Evolutionary transitions during RNA virus experimental evolution

Abstract

One contribution of 13 to a theme issue 'The major synthetic evolutionary transitions'. In their search to understand the evolution of biological complexity, John Maynard Smith and Eörs Szathmáry put forward the notion of major evolutionary transitions as those in which elementary units get together to generate something new, larger and more complex. The origins of chromosomes, eukaryotic cells, multicellular organisms, colonies and, more recently, language and technological societies are examples that clearly illustrate this notion. However, a transition may be considered as anecdotal or as major depending on the specific level of biological organization under study. In this contribution, I will argue that transitions may also be occurring at a much smaller scale of biological organization: the viral world. Not only that, but also that we can observe in real time how these major transitions take place during experimental evolution. I will review the outcome of recent evolution experiments with viruses that illustrate four major evolutionary transitions: (i) the origin of a new virus that infects an otherwise inaccessible host and completely changes the way it interacts with the host regulatory and metabolic networks, (ii) the incorporation and loss of genes, (iii) the origin of segmented genomes from a non-segmented one, and (iv) the evolution of cooperative behaviour and cheating between different viruses or strains during co-infection of the same host.This article is part of the themed issue 'The major synthetic evolutionary transitions'.

Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis

“…This 6 suggests the action of genetic drift, rather than positive selection, leading to a change in the 7 frequency of the two genotypes in the different subpopulations. 8 Similar to the patterns observed for BGMV, a clear geographical segregation was 9 also observed for both EuYMV components, with only minor differences in the assignment 10 of some DNA-A and DNA-B components to the three genetic clusters (South-1, South-2 11 and GO) ( Figure 3). 12 Although it was not possible to define clear genetic clusters for MaYSV DNA-B 13 components based on DAPC analysis, the DNA-A components were split into four groups 14 ( Figure 3).…”

“…For the DNA-A, two 5 major clades were well supported, with isolates sampled in Rio Grande do Sul (RS) and 6 Paraná states (PR) clustered separately from those sampled in Góias (GO) and Mato Grosso 7 do Sul (MS). The same clusters could be observed in the DNA-B tree, except that isolates 8 sampled in MS clustered with those from RS and PR, suggesting a reassortment event. 9 Due to the complex recombination profile of the MaYSV data set (see below), DNA- 10 A and DNA-B phylogenetic trees showed a high degree of incongruence and displayed no 11 obvious pattern of segregation ( Figure 2D).…”

“…4 5 Genetic structure of populations 6 To compare the genetic structure based on DNA-A and DNA-B components, a 7 nonparametric multivariate statistical analysis was performed using DAPC ( Figure 3; Suppl. 8 Table S4). Since DAPC requires predefined groups, the analysis was run sequentially with 9 k values varying from 2 to 10, with the best number of genetic clusters chosen based on the 10 minimum number of k after which the Bayesian Information Criterion (BIC) decreased by 11 an insignificant amount.…”

“…In general, high values of pairwise Nst were 3 observed among different clusters, indicating great differentiation, and fully supporting the 4 subdivision proposed by DAPC analysis. 5 6 Genetic variability 7 Although there is evidence that DNA-B components are more variable than DNA- 8 A components (31) a quantitative and comparative analysis using large intraspecific data 9 sets has not yet been performed. To address this issue, we calculated the average pairwise 10 number of nucleotide differences (nucleotide diversity index, π) for the DNA-A and DNA-…”

Development of a honey bee RNA virus vector based on the genome of Deformed wing virus

“…We showed that the egfp-tagged viruses replicated in the injected pupae increased their loads thousands of times (Figure 2, Figure 7C) suggesting that even a non-essential gene in an RNA virus genome could be relatively stable ( Figure 7C). It is a widely accepted view, that gene exchanges between different virus groups and incorporation of host mRNA or their fragments occur during the RNA virus evolution [40,41]. It is necessary for these foreign inserts to be present in genomic RNA undergoing several rounds of replication events to allow further adjustment to the viral RNA genome context via mutagenesis.…”