Back to the fundamentals: a reply to Basener and Sanford 2018.

Fisher's fundamental theorem of natural selection has haunted theoretical population genetic literature since it was proposed in 1930, leading to numerous interpretations. Most of the confusion stemmed from Fisher's own obscure presentation. By the 1970s, a clearer view of Fisher's theorem had been achieved and it was found that, regardless of its utility or significance, it represents a general theorem of evolutionary biology. Basener and Sanford (J Math Biol 76:1589-1622, 2018) writing in JOMB, however, paint a different picture of the fundamental theorem as one hindered by its assumptions and incomplete due to its failure to explicitly incorporate mutational effects. They argue that Fisher saw his theorem as a "mathematical proof of Darwinian evolution". In this reply, we show that, contrary to Basener and Sanford, Fisher's theorem is a general theorem that applies to any evolving population, and that, far from their assertion that it needed to be expanded, the theorem already implicitly incorporates ancestor-descendant variation. We also show that their numerical simulations produce unrealistic results. Lastly, we argue that Basener and Sanford's motivations were in undermining not merely Fisher's theorem, but the concept of universal common descent itself.

Base composition and translational selection are insufficient to explain codon usage bias in plant viruses.

Viral codon usage bias may be the product of a number of synergistic or antagonistic factors, including genomic nucleotide composition, translational selection, genomic architecture, and mutational or repair biases. Most studies of viral codon bias evaluate only the relative importance of genomic base composition and translational selection, ignoring other possible factors. We analyzed the codon preferences of ssRNA (luteoviruses and potyviruses) and ssDNA (geminiviruses) plant viruses that infect translationally distinct monocot and dicot hosts. We found that neither genomic base composition nor translational selection satisfactorily explains their codon usage biases. Furthermore, we observed a strong relationship between the codon preferences of viruses in the same family or genus, regardless of host or genomic nucleotide content. Our results suggest that analyzing codon bias as either due to base composition or translational selection is a false dichotomy that obscures the role of other factors. Constraints such as genomic architecture and secondary structure can and do influence codon usage in plant viruses, and likely in viruses of other hosts.

TextTB: A Mixed Method Pilot Study Evaluating Acceptance, Feasibility, and Exploring Initial Efficacy of a Text Messaging Intervention to Support TB Treatment Adherence.

Objective. To assess a text messaging intervention to promote tuberculosis (TB) treatment adherence. Methods. A mixed-methods pilot study was conducted within a public pulmonary-specialized hospital in Argentina. Patients newly diagnosed with TB who were 18 or older, and had mobile phone access were recruited and randomized to usual care plus either medication calendar (n = 19) or text messaging intervention (n = 18) for the first two months of treatment. Primary outcomes were feasibility and acceptability; secondary outcomes explored initial efficacy. Results. Feasibility was evidenced by high access to mobile phones, familiarity with texting, most phones limited to basic features, a low rate of participant refusal, and many describing suboptimal TB understanding. Acceptability was evidenced by participants indicating feeling cared for, supported, responsible for their treatment, and many self-reporting adherence without a reminder. Participants in the texting group self-reported adherence on average 77% of the days whereas only 53% in calendar group returned diaries. Exploring initial efficacy, microscopy testing was low and treatment outcomes were similar in both groups. Conclusion. The texting intervention was well accepted and feasible with greater reporting of adherence using text messaging than the diary. Further evaluation of the texting intervention is warranted.

Single-stranded genomic architecture constrains optimal codon usage.

Viral codon usage is shaped by the conflicting forces of mutational pressure and selection to match host patterns for optimal expression. We examined whether genomic architecture (single- or double-stranded DNA) influences the degree to which bacteriophage codon usage differ from their primary bacterial hosts and each other. While both correlated equally with their hosts' genomic nucleotide content, the coat genes of ssDNA phages were less well adapted than those of dsDNA phages to their hosts' codon usage profiles due to their preference for codons ending in thymine. No specific biases were detected in dsDNA phage genomes. In all nine of ten cases of codon redundancy in which a specific codon was overrepresented, ssDNA phages favored the NNT codon. A cytosine to thymine biased mutational pressure working in conjunction with strong selection against non-synonymous mutations appears be shaping codon usage bias in ssDNA viral genomes.