Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation

Form, function, mind: What doesn't compute (and what might)

The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing animal (metazoan) tissues, a non-computational modality, but cell differentiation, which utilizes chromatin-based revisable memory banks and program-like function-calling, via the developmental gene co-expression system unique to the metazoans, has a quasi-computational basis. Multi-attractor dynamical models are argued to be misapplied to global properties of development, and it is suggested that along with computationalism, classic forms of dynamicism are similarly unsuitable to accounting for cognitive phenomena. Proposals are made for treating brains and other nervous tissues as novel forms of excitable matter with inherent properties which enable the intensification of cell-based basal cognition capabilities present throughout the tree of life. Finally, some connections are drawn between the viewpoint described here and active inference models of cognition, such as the Free Energy Principle.

A brief history of galectin evolution

Galectins are a family of carbohydrate-binding proteins found in vertebrates in great abundance and diversity in terms of both structure and ligand-binding properties as well as physiological function. Proteins with clear relationships to vertebrate galectins are already found in primitive Bilateria. The increasing amount of accessible well-annotated bilaterian genomes has allowed us to reveal, through synteny analyses, a new hypothesis about the phylogenetic history of the galectin family in this animal group. Thus, we can trace the genomic localization of the putative ancestral Bilateria galectin back to the scallops as a still very primitive slow-evolving bilaterian lineage. Intriguingly, our analyses show that the primordial galectin of the Deuterostomata most likely exhibited galectin-8-like characteristics. This basal standing galectin is characterized by a tandem-repeat type with two carbohydrate recognition domains as well as by a sialic acid binding property of the N-terminal domain, which is typical for galectin-8. With the help of synteny, the amplification of this potential primordial galectin to the broad galectin cosmos of modern jawed vertebrates can be reconstructed. Therefore, it is possible to distinguish between the paralogs resulting from small-scale duplication and the ohnologues generated by whole-genome duplication. Our findings support a substantially new hypothesis about the origin of the various members of the galectin family in vertebrates. This allows us to reveal new theories on the kinship relationships of the galectins of Gnatostomata. In addition, we focus for the first time on the galectines of the Cyclostomata, which as a sister group of jawed vertebrates providing important insights into the evolutionary history of the entire subphylum. Our studies also highlight a previously neglected member of the galectin family, galectin-related protein 2. This protein appears to be a widespread ohnologue of the original tandem-repeat ancestor within Gnathostomata that has not been the focus of galectin research due to its nonclassical galactose binding sequence motif and the fact that it was lost during mammalian evolution.

Inherency and agency in the origin and evolution of biological functions

Although discussed by 20th century philosophers in terms drawn from the sciences of non-living systems, in recent decades biological function has been considered in relationship to organismal capability and purpose. Bringing two phenomena generally neglected in evolutionary theory (i.e. inherency and agency) to bear on questions of function leads to a rejection of the adaptationist ‘selected effects’ notion of biological function. I review work showing that organisms such as the placozoans can thrive with almost no functional embellishments beyond those of their constituent cells and physical properties of their simple tissues. I also discuss work showing that individual tissue cells and their artificial aggregates exhibit agential behaviours that are unprecedented in the histories of their respective lineages. I review findings on the unique metazoan mechanism of developmental gene expression that has recruited, during evolution, inherent ancestral cellular functionalities into specialized cell types and organs of the different animal groups. I conclude that most essential functions in animal species are inherent to the cells from which they evolved, not selected effects, and that many of the others are optional ‘add-ons’, a status inimical to fitness-based models of evolution positing that traits emerge from stringent cycles of selection to meet external challenges.

Spatial waves and temporal oscillations in vertebrate limb development

The mesenchymal tissue of the developing vertebrate limb bud is an excitable medium that sustains both spatial and temporal periodic phenomena. The first of these is the outcome of general Turing-type reaction-diffusion dynamics that generate spatial standing waves of cell condensations. These condensations are transformed into the nodules and rods of the cartilaginous, and eventually (in most species) the bony, endoskeleton. In the second, temporal periodicity results from intracellular regulatory dynamics that generate oscillations in the expression of one or more gene whose products modulate the spatial patterning system. Here we review experimental evidence from the chicken embryo, interpreted by a set of mathematical and computational models, that the spatial wave-forming system is based on two glycan-binding proteins, galectin-1A and galectin-8 in interaction with each other and the cells that produce them, and that the temporal oscillation occurs in the expression of the transcriptional coregulator Hes1. The multicellular synchronization of the Hes1 oscillation across the limb bud serves to coordinate the biochemical states of the mesenchymal cells globally, thereby refining and sharpening the spatial pattern. Significantly, the wave-forming reaction-diffusion-based mechanism itself, unlike most Turing-type systems, does not contain an oscillatory core, and may have evolved to this condition as it came to incorporate the cell-matrix adhesion module that enabled its pattern-forming capability.

Multiscale modeling of vertebrate limb development

We review the current state of mathematical modeling of cartilage pattern formation in vertebrate limbs. We place emphasis on several reaction-diffusion type models that have been proposed in the last few years. These models are grounded in more detailed knowledge of the relevant regulatory processes than previous ones but generally refer to different molecular aspects of these processes. Considering these models in light of comparative phylogenomics permits framing of hypotheses on the evolutionary order of appearance of the respective mechanisms and their roles in the fin-to-limb transition. This article is categorized under: Analytical and Computational Methods > Computational Methods Models of Systems Properties and Processes > Mechanistic Models Developmental Biology > Developmental Processes in Health and Disease Analytical and Computational Methods > Analytical Methods.

Mathematical modeling of chondrogenic pattern formation during limb development: Recent advances in continuous models

The phenomenon of chondrogenic pattern formation in the vertebrate limb is one of the best studied examples of organogenesis. Many different models, mathematical as well as conceptual, have been proposed for it in the last fifty years or so. In this review, we give a brief overview of the fundamental biological background, then describe in detail several models which aim to describe qualitatively and quantitatively the corresponding biological phenomena. We concentrate on several new models that have been proposed in recent years, taking into account recent experimental progress. The major mathematical tools in these approaches are ordinary and partial differential equations. Moreover, we discuss models with non-local flux terms used to account for cell-cell adhesion forces and a structured population model with diffusion. We also include a detailed list of gene products and potential morphogens which have been identified to play a role in the process of limb formation and its growth.

Complexity: the organizing principle at the interface of biological (dis)order

The term complexity means several things to biologists.When qualifying morphological phenotype, on the one hand, it is used to signify the sheer complicatedness of living systems, especially as a result of the multicomponent aspect of biological form. On the other hand, it has been used to represent the intricate nature of the connections between constituents that make up form: a more process-based explanation. In the context of evolutionary arguments, complexity has been defined, in a quantifiable fashion, as the amount of information, an informatic template such as a sequence of nucleotides or amino acids stores about its environment. In this perspective, we begin with a brief review of the history of complexity theory. We then introduce a developmental and an evolutionary understanding of what it means for biological systems to be complex.We propose that the complexity of living systems can be understood through two interdependent structural properties: multiscalarity of interconstituent mechanisms and excitability of the biological materials. The answer to whether a system becomes more or less complex over time depends on the potential for its constituents to interact in novel ways and combinations to give rise to new structures and functions, as well as on the evolution of excitable properties that would facilitate the exploration of interconstituent organization in the context of their microenvironments and macroenvironments.

The vertebrate limb: An evolving complex of self-organizing systems

The paired appendages (fins or limbs) of jawed vertebrates contain an endoskeleton consisting of nodules, bars and, in some groups, plates of cartilage, or bone arising from replacement of cartilaginous templates. The generation of the endoskeletal elements occurs by processes involving production and diffusion of morphogens, with, variously, positive and negative feedback circuits, adhesion, and receptor dynamics with similarities to the mechanism for chemical pattern formation proposed by Alan Turing. This review presents a unified interpretation of the evolution and functioning of these mechanisms. Studies are described indicating that protocondensations, compacted mesenchymal cell aggregates that prefigure the appendicular skeleton, arise through the adhesive activity of galectin-1, a matricellular protein with skeletogenic homologs in all jawed vertebrates. In the cartilaginous and lobe-finned fishes (and to a variable extent in ray-finned fishes) it additionally cooperates with an isoform of galectin-8 to constitute a self-organizing network capable of generating arrays of preskeletal nodules, bars and plates. Further, in the tetrapods, a putative galectin-8 control module was acquired that may have enabled proximodistal increase in the number of protocondensations. In parallel to this, other self-organizing networks emerged that acted, via Bmp, Wnt, Sox9 and Runx2, as well as transforming factor-β and fibronectin, to convert protocondensations into skeletal tissues. The progressive appearance and integration of these skeletogenic networks over evolution occurred in the context of an independently evolved system of Hox protein and Shh gradients that interfaced with them to tune the spatial wavelengths and refine the identities of the resulting arrays of elements.

The evolutionary origin of digit patterning

The evolution of tetrapod limbs from paired fins has long been of interest to both evolutionary and developmental biologists. Several recent investigative tracks have converged to restructure hypotheses in this area. First, there is now general agreement that the limb skeleton is patterned by one or more Turing-type reaction–diffusion, or reaction–diffusion–adhesion, mechanism that involves the dynamical breaking of spatial symmetry. Second, experimental studies in finned vertebrates, such as catshark and zebrafish, have disclosed unexpected correspondence between the development of digits and the development of both the endoskeleton and the dermal skeleton of fins. Finally, detailed mathematical models in conjunction with analyses of the evolution of putative Turing system components have permitted formulation of scenarios for the stepwise evolutionary origin of patterning networks in the tetrapod limb. The confluence of experimental and biological physics approaches in conjunction with deepening understanding of the developmental genetics of paired fins and limbs has moved the field closer to understanding the fin-to-limb transition. We indicate challenges posed by still unresolved issues of novelty, homology, and the relation between cell differentiation and pattern formation.

'Biogeneric' developmental processes: drivers of major transitions in animal evolution

Using three examples drawn from animal systems, I advance the hypothesis that major transitions in multicellular evolution often involved the constitution of new cell-based materials with unprecedented morphogenetic capabilities. I term the materials and formative processes that arise when highly evolved cells are incorporated into mesoscale matter 'biogeneric', to reflect their commonality with, and distinctiveness from, the organizational properties of non-living materials. The first transition arose by the innovation of classical cell-adhesive cadherins with transmembrane linkage to the cytoskeleton and the appearance of the morphogen Wnt, transforming some ancestral unicellular holozoans into 'liquid tissues', and thereby originating the metazoans. The second transition involved the new capabilities, within a basal metazoan population, of producing a mechanically stable basal lamina, and of planar cell polarization. This gave rise to the eumetazoans, initially diploblastic (two-layered) forms, and then with the addition of extracellular matrices promoting epithelial-mesenchymal transformation, three-layered triploblasts. The last example is the fin-to-limb transition. Here, the components of a molecular network that promoted the development of species-idiosyncratic endoskeletal elements in gnathostome ancestors are proposed to have evolved to a dynamical regime in which they constituted a Turing-type reaction-diffusion system capable of organizing the stereotypical arrays of elements of lobe-finned fish and tetrapods. The contrasting implications of the biogeneric materials-based and neo-Darwinian perspectives for understanding major evolutionary transitions are discussed.This article is part of the themed issue 'The major synthetic evolutionary transitions'.

Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation

BACKGROUND

A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied patterns of nodules, bars and plates, while tetrapod limbs exhibit tandem arrays of few, proximodistally increasing numbers of elements. We applied a comparative genomic and protein evolution approach to understand the origin of the galectin patterning network. Having previously observed a phylogenetic constraint on Gal-1 structure across vertebrates, we asked whether evolutionary changes of Gal-8 could have critically contributed to the origin of the tetrapod pattern.

RESULTS

Translocations, duplications, and losses of Gal-8 genes in Actinopterygii established them in different genomic locations from those that the Sarcopterygii (including the tetrapods) share with chondrichthyans. The sarcopterygian Gal-8 genes acquired a potentially regulatory non-coding motif and underwent purifying selection. The actinopterygian Gal-8 genes, in contrast, did not acquire the non-coding motif and underwent positive selection.

CONCLUSION

These observations interpreted through the lens of a reaction-diffusion-adhesion model based on avian experimental findings can account for the distinct endoskeletal patterns of cartilaginous, ray-finned, and lobe-finned fishes, and the stereotypical limb skeletons of tetrapods.