The Genetics of Adaptation for Eight Microvirid Bacteriophages

Abstract

Theories of adaptive molecular evolution have recently experienced significant expansion, and their predictions and assumptions have begun to be subjected to rigorous empirical testing. However, these theories focus largely on predicting the first event in adaptive evolution, the fixation of a single beneficial mutation. To address longterm adaptation it is necessary to include new assumptions, but empirical data are needed for guidance. To empirically characterize the general properties of adaptive walks, eight recently isolated relatives of the single-stranded DNA (ssDNA) bacteriophage uX174 (family Microviridae) were adapted to identical selective conditions. Three of the eight genotypes were adapted in replicate, for a total of 11 adaptive walks. We measured fitness improvement and identified the genetic changes underlying the observed adaptation. Nearly all phages were evolvable; nine of the 11 lineages showed a significant increase in fitness. However, fitness plateaued quickly, and adaptation was achieved through only three substitutions on average. Parallel evolution was rampant, both across replicates of the same genotype as well as across different genotypes, yet adaptation of replicates never proceeded through the exact same set of mutations. Despite this, final fitnesses did not vary significantly among replicates. Final fitnesses did vary significantly across genotypes but not across phylogenetic groupings of genotypes. A positive correlation was found between the number of substitutions in an adaptive walk and the magnitude of fitness improvement, but no correlation was found between starting and ending fitness. These results provide an empirical framework for future adaptation theory.

Number of adaptive steps to a local fitness peak

“…Our result (25) shows that the walk should last longer in systems with smaller κ. This may be checked by measuring the mean walk length in populations with κ = −1 [16], κ → 0 [15] and κ > 0 [11]. To find the dependence of walk length properties on L, varying the sequence length may not be experimentally viable but it should be possi-ble to set up experiments along the lines of [9] and vary the initial fitness rank.…”

“…The fitness distribution p(f ) lies in the domain of the extreme value distribution given by Weibull distribution for κ < 0, Gumbel distribution if κ → 0 and Fréchet distribution for κ > 0. Although much of the experimental data on distribution of beneficial mutations is consistent with κ → 0 [9,15], recent works also support κ < 0 [16] and κ > 0 [11]. The adaptive walk in the limits κ → ±∞ is well studied theoretically.…”

A New Microviridae Phage Isolated from a Failed Biotechnological Process Driven by Escherichia coli

“…In an evolutionary study of eight Microviridae phages, Rokyta and colleagues observed that the majority of mutations detected at the end of an evolutionary walk were missense changes that occurred in genes coding for structural proteins (gpF, gpG, gpH, and gpJ) (23). Five missense mutations were found in the G gene.…”

“…Many studies have been conducted to better understand how ssDNA viruses evolve, and at least two different approaches have been used to investigate Microviridae evolution. The first approach involves replication of viruses in a chemostat with and without different selective pressures for many generations (15)(16)(17)(18)(19)(20)(21)(22)(23). The second approach is based on isolating and sequencing novel members of the virus family (24) and surveying environmental sequences (25).…”

A kompenzáló evolúció rendszerszintű vizsgálata élesztőben

“…Minél nagyobb hatása van egy gén elvesztésének, annál könnyebb ezt a hatást enyhíteni. Korábbi kis skálájú vizsgálatok is találtak ilyen összefüggést [Moore et al, 2000, Estes and Lynch, 2003, Poon and Chao, 2005, Rokyta et al, 2009, és nemrég napvilágot látott több publikáció is, melyek nagyobb skálán és más organizmusok esetén is megerősítették eredményünket [Couce andTenaillon, 2015, Blank et al, 2014]. Több okból is kialakulhat a megfigyelt mintázat.…”