Evolutionary Developmental Biology Studies Research Articles

Transcriptional Network Structure Has Little Effect on the Rate of Regulatory Evolution in Yeast

Studies in evolutionary developmental biology suggest that the structure of genetic pathways may bias the fixation of natural variation toward particular nodes in these pathways. In an attempt to test this trend genome wide, we integrated several previously published data sets to examine whether the position of genes in the whole-genome transcriptional network of Saccharomyces cerevisiae is associated with the amount of cis-regulatory expression divergence between S. cerevisiae and its sibling species Saccharomyces paradoxus. We find little evidence for an association between connectivity and divergence in the global network that combines data from multiple conditions. However, relationships between connectivity and divergence are apparent in some of the smaller subnetworks. Despite a slight tendency for genes with more transcriptional interactions to show greater divergence, these differences explain no more than a small fraction of variation in evolutionary rates. These results suggest that the systems biology focus on large interactomes may miss some critical details of local interactions. More detailed experimental analysis will be needed to define the genetic pathways that control specific phenotypic traits and quantify the rate of regulatory changes at different points in these pathways.

Defending Evo-Devo: A Response to Hoekstra and Coyne

The study of evolutionary developmental biology (“evo-devo”) has recently experienced a dramatic surge in popularity among researchers and theorists concerned with evolution. However, some biologists and philosophers remain skeptical of the claims of evo-devo. This paper discusses and responds to the recent high profile criticisms of evo-devo presented by biologists Hopi E. Hoekstra and Jerry A. Coyne. I argue that their objections are unconvincing. Indeed, empirical research supports the main tenets of evo-devo, including the claim that morphological evolution is the result of cis-regulatory change and the distinction that evo-devo draws between morphological and physiological traits.

Development of the embryo, larva and early juvenile of Nile tilapia Oreochromis niloticus (Pisces: Cichlidae). Developmental staging system

We described the developmental stages for the embryonic, larval and early juvenile periods of Nile tilapia Oreochromis niloticus to elucidate sequential events of craniofacial development. Craniofacial development of cichlids, especially differentiation and morphogenesis of the pharyngeal skeleton, progresses until about 30 days postfertilization (dpf). Because there is no comprehensive report describing the sequential processes of craniofacial development up to 30 dpf, we newly defined 32 stages using a numbered staging system. For embryonic development, we defined 18 stages (stages 1-18), which were grouped into seven periods named the zygote, cleavage, blastula, gastrula, segmentation, pharyngula and hatching periods. For larval development, we defined seven stages (stages 19-25), which were grouped into two periods, early larval and late larval. For juvenile development until 30 dpf, we defined seven stages (stages 26-32) in the early juvenile period. This developmental staging system for Nile tilapia O. niloticus will benefit researchers investigating skeletogenesis throughout tilapia ontogeny and will also facilitate comparative evolutionary developmental biology studies of haplochromine cichlids, which comprise the species flocks of Lakes Malawi and Victoria.

A grand new view from the embryo

The field of `evo-devo', the study of evolutionary developmental biology, is one of the most exciting in modern biology. Its appeal lies in the promise of delivering answers to the age-old question of where did we come from? The answers come from not one but two perspectives, which are intimately

67 Human Bauplan Anomalies

The german term Bauplan means body-plan, but captures also the idea of the architectural constraints existing in such a functional design. There are only a few animal Bauplane, and each phylum is characterized by one of them. Major Bauplan's modifications within a taxon are not tolerated. The concept is common between the zoologists, but usually is not employed in human pathology. Our hypothesis is that an approach to the birth defects in terms of basic body-plan results in a better understanding of the human ontogenetic and phylogenetic development. We observed 30 interrupted pregnancies owing to severe structural fetal malformations. A pathological study was performed in all the fetuses. We found the following syndromes and anomalies: Meckel-Gruber syndrome 1; Cantrell's pentalogy 1; Ivemark syndrome 1; Omphalocele-radial hypoplasia complex 1; Triploid syndrome 1; Malformative associations including encephalic anomalies 3; SNC isolated abnormalities (comprehensive of 10 neural tube defects) 16; Gastroschisis 1; Complex cardiac anomalies 3; Kidney defects, including bilateral renal agenesis 2; According to our study, three major Bauplan defects are detectable in the aborted fetuses. They are concerning with: (1) cephalization, (2) laterality, (3) closure of the fetal body surface, and all of them are related to a midline pathology. These results are in agreement with the belonging of our species to the chordates deuterostomata and suggest that the human Bauplan begins to appear in the early blastogenesis, when the nothocord appears and neurulation occurs. In this period the embryo seems to act as a single morphogenetic unit, so that blastogenetic defects are frequently multisystem abnormalities. 1/3 of the fetuses presented complex malformative disorders. Besides being a source for studies of evolutionary developmental biology (Evo-Devo), the investigation on human blastogenesis and organogenesis through an oriented evaluation of the birth defects could have in the future unexpected therapeutic relevance.

DEFINING A MEETING PLACE: MODULARITY IN DEVELOPMENT AND EVOLUTION

Modularity describes the general idea that biological systems at many hierarchical levels are not uniformly interconnected, but rather composed of subparts: discrete elements of the phenotype possess a degree of internal integration stronger than their external connectivity, and maintain their identity and function independent of the context in which they are embedded. The behavior or function of a module reflects the integration, not simply the sum, of its constituents; and although modules are biological individuals (Hull 1980; Roth 1991), they must also show external connectivity and interaction (an individual in isolation is not a module; Bolker 2000). We readily recognize as modules individual body parts such as bones, limbs, or segments; DNA sequences that constitute specific genes or regulatory motifs; and process modules (Gilbert and Bolker 2000) ranging from courtship displays to intercellular signal transduction pathways. Evolutionary biology relies on a working assumption that it is both feasible and biologically justifiable to view the phenotype as modular, treating different aspects (whether structures or genes) as largely dissociable entities that respond to selection in a relatively independent manner. The success of this paradigm offers strong evidence that the hypothesis of modularity accords well with biological reality. In fact, most of the analytical tools for describing the evolution of organisms rest (explicitly or otherwise) on the premise that one can delineate distinct characters (Bolker 2000). Beyond its central importance to evolutionary biology, the concept of modularity has been described as a potential meeting place for evolutionary and developmental biologists, and thus a promising bridge for interdisciplinary studies of evolutionary developmental biology (EDB or evo-devo; Von Dassow and Munro 1999; Bolker 2000; Gass and Bolker 2003). In support of that claim, Gerhard Schlosser and Gunter Wagner convened a workshop comprising developmental biologists studying specific model systems, evolutionary biologists interested in the origins and long-term significance of modularity, and philosophers and theorists with ideas about how to think about the concept. The resulting volume demonstrates that modularity is indeed an interesting and fruitful way to think about development, evolution and their interrelationship-and that we still have a long way to go. The diverse collection of papers also highlights the complexities of studying a concept that, while intuitively obvious, is surprisingly difficult to define in a precise and universally acceptable way.

An integrated physical and genetic map of the nematode Pristionchus pacificus.

The free-living nematode Pristionchus pacificus is one of several species that have recently been developed as a satellite system for comparative functional studies in evolutionary developmental biology. Comparisons of developmental processes between P. pacificus and the well established model organism Caenorhabditis elegans at the cellular and genetic levels provide detailed insight into the molecular changes that shape evolutionary transitions. To facilitate genetic analysis and cloning of mutations in P. pacificus, we previously generated a BAC-based genetic linkage map for this organism. Here, we describe the construction of a physical map of the P. pacificus genome based on AFLP fingerprint analysis of 7747 BAC clones. Most of the SSCP markers used to generate the genetic linkage map were derived from BAC ends, so that the physical genome map and the genetic map can be integrated. The contigs that make up the physical map are evenly distributed over the genetic linkage map and no clustering is observed, indicating that the physical map provides a valid representation of the P. pacificus genome. The integrated genome map thus provides a framework for positional cloning and the study of genome evolution in nematodes.

From evolutionary developmental biology to genomics: towards a genome map of the free-living nematode Pristionchus pacificus

Case studies in evolutionary developmental biology have concentrated on various ontogenetic processes in arthropods, nematodes and chordates. In nematodes, one well-studied process is the formation of the vulva. Cellular, genetic and molecular comparative studies of vulva development between Pristionchus pacificus and Caenorhabditis elegans indicated the existence of multiple changes during the evolution of this process. Besides macro-evolutionary alterations, the study of more closely related species of the genus Pristionchus showed that several aspects of vulva development differ at the micro-evolutionary level. To facilitate a more detailed mechanistic understanding of the molecular changes involved in vulval evolution, a genetic linkage map of P. pacificus has been generated, which allows both, macro- and micro-evolutionary processes to be studied in greater details.

Phylogeny, fossils, and model systems in the study of evolutionary developmental biology

The emerging field of evolutionary developmental biology (evo-devo) continues to operate largely under a single paradigm. In this paradigm developmental regulatory genes and processes are compared among a collection of “model organisms” selected primarily on the basis of their historical utility in the study of development. This approach has proven to be extremely informative, revealing an unexpected deep evolutionary conservation among developmental genes and genetic systems. Despite its success, concern has been expressed regarding its limitations. We discuss the “model organism” paradigm in evo-devo research. Based on our interpretation of its limitations, we propose a separate but complementary approach that is centered on “model groups.” These groups are selected on the basis of their taxonomic affinity and their relevance to questions of interest to evo-devo biologists. We further discuss the Tetraodontiformes (Teleostei, Pisces) as an example of a “model group” for the evo-devo study of vertebrate skeletal elements.