Phylo-evo-devo: combining phylogenetics with evolutionary developmental biology

As a result of the integration of molecular and morphological approaches for the reconstruction of phylogenies, and of the intertwining of developmental and evolutionary biology, further prospects are open for a fruitful interaction between these two fields in what we may call a phylo-evo-devo approach.     

Toward a new synthesis: population genetics and evolutionary developmental biology

Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.     

Transformationalism,taxism, and developmental biology in systematics

Issues concerning transformational and taxic comparisons are central to understanding the impact of the recent proliferation of molecular developmental data on evolutionary biology. More importantly, an understanding of taxism and transformationalism in comparative biology is critical to assessing the impact of the recent developmental data on systematic theory and practice. We examine the philosophical and practical aspects of the transformational approach and the relevance of this approach to recent molecular-based developmental data. We also examine the theoretical basis of the taxic approach to molecular developmental data and suggest that developmental data are perfectly amenable to the taxic approach. Two recent examples from the molecular developmental biology literature--the evolution of insect wings and the evolution of dorsal ventral inversion in vertebrates and invertebrates--are used to compare the taxic and transformational approaches. We conclude that the transformational approach is entirely appropriate for ontogenetic studies and furthermore can serve as an excellent source of hypotheses about the evolution of characters. However, the taxic approach is the ultimate arbiter of these hypotheses.     

The morphogenesis of evolutionary developmental biology

The early studies of evolutionary developmental biology (Evo-Devo) come from several sources. Tributaries flowing into Evo-Devo came from such disciplines as embryology, developmental genetics, evolutionary biology, ecology, paleontology, systematics, medical embryology and mathematical modeling. This essay will trace one of the major pathways, that from evolutionary embryology to Evo-Devo and it will show the interactions of this pathway with two other sources of Evo-Devo: ecological developmental biology and medical developmental biology. Together, these three fields are forming a more inclusive evolutionary developmental biology that is revitalizing and providing answers to old and important questions involving the formation of biodiversity on Earth. The phenotype of Evo-Devo is limited by internal constraints on what could be known given the methods and equipment of the time and it has been framed by external factors that include both academic and global politics.     

The types of homology and their significance for evolutionary biology and phylogenetics

This paper comments on recently revived discussion about the most adequate definition of homology. Homologues are considered as similarities of complex structures or patterns which are based on a continuity of biological information or instruction. Dependent on the level of comparison four types of homology are defined: (1) Iterative ( = serial = homonomy), (2) ontogenetic, (3) di- or polymorphic, and (4) supraspecific homology. The significance of all four types for evolutionary biology and phylogenetic analysis is outlined.     

Toward the synthesis of taxonomy,ontogeny, and phylogenetics: A new concept of <Emphasis Type=Italic>Ontogenetic Systematics</Emphasis>

Over the past decade, the morphological paradigm in the traditional field of systematics and evolutionary biology has been challenged and has actually been replaced by the molecular paradigm. In this study, an attempt is made to evaluate the current state of the problem concerning the relationship between the fundamentals of systematics and evolution. It is shown that the interrelatedness of evolution, ontogeny, systematics, and phylogenetics is deeply underestimated in the approaches used in recent research. Instead of considering the above fields of biology as separate categories, as is common in recent studies, the synthetic concept of ontogenetic systematics is proposed, which unifies them into an integrated process.     

Mitochondrial gene rearrangements: new paradigm in the evolutionary biology and systematics

Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression mechanism evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mt gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms.     

Beyond Arabidopsis. Translational biology meets evolutionary developmental biology

Developmental processes shape plant morphologies, which constitute important adaptive traits selected for during evolution. Identifying the genes that act in developmental pathways and determining how they are modified during evolution is the focus of the field of evolutionary developmental biology, or evo-devo. Knowledge of genetic pathways in the plant model Arabidopsis serves as the starting point for investigating how the toolkit of developmental pathways has been used and reused to form different plant body plans. One productive approach is to identify genes in other species that are orthologous to genes known to control developmental pathways in Arabidopsis and then determine what changes have occurred in the protein coding sequence or in the gene's expression to produce an altered morphology. A second approach relies on natural variation among wild populations or crop plants. Natural variation can be exploited to identify quantitative trait loci that underlie important developmental traits and, thus, define those genes that are responsible for adaptive changes. The possibility of applying comparative genomics approaches to Arabidopsis and related species promises profound new insights into the interplay of evolution and development.     

Driving developmental and evolutionary change: A systems biology view

Embryonic development is underpinned by ～50 core processes that drive morphogenesis, growth, patterning and differentiation, and each is the functional output of a complex molecular network. Processes are thus the natural and parsimonious link between genotype and phenotype and the obvious focus for any discussion of biological change. Here, the implications of this approach are explored. One is that many features of developmental change can be modeled as mathematical graphs, or sets of connected triplets of the general form <noun><verb><noun>. In these, the verbs (edges) are the outputs of the processes that drive change and the nouns (nodes) are the time-dependent states of biological entities (from molecules to tissues). Such graphs help unpick the multi-level complexity of developmental phenomena and may help suggest new experiments. Another comes from analyzing the effect of mutation that lead to tinkering with the dynamic properties of these processes and to congenital abnormalities; if these changes are both inherited and advantageous, they become evolutionary modifications. In this context, protein networks often represents what classical evolutionary genetics sees as genes, and the realization that traits reflect the output processes of complex networks, particularly for growth, patterning and pigmentation, rather than anything simpler clarifies some problems that the evolutionary synthesis of the 1950s has found hard to solve. In the wider context, most processes are used many times in development and cooperate to produce tissue modules (bones, branching duct systems, muscles etc.). Their underlying generative networks can thus be thought of as genomic modules or subroutines.     

A semiotic framework for evolutionary and developmental biology

This work aims at constructing a semiotic framework for an expanded evolutionary synthesis grounded on Peirce's universal categories and the six space/time/function relations [Taborsky, E., 2004. The nature of the sign as a WFF--a well-formed formula, SEED J. (Semiosis Evol. Energy Dev.) 4 (4), 5-14] that integrate the Lamarckian (internal/external) and Darwinian (individual/population) cuts. According to these guide lines, it is proposed an attempt to formalize developmental systems theory by using the notion of evolving developing agents (EDA) that provides an internalist model of a general transformative tendency driven by organism's need to cope with environmental uncertainty. Development and evolution are conceived as non-programmed open-ended processes of information increase where EDA reach a functional compromise between: (a) increments of phenotype's uniqueness (stability and specificity) and (b) anticipation to environmental changes. Accordingly, changes in mutual information content between the phenotype/environment drag subsequent changes in mutual information content between genotype/phenotype and genotype/environment at two interwoven scales: individual life cycle (ontogeny) and species time (phylogeny), respectively. Developmental terminal additions along with increment minimization of developmental steps must be positively selected.     

Annelids in evolutionary developmental biology and comparative genomics

Annelids have had a long history in comparative embryology and morphology, which has helped to establish them in zoology textbooks as an ideal system to understand the evolution of the typical triploblastic, coelomate, protostome condition. In recent years there has been a relative upsurge in embryological data, particularly with regard to the expression and function of developmental control genes. Polychaetes, as well as other annelids such as the parasitic leech, are now also entering the age of comparative genomics. All of this comparative data has had an important impact on our views of the ancestral conditions at various levels of the animal phylogeny, including the bilaterian ancestor and the nature of the annelid ancestor. Here we review some of the recent advances made in annelid comparative development and genomics, revealing a hitherto unsuspected level of complexity in these ancestors. It is also apparent that the transition to a parasitic lifestyle leads to, or requires, extensive modifications and derivations at both the genomic and embryological levels.     

Fluctuating asymmetry and developmental instability in evolutionary biology: past, present and future

The role of developmental instability (DI), as measured by fluctuating asymmetry (FA), in evolutionary biology has been the focus of a wealth of research for more than half a century. In spite of this long period and many published papers, our current state of knowledge reviewed here only allows us to conclude that patterns are heterogeneous and that very little is known about the underlying causes of this heterogeneity. In addition, the statistical properties of FA as a measure of DI are only poorly grasped because of a general lack of understanding of the underlying mechanisms that drive DI. If we want to avoid that this area of research becomes abandoned, more efforts should be made to understand the observed heterogeneity, and attempts should be made to develop a unifying statistical protocol. More specifically, and perhaps most importantly, it is argued here that more attention should be paid to the usefulness of FA as a measure of DI since many factors might blur this relationship. Furthermore, the genetic architecture, associations with fitness and the importance of compensatory growth should be investigated under a variety of stress situations. In addition, more focus should be directed to the underlying mechanisms of DI as well as how these processes map to the observable phenotype. These insights could yield more efficient statistical models and a unified approach to the analysis of patterns in FA and DI. The study of both DI and canalization is indispensable to obtain better insights in their possible common origin, especially because both have been suggested to play a role in both micro- and macro-evolutionary processes.     

Ontogeny, systematics, and phylogenetics: Perspectives of future synthesis and a new model of the evolution of bilateria

Ontogeny is considered as a process that allows linking two key components of biological systematics in an objective way: historically independent character attribution and phylogeny. It is proposed to designate the general theory that unifies the ??static?? traditional taxonomy and the dynamic evolutionary process on the basis of ontogenetic transformation of shapes of organisms as the ontogenetic systematics. One of the important practical applications is a new model of the evolution of bilaterian animals, which supposes an ancestral status of clonal asexual reproduction and its multiple reduction in different lines of Bilatera.     

Michael Akam and the rise of evolutionary developmental biology

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.     

The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications

Glutamine synthetase exists in at least two related forms, GSI and GSII, the sequences of which have been used in evolutionary molecular clock studies. GSI has so far been found exclusively in bacteria, and GSII has been found predominantly in eukaryotes. To date, only a minority of bacteria, including rhizobia, have been shown to express both forms of GS. The sequences of equivalent internal fragments of the GSI and GSII genes for the type strains of 16 species of rhizobia have been determined and analyzed. The GSI and GSII data sets do not produce congruent phylogenies with either neighbor-joining or maximum-likelihood analyses. The GSI phylogeny is broadly congruent with the 16S rDNA phylogeny for the same bacteria; the GSII phylogeny is not. There are three striking rearrangements in the GSII phylograms, all of which might be explained by horizontal gene transfer to Bradyrhizobium (probably from Mesorhizobium), to Rhizobium galegae (from Rhizobium), and to Mesorhizobium huakuii (perhaps from Rhizobium). There is also evidence suggesting intrageneric DNA transfer within Mesorhizobium. Meta-analysis of both GS genes from the different genera of rhizobia and other reference organisms suggests that the divergence times of the different rhizobium genera predate the existence of legumes, their host plants.