TY - JOUR

T1 - Double-replica theory for evolution of genotype-phenotype interrelationship

AU - Pham, Tuan Minh

AU - Kaneko, Kunihiko

PY - 2023/4/21

Y1 - 2023/4/21

N2 - The relationship between genotype and phenotype plays a crucial role in determining the function and robustness of biological systems. Here the evolution progresses through the change in genotype, whereas the selection is based on the phenotype, and the genotype-phenotype relation also evolves. The theory for such phenotypic evolution remains poorly developed, in contrast to evolution under the fitness landscape determined by genotypes. Here we provide a statistical-physics formulation of this problem by introducing replicas for genotype and phenotype. We apply it to an evolution model in which phenotypes are given by spin configurations; genotypes are an interaction matrix for spins to give the Hamiltonian, and the fitness depends only on the configuration of a subset of spins called the target. We describe the interplay between the genetic variations and phenotypic variances by noise in this model by our approach that extends the replica theory for spin glasses to include a spin replica for phenotypes and a coupling replica for genotypes. Within this framework we obtain a phase diagram of the evolved phenotypes against the noise and selection pressure, where each phase is distinguished by the fitness and overlaps for genotypes and phenotypes. Among the phases, a robust fitted phase, relevant to biological evolution, is achieved under the intermediate level of noise (temperature), where robustnesses to noise and to genetic mutation are correlated, as a result of replica symmetry. We also find a tradeoff between maintaining a high fitness level of phenotype and acquiring a robust pattern of genes as well as the dependence of this tradeoff on the ratio between the size of the functional (target) part to that of the remaining nonfunctional (non-target) one. The selection pressure needed to achieve high fitness increases with the fraction of target spins.

AB - The relationship between genotype and phenotype plays a crucial role in determining the function and robustness of biological systems. Here the evolution progresses through the change in genotype, whereas the selection is based on the phenotype, and the genotype-phenotype relation also evolves. The theory for such phenotypic evolution remains poorly developed, in contrast to evolution under the fitness landscape determined by genotypes. Here we provide a statistical-physics formulation of this problem by introducing replicas for genotype and phenotype. We apply it to an evolution model in which phenotypes are given by spin configurations; genotypes are an interaction matrix for spins to give the Hamiltonian, and the fitness depends only on the configuration of a subset of spins called the target. We describe the interplay between the genetic variations and phenotypic variances by noise in this model by our approach that extends the replica theory for spin glasses to include a spin replica for phenotypes and a coupling replica for genotypes. Within this framework we obtain a phase diagram of the evolved phenotypes against the noise and selection pressure, where each phase is distinguished by the fitness and overlaps for genotypes and phenotypes. Among the phases, a robust fitted phase, relevant to biological evolution, is achieved under the intermediate level of noise (temperature), where robustnesses to noise and to genetic mutation are correlated, as a result of replica symmetry. We also find a tradeoff between maintaining a high fitness level of phenotype and acquiring a robust pattern of genes as well as the dependence of this tradeoff on the ratio between the size of the functional (target) part to that of the remaining nonfunctional (non-target) one. The selection pressure needed to achieve high fitness increases with the fraction of target spins.

KW - SLOW INTERACTIONS

KW - COUPLED DYNAMICS

KW - FAST SPINS

KW - ROBUSTNESS

KW - EVOLVABILITY

KW - EXPRESSION

KW - NETWORKS

KW - NOISE

KW - MODEL

U2 - 10.1103/PhysRevResearch.5.023049

DO - 10.1103/PhysRevResearch.5.023049

M3 - Journal article

VL - 5

JO - Physical Review Research

JF - Physical Review Research

SN - 2643-1564

IS - 2

M1 - 023049

ER -