Evolutionary dimension reduction in phenotypic space
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large number of degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in response to environmental changes are effectively restric...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
American Physical Society
2020-02-01
|
| Series: | Physical Review Research |
| Online Access: | http://doi.org/10.1103/PhysRevResearch.2.013197 |
| _version_ | 1797211570639470592 |
|---|---|
| author | Takuya U. Sato Kunihiko Kaneko |
| author_facet | Takuya U. Sato Kunihiko Kaneko |
| author_sort | Takuya U. Sato |
| collection | DOAJ |
| description | In general, cellular phenotypes, as measured by concentrations of cellular components, involve large number of degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in response to environmental changes are effectively restricted to a low-dimensional subspace. Thus, uncovering the origin and nature of such a drastic dimension reduction is crucial to understanding the general characteristics of biological adaptation and evolution. Herein, we first formulated the dimension reduction in terms of dynamical systems theory: considering the steady growth state of cells, the reduction is represented by the separation of a few large singular values of the inverse Jacobian matrix around a fixed point. We then examined this dimension reduction by numerical evolution of cells consisting of thousands of chemicals whose concentrations determine phenotype. The model cells grow with catalytic reactions governed by genetically determined networks, which evolve to increase cellular fitness, i.e., growth speed. As a result of the evolution, phenotypic changes due to mutations and external perturbations were found to be mainly restricted to a one-dimensional subspace. One singular value of the inverse Jacobian matrix at a fixed point of concentrations was significantly larger than the others. The major phenotypic changes due to mutations and external perturbations occur along the corresponding left-singular vector, which leads to phenotypic constraint, and fitness dominantly changes in the same direction. Once such phenotypic constraint is acquired, phenotypic evolution to a novel environment takes advantage of this restricted phenotypic direction. This results in the convergence of phenotypic pathways across genetically different strains, as is experimentally observed, while accelerating further evolution. We also confirmed that this one-dimensional constraint on phenotypic changes is imposed even by evolution under fluctuating conditions with environmental changes occurring every few generations, where the fitness for each condition is embedded into the evolving one-dimensional direction for major phenotypic changes. Thus, while genetic evolution can be random, phenotypic evolution appears to be constrained. |
| first_indexed | 2024-04-24T10:28:36Z |
| format | Article |
| id | doaj.art-df802b3577a048abb68952d34901dff5 |
| institution | Directory Open Access Journal |
| issn | 2643-1564 |
| language | English |
| last_indexed | 2024-04-24T10:28:36Z |
| publishDate | 2020-02-01 |
| publisher | American Physical Society |
| record_format | Article |
| series | Physical Review Research |
| spelling | doaj.art-df802b3577a048abb68952d34901dff52024-04-12T16:50:15ZengAmerican Physical SocietyPhysical Review Research2643-15642020-02-012101319710.1103/PhysRevResearch.2.013197Evolutionary dimension reduction in phenotypic spaceTakuya U. SatoKunihiko KanekoIn general, cellular phenotypes, as measured by concentrations of cellular components, involve large number of degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in response to environmental changes are effectively restricted to a low-dimensional subspace. Thus, uncovering the origin and nature of such a drastic dimension reduction is crucial to understanding the general characteristics of biological adaptation and evolution. Herein, we first formulated the dimension reduction in terms of dynamical systems theory: considering the steady growth state of cells, the reduction is represented by the separation of a few large singular values of the inverse Jacobian matrix around a fixed point. We then examined this dimension reduction by numerical evolution of cells consisting of thousands of chemicals whose concentrations determine phenotype. The model cells grow with catalytic reactions governed by genetically determined networks, which evolve to increase cellular fitness, i.e., growth speed. As a result of the evolution, phenotypic changes due to mutations and external perturbations were found to be mainly restricted to a one-dimensional subspace. One singular value of the inverse Jacobian matrix at a fixed point of concentrations was significantly larger than the others. The major phenotypic changes due to mutations and external perturbations occur along the corresponding left-singular vector, which leads to phenotypic constraint, and fitness dominantly changes in the same direction. Once such phenotypic constraint is acquired, phenotypic evolution to a novel environment takes advantage of this restricted phenotypic direction. This results in the convergence of phenotypic pathways across genetically different strains, as is experimentally observed, while accelerating further evolution. We also confirmed that this one-dimensional constraint on phenotypic changes is imposed even by evolution under fluctuating conditions with environmental changes occurring every few generations, where the fitness for each condition is embedded into the evolving one-dimensional direction for major phenotypic changes. Thus, while genetic evolution can be random, phenotypic evolution appears to be constrained.http://doi.org/10.1103/PhysRevResearch.2.013197 |
| spellingShingle | Takuya U. Sato Kunihiko Kaneko Evolutionary dimension reduction in phenotypic space Physical Review Research |
| title | Evolutionary dimension reduction in phenotypic space |
| title_full | Evolutionary dimension reduction in phenotypic space |
| title_fullStr | Evolutionary dimension reduction in phenotypic space |
| title_full_unstemmed | Evolutionary dimension reduction in phenotypic space |
| title_short | Evolutionary dimension reduction in phenotypic space |
| title_sort | evolutionary dimension reduction in phenotypic space |
| url | http://doi.org/10.1103/PhysRevResearch.2.013197 |
| work_keys_str_mv | AT takuyausato evolutionarydimensionreductioninphenotypicspace AT kunihikokaneko evolutionarydimensionreductioninphenotypicspace |