The DOI matches its Crossref record; 431 of the 435 references it cites were found in a registry or an index.
From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics
Open accessAbstract
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis.
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“They all share a remarkable universal pattern of organization, including neutrality, characterized by flat regions where different genotypes have the same fitness [29] (see also Catalán et al. [218]).”
From Fundamental constraints to the logic of living systems (2024) · cites this paper as [29]
Citations
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Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution
Johnston, I. G., Dingle, K., Greenbury, S. F., Camargo, C. Q., Doye, J. P. K., Ahnert, S. E., & Louis, A. A. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2113883119 · Cited by 137
Self-citationThe structure of genotype-phenotype maps makes fitness landscapes navigable
Greenbury, S. F., Louis, A. A., & Ahnert, S. E. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01867-z · Cited by 77
Self-citationReinforcement learning informs optimal treatment strategies to limit antibiotic resistance
Weaver, D. T., King, E. S., Maltas, J., & Scott, J. G. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2303165121 · Cited by 55
Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes
Dingle, K., Ghaddar, F., Šulc, P., & Louis, A. A. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab280 · Cited by 46
Self-citationFundamental constraints to the logic of living systems
Solé, R., Kempes, C. P., Corominas-Murtra, B., De Domenico, M., Kolchinsky, A., Lachmann, M., Libby, E., Saavedra, S., Smith, E., & Wolpert, D. (2024) · Interface Focus · doi:10.1098/rsfs.2024.0010 · Cited by 34
“They all share a remarkable universal pattern of organization, including neutrality, characterized by flat regions where different genotypes have the same fitness [29] (see also Catalán et al .”
Background
Metadata
- Authors
- Manrubia, S., Cuesta, J. A., Aguirre, J., Ahnert, S. E., Altenberg, L., Cano, A. V., Catalán, P., Diaz-Uriarte, R., Elena, S. F., García-Martín, J. A., Hogeweg, P., Khatri, B. S., Krug, J., Louis, A. A., Martin, N. S., Payne, J. L., Tarnowski, M. J., & Weiß, M.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- Universidad de Zaragoza (ES)
- University of Cambridge (GB)
- University of Hawaiʻi at Mānoa (US)
- SIB Swiss Institute of Bioinformatics (CH)
- Universidad Carlos III de Madrid (ES)
- Santa Fe Institute (US)
- Utrecht University (NL)
- The Francis Crick Institute (GB)
- University of Cologne (DE)
- University of Oxford (GB)
- University of Bristol (GB)
- Corresponding author
- Manrubia, Susanna
- ORCID
- Venue
- Physics of Life Reviews
- Publisher
- Elsevier BV
- Published
- 2021-09
- Volume
- 38
- Pages
- 55-106
- ISSN
- 1571-0645 (ISSN-L)
- OpenAlex
- W3003432383
- Cited by
- 88
- References
- 435
- Citations by year
- 2026: 14 · 2025: 15 · 2024: 20 · 2023: 14 · 2022: 12 · 2021: 11
- FWCI
- 2.10
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Physics of Life Reviews (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by-nc-nd)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by-nc-nd)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- e-Archivo (Carlos III University of Madrid) (submittedVersion, other-oa)
- Hispana (submittedVersion)
- Biblos-e Archivo (Universidad Autónoma de Madrid) (submittedVersion, public-domain)
- arXiv (Cornell University)
- ETH Zürich Research Collection
- Funders
- Gatsby Charitable Foundation
- European Commission (FIS2015-64349-P, PGC2018-098186-B-I00, SEV 2017-0712)
- Deutsche Forschungsgemeinschaft
- Engineering and Physical Sciences Research Council
- Biotechnology and Biological Sciences Research Council (BB/L01386X/1)
- Silicon Valley Community Foundation (F QXi-RFP-IPW-1913)
- Ministerio de Ciencia e Innovación
- Stanford University
- European Regional Development Fund
- Ohio State University
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (EP/L016494/1, PP00P3_170604)
- Ministerio de Economía y Competitividad
- National Science Foundation (0931642, BFU2015-65037-P, BFU2015-67302-R, DMS 0931642)
- Generalitat Valenciana
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Social Sciences › Arts and Humanities › History and Philosophy of Science › Philosophy of Biology and Scientific Explanation
- Keywords
- genotype-phenotype mapping, evolutionary dynamics, fitness, molecular phenotypes, synthetic biology
- MeSH terms
- Genotype, Phenotype
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