Emergence of species in evolutionary simulated annealing

TL;DR

This paper models how mutation rates influence the emergence of species in asexual populations, revealing dynamics of fitness, protein interactions, and mutation rate evolution through simulations.

Contribution

It introduces a first principles model linking molecular properties to population dynamics, showing how mutation rates and species formation evolve in simulated asexual populations.

Findings

Species form at low mutation rates but are lost at high mutation rates.

Populations initially maintain high mutation rates before evolving lower rates.

Fitness increases in punctuated steps via epistatic events.

Abstract

Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and interactions of proteins encoded in their genomes. Simulating evolution of populations, we found that fitness increases in punctuated steps via epistatic events, leading to formation of stable and functionally interacting proteins. At low mutation rates, species - populations of organisms with identical genotypes - form, while at higher mutation rates, species are lost through delocalization in sequence space without an apparent loss of fitness. However, when mutation rate was a selectable trait, the population initially maintained high mutation rate until a high fitness level is reached, after which organisms with low mutation rates are gradually selected, with the population eventually reaching mutation rates comparable to those of modern DNA-based organisms. These results provide microscopic insights into the dynamic fitness landscape of asexual populations of unicellular organisms.