Biology subjects

Rose, C. J.

Publications and source records attributed to Rose, C. J..

4 recordsLinked to original sources

bioRxiv2024

Hurdles to Horizontal Gene Transfer: Synonymous variation determines antibiotic resistance phenotype across species

Evidence that synonymous mutations and synonymous gene variants have fitness effects have accumulated recently. Since horizontal gene transfer represents a change in the genome of expression of the transferred gene, we hypothesized that the codon usage preferences of a horizontally transferred gene could determine the conferred fitness advantage or disadvantage, condition the immediate success of the transfer and in the longer term orient transfers. To test this hypothesis, we characterized resistance levels of synonymous variants of a gentamicin resistance gene, inserted into a broad-host range plasmid and transformed into three different bacterial species Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. We revealed a strong species effect, explained in part by differences in plasmid copy number between host species. Importantly, the relative levels of resistance conferred by each synonymous variant were not conserved across species, indicating that these phenotypic effects are due to differing compatibility between the transferred variants and the receiver bacterial genomes. This species-variant interaction confirms that the codon composition of a gene can be a determinant of post-horizontal gene transfer success. However, the similarity in codon usage between the synonymous variants and the host genome only explained the phenotypic differences between variants in one species, P. aeruginosa. Further investigations of the effects of local codon usage, translation bottlenecks and internal Shine-Dalgarno sequences did not reveal common universal mechanisms across our three bacterial species and point to multiple paths leading from the synonymous sequence to phenotype and a species-specific sensitivity to these different paths.

evolutionary biology↗

bioRxiv2021

Beyond Fitness Decoupling: Tradeoff-breaking during Evolutionary Transitions in Individuality

Evolutionary transitions in individuality (ETIs) involve the formation of Darwinian collectives from Darwinian particles. The transition from cells to multicellular life is a prime example. During an ETI, collectives become units of selection in their own right. However, the underlying processes are poorly understood. One observation used to identify the completion of an ETI is an increase in collective-level performance accompanied by a decrease in particle-level performance, for example measured by growth rate. This seemingly counterintuitive dynamic has been referred to as "fitness decoupling" and has been used to interpret both models and experimental data. Using a mathematical approach, we show this concept to be problematic in that the fitness of particles and collectives can never decouple--calculations of particle and collective fitness performed over appropriate and equivalent time intervals are necessarily the same. By way of solution, we draw attention to the value of mechanistic approaches that emphasise traits, and tradeoffs among traits, as opposed to fitness. This trait-based approach is sufficient to capture dynamics that underpin evolutionary transitions. In addition, drawing upon both experimental and theoretical studies, we show that while early stages of transitions might often involve tradeoffs among particle traits, later--and critical--stages are likely to involve the rupture of such tradeoffs. Thus, tradeoff-breaking stands as a useful marker for ETIs.

evolutionary biology↗

bioRxiv2020

Analysis of an experimental transition in individuality challenges the need to assign traits to levels

Major evolutionary transitions in individuality, at any level of the biological hierarchy, occur when groups participate in Darwinian processes as units of selection in their own right. Identifying transitions in individuality can be problematic because apparent selection at one level of the biological hierarchy may be a by-product of selection occurring at another level. Here we discuss approaches to this "levels-of-selection" problem and apply them to a previously published experimental exploration of the evolutionary transition to multicellularity. In these experiments groups of the bacterium Pseudomonas fluorescens were required to reproduce via life cycles involving soma- and germline-like phases. The rate of transition between the two cell types was a focus of selection, and might be regarded as a property of groups, cells, or even genes. By examining the experimental data under several established philosophical frameworks, we argue that in the Pseudomonas experiments, bacterial groups acquired Darwinian properties sufficient to allow the evolution of traits adaptive at the group level.

evolutionary biology↗

bioRxiv2018

Meta-population structure and the evolutionary transition to multicellularity

AO_SCPLOWBSTRACTC_SCPLOWThe evolutionary transition to multicellularity has occurred on numerous occasions, but transitions to complex life forms are rare. While the reasons are unclear, relevant factors include the intensity of within-versus between-group selection that are likely to have shaped the course of life cycle evolution. A highly structured environment eliminates the possibility of mixing between evolving lineages, thus ensuring strong competition between groups. Less structure intensifies competition within groups, decreasing opportunity for group-level evolution. Here, using populations of the bacterium Pseudomonas fluorescens, we report the results of experiments that explore the effect of lineage mixing on the evolution of nascent multicellular groups. Groups were propagated under regimes requiring reproduction via a life cycle replete with developmental and dispersal (propagule) phases, but in one treatment lineages never mixed, whereas in a second treatment, cells from different lineages experienced intense competition during the dispersal phase. The latter treatment favoured traits promoting cell growth at the expense of traits underlying group fitness - a finding that is supported by results from a mathematical model. Together our results show that the transition to multicellularity benefits from ecological conditions that maintain discreteness not just of the group (soma) phase, but also of the dispersal (germline) phase.

evolutionary biology↗