Rupert Riedl's Order in Living Organisms proposed a systems theory of evolution decades before the concepts it pioneered-burden, internal selection, the imitative epigenotype-became recognizable problems on the agenda of evolutionary biology. This paper traces how these ideas were received and operationalized across morphology and phylogenetics, evolutionary quantitative genetics, evo-devo, and theoretical biology. Drawing on citation analysis, archival correspondence, and interviews, I then ask why, despite this documented influence, Riedl's ideas proved so difficult to assimilate. I argue that two main factors conspired against their wider circulation: the tightly integrated structure of his theoretical system, which resisted the selective appropriation that allows ideas to travel across disciplinary boundaries, and a sustained resistance from a neo-Darwinian orthodoxy that dismissed his morphological framework as incompatible with the Modern Synthesis. Riedl's legacy, I conclude, lies less in direct citation than in the intellectual lineages through which his students and readers translated and operationalized his insights, carrying them from the periphery toward the center of contemporary evolutionary biology.
Synaptonemal complex protein 3 (Scp3), a structural component of the synaptonemal complex, serves as a key molecular marker for studying meiosis and germ cell development in teleosts. To elucidate the molecular mechanisms of germ cell meiosis and identify critical windows for sex differentiation in turbot (Scophthalmus maximus), a flatfish of considerable economic value in global aquaculture, this study cloned the full-length cDNA sequence of the scp3 gene. The obtained sequence is 1094 bp in length, containing an open reading frame of 717 bp that encodes a polypeptide of 238 amino acids, with bioinformatic analyses revealing characteristic coiled-coil domains. Tissue distribution analysis demonstrated that scp3 expression was predominantly restricted to the gonads. Quantitative PCR in an all-female lineage revealed that transcripts were initially detectable at 25 days post-hatching (dph), remained low until 55 dph, and increased significantly thereafter, peaking after 80 dph (p < 0.05). In situ hybridization localized scp3 mRNA to the cytoplasm of early primary oocytes. The expression window, initiating at 25 dph and intensifying from 60 dph, aligns with the initiation of meiotic prophase I and precedes morphological sex differentiation. These results indicate that scp3 functions as a reliable noninvasive molecular marker for the onset of meiosis in female turbot and may play a specific role in oocyte proliferation. This study provides a crucial theoretical foundation and key temporal information for further elucidating the molecular mechanism of sex differentiation and advancing all-female population cultivation in turbot.
Rupert Riedl did not use the term evolvability, but his writings and teachings in the 1970s and 1980s were important precursors and influences on the research that became associated with the term when it appeared in the 1990s. Riedl served as a motivator for many researchers that later took up questions related to evolvability, and also had an indirect influence in that Riedl-inspired researchers created a research program to combine the systems thinking that Riedl championed with the theoretical population genetics of the modern synthesis. Notably, this was despite a near-total absence of population perspectives in Riedl's personal research. In this essay I review some of Riedl's perspectives on evolvability, speculate on his influence on later evolvability research, and review what we have later learned about the questions and perspectives initiated by him.
What lies behind the extraordinary phenotypic plasticity of sponges? We used this question to conduct a systematic review of how "phenotypic plasticity" is approached in the literature regarding the phylum Porifera. First, we gathered information on what the literature says about plasticity in sponges. Next, we analyzed its usage contexts, distinguishing between plasticity as a general feature versus a specific process linked to environmental triggers or genetic variation. Thus, we critique the overuse of synonymous terms that fail to capture the concept's complexity and advocate for greater precision to advance research. Finally, we advocate for precise and consistent terminology as an essential requirement for advancing research on sponge phenotypic plasticity. Phenotypic plasticity in sponges is a multifaceted phenomenon. We focused on the rationale behind the term's use and its underlying biological assumptions, proposing a categorization into three levels: (1) intraindividual/cellular plasticity, regarding modifications in a single organism's structures; (2) individual plasticity, involving whole-organism adaptation; and (3) population-level plasticity, where variability occurs among individuals of the same species. This framework distinguishes between changes within a single organism and broader variation patterns, highlighting scale-specific biological constraints. Recognizing sponges as highly plastic organisms was only the beginning. We advanced our comprehension by addressing key evolutionary questions and knowledge gaps that remain essential to guide future research on the molecular, ecological, and evolutionary implications of plasticity in this phylum.
In this article I am tracing the intellectual trajectory and historical context of Rupert Riedl's contributions to evolutionary theory, the book Order in Living Organisms (1978) and the accompanying article in the Quarterly Review of Biology (1977). These publications appeared at about the same time as Steven J. Gould's Ontogeny and Phylogeny as well as the "Spandrels" paper by Gould and Lewontin which initiated a major re-orientation of evolutionary biology. Riedl's work anticipated two major developments, the notion of developmental constraints in evolutionary developmental biology and the idea of evolvability. The factors that likely have limited the bibliometric impact of Riedl's work are also discussed.
Pigmentation has long served as a powerful system for exploring gene-trait relationships, yet much of the field has focused on a relatively narrow group of well-established genes involved in melanin production and pigment cell differentiation. Recent advances, however, have allowed pigmentation to be studied through a more comprehensive framework. By combining artificial intelligence (AI)-driven phenotyping with genomic mapping approaches such as genome-wide association studies, QTL mapping, and structural variant analysis, a broader range of pigmentation regulators has been identified across diverse animal taxa. This review highlights studies where AI methods, including deep learning, self-supervised modeling, and pattern recognition, have been used to quantify complex pigmentation traits in animals. These approaches have enabled the discovery of non-classical pigmentation genes involved in membrane trafficking, intracellular signaling, structural organization, and non-coding regulation. Rather than displacing the classical pigmentation paradigm, these findings extend it, revealing a wider set of genetic contributors to coloration and pattern diversity. We introduce the term AI-pigmentomics to describe the integration of AI-driven phenotyping with genomic mapping, as part of the broader emergence of AI-omics. Together, AI and genomic mapping are reshaping our understanding of pigmentation by uncovering unexpected biological mechanisms and providing a framework for investigating pigmentation in both model and non-model species.
Blastoderm formation represents a key transition from a syncytial to a cellular embryo and provides the basis for subsequent embryonic patterning in insects. In most insect models, this transition occurs through synchronous cellularization, producing a uniform blastoderm that is patterned only afterward. Whether this sequence represents a common developmental principle across insects remains unclear. Here, we show that in the carpenter ant Camponotus floridanus, cellularization proceeds progressively rather than synchronously and establishes spatially differentiated blastoderm domains. Cellularization initiates at the anterior and progresses posteriorly, while a second front from the posterior advances in the opposite direction. These opposing fronts converge at the site where the germline capsule subsequently forms. At the same time, a regionalized blastoderm rather than a uniform blastoderm is established. The extraembryonic tissues amnion, serosa, and trophocytes emerge along progressive cellularization through coordinated morphogenetic dynamics and exhibit a distinct mode of organization. Our data present a revised understanding of cellularization of blastoderm in insects and broaden the comparative framework of embryogenesis described in model organisms.
Rupert Riedl showed in his "Order in Living Organisms" that morphology can produce law statements and is, therefore, a proper, that is, nomothetic, science. Furthermore, he coined useful terms (interphene and metaphene) and concepts (burden, cadre and minimal homology). Notwithstanding certain flaws-he used "laws in evolution" and "verification of a theory" although claiming to be in accordance with Popper's hypothetico-deductivism-and an almost complete absence of synecological relationships in his evolutionary explanations, his scientific legacy still forms a basis of a "logic of morphology" and an "evolutionary morphology," especially through the works of his students.
Asymmetry in a bilateral organism refers to the difference in the expression of a trait between right and left sides, which may result from genetic or environmental disturbances. Using geometric morphometrics and a phylogenetic approach, we studied asymmetry in dorsal and ventral views of the skulls of anuran species, representing 22 families, 16 of which belong to the Hyloidea clade. The cranial regions with the most pronounced shape asymmetry were identified. To discern species with elevated levels of asymmetry and to hypothesize its evolutionary trends across phylogeny we implemented the asymmetry index. Significant asymmetric skull shape variation was found between right and left sides, associated with the upper area of the mandibular joint and the anterior area of the nasals in dorsal view. In ventral view, the greatest variation was in the vomers and the ala of the parasphenoid. The degree of size-related asymmetry varied among species. Character mapping results indicate that cranial asymmetry is a conserved and widespread trait in the Hyloidea clade, representing an ancestral condition across both dorsal and ventral regions of the skull. The observed asymmetries were found in traits that develop later in their ontogeny, which would imply that as they establish fewer developmental dependencies with other traits and, consequently, are less phylogenetically constrained. The asymmetries we found belong to this category and would be more prone to change during evolution.
The ParaHox homeobox genes Gsx, Xlox, and Cdx are evolutionarily related to Hox genes and form part of the ANTP-class homeobox gene repertoire. Comparative genomic data indicate that ParaHox genes were already present before the cnidarian-bilaterian split. Across metazoans, ParaHox genes often show conserved associations with the anteroposterior body axis and have been implicated in both gut patterning and neural development, although gene complements and genomic organization vary substantially among lineages. To investigate ParaHox gene deployment in Gnathifera, we identified orthologs of Gsx and Cdx across gnathiferan lineages, including Chaetognatha, Monogononta, Bdelloidea, Seisonidea, and Acanthocephala, but found no evidence of Xlox, indicating a reduced ParaHox gene complement. We analyzed the genomic organization and embryonic expression of Gsx and Cdx in the monogonont rotifer Brachionus manjavacas (Bm). Genomic mapping revealed a dispersed ParaHox configuration, with Bm-Gsx and Bm-Cdx separated by 4.4 Mb. Using whole-mount in situ hybridization, we detected Bm-Gsx expression in neurons of the foot region, as well as in a small number of cells with neuronal characteristics and probable involvement in stomatogastric system development. Bm-Cdx was expressed in FMRFamide-positive cells associated with the bladder, consistent with a neuroepithelial identity. Together, these data indicate that in rotifers, ParaHox gene expression is predominantly associated with neural structures. We propose that this pattern represents a derived condition reflecting the compact body plan and reduced gut organization characteristic of rotifers, highlighting the evolutionary flexibility of ParaHox gene deployment under lineage-specific developmental constraints.
The diverse and colorful patterns found in organisms serve various functions. In Pachyrhynchus weevils, these colors and patterns composed of 3D photonic architectures function as signals for sexual selection and aposematism. Previous study of photonic structure suggests the involvement of specific genes in color regulation in Pachyrhynchus weevils. However, the genes responsible for scale coloring in Pachyrhynchus weevils have remained unknown. In this study, RNA-seq was conducted in P. nobilis at 6 h and 24 h after emergence, comparing elytra (no-scale) and scale tissues during the period of coloring. qPCR validation was performed across three species ( P. nobilis , P. sarcitis , and P. orbifer ). RNA-seq analysis identified 3172 and 2890 DEGs at 6 h and 24 h after emergence, respectively, with up-regulated DEGs increasing over time. The candidate genes were selected based on functional annotations related to scale development (C-type lectins, cuticle proteins, and Yellow family proteins), and KEGG pathway analysis. qPCR validation revealed species-specific expression patterns: C-type lectin-encoding gene was expressed in P. nobilis and P. sarcitis but absent in P. orbifer , while Hedgehog-like protein-encoding gene was exclusively detected in P. orbifer . Temporal analysis showed significant differences in Wnt signaling pathway between developmental stages in P. orbifer , and marginal significance in calcium signaling pathway gene in P. sarcitis . This study suggests that these specific genes may play roles in color regulation during scale development in Pachyrhynchus weevils, with varying expression at different time points after emergence or among species.
Transcription factors are typically thought to play a limited role in developmental evolution due to their high pleiotropic nature. However, such constraints may be relaxed following gene duplication or when proteins are organized into structural and functional modules, opening avenues for evolutionary innovation. Here, we integrate expression and genomic data to investigate the evolutionary dynamics of Hox gene duplicates in the allotetraploid frog Xenopus laevis. Despite overall conservation across the Hox clusters, we find that HoxB4L has acquired expression during maternally regulated stages and is evolving under positive selection. Protein-level changes include the number, length, and sequence of functionally important protein regions. Our results indicate that HoxB4L has escaped ancestral constraints and is undergoing maternal neofunctionalization as a result of cis-regulatory divergence and structural protein modifications. These findings illustrate how transcription factors can overcome developmental constraints and contribute to novel functions during early development.
Bivalve planktonic development is a critical phase during which larvae must secrete the first calcium carbonate shell, the prodissoconch I (PD I). As PD I formation is in close contact with seawater, this process can be negatively affected by adverse seawater carbonate chemistry. It is hypothesized that bivalves can regulate shell formation under environmental stress through biologically controlled biomineralization involving a complex extracellular shell proteome. However, the plasticity of this regulatory mechanism during PD I development is unknown. We assessed the PD I shell proteome of the Hong Kong oyster (Magallana hongkongensis) in carbonate chemistry that was adverse or favorable for biomineralization to understand the regulatory capacity of larval shell formation. While survival rates were not affected in adverse carbonate chemistry, there were significant changes, including the upregulation of several calcium-binding proteins and downregulation of proton-generating processes and putative calcification inhibitors. With 198 sequences, the oyster larval shell proteome was twice to over six times larger than those reported for other bivalve species at the same developmental stage. However, in adverse carbonate chemistry, the oyster larval shells were thinner and smaller, and protein diversity decreased to 131 sequences, with overall lower functional redundancy and reduced expression of structural proteins, indicating potential trade-offs. The proteomic and shell structural data also suggest that direct cellular control and biologically induced mechanisms, which will require further investigation, may be involved in PD I formation.
Cell proliferation is a key driver of morphogenesis and body plan transformation in multicellular animals, yet its spatial organization remains poorly understood in many non-segmented spiralians. In this study, we examine the dynamics of cell division during larval growth and metamorphosis in the larvae and early juveniles of the phoronid Phoronopsis harmeri, using EdU incorporation, anti-phospho-histone H3 immunostaining, confocal laser scanning microscopy, and electron microscopy. Early larval proliferation is partly regionalized from the outset and becomes progressively more localized toward metamorphosis. We identify a tripartite organization of proliferative activity: (1) posterior ring-shaped domains in the telotroch that persist through metamorphosis and support elongation and anal chamber formation; (2) regional proliferative zones at tentacle bases, preoral and postoral regions; and (3) scattered proliferation driving the expansion of the trunk epidermis. This coexistence of posterior, regional, and scattered patterns underscores the developmental plasticity of phoronids and the diversity of growth strategies within Spiralia. Posterior proliferative domains in phoronids contribute important context to homology-convergence debates on posterior growth across spiralians, but are not decisive by themselves; viewed with the distributed epithelial proliferation, they underscore the coexistence of multiple proliferative programs within a single life cycle. In addition, we identify atypical mitotic characteristics in this species, including unconventional metaphase organization and signs of interkinetic nuclear migration in larval epithelia. Our results suggest that phoronids provide a valuable model for exploring how diverse architectures of cell proliferation contribute to larval growth, body elongation, and morphogenetic compartmentalization in Lophotrochozoa.
Experimental studies have demonstrated that nutritional changes during development can result in phenotypic changes to mammalian cheek teeth. This developmental plasticity of tooth morphology is an example of phenotypic plasticity. Because tooth development occurs through complex interactions between manifold processes, there are many potential mechanisms which can contribute to a tooth's norm of reaction. Determining the identity of those mechanisms and the relative importance of each of them is one of the main challenges to understanding phenotypic plasticity. Quantitative proteomics combined with experimental studies allow for the identification of potential molecular contributors to a plastic response through quantification of expressed gene products. Here, we present the results of a quantitative proteomics analysis of mature upper first molars in Mus musculus from a controlled feeding experiment. Pregnant and nursing mothers were fed either a low-dietary protein (10%) treatment diet or control (20%) diet. Low-dietary protein was not associated with reduced molar size or skull length. However, expression of tooth-related proteins, immune system proteins, and actin-based myosin proteins were significantly altered in our low-dietary protein proteomics sample. The differential expression of immune proteins along with systematic reduction in actin-based myosin protein expression are novel discoveries for tooth proteomics studies. We propose that studies that aim to elucidate specific mechanisms of molar phenotypic plasticity should prioritize investigations into the relationships between IGF regulation and tooth development and actin-based myosin expression and tooth development.
