Evolutionary Developmental Biology (Evo-Devo): Past, Present, and Future

The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species

Design of biomaterials and cellular scaffolds for tissue-engineering applications and regenerative medicine requires a precise understanding of the principles underlying multicellular patterning. Adhesion, migration, division, differentiation, and apoptosis are characteristic cellular behaviors, the engineering of which has the potential to allow creation of custom, multicellular structures. These cellular events occur naturally during embryonic and postembryonic development of multicellular organisms. Development thus offers the opportunity to learn about the design principles and molecular mechanisms that guide cellular patterning. A key finding in developmental biology is that a limited set of conserved molecular signaling pathways act at multiple times and locations throughout the embryo to introduce cell-fate asymmetries in homogenous populations of cells. In turn, these asymmetries serve as starting points for the patterning of new organs. These signaling pathways interact quantitatively at multiple levels, including signaling cues, post-translational regulation, and gene-regulatory networks, to guide multicellular patterning. How does the quantitative performance of these signaling networks ensure the intended phenotype pattern? How do changes in the quantitative performance of these networks, possibly over the course of evolution, give rise to new phenotypes? These are the central questions pursued in this thesis. In order to answer such questions, we used vulva formation in the nematode Caenorhabditis elegans as a model system of cellular patterning. We formulated a mathematical model of the molecular network underlying cellular-fate specification in this system. Computational analysis of this molecular network reveals that cell–cell coupling through lateral LIN-12/Notch signaling amplifies the perception of the gradient in the epidermal-growth-factor-like soluble cue, LIN-3. Thus, the gradient in LIN-3 concentration produces an even steeper difference in LIN-3-mediated intracellular signals between adjoining cells. Such gradient amplification may be particularly important in converting a shallow, graded-specification signal into a spatial pattern of distinct fate choices. Through quantitative perturbations of interaction strengths between components of the vulval patterning network, we further show that our modeling approach can correctly predict phenotype patterns observed in C. elegans mutation studies. This study generated a framework for quantitative analysis of molecular networks that links quantitative molecular perturbations to patterning outcomes. This framework will prove useful in the analysis of other systems involving cellular fate decisions and in tissue engineering applications where the generation of precise cell patterns is needed. We demonstrate the generality of our approach through an application to evolutionary developmental biology. Since molecular connectivity of the vulva patterning network of several closely related Caenorhabditis species is preserved, we correctly predict the quantitative diversification that must have occurred in this network during species evolution.

One of the central issues in evolutionary developmental biology is how we can formulate the relationships between evolutionary and developmental processes. Two major models have been proposed: the 'funnel-like' model, in which the earliest embryo shows the most conserved morphological pattern, followed by diversifying later stages, and the 'hourglass' model, in which constraints are imposed to conserve organogenesis stages, which is called the phylotypic period. Here we perform a quantitative comparative transcriptome analysis of several model vertebrate embryos and show that the pharyngula stage is most conserved, whereas earlier and later stages are rather divergent. These results allow us to predict approximate developmental timetables between different species, and indicate that pharyngula embryos have the most conserved gene expression profiles, which may be the source of the basic body plan of vertebrates.

Changes in the developmental processes and developmental mechanisms can result in the modification of morphological structures and in the evolution of phenotypic novelty. But how do developmental processes evolve? One striking finding in modern biology is the confrontation of morphological diversity in multicellular organisms with the conserved blueprint of life-the small number of conserved signaling pathways and transcriptional regulators. Evolutionary developmental biology (evo-devo) tries to explain this discrepancy between macroscopic diversity and molecular uniformity. Selected case studies in evo-devo models allowed detailed insight into the mechanisms of evolutionary changes and might help solving this problem. Here, I compare the formation of vulva development between Caenorhabditis elegans and the evo-devo model Pristionchus pacificus. More than 3 decades of work in C. elegans and 15 years in P. pacificus provide an insight into the molecular mechanisms of developmental change during vulva evolution. C. elegans and P. pacificus differ first, in the type of the signaling system used for vulva induction; second, the cells required for the inductive interactions; third, the logic of the signal system, and finally, the sequence and structure of peptide domains in otherwise conserved proteins. Nonetheless, the vulva is formed from the same three cells in both nematodes. I discuss redundancy as an evolutionary mechanism to explain developmental systems drift, a theory predicting conserved morphological structures to be generated by diverse molecular regulatory networks.

The question of vertebrate head segmentation has become one of the central issues in Evolutionary Developmental Biology. Beginning as a theory based in comparative anatomy, a segmental theory of the head has been adopted and further developed by comparative embryologists. With the use of molecular and cellular biology, and in particular analyses of the Hox gene complex, the question has been addressed at new levels, but it remains unresolved. In this review, vertebrate head segmentation is reevaluated, by introducing findings from experimental embryology and evolutionary biology. Developmental biology has shown that pattern is generated through hierarchically organized and causally linked series of events. The question of head segmentation can be viewed as a question of generative constraint, that is whether segmentation in the head is imposed by underlying segmental patterns, as it is in the trunk. In this respect, amphioxus appears to be segmented along the entire anteroposterior axis, with myotomes and peripheral nerves repeating with the same rhythm (somitomerism). Similarly, in the vertebrate trunk, the segmental patterns shared by myotomes, peripheral nerves and vertebrae are derived from the somites. However, in the head of vertebrates there is no such mesodermal pattern, although neuromerism and branchiomerism do indicate the presence of constraints derived from rhombomeres and pharyngeal pouches, respectively. These data fit better the concept of dual metamerism of the vertebrate body proposed by Romer (1972), than the traditional head cavity-based segmental model by Goodrich (1930).

A challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used to investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As a phylum of the sister group to chordates, echinoderms extensively contributed to our knowledge of embryonic patterning, organ development and cell-type evolution. Echinoderms display a variety of larval forms with diverse shapes, making them a suitable group to compare the evolution of embryonic developmental strategies. However, because of the laboratory accessibility and the already available techniques, most studies focus on sea urchins and sea stars mainly. As a comparative approach, the field would benefit from including information on other members of this group, like the sea cucumbers (holothuroids), for which little is known on the molecular basis of their development. Here, we review the spawning and culture methods, the available morphological and molecular information, and the current state of genomic and transcriptomic resources on sea cucumbers. With the goal of making this system accessible to the broader community, we discuss how sea cucumber embryos and larvae can be a powerful system to address the open questions in evo-devo, including understanding the origins of bilaterian structures.

Michael Akam has been awarded the 2007 Kowalevsky medal for his many research accomplishments in the area of evolutionary developmental biology. We highlight three tributaries of Michael’s contribution to evolutionary developmental biology. First, he has made major contributions to our understanding of development of the fruit fly, Drosophila melanogaster. Second, he has maintained a consistent focus on several key problems in evolutionary developmental biology, including the evolving role of Hox genes in arthropods and, more recently, the evolution of segmentation mechanisms. Third, Michael has written a series of influential reviews that have integrated progress in developmental biology into an evolutionary perspective. Michael has also made a large impact on the field through his effective mentorship style, his selfless promotion of younger colleagues, and his leadership of the University Museum of Zoology at Cambridge and the European community of evolutionary developmental biologist.

Evolutionary developmental biology (EVO-DEVO) tries to decode evolutionary constraints on the stages of embryonic development. Two models—the “funnel-like” model and the “hourglass” model—have been proposed by investigators to illustrate the fluctuation of selective pressure on these stages. However, selective indices of stages corresponding to mammalian preimplantation embryonic development (PED) were undetected in previous studies. Based on single cell RNA sequencing of stages during human PED, we used coexpression method to identify gene modules activated in each of these stages. Through measuring the evolutionary indices of gene modules belonging to each stage, we observed change pattern of selective constraints on PED for the first time. The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages. Previous EVO-DEVO studies concerning the whole embryo development neglected the fluctuation of selective pressure in these earlier stages, and the fluctuation was potentially correlated with events of earlier stages, such as zygote genome activation (ZGA). Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development. Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.

Evolutionary developmental biology has encouraged a change of research emphasis from the sorting of phenotypic variation by natural selection to the production of that variation through development. Some morphologies are more readily generated than others, and developmental mechanisms can limit or channel evolutionary change. Such biases determine how readily populations are able to respond to selection, and have been postulated to explain stasis in morphological evolution and unexplored morphologies. There has been much discussion about evolutionary constraints but empirical data testing them directly are sparse. The spectacular diversity in butterfly wing patterns is suggestive of how little constrained morphological evolution can be. However, for wing patterns involving serial repeats of the same element, developmental properties suggest that some directions of evolutionary change might be restricted. Here we show that despite the developmental coupling between different eyespots in the butterfly Bicyclus anynana, there is great potential for independent changes. This flexibility is consistent with the diversity of wing patterns across species and argues for a dominant role of natural selection, rather than internal constraints, in shaping existing variation.

Many scientists and philosophers of science are troubled by the relative isolation of developmental from evolutionary biology. Reconciling the science of development with the science of heredity preoccupied a minority of biologists for much of the twentieth century, but these efforts were not corporately successful. Mainly in the past fifteen years, however, these previously dispersed integrating programmes have been themselves synthesized and so reinvigorated. Two of these more recent synthesizing endeavours are evolutionary developmental biology (EDB, or "evo-devo") and developmental systems theory (DST). While the former is a bourgeoning and scientifically well-respected biological discipline, the same cannot be said of DST, which is virtually unknown among biologists. In this review, we provide overviews of DST and EDB, summarize their key tenets, examine how they relate to one another and to the study of epigenetics, and survey the impact that DST and EDB have had (and in future should have) on biological theory and practice.

Inferences from dependencies in development, or from conserved traits, structures, or genes, have become a central and ubiquitous tool in evolutionary developmental biology. An element with many downstream consequences of its operation in an adaptive system should be conserved because its deletion or change would likely have massively deleterious effects. Thus, substantial observed dependencies should predict conservation, and vice versa. Dependencies and conservation are both matters of degree, generating an ordering of rates of evolutionary change. I trace four independent sources for this idea with subtle differences in their application. The origins of the use of genetic pleiotropy to predict conservation is complex and progressed in multiple stages, with partial awareness emerging in the 1960s, and grew erratically in use without becoming a major theme until the 1990s. Since 2000 it has grown to become an essential tool and applied in an expanding number of ways. I distinguish and illustrate “top-down” and “bottom up” approaches, though people now working from one direction often recruit collaborators from the other. Other approaches have had diverse inspirations and points of initial application. Rupert Riedl’s notion of “burden” was applied primarily to morphological traits, with an elaborated account of organizational factors modulating entrenchment. Wallace Arthur explored dependency in “morphogenetic trees,” utilizing as his inspiration cellular descent trees in metazoans. Bill Wimsatt looked for “generative entrenchment” in factors both internal and external to the developing system to analyze innate behavior. Entrenchment was later extended to analyze development in Drosophila and to construct multi-locus population genetic models of gene control networks, yielding new results that illuminate relations between micro and meso-evolution. Applications of generative entrenchment to cultural and technological evolution are also sketched, where development of individuals and other social entities must play a central role.

The power of evo-devo to explore evolutionary constraints: experiments with butterfly eyespots

It has been said that many original ideas reflect a convergence of related thought that coalesces into a unified representation of what many have been thinking. This is certainly true for the subfield of maternal effects evolution. The study of maternal effects has a long history. The first two

The fields of developmental biology, biomedicine, and artificial life are being revolutionized by advances in synthetic morphology. The next phase of synthetic biology and bioengineering is resulting in the construction of novel organisms (biobots), which exhibit not only morphogenesis and physiology but functional behavior. It is now essential to begin to characterize the behavioral capacity of novel living constructs in terms of their ability to make decisions, form memories, learn from experience, and anticipate future stimuli. These synthetic organisms are highly diverse, and often do not resemble familiar model systems used in behavioral science. Thus, they represent an important context in which to begin to unify and standardize vocabulary and techniques across developmental biology, behavioral ecology, and neuroscience. To facilitate the study of behavior in novel living systems, we present a primer on techniques from the behaviorist tradition that can be used to probe the functions of any organism – natural, chimeric, or synthetic – regardless of the details of their construction or origin. These techniques provide a rich toolkit for advancing the fields of synthetic bioengineering, evolutionary developmental biology, basal cognition, exobiology, and robotics.

What drives evolution? This was one of the main questions raised at the final ZOONET meeting in Budapest, Hungary, in November 2008. The meeting marked the conclusion of ZOONET, an EU-funded Marie-Curie Research Training Network comprising nine research groups from all over Europe (Max Telford, University College London; Michael Akam, University of Cambridge; Detlev Arendt, EMBL Heidelberg; Maria Ina Arnone, Stazione Zoologica Anton Dohrn Napoli; Michalis Averof, IMBB Heraklion; Graham Budd, Uppsala University; Richard Copley, University of Oxford; Wim Damen, University of Cologne; Ernst Wimmer, University of Göttingen). ZOONET meetings and practical courses held during the past four years provided researchers from diverse backgrounds--bioinformatics, phylogenetics, embryology, palaeontology, and developmental and molecular biology--the opportunity to discuss their work under a common umbrella of evolutionary developmental biology (Evo Devo). The Budapest meeting emphasized in-depth discussions of the key concepts defining Evo Devo, and bringing together ZOONET researchers with external speakers who were invited to present their views on the evolution of animal form. The discussion sessions addressed four main topics: the driving forces of evolution, segmentation, fossils and phylogeny, and the future of Evo Devo.