Systems Biology
- LAST REVIEWED: 26 September 2022
- LAST MODIFIED: 26 September 2022
- DOI: 10.1093/obo/9780199941728-0010
- LAST REVIEWED: 26 September 2022
- LAST MODIFIED: 26 September 2022
- DOI: 10.1093/obo/9780199941728-0010
Introduction
The exact meaning of the term systems biology is debated, yet most biologists agree that it refers to the study of organismal properties that cannot be reduced to the functions of single genes or other individual components. That is, systems biology is about the traits—be they physiological, developmental, or behavioral—that arise out of interactions between components. Some systems biologists emphasize not the subject matter of the field, but instead the methodology, which combines experimental perturbations with high-throughput quantitative measurements and mathematical modeling. The goal is to understand how complex biological systems achieve function through iterative cycles of data gathering and model-based prediction. Evolutionary biology intersects with systems biology in two ways. First, evolution provides a means of understanding the current structure and function of biological systems. For example, many studies have found that networks of biological interactions do not have topologies consistent with random connections between pairs of components. The departures from random expectation must have evolutionary explanations, and both adaptive and nonadaptive explanations have been proposed and debated. Second, systems biology holds the promise of replacing unrealistically simple representations of the mapping between genotype and phenotype —a key element of all evolutionary models—with more meaningful ones. Thus, systems biology can expand and enrich our understanding of complex-trait evolution. This article aims to provide entry points into the literature of evolutionary systems biology from its historical roots to its current incarnations. Particular attention is paid to the organizational features and functional properties of complex biological systems. System organization is typically investigated in terms of networks of interacting components, such as genes or proteins. Organizational features of interest range from the global level of overall network topology to the local level of modules and regulatory motifs. Functional properties of interest include modularity, evolvability, and robustness to perturbations, such as environmental fluctuations and mutations. The field of evolutionary systems biology spans a range of organisms and analytical approaches, addresses a range of questions, and, indeed, has several alternative definitions. The works compiled here were chosen to reflect this diversity, to highlight major developments and insights, and to enable more extensive forays into the literature.
General Overviews
Although the field of systems biology has roots going back decades (see Forerunners of Modern Systems Biology), most scientists would place the start of its modern form around the late 1990s or early 2000s. The first review articles heralding the new field appeared in the early 2000s, whereas the first textbooks appeared a few years later (see Systems Biology). Although the foundational works of evolutionary systems biology emerged at about the same time as those of modern systems biology (see Historical Background), the field was not called evolutionary systems biology until around 2004 (see O’Malley 2012, cited under Alternative Definitions). Reviews and edited volumes on evolutionary systems biology followed soon after that (see Evolutionary Systems Biology).
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Article
- Adaptation
- Adaptive Radiation
- Altruism
- Amniotes, Diversification of
- Ancient DNA
- Bacterial Species Concepts
- Behavioral Ecology
- Canalization and Robustness
- Cancer, Evolutionary Processes in
- Character Displacement
- Coevolution
- Cognition, Evolution of
- Constraints, Evolutionary
- Contemporary Evolution
- Convergent Evolution
- Cooperation and Conflict: Microbes to Humans
- Cooperative Breeding in Insects and Vertebrates
- Creationism
- Cryptic Female Choice
- Darwin, Charles
- Darwinism
- Disease Virulence, Evolution of
- Diversification, Diversity-Dependent
- Eco-Evolutionary Dynamics
- Ecological Speciation
- Endosymbiosis
- Epigenetics and Behavior
- Epistasis and Evolution
- Eusocial Insects as a Model for Understanding Altruism, Co...
- Eusociality
- Evidence of Evolution, The
- Evolution
- Evolution and Development: Genes and Mutations Underlying ...
- Evolution and Development of Individual Behavioral Variati...
- Evolution, Cultural
- Evolution of Animal Mating Systems
- Evolution of Antibiotic Resistance
- Evolution of New Genes
- Evolution of Plant Mating Systems
- Evolution of Specialization
- Evolutionary Biology of Aging
- Evolutionary Biomechanics
- Evolutionary Computation
- Evolutionary Developmental Biology
- Evolutionary Ecology of Communities
- Experimental Evolution
- Extinction
- Field Studies of Natural Selection
- Fossils
- Founder Effect Speciation
- Frequency-Dependent Selection
- Fungi, Evolution of
- Gene Duplication
- Gene Expression, Evolution of
- Gene Flow
- Genetics, Ecological
- Genome Evolution
- Geographic Variation
- Gradualism
- Group Selection
- Heterochrony
- Heterozygosity
- History of Evolutionary Thought, 1860–1925
- History of Evolutionary Thought before Darwin
- History of Evolutionary Thought Since 1930
- Human Behavioral Ecology
- Human Evolution
- Hybrid Speciation
- Hybrid Zones
- Hybridization and Diversification
- Identifying the Genomic Basis Underlying Phenotypic Variat...
- Inbreeding and Inbreeding Depression
- Inclusive Fitness
- Innovation, Evolutionary
- Islands as Evolutionary Laboratories
- Kin Selection
- Land Plants, Evolution of
- Landscape Genetics
- Landscapes, Adaptive
- Language, Evolution of
- Latitudinal Diversity Gradient, The
- Macroevolution
- Macroevolution, Clade-Level Interactions and
- Macroevolutionary Rates
- Male-Male Competition
- Mass Extinction
- Mate Choice
- Maternal Effects
- Mating Tactics and Strategies
- Medicine, Evolutionary
- Meiotic Drive
- Mimicry
- Modern Synthesis, The
- Molecular Clocks
- Molecular Phylogenetics
- Mutation Rate and Spectrum
- Mutualism, Evolution of
- Natural Selection in Human Populations
- Natural Selection in the Genome, Detecting
- Neutral Theory
- New Zealand, Evolutionary Biogeography of
- Niche Construction
- Niche Evolution
- Non-Human Animals, Cultural Evolution in
- Origin and Early Evolution of Animals
- Origin of Amniotes and the Amniotic Egg
- Origin of Eukaryotes
- Origin of Life, The
- Paradox of Sex
- Parallel Speciation
- Parental Care, Evolution of
- Parthenogenesis
- Personality Differences, Evolution of
- Pest Management, Evolution and
- Phenotypic Plasticity
- Phylogenetic Comparative Methods and Tests of Macroevoluti...
- Phylogenetic Trees, Interpretation of
- Phylogeography
- Polyploid Speciation
- Population Genetics
- Population Structure
- Post-Copulatory Sexual Selection
- Psychology, Evolutionary
- Punctuated Equilibria
- Quantitative Genetic Variation and Heritability
- Reaction Norms, Evolution of
- Reinforcement
- Reproductive Proteins, Evolution of
- Selection, Directional
- Selection, Disruptive
- Selection Gradients
- Selection, Natural
- Selection, Sexual
- Selective Sweeps
- Selfish Genes
- Sequential Speciation and Cascading Divergence
- Sexual Conflict
- Sexual Selection and Speciation
- Sexual Size Dimorphism
- Speciation
- Speciation Continuum
- Speciation Genetics and Genomics
- Speciation, Geography of
- Speciation, Sympatric
- Species Concepts
- Species Delimitation
- Sperm Competition
- Stasis
- Systems Biology
- Taxonomy and Classification
- Tetrapod Evolution
- The Philosophy of Evolutionary Biology
- Theory, Coalescent
- Trends, Evolutionary
- Vertebrates, Origin of
- Wallace, Alfred Russel