Toward understanding of evolutionary constraints: experimental and theoretical approaches

Abstract

Although organisms have diversified remarkably through evolution, they do not exhibit unlimited variability. During evolution, the phenotypic changes do not occur at random; instead, they are directional and restricted by the constraints imposed on them. Despite the perceived importance of characterizing the unevenness of these changes, studies on evolutionary constraints have been primarily qualitative in nature. In this review, we focus on the recent studies of evolutionary constraints, which are based on the quantification of high-dimensional phenotypic and genotypic data. Furthermore, we present a theoretical analysis that enables us to predict evolutionary constraints on the basis of phenotypic fluctuation, modeled on the fluctuation-response relationship in statistical physics. The review lays emphasis on the tight interactions between experimental and theoretical analyses in evolutionary biology that will contribute to a better understanding of evolutionary constraints.

Keywords: Developmental hourglass model; Evolutionary constraints; Evolutionary fluctuation–response relationship; Microbial laboratory evolution.

Fig. 1

Laboratory evolution of E. coli under antibiotics. a, b The time courses of the increase in MIC for enoxacin (ENX) and Cefixime (CFIX) in 90-day laboratory evolution, respectively. Four parallel series of experiments were performed. c Changes in MICs for other antibiotics in ENX-resistant strains, respectively. The radial axis depicts the log2-transformed relative MIC to the parent strain. The thick black line indicates MICs of the parent strain, and the colored thick lines indicate relative MICs of four parallel-evolved ENX resistant strains. d Comparisons between observed and predicted MICs calculated by using expression levels of 8 genes. See reference Suzuki et al. (2014)) for details

Fig. 2

Potential mechanism behind animal body plan conservation. In accordance with the prediction of the developmental hourglass model (Duboule 1994), body plan establishing, mid-embryonic stages (bottle-neck part of the hourglass) were persistently conserved through the vertebrate evolution. The nested hourglasses represent evolutionary diversity in the different evolutionary scales, implying that environmental factors are not powerful enough to diversify the mid-embryonic period. This conserved period was significantly enriched with genes having pleiotropic expressions (left, dark circles represent genes with temporarily and spatially pleiotropic expressions), suggesting that pleiotropic constraint contributed to the body plan conservation (Raff 1996)

Fig. 3

Evolutionary fluctuation-response relationship in replicating cell model. a Schematic representation of the replicating cell model. A cell has an intracellular catalytic reaction network, by which the amount of each chemical changes over time in a stochastic manner. The nutrient chemicals are transported into the cell with the aid of other chemical components (transporter). The cell will divide into two daughter cells when the total amount of chemicals in the cell exceeds a given threshold. b Relationship between V_ip and V_g. V_ip and V_gwere calculated based on the simulation results of randomly generated networks with various mutation rates m (the number of randomly replaced reaction paths divided by the total number of paths). The solid line is the y = x for the reference. Reproduced from (Furusawa and Kaneko 2015)