Phenotype ontologies: The bridge between genomics and evolution

Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
Trends in Ecology & Evolution (Impact Factor: 16.2). 08/2007; 22(7):345-50. DOI: 10.1016/j.tree.2007.03.013
Source: PubMed


Understanding the developmental and genetic underpinnings of particular evolutionary changes has been hindered by inadequate databases of evolutionary anatomy and by the lack of a computational approach to identify underlying candidate genes and regulators. By contrast, model organism studies have been enhanced by ontologies shared among genomic databases. Here, we suggest that evolutionary and genomics databases can be developed to exchange and use information through shared phenotype and anatomy ontologies. This would facilitate computing on evolutionary questions pertaining to the genetic basis of evolutionary change, the genetic and developmental bases of correlated characters and independent evolution, biomedical parallels to evolutionary change, and the ecological and paleontological correlates of particular types of change in genes, gene networks and developmental pathways.


Available from: Melissa A Haendel
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    • "The ontology was edited in OBO-Edit (Day-Richter et al., 2007). All characters were mapped to ontology terms similarly as in Mabee et al. (2007a,b), Sereno (2007), Dahdul et al. (2010a), and Balhoff et al. (2010). Because we are not interested in specific qualities, we have used a simpler mapping of characters to ontology terms than the more elaborate Entity-Quality syntax implemented in Phenex (Balhoff et al., 2010; Dahdul et al., 2010a). "
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    ABSTRACT: Complexity is an important aspect of evolutionary biology, but there are many reasonable concepts of complexity, and its objective measurement is an elusive matter. Here we develop a simple measure of complexity based on counts of elements, incorporating the hierarchical information as represented in anatomical ontologies. Neomorphic and transformational characters are used to identify novelties and individuated morphological regions, respectively. By linking the characters to terms in an anatomical ontology a node-driven approach is implemented, where a node ontology and a complexity score are inferred from the optimization of individual characters on each ancestral or terminal node. From the atomized vector of character scorings, the anatomical ontology is used to integrate the hierarchical structure of morphology in terminals and ancestors. These node ontologies are used to calculate a measure of complexity that can be traced on phylogenetic trees and is harmonious with usual phylogenetic operations. This strategy is compared with a terminal-driven approach, in which the complexity scores are calculated only for terminals, and optimized as a continuous character on the internal nodes. These ideas are applied to a real dataset of 166 araneomorph spider species scored for 393 characters, using Spider Ontology (SPD,; complexity scores and transitions are calculated for each node and branch, respectively. This result in a distribution of transitions skewed towards simplification; the transitions in complexity have no apparent correlation with character branch lengths. The node-driven and terminal-driven estimations are generally correlated in the complexity scores, but have higher divergence in the transition values. The structure of the ontology is used to provide complexity scores for organ systems and body parts of the focal groups.
    Cladistics 04/2014; 30(6). DOI:10.1111/cla.12075 · 6.22 Impact Factor
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    • "Different anatomy ontologies specify the organismal components for multiple species, and – on a smaller scale of granularity – the developmental relations and features of cell types are characterized by the Celltype Ontology [18]. Phenotype ontologies are also available for multiple species and are widely used for the annotation of the abnormalities observed in mutagenesis experiments [19-21] as well as for the characterization of diseases and drug effects [22]. "
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    ABSTRACT: Over the past 15 years, the biomedical research community has increased its efforts to produce ontologies encoding biomedical knowledge, and to provide the corresponding infrastructure to maintain them. As ontologies are becoming a central part of biological and biomedical research, a communication channel to publish frequent updates and latest developments on them would be an advantage. Here, we introduce the JBMS thematic series on Biomedical Ontologies. The aim of the series is to disseminate the latest developments in research on biomedical ontologies and provide a venue for publishing newly developed ontologies, updates to existing ontologies as well as methodological advances, and selected contributions from conferences and workshops. We aim to give this thematic series a central role in the exploration of ongoing research in biomedical ontologies and intend to work closely together with the research community towards this aim. Researchers and working groups are encouraged to provide feedback on novel developments and special topics to be integrated into the existing publication cycles.
    Journal of Biomedical Semantics 03/2014; 5(1):15. DOI:10.1186/2041-1480-5-15 · 2.26 Impact Factor
    • "The development of glossaries (e.g. Richter et al. 2010), and particularly of ontologies (Vogt et al. 2010, 2011 for theoretical background) is intended to resolve this problem (see also Mabee et al. 2007, Deans et al. 2012). We too have attempted elsewhere to summarize certain aspects of what we elaborate on here, including in a short essay in a volume published by the German Zoological Society on occasion of the 100th yearly meeting of the society (Richter 2007) and in a short overview of the descriptive and comparative aspects of Evolutionary Morphology (Wirkner and Richter 2010). "
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    ABSTRACT: Throughout the history of biology since the time of Goethe, morphology as a discipline has been not only descriptive but explanatory too. Both, morphology itself and its central concept, homology, are pre-Darwinian in origin, and as a result dubious in the eyes of many. Although morphology has taken evolution into account since Darwin, its contribution as a scientific discipline to evolutionary biology is a matter of dispute. This paper can be regarded as the conceptualization of a research program for Evolutionary Morphology, a term we use to characterize the field in evolutionary biology which includes the description, comparison and explanation of all the predicates (i.e. form and function) of phenotypic objects. Evolutionary Morphology deserves a central place in an extended evolutionary synthesis. The descriptive aspect of Evolutionary Morphology describes and documents the form of parts of an organism (referred to here as morphemes). In comparative morphology, evolutionary units are identified and their homology between species is tested. Then, within the framework of phylogenetic analyses, putatively homologous evolutionary units (character states) are arranged in transformation series (characters in cladistic terminology), tested against each other and, ultimately, ordered chronologically. Establishing the relative chronological order of evolutionary units is the main goal of the phylogenetic analyses conducted in Evolutionary Morphology. Phylogenetic analyses form the basis of the explanatory aspect of Evolutionary Morphology, the area of ‘causal morphology’. Evolutionary units are the result of adaptation and need to be studied in terms of potential selective forces. Their evolvability, however, is limited by material constraints. In addition, coherence may exist both between morphemes (e.g. by architectural constraints) and between evolutionary units, and this too is important for our understanding of evolutionary transformations. In this context, it is crucial to note that to reach a causal understanding of the predicates of morphemes, it is important to remember that they all undergo a process of development, and that ultimately, changes in developmental pathways are responsible for changes in the predicates in adults. Understanding these developmental pathways and the genetics behind them is indispensable if we are to understand morpheme form and the transformation of evolutionary units. The discipline of Evolutionary Developmental Biology (evo-devo) focuses on precisely these questions. Its results, yet, do not replace those of Evolutionary Morphology but supplement them. None of the aspects of the area of ‘causal morphology’ listed is exclusive; they are complementary in their contribution to our understanding of phenotypes. They all embody different approaches which are indispensable to our understanding of form. Evolutionary Morphological investigations take place within research cycles, which implies that findings in the area of causal morphology might influence the descriptive and comparative studies of the next research cycle.
    Journal of Zoological Systematics and Evolutionary Research 03/2014; 52(4). DOI:10.1111/jzs.12061 · 1.68 Impact Factor
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