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Non-adaptive origins of interactome complexity.

ABSTRACT: The boundaries between prokaryotes, unicellular eukaryotes and multicellular eukaryotes are accompanied by orders-of-magnitude reductions in effective population size, with concurrent amplifications of the effects of random genetic drift and mutation. The resultant decline in the efficiency of selection seems to be sufficient to influence a wide range of attributes at the genomic level in a non-adaptive manner. A key remaining question concerns the extent to which variation in the power of random genetic drift is capable of influencing phylogenetic diversity at the subcellular and cellular levels. Should this be the case, population size would have to be considered as a potential determinant of the mechanistic pathways underlying long-term phenotypic evolution. Here we demonstrate a phylogenetically broad inverse relation between the power of drift and the structural integrity of protein subunits. This leads to the hypothesis that the accumulation of mildly deleterious mutations in populations of small size induces secondary selection for protein-protein interactions that stabilize key gene functions. By this means, the complex protein architectures and interactions essential to the genesis of phenotypic diversity may initially emerge by non-adaptive mechanisms.

SUBMITTER: Fernandez A

PROVIDER: S-EPMC3121905 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature

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Non-adaptive origins of interactome complexity.

Fernández Ariel A Lynch Michael M

Nature 20110518 7352

The boundaries between prokaryotes, unicellular eukaryotes and multicellular eukaryotes are accompanied by orders-of-magnitude reductions in effective population size, with concurrent amplifications of the effects of random genetic drift and mutation. The resultant decline in the efficiency of selection seems to be sufficient to influence a wide range of attributes at the genomic level in a non-adaptive manner. A key remaining question concerns the extent to which variation in the power of rando ...[more]

PMID: 21593762

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Project description:Duplication and divergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in the context of eye evolution by using new approaches to understand patterns of gene duplication during the evolution of metazoan genomes. We hypothesize that 1) genes involved in eye development and phototransduction have duplicated and are retained at higher rates in animal clades that possess more distinct types of optical design; and 2) genes with functional relationships were duplicated and lost together, thereby preserving genetic networks. To test these hypotheses, we examine the rates and patterns of gene duplication and loss evident in 19 metazoan genomes, including that of Daphnia pulex - the first completely sequenced crustacean genome. This is of particular interest because the pancrustaceans (hexapods+crustaceans) have more optical designs than any other major clade of animals, allowing us to test specifically whether the high amount of disparity in pancrustacean eyes is correlated with a higher rate of duplication and retention of vision genes.Using protein predictions from 19 metazoan whole-genome projects, we found all members of 23 gene families known to be involved in eye development or phototransduction and deduced their phylogenetic relationships. This allowed us to estimate the number and timing of gene duplication and loss events in these gene families during animal evolution. When comparing duplication/retention rates of these genes, we found that the rate was significantly higher in pancrustaceans than in either vertebrates or non-pancrustacean protostomes. Comparing patterns of co-duplication across Metazoa showed that while these eye-genes co-duplicate at a significantly higher rate than those within a randomly shuffled matrix, many genes with known functional relationships in model organisms did not co-duplicate more often than expected by chance.Overall, and when accounting for factors such as differential rates of whole-genome duplication in different groups, our results are broadly consistent with the hypothesis that genes involved in eye development and phototransduction duplicate at a higher rate in Pancrustacea, the group with the greatest variety of optical designs. The result that these genes have a significantly high number of co-duplications and co-losses could be influenced by shared functions or other unstudied factors such as synteny. Since we did not observe co-duplication/co-loss of genes for all known functional modules (e.g. specific regulatory networks), the interactions among suites of known co-functioning genes (modules) may be plastic at the temporal scale of analysis performed here. Other factors in addition to gene duplication - such as cis-regulation, heterotopy, and co-option - are also likely to be strong factors in the diversification of eye types.

Project description:BackgroundThe concept of complexity is used in palliative care (PC) to describe the nature of patients' situations and the extent of resulting needs and care demands. However, the term or concept is not clearly defined and operationalised with respect to its particular application in PC. As a complex problem, a care situation in PC is characterized by reciprocal, nonlinear relations and uncertainties. Dealing with complex problems necessitates problem-solving methods tailored to specific situations. The theory of complex adaptive systems (CAS) provides a framework for locating problems and solutions. This study aims to describe criteria contributing to complexity of PC situations from the professionals' view and to develop a conceptual framework to improve understanding of the concept of "complexity" and related elements of a PC situation by locating the complex problem "PC situation" in a CAS.MethodsQualitative interview study with 42 semi-structured expert (clinical/economical/political) interviews. Data was analysed using the framework method. The thematic framework was developed inductively. Categories were reviewed, subsumed and connected considering CAS theory.ResultsThe CAS of a PC situation consists of three subsystems: patient, social system, and team. Agents in the "system patient" are allocated to further subsystems on patient level: physical, psycho-spiritual, and socio-cultural. The "social system" and the "system team" are composed of social agents, who affect the CAS as carriers of characteristics, roles, and relationships. Environmental factors interact with the care situation from outside the system. Agents within subsystems and subsystems themselves interact on all hierarchical system levels and shape the system behaviour of a PC situation.ConclusionsThis paper provides a conceptual framework and comprehensive understanding of complexity in PC. The systemic view can help to understand and shape situations and dynamics of individual care situations; on higher hierarchical level, it can support an understanding and framework for the development of care structures and concepts. The framework provides a foundation for the development of a model to differentiate PC situations by complexity of patients and care needs. To enable an operationalisation and classification of complexity, relevant outcome measures mirroring the identified system elements should be identified and implemented in clinical practice.

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Non-adaptive origins of interactome complexity.

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Non-adaptive origins of interactome complexity.

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