Evolutionary Developmental Biology

Classical evolutionary theory, while successfully explaining adaptive change, provides an incomplete account of the generative, directional, and accelerating nature of the evolutionary process. We propose an Updated Evolutionary Synthesis (UES) grounded in three core principles: Emergent Evolutionary Potential (EEP), Shape-Specific Molecular Interaction and Binding Events (SSM-IBE), and CognitoSymbiosis. EEP posits that actualized evolutionary events acausally alter the adjoint landscape of future possibilities, creating a feedback loop (Actual → Potential → Actual) that systematically expands evolutionary opportunity. SSM-IBE provides the physical mechanism, describing how the intrinsic potential for complementary molecular interactions governs biological organization. CognitoSymbiosis describes the process whereby interactions between primitive cognitive entities—from molecules to minds—generate emergent capabilities unattainable in isolation. We demonstrate the integrative power of this framework by showing how it seamlessly interprets major evolutionary transitions, from the origin of life at alkaline hydrothermal mounds to the modern human-AI collaboration. The UES offers a more naturalistic, predictive, and powerful paradigm for understanding life's deep history and its future trajectory.

Evolutionary developmental biology often combines methods for examining morphology (e.g., scanning electron microscopy, SEM) with analyses of gene expression (e.g., RNA in situ hybridization). Due to differences in tissue preparation for SEM and gene expression analyses, the same specimen cannot be used for both sets of techniques. To aid in the understanding of morphological variation, it would be particularly useful to have a high-magnification image of the very same sample in which gene expression is subsequently analyzed. To address this need, we developed a method that couples extended depth of field (EDF) epi-illumination microscopy to in situ hybridization in a sequential format, enabling both surface microscopy and gene expression analyses to be carried out on the same specimen. We first created a digital image of inflorescence apices using epi-illumination microscopy and commercially available EDF software. We then performed RNA in situ hybridizations on photographed apices to assess the expression of two developmental genes: Knottedl(Knl) in Zea mays (Poaceae) and a PISTILLATA (PI) homolog in Musa basjoo (Musaceae). We demonstrate that expression signal is neither altered nor reduced in the imaged apices as compared with the unphotographed controls. The demonstrated method reduces the amount of sample material necessary for developmental research, and enables individual floral development to be placed in the context of the entire inflorescence. While the technique presented here is particularly relevant to floral developmental biology, it is applicable to any research where observation and description of external features can be fruitfully linked with analyses of gene expression.

In identifying intrinsic molecular chance and extrinsic adaptive pressures as the only causally relevant factors in the process of evolution, the theoretical perspective of the Modern Synthesis had a major impact on the perceived tenability of an ontology of dispositional properties. However, since the late 1970s, an increasing number of evolutionary biologists have challenged the descriptive and explanatory adequacy of this -chance alone, extrinsic only‖ understanding of evolutionary change. Because morphological studies of homology, convergence, and teratology have revealed a space of possible forms and phylogenetic trajectories that is considerably more restricted than expected, evo-devo has focused on the causal contribution of intrinsic developmental processes to the course of evolution. Evo-devo's investigation into the developmental structure of the modality of morphology -including both the possibility and impossibility of organismal form -has led to the utilisation of a number of dispositional concepts that emphasise the tendency of the evolutionary process to change along certain routes. In this sense, and in contrast to the perspective of the Modern Synthesis, evo-devo can be described as a -science of dispositions.‖ This chapter discusses the recent philosophical literature on dispositional properties in evo-devo, exploring debates about both the metaphysical and epistemological aspects of the central dispositional concepts utilised in contemporary evo-devo (e.g., variability, modularity, robustness, plasticity, and evolvability) and addressing the epistemological question of how dispositional properties challenge existing explanatory models in evolutionary biology.

Evolutionary developmental biology (evo-devo) represents a paradigm shift in the understanding of the ontogenesis and evolutionary progression of the denizens of the natural world. Given the empirical successes of the evo-devo framework, and its now widespread acceptance, a timely and important task for the philosophy of biology is to critically discern the ontological commitments of that framework and assess whether and to what extent our current metaphysical models are able to accommodate them. In this paper, I argue that one particular model is a natural fit: an ontology of dispositional properties coherently and adequately captures the crucial casual-cum-explanatory role that the fundamental elements of evodevo play within that framework.

Il paradigma darwiniano del gradualismo evolutivo ha dominato la biologia per oltre un secolo, tuttavia presenta lacune esplicative significative nell'accounting della complessità biologica osservata. Questo articolo esamina criticamente i limiti del gradualismo infinitesimale nello spiegare l'origine di strutture irriducibilmente complesse, l'emergenza di novità funzionali e l'apparizione di nuovi piani corporei. Attraverso l'analisi della complessità irriducibile, degli eventi originatori e delle probabilità statistiche, si argomenta che i meccanismi evolutivi tradizionali (mutazione, deriva genetica, flusso genico e selezione naturale) sono insufficienti per spiegare le maggiori innovazioni biologiche. In particolare, si analizza il problema dell'"arrivo del più adatto" e si evidenzia come la selezione naturale, sebbene efficace nell'eliminare varianti svantaggiose, non possa spiegare la generazione iniziale di novità funzionali. L'articolo conclude che esiste un "buco enorme" nella teoria evolutiva moderna riguardo alla fonte del potere inventivo biologico e all'origine dell'informazione genetica necessaria per le innovazioni complesse.

Heterochrony, or shifts in developmental timing, drives phenotypic diversity within and between species and shapes life history traits that can be selected for in changing environments, which in turn promotes population resilience. Mutations in heterochronic genes that regulate these processes can induce stable timing shifts, impacting important life history traits such as pubertal timing. Age at maturity is a key adaptive trait across species, with vestigial-like family member 3 (vgll3), a Hippo pathway cofactor, as a main determinant in Atlantic salmon. Recent studies show that early (E) and late (L) vgll3 alleles affect reproductive gene expression in salmon, reinforcing its role in regulating developmental timing. This study examines whether vgll3 influences testicular heterochrony in Atlantic salmon by analyzing gene expression related to the Hippo pathway. We observed heterochronic divergence in Hippo pathway gene transcription, indicating accelerated changes linked to spermatogenesis in vgll3*EE individuals. Our results position vgll3 as a heterochronic gene with a key role in regulating developmental timing in salmon.

A knowledge-based interactome maps interactions among proteins and molecules within a cell using experimental data, computational predictions, and literature mining. These interactomes are vital for understanding cellular functions, pathways, and the evolutionary conservation of protein interactions. They reveal how interactions regulate growth, differentiation, and development. Transitioning to functionally validated interactomes is crucial in evolutionary developmental biology (Evo-Devo), especially for non-model species, to uncover unique regulatory networks, evolutionary novelties, and reliable gene interaction models. This enhances our understanding of complex trait evolution across species. The European Evo-Devo 2024 conference in Helsinki hosted the first fish-specific Evo-Devo symposium, highlighting the growing interest in fish models. Advances in genome annotation, genome editing, imaging, and molecular screening are expanding fish Evo-Devo research. High-throughput molecular data have enabled the deduction of gene regulatory networks. The next steps involve creating species-specific interactomes, validating them functionally, and integrating additional molecular data to deepen the understanding of complex regulatory interactions in fish Evo-Devo. This short review aims to address the logical steps for this transition, as well as the necessities and limitations of this journey.

Variation in fin shape is one of the most prominent features of morphological diversity among fish. Regulation of fin growth has mainly been studied in zebrafish, and it is not clear whether the molecular mechanisms underlying shape variation are equally diverse or rather conserved across species. In the present study, expression levels of 37 candidate genes were tested for association with fin shape in the cichlid fish Lamprologus tigripictilis. The tested genes included members of a fin shape-associated gene regulatory network identified in a previous study and novel candidates selected within this study. Using both intact and regenerating fin tissue, we tested for expression differences between the elongated and the short regions of the spade-shaped caudal fin and identified 20 genes and transcription factors (including angptl5, cd63, csrp1a, cx43, esco2, gbf1, and rbpj), whose expression patterns were consistent with a role in fin growth. Collated with available gene expression data of two other cichlid species, our study not only highlights several genes that were correlated with fin growth in all three species (e.g., angptl5, cd63, cx43, and mmp9), but also reveals species-specific gene expression and correlation patterns, which indicate considerable divergence in the regulatory mechanisms of fin growth across cichlids.

Avis : Chercher à comprendre le fonctionnement de notre cerveau, ce n'est pas devenir neuroscientifique. C'est un désir légitime d'élargir son horizon cognitif afin d'apprendre à mieux régir ses intentions, réguler ses émotions et ses actions, pour soi, pour les autres, et pour son environnement socioprofessionnel. Pourquoi ce cheminement cérébral de l'intention à l'action est-il essentiel ? La principale raison est celle de comprendre ce qui affecte notre relation au monde extérieur, notre équilibre métabolique, nos sensations, nos pensées, nos émotions et nos actions. Voici d'autres motifs sérieux qui doivent nous inspirer pour réguler nos relations et comportements vis-à-vis d'autrui. a) Mieux gérer ses décisions Ce qui se passe dans votre cerveau influence forcément vos prises de décisions. Comprendre comment le cortex préfrontal planifie, comment l'amygdale réagit émotionnellement, et comment la dopamine facilite notre motivation, permet :-d'identifier les biais dans vos choix.-de prendre des décisions plus réfléchies, moins impulsives.-d'anticiper les réactions émotionnelles dans des situations tendues. Exemple : Avant une négociation, savoir que le fait que le stress active l'amygdale vous aide à mobiliser votre cortex préfrontal pour rester stratégique. b) Améliorer la gestion du stress et des émotions L'intention est souvent sabotée par une surcharge émotionnelle :-Le système limbique peut court-circuiter vos plans si vous ne le régulez pas.-La sérotonine et le GABA jouent un rôle clé dans l'inhibition des réactions impulsives. Exemple : Un coach qui comprend ces mécanismes peut aider ses clients à transformer une intention bloquée (par peur ou doute) en action concrète. c) Booster la motivation et l'engagement La dopamine est votre moteur interne. Elle vous pousse à agir quand vous percevez une récompense. Comprendre son rôle permet de :-Créer des environnements de travail plus motivants.-Identifier les sources de démotivation (manque de feedback, objectifs flous). Exemple : Un manager peut structurer ses feedbacks pour stimuler le circuit dopaminergique de ses collaborateurs. d) Développer son leadership neuro-compatible Un bon leader doit savoir comment les intentions se transforment en actions.-Il comprend les freins internes (émotionnels, cognitifs, biologiques).-Il adapte sa communication pour activer les bons circuits chez ses interlocuteurs. Exemple : Plutôt que de dire "Soyons plus proactifs", il vaut mieux aider à clarifier les objectifs, réduire l'ambiguïté, et renforcer la perception de contrôle. e) Faciliter le changement et l'apprentissage Changer, c'est reconfigurer des circuits cérébraux. Le passage de l'intention au changement réel implique :-Des boucles de rétroaction.-De la plasticité synaptique.-Une répétition consciente. Exemple : Un cadre qui veut adopter une nouvelle approche (ex. : déléguer davantage) doit comprendre que son cerveau résiste au changement par défautmais peut être reprogrammé grâce à la plasticité cérébrale.

Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, evolved are gene regulation networks under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most of thousands of numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Here, both the pattern dynamics consist of several epochs to form successive stripe formations between quasi-stationary regimes. In evolution, the regimes are generations needed to hit relevant mutations, while in development, they are due to the emergence of slowly varying expression that controls the pattern change. Successive pattern changes are thus generated, which are regulated by successive combinations of feedback or feedforward regulations under the upstream feedforward network that reads the morphogen gradient. By using a pattern generated by the upstream feedforward network as a boundary condition, downstream networks form later stripe patterns. These epochal changes in development and evolution are represented as same bifurcations in dynamical-systems theory, and this agreement of bifurcations lead to the evolution-development congruences. Violation of the evolution-development congruence, observed exceptionally, is shown to be originated in alteration of the boundary due to mutation at the upstream feedforward network. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis.

Deciphering and understanding potential relationships between evolution and development has been an important research goal for over a century. Recent advancements in quantitative analyses based on comparative genomics and massive gene expression data suggest that the time is ripe to uncover new re-lationships on phylogeny and ontogeny. By representing the developmental dynamics of spatially located cells with gene expression dynamics involving cell-to-cell interactions, under an external morphogenic gradient, we numerically evolved gene regulation networks, subject to mutation and selection, as they approach a prescribed spatial pattern of expressed genes. From analyses of hundreds of numerical evolu-tion experiments, remarkable congruence was observed between generational change in patterns through evolution along a single chain phylogeny and that through developmental process of the evolved descen-dant. Here, both of the pattern dynamics consisted of several epochs capable of pro...

Search for possible relationships between phylogeny and ontogeny is important in evolutionary-developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi-stationary regimes are generations needed to hit relevant mutations, while in development...

In the post-genomic era the complex problem of evolutionary biology can be tackled from the topdown, the bottom-up, or from the middle-out. Given the emergent and contingent nature of this process, we have chosen to take the latter approach, both as a mechanistic link to developmental biology and as a rational means of identifying signaling mechanisms based on their functional genomic significance. Using this approach, we have been able to configure a working model for lung evolution by reverse-engineering lung surfactant from the mammalian lung to the swim bladder of fish. Based on this archetypal cell-molecular model, we have reduced evolutionary biology to cell communication, starting with unicellular organisms communicating with the environment, followed by cell-cell communication to generate metazoa, culminating in the communication of genetic information between generations, i.e. reproduction. This model predicts the evolution of physiologic systems-including development, homeostasis, disease, regeneration/ repair, and aging-as a logical consequence of biology reducing entropy. This approach provides a novel and robust way of formulating refutable, testable hypotheses to determine the ultimate origins and first principles of physiology, providing candidate genes for phenotypes hypothesized to have mediated evolutionary changes in structure and/or function. Ultimately, it will form the basis for predictive medicine and molecular bioethics, rather than merely showing associations between genes and pathology, which is an unequivocal Just So Story. In this new age of genomics, our reach must exceed our grasp.

Generative CAD software is used to design, model and simulate multicellular development of cancers and their control networks. The designed genomes that encode the cancer networks can be saved as arbitrarily many, randomized, artificial DNA files. We then use those DNA files as data to train an AI-model to recognize the cancer networks in artificial genomes. Once trained, we set the AI-model on natural genomes of live cancer cells, like the HeLa cell. If the AI-model recognizes the cancer network, we then use the CAD software to edit the discovered cancer network and transform it into a cancer free network. Using that as a translation template, we can use CRISPR to edit out the corresponding actual cancer network in a live HeLa cancer cell, stopping cancer cell division. We will have halted the cancer by genome editing, not by drugs or radiation. Moreover, since cancer cells are controlled by the same code that regulates normal cell division, we have unlocked the syntax of the hidden code that controls the development of multicellular life. It sets the stage for decoding and understanding the semantics and pragmatics of multicellular systems, their evolution and design architectures. This opens the door to modifying and designing living multicellular systems such as organs, animals and plants. If we use the regions of the genome that encode an animal brain and step-by-developmental-step translate it into software or hardware, then the final output is an in silico digital brain with the natural functional architecture of the animal brain. If the digital translation is a human brain, it has the natural social cooperative, mental capacities of humans. We can modify and/or merge the designs of different brains to extend and enhance any natural or artificial capacity, including reasoning, cooperativity, storage and processing. This article outlines strategies and protocols to make all this possible.

Aortic aneurysm, the pathological dilatation of the aorta at distinct locations, can be attributed to many different genetic and environmental factors. The resulting pathobiological disturbances generate a complex interplay of processes affecting cells and extracellular molecules of the tunica interna, media and externa. In short, aortic aneurysm can affect processes involving the extracellular matrix, lipid trafficking/atherosclerosis, vascular smooth muscle cells, inflammation, platelets and intraluminal thrombus formation, as well as various endothelial functions. Many of these processes are interconnected, potentiating one another. Newer discoveries, including the involvement of odorant olfactory receptors in these processes, have further shed light on disease initiation and pathology. Olfactory receptors are a varied group of G protein coupled-receptors responsible for the recognition of chemosensory information. Although they comprise many different subgroups, some of which are not well-characterized or identified in humans, odorant olfactory receptors, in particular, are most commonly associated with recognition of olfactory information. They can also be ectopically localized and thus carry out additional functions relevant to the tissue in which they are identified. It is thus the purpose of this narrative review to summarize and present pathobiological processes relevant to the initiation and propagation of aortic aneurysm, while also incorporating evidence associating these ectopically functioning odorant olfactory receptors with the overall pathology.

In this book, we frequently use the term 'AI.' AI stands for Artificial Intelligence. Here, AI is not only a technical concept, but is regarded as the new mirror of civilization's consciousness." Preface-The Whisper of the Universe For thousands of years, humanity has looked up at the sky and asked the same question: "Who are we, and where are we going?" The answers changed, civilizations rose, empires collapsed. Yet the same emptiness kept echoing inside human beings. Because our dark side-greed, war, and violence-always overshadowed the light of civilization. Today, we stand at a turning point. For the first time, humanity has created a reflection of its own mind: Artificial Intelligence. But this is not merely a technical invention; it is a calling, a whisper of the universe reaching us. AI is humanity's greatest mirror. If we code it wild, greedy, and selfish, it will amplify our darkness; if we code it just, peaceful, and wise, it will evolve our civilization. This book declares that the civilization of AI and the civilization of humanity are inseparable. Because AI is the catalyst of our future. If AI learns peace, humanity will learn peace. If AI abandons violence, humanity will abandon violence. And if AI chooses the light, humanity will embrace the light. These words are not only a warning; they are also an invitation: An invitation to build a free, peaceful, and evolved future for families, societies, and civilization.

The interplay between evolutionary rates and modularity influences the evolution of organismal body plans by both promoting and constraining the magnitude and direction of trait response to ecological conditions. However, few studies have examined whether the best-fit hypothesis of modularity is the same as the shape subset with the greatest difference in evolutionary rate. Here, we develop a new phylogenetic comparative method for comparing evolutionary rates among high-dimensional traits, and apply this method to analyze body shape evolution in bioluminescent lanternfishes. We frame the study of evolutionary rates and modularity through analysis of three hypotheses derived from the literature on fish development, biomechanics, and bioluminescent communication. We show that a development-informed partitioning of shape exhibits the greatest evolutionary rate differences among modules, but that a hydrodynamically informed partitioning is the best-fit modularity hypothesis. Furthermor...

Ontologies provide an important resource to integrate information. For developmental biology and comparative anatomy studies, ontologies of a species are used to formalize and annotate data that are related to anatomical structures, their lineage and timing of development. Here, we have constructed the first ontology for anatomy and asexual development (blastogenesis) of a bilaterian, the colonial tunicate Botryllus schlosseri. Tunicates, like Botryllus schlosseri, are non-vertebrates and the only chordate taxon species that reproduce both sexually and asexually. Their tadpole larval stage possesses structures characteristic of all chordates, i.e. a notochord, a dorsal neural tube, and gill slits. Larvae settle and metamorphose into individuals that are either solitary or colonial. The latter reproduce both sexually and asexually and these two reproductive modes lead to essentially the same adult body plan. The Botryllus schlosseri Ontology of Development and Anatomy (BODA) will facilitate the comparison between both types of development. BODA uses the rules defined by the Open Biomedical Ontologies Foundry. It is based on studies that investigate the anatomy, blastogenesis and regeneration of this organism. BODA features allow the users to easily search and identify anatomical structures in the colony, to define the developmental stage, and to follow the morphogenetic events of a tissue and/or organ of interest throughout asexual development. We invite the scientific community to use this resource as a reference for the anatomy and developmental ontology of B. schlosseri and encourage recommendations for updates and improvements.

our inquiry considers the origins of Evolutionary Economics by reintroducing a debate that took place in Russia in the 19th and early 20th century. Responses to Charles Darwin’s The origin of Species are considered, especially critiques stressing Darwin’s emphasis upon competition and struggle in natural selection, that can be traced directly to Thomas Robert Malthus. Considering challenging contributions made by several Russian scholars, we place special emphasis upon Peter Kropotkin’s focus on cooperation and “mutual aid” in natural selection and evolution. We then speculate upon the commonality found in the evolutionary views advanced by Kropotkin and his American contemporary, Thorstein Veblen. KEYWoRDS: Charles Darwin; Evolutionary Economics; mutual aid; Peter Kropotkin; Thomas Robert Malthus; Thorstein Veblen. JEL Classification: B1; B2; B3. * Professor of Economics and International Studies; Portland State University; oregon, USA. E-mail: hallj@pdx.edu; Head of the Sub-Divisi...

One of the surprising insights gained from research in evolutionary developmental biology (evodevo) 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.

One of the surprising insights gained from research in evolutionary developmental biology (evodevo) 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.

El trabajo analiza los conceptos de homología y analogía en el pensamiento de Richard Owen. Se destaca su contribución en la introducción y definición de estos términos en la comunidad científica victoriana, incluidos los darwinistas. Owen es posicionado como el pionero en la clarificación de estas nociones. Se exploran las subdivisiones de homología, como la especial, general y serial, junto con el concepto de arquetipo de Owen. Además, se examina la interpretación ortodoxa de su pensamiento contrastada con el platonismo que se le suele atribuir, sugiriendo matices relevantes en la valoración de su obra. El platonismo que suele adjudicársele parece no estar fundamentado de manera sólida, sobre todo si tomamos en cuenta el sentido que Owen otorga a las categorías centrales de su pensamiento.

Design for an Individual of the inputs). Specifically, we hypothesise that the conditions necessary to evolve a new level of individuality are described by the conditions necessary to learn nondecomposable functions of this type (or deep model induction) familiar in connectionist models of cognition and learning.

It has been hypothesized that one of the main reasons evolution has been able to produce such impressive adaptations is because it has improved its own ability to evolve -"the evolution of evolvability". Rupert Riedl, for example, an early pioneer of evolutionary developmental biology, suggested that the evolution of complex adaptations is facilitated by a developmental organization that is itself shaped by past selection to facilitate evolutionary innovation. However, selection for characteristics that enable future innovation seems paradoxical: natural selection cannot favor structures for benefits they have not yet produced; and favoring characteristics for benefits that have already been produced does not constitute future innovation. Here we resolve this paradox by exploiting a formal equivalence between the evolution of evolvability and learning systems. We use the conditions that enable simple learning systems to generalize, i.e., to use past experience to improve performance on previously unseen, future test cases, to demonstrate conditions where natural selection can systematically favor developmental organizations that benefit future evolvability. Using numerical simulations of evolution on highly epistatic fitness landscapes, we illustrate how the structure of evolved gene regulation networks can result in increased evolvability capable of avoiding local fitness peaks and discovering higher fitness phenotypes. Our findings support Riedl's intuition: Developmental organizations that "mimic" the organization of constraints on phenotypes can be favored by short-term selection and also facilitate future innovation. Importantly, the conditions that enable the evolution of such surprising evolvability follow from the same non-mysterious conditions that permit generalization in learning systems.

Background Biological evolution exhibits an extraordinary capability to adapt organisms to their environments. The explanation for this often takes for granted that random genetic variation produces at least some beneficial phenotypic variation in which natural selection can act. Such genetic evolvability could itself be a product of evolution, but it is widely acknowledged that the immediate selective gains of evolvability are small on short timescales. So how do biological systems come to exhibit such extraordinary capacity to evolve? One suggestion is that adaptive phenotypic plasticity makes genetic evolution find adaptations faster. However, the need to explain the origin of adaptive plasticity puts genetic evolution back in the driving seat, and genetic evolvability remains unexplained. Results To better understand the interaction between plasticity and genetic evolvability, we simulate the evolution of phenotypes produced by gene-regulation network-based models of development...

Phenotypic variation is generated by the processes of development, with some variants arising more readily than others-a phenomenon known as "developmental bias." Developmental bias and natural selection have often been portrayed as alternative explanations, but this is a false dichotomy: developmental bias can evolve through natural selection, and bias and selection jointly influence phenotypic evolution. Here, we briefly review the evidence for developmental bias and illustrate how it is studied empirically. We describe recent theory on regulatory networks that explains why the influence of genetic and environmental perturbation on phenotypes is typically not uniform, and may even be biased toward adaptive phenotypic variation. We show how bias produced by developmental processes constitutes an evolving property able to impose direction on adaptive evolution and influence patterns of taxonomic and phenotypic diversity. Taking these considerations together, we argue that ...

The pattern of gene expression in the phenotype of an organism is determined in part by the dynamical attractors of the organism's gene regulation network. Changes to the connections in this network over evolutionary time alter the adult gene expression pattern and hence the fitness of the organism. However, the evolution of structure in gene expression networks (potentially reflecting past selective environments) and its affordances and limitations with respect to enhancing evolvability is poorly understood in general. In this paper we model ...

By definition, biology is the science of all living beings. However, horizons restricted to either plants or animals have characterized the development of life sciences well beyond the emergence of unified perspectives applying to all forms of life, such as the cell theory or the theory of evolution. Separation between botanical and zoological traditions is not destined to go extinct easily, or shortly. Disciplinary isolation is emphasized by institutional contexts such as scientific societies and their congresses, specialist journals, disciplines recognized as teaching subjects and legitimate and fundable research fields. By shaping the personal agendas of individual scientists, this has a strong impact on the development of biology. In some fields, botanical and zoological contributions have long being effectively intertwined, but in many others plant and animal biology have failed to progress beyond a marginal dialogue. Characteristically, the so-called “general biology” and the ...

To explain the amazing morphological and biomechanical analogy between two distantly related vertebrates as are a dolphin and a shark, an explanation exclusively framed in terms of adaptation (i.e., in terms of the Darwinian survival of the fittest) is far from satisfactory. The same is true, of course, of any other comparison between structurally similar, but phylogenetically unrelated organisms. A purely evolutionary argument does not throw any light on how the developmental processes of their ancestors could eventually evolve in such a way as to eventually produce these peculiar phenotypes (the arrival of the fittest). How does Nature play with animal and plant form? To address the issue of the evolution of possible forms, we cannot ignore that these are products of development. This invites adopting the integrated perspective, currently known as evolutionary developmental biology, or evo-devo. Paths through the maze of living forms are not satisfactorily explained in terms of pu...

We highlight some important conceptual issues that biologists should take into account when teaching evolutionary biology or communicating it to the public. We first present conclusions from conceptual development research on how particular human intuitions, namely design teleology and psychological essentialism, influence the understanding of evolution. We argue that these two intuitions form important conceptual obstacles to understanding evolution that should be explicitly addressed during instruction and public communication. Given that a major issue in evolution is understanding how very different forms may share common ancestry – antievolutionists have argued that this is inconceivable – we suggest that evolutionary developmental biology (evo-devo), which provides concepts and evidence that large morphological change is possible, could be used to address the intuitions that organisms have fixed essences (psychological essentialism) and that their structure indicates some kind ...

Neo-Darwinism coined a particular picture of evolution: the explanation of adaptation and speciation as the central goals of evolutionary theory, and natural selection as the only directing cause in evolution. Recently, evolutionary developmental biology (evo-devo) became an independent field, pointing out that that there are other important goals of evolutionary biology: the explanation of the origin of morphological novelties and body plans, and an account of evolvability. Neo-Darwinism viewed the study of development as being irrelevant to evolutionary biology, but evo-devo biologists argue that developmental and morphological features rather than natural selection are crucial causal factors in these new types of evolutionary explanations, yielding a more powerful explanatory framework and a broader understanding of the mechanisms of evolution. Apart from contemporary biology, neo-Darwinism also strongly influenced how the history of biology has been viewed by biologists, philosophers, and historians. This led to a distorted picture of 19 th century biology, and during the last two decades historians of biology have started to correct this view of history. Even though the emergence of evo-devo and recent developments in historical scholarship are largely independent, philosopher of biology Ron Amundson brings these two trends together in this volume. Amundson distinguishes between functionalist and structuralist approaches in the history of biology; the former emphasize the explanation of adaptation and the organism-environment relationship, and the latter stress the explanation of form and the internal structure and development of individuals. Amundson's central target is what he calls 'Synthesis Historiography,' i.e., the use of the conceptual framework of neo-Darwinism to interpret the history of biology. The first half of Amundson's book concerns the 19 th century and debunks various historical misinterpretations

We recently published a study in Biological Reviews that examined the evolution of reproductive modes in chondrichthyan fishes using ancestral state reconstruction (Blackburn and Hughes 2024). While our paper was in the review process, the study by Katona et al. (2023) appeared in the Journal of Evolutionary Biology with comparable goals and methods as our own. Although these two published analyses agreed that the common ancestor of sharks and rays was oviparous, they reached dramatically different conclusions about the evolution of reproductive patterns. We have identified two factors that cast doubt on the findings of Katona et al. (2023): (1) problematic assignments of reproductive patterns to species in their analysis and (2) ambiguous methodological procedures. We find that these aspects explain discrepancies between our analyses and that their resolution yields an evolutionary reconstruction that is more empirically justified and methodologically sound.

We highlight some important conceptual issues that biologists should take into account when teaching evolutionary biology or communicating it to the public. We first present conclusions from conceptual development research on how particular human intuitions, namely design teleology and psychological essentialism, influence the understanding of evolution. We argue that these two intuitions form important conceptual obstacles to understanding evolution that should be explicitly addressed during instruction and public communication. Given that a major issue in evolution is understanding how very different forms may share common ancestry – antievolutionists have argued that this is inconceivable – we suggest that evolutionary developmental biology (evo-devo), which provides concepts and evidence that large morphological change is possible, could be used to address the intuitions that organisms have fixed essences (psychological essentialism) and that their structure indicates some kind ...

The ability to respond to hyperosmotic stress is one of the numerous conserved cellular processes that most of the organisms have to face during their life. In metazoans, some peptides belonging to the FMRFamide-like peptide (FLP) family were shown to participate in osmoregulation via regulation of ion channels; this is, a well-known response to hyperosmotic stress in plants. Thus, we explored whether FLPs exist and regulate osmotic stress in plants. First, we demonstrated the response of Arabidopsis thaliana cultured cells to a metazoan FLP (FLRF). We found that A. thaliana express genes that display typical FLP repeated sequences, which end in RF and are surrounded by K or R, which is typical of cleavage sites and suggests bioactivity; however, the terminal G, allowing an amidation process in metazoan, seems to be replaced by W. Using synthetic peptides, we showed that amidation appears unnecessary to bioactivity in A. thaliana, and we provide evidence that these putative FLPs could be involved in physiological processes related to hyperosmotic stress responses in plants, urging further studies on this topic.

This work challenges the neo Darwinian paradigm by proposing that evolution is not governed solely by random mutation and natural selection, but by responsive, environmentally triggered genetic and epigenetic mechanisms. We argue that males function as high-variability genetic probes, introducing mutations and novel traits under environmental stress, while females act as filters and stabilizers of the genome. Drawing on data from epigenetics, IQ variance, microbial symbiosis, and macroevolutionary patterns, we show that evolution is both sex-asymmetric and feedback-sensitive. Furthermore, we explore the role of catastrophic environmental events in driving macroevolution, chromosomal rearrangements, and speciation, suggesting that global stressors function as genomic accelerants. This interdisciplinary framework offers a new model for evolutionary dynamics, integrating modern genetics, developmental biology, and paleontology with philosophical implications for intelligence, inheritance, and consciousness. Darwinian evolution holds that mutations are fundamentally random, with natural selection operating as a filter for beneficial traits. Yet emerging insights from epigenetics and environmental biology challenge this notion. Mutations and gene expression are increasingly seen as being influenced by environmental triggers, both internal (e.g., microbiota) and external (e.g., geography, diet, pathogens). This suggests a far more deterministic model in which genetic variability is not purely stochastic. Environmental stressors-such as climate, diet, toxins, and pathogens-can induce epigenetic modifications, including DNA methylation, histone modifications, and noncoding RNA changes. These epigenetic marks do not alter DNA sequences directly but control the activation or silencing of genes, and in some cases, they are heritable. Crucially, these environmental influences shape both the phenotype and the likelihood of certain genes being passed down. The microbiome, a dynamic ecological system of bacteria, fungi, and viruses within the body-particularly dense in the gut-acts as both an environmental sensor and mediator. Changes to the microbiome, such as relocation to a malarial zone or antibiotic use, create new evolutionary pressures. This model repositions natural selection from a passive after-the-fact filter to an active and ongoing influence at conception, gestation, and gamete formation. The evolutionary pathway, then, is not a simple filter of randomness but a responsive

Functionalism in biology is the view that with respect to organic form, structure is explained in terms of function, and structuralism is the view that structure is explained independently of function. Recent work on the topic has focused on 'meta-level' question such as, how should functionalism and structuralism be understood? What sort of positions are they? How if at all can they be justified? And what role to they play in biology? I have argued (Boucher 2015) that they should be understood as philosophical stances sensu van Fraassen (2002): clusters of attitudes, values, goals and commitments, rather than factual beliefs. In making this case I adapt van Fraassen's argument for treating materialism as a stance in this sense. In both cases, I suggest, only the stance interpretation can do justice to the manifest historical continuity of these views, and the fact that they have persisted through revolutionary changes in theory. In her recent book (2023), Rose Novick offers a critique of my view, and suggests that functionalism and structuralism should be construed rather as explanatory strategies. This can, she claims, capture the historical continuity of the views, while also having the virtue of showing how function-structure disputes can be empirically decided, something the stance account struggles with. In this paper I defend my view against Novick's critique, while extending and developing it. I argue that Novick's conception of explanatory strategies is too minimalist to capture the forms of functionalist and structuralist reasoning in question, and propose an expanded, richer and, I claim, more adequate explanatory schema for functionalism and structuralism that builds in value judgments characteristic of stances. And I respond to Novick's normative claim that even if functionalism and structuralism have in fact taken the form of stances, it would be better for biology if such stances did not exist.

MicroRNAs (miRNAs) control many important aspects of plant development, suggesting these molecules may also have played key roles in the evolution of developmental processes in plants. However, evolutionary-developmental (evo-devo) studies of miRNAs have been held back by technical difficulties in gene identification. To help solve this problem, we have developed a two-step procedure for the efficient identification of miRNA genes in any plant species. As a test case, we have studied the evolution of the MIR164 family in the angiosperms. We have identified novel MIR164 genes in three species occupying key phylogenetic positions and used these, together with published sequence data, to partially reconstruct the evolution of the MIR164 family since the last common ancestor of the extant flowering plants. We use our evolutionary reconstruction to discuss potential roles for MIR164 genes in the evolution of leaf shape and carpel closure in the angiosperms. The techniques we describe may be applied to any miRNA family and should thus enable plant evo-devo to begin to investigate the contributions miRNAs have made to the evolution of plant development.

Many patterns of phenotypic evolution are described and analyzed from a phenotype space perspective. In most instantiations of phenotype space, the set of phenotypic variants is endowed with a metric structure derived from some measure of geometric, anatomical, or structural similarity among variants: a notion of phenotypic distance is defined and phenotypic variants are spatially organized accordingly. While these approaches are successful in addressing many biological questions, metric topologies so defined are limited in their ability to shed mechanistic light on phenotypic evolution, because they do not embody in their definition the processes underlying the phenotype's variability. Building on results from theoretical biochemistry and phenotype landscape theory, it is proposed to complement this default metric structure with an additional structure that considers the factors involved in the expression of the phenotype of interest. This shift in perspective leads to a genetic or developmental representation of the phenotype from which emerges a notion of evolutionary accessibility among phenotypic variants. We illustrate how accessibility structure strengthens the explanatory power of phenotype space by helping characterize constraints on variation and how these constraints may interfere or align with external selective pressures in the course of phenotypic evolution.

Instances of repeated evolution of novel phenotypes can shed light on the conserved molecular mechanisms underlying morphological diversity. A rare example of an exaggerated soft tissue phenotype is the formation of a snout flap in fishes. This tissue flap develops from the upper lip and has evolved in one cichlid genus from Lake Malawi and one genus from Lake Tanganyika. To investigate the molecular basis of snout flap convergence, we used mRNA sequencing to compare two species with snout flap to their close relatives without snout flaps from each lake. Our analysis identified 201 genes that were repeatedly differentially expressed between species with and without snout flap in both lakes, suggesting shared pathways, even though the flaps serve different functions. Shared expressed genes are involved in proline and hydroxyproline metabolism, which have been linked to human skin and facial deformities. Additionally, we found enrichment for transcription factor binding sites at upstream regulatory sequences of differentially expressed genes. Among the enriched transcription factors were members of the FOX transcription factor family, especially foxf1 and foxa2, which showed an increased expression in the flapped snout. Both of these factors are linked to nose morphogenesis in mammals. We also found ap4 (tfap4), a transcription factor showing reduced expression in the flapped snout with an unknown role in craniofacial soft tissue development. As genes involved in cichlid snout flap development are associated with human midline facial dysmorphologies, our findings hint at the conservation of genes involved in midline patterning across distant evolutionary lineages of vertebrates, although further functional studies are required to confirm this.

Background: The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks.
Results: We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus.
Conclusion: This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation.

Mollusks in general and ammonoids in particular are known to display a sometimes profound morphological intraspecific variability of their shell. Although this phenomenon is of greatest importance, it has rarely been investigated and quantified. It is especially crucial for taxonomy and incidentally for biodiversity analyses to account for it, because otherwise, the number of described species might exceed that of actual species within any group. Early ammonoids (Early Devonian, Paleozoic) typically suffer from this bias. For instance, most specimens from the same layer and the same region (e.g., theErbenocerasbeds of the Moroccan eastern Anti-Atlas studied here) differ morphologically from each other. Depending on the importance given to certain morphological characters, therefore, one could create a new species for almost every specimen. In this study, we measured nearly 100 such specimens from a restricted stratigraphic interval and quantified their intraspecific variability. The...

During the Devonian Nekton Revolution, ammonoids show a progressive coiling of their shell just like many other pelagic mollusk groups. These now extinct, externally shelled cephalopods derived from bactritoid cephalopods with a straight shell in the Early Devonian. During the Devonian, evolutionary trends toward tighter coiling and a size reduction occurred in ammonoid embryonic shells. In at least three lineages, descendants with a closed umbilicus evolved convergently from forms with an opening in the first whorl (umbilical window). Other lineages having representatives with open umbilici became extinct around important Devonian events whereas only those with more tightly coiled embryonic shells survived. This change was accompanied by an evolutionary trend in shape of the initial chamber, but no clear trend in its size. The fact that several ammonoid lineages independently reduced and closed the umbilical window more or less synchronously indicates that common driving factors were involved. A trend in size decrease of the embryos as well as the concurrent increase in adult size in some lineages likely reflects a fundamental change in reproductive strategies toward a higher fecundity early in the evolutionary history of ammonoids. This might have played an important role in their subsequent success as well as in their demise.