Hierarchical genotype networks and incipient ecological speciation in Q$\beta$ phage quasispecies

TL;DR

This study uses deep-sequencing to analyze the structure of viral genotype networks in Qβ phage, revealing hierarchical organization, local topological features, and early divergence patterns in quasispecies evolution.

Contribution

It introduces a detailed analysis of genotype network topology and hierarchical structure in viral populations, highlighting the role of structural motifs and divergence under different conditions.

Findings

Genotype networks exhibit hierarchical clustering around a core sequence.

Local network topology is governed by structural motifs like tetrahedrons, triangles, and squares.

Early divergence shows overlapping populations connected by short mutational paths.

Abstract

Understanding how viral mutant spectra organize and explore genotype space is essential for unraveling the mechanisms driving evolution at the finest scale. Here we use deep-sequencing data of an amplicon in the A2 protein of the RNA bacteriophage Q$\beta$ to reconstruct genotype networks with tens of thousands of different haplotypes. The study of populations evolved under different temperature regimes uncovers generic topological features conditioned by fundamental structural motifs of genotype networks -- tetrahedrons, triangles, and squares -- that govern their local architecture. Mutant swarms display a hierarchical structure where sequences cluster around a highly connected and abundant sequence core that sustains population diversity. The immediate neighborhood of this core is comprehensively sampled, with no signs of selection, while a few mutations away sampling becomes dynamical and sparse, showing signs of purifying selection. By aggregating genotype networks from populations adapted to different temperatures, we capture the early stages of evolutionary divergence, with overlapping populations that remain connected through short mutational paths. Even at the time scale of these experiments, evolutionary pathways might be multiple, preventing the backward reconstruction of unique trajectories once mutations have been fixed. This analysis provides a detailed view of the local, fine-scale processes shaping viral quasispecies evolution and underscores the usefulness of genotype networks as an enlightening visualization of the organization of mutant swarms.