome, and both are expressed in the olfactory organ, revealing that the genetic components of the present-day VNS existed in the common ancestor of all extant vertebrates. Additionally, all three VNS genes, Trpc2, V1Rs, and vomeronasal type 2 receptors (V2Rs), are found in the elephant shark genome. Because V1Rs and V2Rs are related to two families of taste receptors, we also searched the early diverging vertebrate genomes for taste system genes and found them in the shark genome but not in the lamprey. Coupled with known distributions of the genetic components of the vertebrate main olfactory system, our results suggest staggered origins of vertebrate sensory systems. These findings are important for understanding the evolution of vertebrate sensory systems and illustrate the utility of the genome sequences of early diverging vertebrates for uncovering the evolution of vertebrate-specific traits.

Duplication and divergence of fgf8 functions in teleost development and evolution

Fibroblast growth factors play critical roles in many aspects of embryo patterning that are conserved across broad phylogenetic distances. To help understand the evolution of fibroblast growth factor functions, we identified members of the Fgf8/17/18-subfamily in the three-spine stickleback Gasterosteus aculeatus, and investigated their evolutionary relationships and expression patterns. We found that fgf17b is the ortholog of tetrapod Fgf17, whereas the teleost genes called fgf8 and fgf17a are duplicates of the tetrapod gene Fgf8, and thus should be called fgf8a and fgf8b. Phylogenetic analysis supports the view that the Fgf8/17/18-subfamily expanded during the ray-fin fish genome duplication. In situ hybridization experiments showed that stickleback fgf8 duplicates exhibited common and unique expression patterns, indicating that tissue specialization followed the gene duplication event. Moreover, direct comparison of stickleback and zebrafish embryonic expression patterns of fgf8 co-orthologs suggested lineage-specific independent subfunction partitioning and the acquisition or the loss of ortholog functions. In tetrapods, Fgf8 plays an important role in the apical ectodermal ridge of the developing pectoral appendage. Surprisingly, differences in the expression of fgf8a in the apical ectodermal ridge of the pectoral fin bud in zebrafish and stickleback, coupled with the role of fgf16 and fgf24 in teleost pectoral appendage show that different Fgf genes may play similar roles in limb development in various vertebrates.

The formation of the theory of homology in biological sciences

Homology is among the most important comparative concepts in biology. Today, the evolutionary reinterpretation of homology is usually conceived of as the most important event in the development of the concept. This paradigmatic turning point, however important for the historical explanation of life, is not of crucial importance for the development of the concept of homology itself. In the broadest sense, homology can be understood as sameness in reference to the universal guarantor so that in this sense the different concepts of homology show a certain kind of "metahomology". This holds in the old morphological conception, as well as in the evolutionary usage of homology. Depending on what is (or was) taken as a guarantor, different types of homology may be distinguished (as idealistic, historical, developmental etc.). This study represents a historical overview of the development of the homology concept followed by some clues on how to navigate the pluralistic terminology of modern approaches to homology.

The developmental genetics of homology

Homology is an essential idea of biology, referring to the historical continuity of characters, but it is also conceptually highly elusive. The main difficulty is the apparently loose relationship between morphological characters and their genetic basis. Here I propose that it is the historical continuity of gene regulatory networks rather than the expression of individual homologous genes that underlies the homology of morphological characters. These networks, here referred to as 'character identity networks', enable the execution of a character-specific developmental programme.

Growth from two transient apical initials in the meristem of Selaginella kraussiana

A major transition in land plant evolution was from growth in water to growth on land. This transition necessitated major morphological innovations that were accompanied by the development of three-dimensional apical growth. In extant land plants, shoot growth occurs from groups of cells at the apex known as meristems. In different land plant lineages, meristems function in different ways to produce distinct plant morphologies, yet our understanding of the developmental basis of meristem function is limited to the most recently diverged angiosperms. To redress this balance, we have examined meristem function in the lycophyte Selaginella kraussiana. Using a clonal analysis, we show that S. kraussiana shoots are derived from the activity of two short-lived apical initials that facilitate the formation of four axes of symmetry in the shoot. Leaves are initiated from just two epidermal cells, and the mediolateral leaf axis is the first to be established. This pattern of development differs from that seen in flowering plants. These differences are discussed in the context of the development and evolution of diverse land plant forms.

Origin and evolution of the vertebrate vomeronasal system viewed through system-specific genes

Tetrapods have two distinct nasal chemosensory systems, the main olfactory system and the vomeronasal system (VNS). Defined by certain morphological components, the main olfactory system is present in all groups of vertebrates, while the VNS is found only in tetrapods. Previous attempts to identify a VNS precursor in teleost fish were limited by functional and morphological characters that could not clearly distinguish between homologous and analogous systems. In the past decade, several genes that specifically function in the VNS have been discovered. Here we first describe recent evolutionary studies of mammalian VNS-specific genes. We then review evidence showing the presence and tissue-specific expression of the VNS-specific genes in teleosts, as well as co-expression patterns of these genes in specific regions of the teleost olfactory epithelium. We propose that a VNS precursor exists in teleosts and that its evolutionary origin predated the separation between teleosts and tetrapods.

Information about a form (on the dynamic laws of morphogenesis)

How a developing embryo becomes "informed" about its form?" This problem remains obscure and controversial. We argue that the "information about a form" is distributed throughout three main components: the dynamic laws, the parameters and the initial/boundary conditions. In the absence of a dynamic law two other components are "blind", that is, do not contain any unambiguous information. We present a version of a dynamic law of morphogenesis, based upon the presumption of a feedback between passive and active mechanical stresses. We explore several models of shape formation based upon this law and show that, as depending upon the parameters values, they generate a large set of realistic shapes. Genetic and epigenetic basis of the models parameters is discussed.

Petaloidy and petal identity MADS-box genes in the balsaminoid genera Impatiens and Marcgravia

Impatiens and Marcgravia have striking morphological innovations associated with the flowers. One of the sepals in Impatiens is spurred and petaloid, while in Marcgravia the petals are fused into a cap and nectary cups are associated with the inflorescence. Balsaminaceae (Impatiens) and Marcgraviaceae have surprisingly been shown to be closely related, since both belong to the balsaminoid clade of Ericales (basal asterids). However, several thorough morphological studies thus far have not revealed shared derived characters (synapomorphies) that support a close relationship between these families. In the balsaminoid clade, transitions from entirely green flowers to flowers with heterotopic petaloid organs can be observed. The primary role of class B genes in core eudicots is to specify the identity of petal and stamen floral organs. E-class genes, of which SEP3 is a representative, have been identified as redundant mediators that confer transcriptional activation potential on protein complexes that specify organ identity. Given the conserved function of organ-identity MADS-box genes in model plants, but the rapid molecular evolution in angiosperms, it remains controversial whether these genes have been involved in shaping floral diversity. We have identified a SEP3-like gene and a total of five class B genes from Impatiens hawkeri and Marcgravia umbellata and report their quantitative expression in the floral organs. In Impatiens, two AP3/DEF-like genes were identified with strongly divergent C-terminal domains, one truncated and one unusually long. Both genes show a gradual decrease in expression towards the outer perianth organs, but no GLO-like gene expression is observed in the petaloid sepal. Remarkably, SEP3-like gene expression in the Impatiens perianth is absent from the green sepals but present in the petaloid sepal and in the petals. Dimeric protein interactions of the cloned Impatiens genes were studied in yeast and by using gel retardation. In Marcgravia, strong overlapping class B gene expression is limited to the stamens, but a SEP3-like gene is strongly expressed in the Marcgravia nectary, indicating that both Impatiens and Marcgravia show heterotopic expression of a SEP3-like gene. We discuss several candidate mechanisms for heterotopic petaloidy involving modified gene expression and protein interaction of SEP3-like and class B genes.

Recursive causality in evolution: a model for epigenetic mechanisms in cancer development

Interactions between adaptative and selective processes are illustrated in the model of recursive causality as defined in Rupert Riedl's systems theory of evolution. One of the main features of this theory also termed as theory of evolving complexity is the centrality of the notion of 'recursive' or 'feedback' causality - 'the idea that every biological effect in living systems, in some way, feeds back to its own cause'. Our hypothesis is that "recursive" or "feedback" causality provides a model for explaining the consequences of interacting genetic and epigenetic mechanisms which are known to play a key role in development of cancer. Epigenetics includes any process that alters gene activity without changes of the DNA sequence. The most important epigenetic mechanisms are DNA-methylation and chromatin remodeling. Hypomethylation of so-called oncogenes and hypermethylation of tumor suppressor genes appear to be critical determinants of cancer. Folic acid, vitamin B12 and other nutrients influence the function of enzymes that participate in various methylation processes by affecting the supply of methyl groups into a variety of molecules which may be directly or indirectly associated with cancerogenesis. We present an example from our own studies by showing that vitamin D3 has the potential to de-methylate the osteocalcin-promoter in MG63 osteosarcoma cells. Consequently, a stimulation of osteocalcin synthesis can be observed. The above mentioned enzymes also play a role in development and differentiation of cells and organisms and thus illustrate the close association between evolutionary and developmental mechanisms. This enabled new ways to understand the interaction between the genome and environment and may improve biomedical concepts including environmental health aspects where epigenetic and genetic modifications are closely associated. Recent observations showed that methylated nucleotides in the gene promoter may serve as a target for solar UV-induced mutations of the p53 tumor suppressor gene. This illustrates the close interaction of genetic and epigenetic mechanisms in cancerogenesis resulting from changes in transcriptional regulation and its contribution to a phenotype at the micro- or macroevolutionary level. Above-mentioned interactions of genetic and epigenetic mechanisms in oncogenesis defy explanation by plain linear causality, things like the continuing adaptability of complex systems. They can be explained by the concept of recursive causality and has introduced molecular biology into the realm of cognition science and systems theory: based on the notion of so-called feedback- or recursive causality a model for epigenetic mechanisms with relevance for oncology and biomedicine is provided.

Phenogenetic drift in evolution: the changing genetic basis of vertebrate teeth

Vertebrate mineralized tissues are vital to the adaptive evolution of various traits. Among these traits is the tooth, which consists of two characteristic mineralized tissues, a highly mineralized surface layer (enamel in tetrapods and enameloid in fish) and a softer body (dentin), both supported by basal bone. However, enamel and enameloid are significantly different in development, and dentin shows many histological variations; hence their evolution has been intensively studied. Nevertheless, their genetic basis has been revealed only in tetrapods. We previously reported that many genes involved in tetrapod tissue mineralization arose from a common ancestor and constitute the secretory calcium-binding phosphoprotein (SCPP) gene family. Now we show that teleost fish also use many SCPPs for enameloid and dentin mineralization, but none of these directly corresponds to tetrapod SCPPs. This finding suggests that teleost and tetrapod SCPP genes have experienced independent parallel duplication histories. Thus, through phenogenetic drift, the tooth has remained a stable trait in jawed vertebrates, while evolving distinct genetic bases in teleosts and tetrapods. The characteristics of teleost SCPP genes and their expression domains in tooth development suggest the possibility that enameloid arose from dentin and enamel from enameloid more than once in vertebrate evolution. In fugu (puffer fish), expression of SCPP genes is also detected in an unusual beak-like structure that shelters numerous teeth. Their expression pattern suggests that the jaw consists of the dentin beak and supportive bone. These findings illustrate the complexity of the homology concept in understanding evolution, particularly the evolution of mineralized tissues.

Phylogeny and evo-devo: Characters, homology, and the historical analysis of the evolution of development

The concept of homology continues to attract more and more commentary. In systematic and evolutionary biology the meaning of homology as synapomorphic similarity inherited from a common ancestor has gained wide acceptance over the last three or four decades. In recent years, however, developmental biologists, in particular, have argued for a new approach to, and new definition for, homology that revolves around the desire to make it more process-oriented and more mechanistic. These efforts raise questions about the relationship between developmental and evolutionary biology as well as how the evolution of development is to be studied. It is argued in this paper that this new approach to homology seemingly decouples developmental biology from the study of the evolution of development rather than to facilitate that study. In contrast, applying the notion of historical, phylogenetic homology to developmental data is inherently comparative and therefore evolutionary.

Homology and ontogeny: pattern and process in comparative developmental biology

In this article the interface between development and homology is discussed. Development is here interpreted as a sequence of evolutionarily independent stages. Any approach stressing the importance of specific developmental stages is rejected. A homology definition is favoured which includes similarity, and complexity serves as a test for homology. Complexity is seen as the possibility of subdividing a character into evolutionarily independent corresponding substructures. Topology as a test for homology is critically discussed because corresponding positions are not necessarily indicative of homology. Complexity can be used twofold for homology assessments of development: either stages or processes of development are homologized. These two approaches must not be con-flated. This distinction leads to the conclusion that there is no ontogenetic homology "criterion".

Conservation and co-option in developmental programmes: the importance of homology relationships

One of the surprising insights gained from research in evolutionary developmental biology (evo-devo) is that increasing diversity in body plans and morphology in organisms across animal phyla are not reflected in similarly dramatic changes at the level of gene composition of their genomes. For instance, simplicity at the tissue level of organization often contrasts with a high degree of genetic complexity. Also intriguing is the observation that the coding regions of several genes of invertebrates show high sequence similarity to those in humans. This lack of change (conservation) indicates that evolutionary novelties may arise more frequently through combinatorial processes, such as changes in gene regulation and the recruitment of novel genes into existing regulatory gene networks (co-option), and less often through adaptive evolutionary processes in the coding portions of a gene. As a consequence, it is of great interest to examine whether the widespread conservation of the genetic machinery implies the same developmental function in a last common ancestor, or whether homologous genes acquired new developmental roles in structures of independent phylogenetic origin. To distinguish between these two possibilities one must refer to current concepts of phylogeny reconstruction and carefully investigate homology relationships. Particularly problematic in terms of homology decisions is the use of gene expression patterns of a given structure. In the future, research on more organisms other than the typical model systems will be required since these can provide insights that are not easily obtained from comparisons among only a few distantly related model species.

Birth, life and death of developmental control genes: new challenges for the homology concept

Understanding the interrelationship between the phylogeny of developmental control genes and the evolution of morphological features is a central goal of evolutionary developmental biology (evo-devo). It requires that one distinguishes properly between gene genealogy and function. Gene duplication, gene loss and speciation in combination with differential changes in gene function can generate complex evolutionary scenarios that require additional terms beyond homology for a proper description. Use and possible misuse of these terms, including "orthology", "paralogy" and "subfunctionalization", is exemplified with AGAMOUS-like genes encoding transcription factors involved in flower and fruit development. This MADS-box gene subfamily demonstrates that homologous genes in different species with (almost) identical functions can be paralogues rather than orthologues, corroborating that functional similarity of genes is not a valid criterion for orthology. Homeosis fails some tests of homology, but might be of greater evolutionary importance than previously assumed, justifying yet another term, "homocracy". It describes organs that share the expression of the same patterning genes, irrespective of the homology of these organs. All in all this article opts for a careful use of a limited and well-chosen set of terms describing gene relationships and function, rather than the inflationary production of novel terms that may seem to be precise, but whose obscurity hampers communication.

The genetic basis of aging: an evolutionary biologist's perspective

This Perspective discusses recent progress in the study of the genetic basis of aging from the viewpoint of an evolutionary biologist. Work in this area has revealed that homologous genes and pathways play a role in determining life span in many different species. Because life span is a complex polygenic trait, however, these findings provide information about only a small portion of the genetic basis of this trait. Additionally, because the model organisms used to study aging have been exposed to similar laboratory conditions that can lead to unintentional artificial selection, some of the similarities among these organisms might have resulted from such selection. It is not yet clear whether the results found in model organisms will extend to organisms in a natural environment. A few species are known for which there are natural populations that differ in life span and patterns of senescence, and they should be useful for assessing whether the genetic mechanisms identified in the laboratory also operate in the wild.

The phenogenetic logic of life

For nearly a century we have understood that life works through genes, and so have had an elegant theory for general evolution. But this did not explain the kinds of traits that characterize organisms, nor how genes produce them. Advances in recent decades have opened the way for an understanding of the phenogenetic logic or relational principles of life, by which a few basic characteristics of genomes produce biological phenotypes through some basic developmental processes. This logic provides a general explanation of the nature and source of organismal design, and a powerful programme for research.

Wing venation and Distal-less expression in Heliconius butterfly wing pattern development

Here we show that major color pattern elements of Heliconius butterfly wings develop independently of wing venation. We recovered a hybrid Heliconius displaying a mutant phenotype with a severe vein deficiency. Although this butterfly lacked most of its wing veins, the large, melanic banding patterns typical of the genus were conserved across the entire wing. The only obvious correlation between vein reduction and pigment patterns was a loss of vein-associated melanin stripes near the distal margin of the wings. We examined the expression of the eyespot-associated transcription factor Distal-less in a banded and a spotted species of Heliconius and found no obvious relationship between protein expression and the band or spot patterns typical of the genus. Together, our results suggest that the melanic bands and spots in Heliconius are unlikely to be derived from an eyespot determination system. We propose that major elements of Heliconius wing pattern formation are based primarily on a complex, whole-wing proximodistal axis system.

Latent homologues for the neural crest as an evolutionary novelty

The neural crest is a craniate synapomorphy and a bona fide evolutionary novelty. Recently, researchers considering intriguingly similar patterns of gene expression, cell behaviors, and embryogenetic processes in noncraniate deuterostomes have suggested that cephalochordates, urochordates, and echinoderms or their ancestors might have possessed cells that were precursors to the neural crest or its constituent cells. To emphasize the caution with which similarities at genetic, cellular, or embryological levels should be interpreted as substantiations for cell, germ layer, or tissue homologies, we present and evaluate additional tantalizing evidence that could be considered as documenting neural crest precursors in precraniates. Furthermore, we propose an evolutionary context--latent homologue--within which these data should be interpreted.