Insights from a general,full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging*

Factors that influence the distribution, abundance, and diversification of species can simultaneously affect multiple evolutionary lineages within or across communities. These include changes to the environment or inter-specific ecological interactions that cause ranges of multiple species to contract, expand, or fragment. Such processes predict temporally clustered evolutionary events across species, such as synchronous population divergences and/or changes in population size. There have been a number of methods developed to infer shared divergences or changes in population size, but not both, and the latter has been limited to approximate methods. We introduce a full-likelihood Bayesian method that uses genomic data to estimate temporal clustering of an arbitrary mix of population divergences and population-size changes across taxa. Using simulated data, we find that estimating the timing and sharing of demographic changes tends to be inaccurate and sensitive to prior assumptions, which is in contrast to accurate, precise, and robust estimates of shared divergence times. We also show that previous estimates of co-expansion among five Alaskan populations of three-spine sticklebacks (Gasterosteus aculeatus) were likely driven by prior assumptions and ignoring invariant characters. We conclude by discussing potential avenues to improve the estimation of synchronous demographic changes across populations.     

Long-Term Persistence with Injectable Therapy in Relapsing-Remitting Multiple Sclerosis: An 18-Year Observational Cohort Study

Disease modifying therapies (DMTs) reduce the frequency of relapses and accumulation of disability in multiple sclerosis (MS). Long-term persistence with treatment is important to optimize treatment benefit. This long-term, cohort study was conducted at the Calgary MS Clinic. All consenting adults with relapsing-remitting MS who started either glatiramer acetate (GA) or interferon-β 1a/1b (IFN-β) between January 1^st, 1996 and July 1^st, 2011 were included. Follow-up continued to February 1^st, 2014. Time-to-discontinuation of the initial and subsequently-prescribed DMTs (switches) was analysed using Kaplan-Meier survival analyses. Group differences were compared using log-rank tests and multivariable Cox regression models. Analysis included 1471 participants; 906 were initially prescribed GA and 565 were initially prescribed IFN-β. Follow-up information was available for 87%; 29 (2%) were lost to follow-up and 160 (11%) moved from Southern Alberta while still using DMT. Median time-to-discontinuation of all injectable DMTs was 11.1 years. Participants with greater disability at treatment initiation, those who started treatment before age 30, and those who started between 2006 and 2011 were more likely to discontinue use of all injectable DMTs. Median time-to-discontinuation of the initial DMT was 8.6 years. Those initially prescribed GA remained on treatment longer. Of 610 participants who discontinued injectable DMT, 331 (54%) started an oral DMT, or a second-line DMT, or resumed injectable DMT after 90 days. Persistence with injectable DMTs was high in this long-term population-based study. Most participants who discontinued injectable DMT did not remain untreated. Further research is required to understand treatment outcomes and outcomes after stopping DMT.     

Ants provide nutritional and defensive benefits to the carnivorous plant Sarracenia minor

Ants can have important, but sometimes unexpected, effects on the plants they associate with. For carnivorous plants, associating with ants may provide defensive benefits in addition to nutritional ones. We examined the effects of increased ant visitation and exclusion of insect prey from pitchers of the hooded pitcher plant Sarracenia minor, which has been hypothesized to be an ant specialist. Visitation by ants was increased by placing PVC pipes in the ground immediately adjacent to 16 of 32 pitcher plants, which created nesting/refuge sites. Insects were excluded from all pitchers of 16 of the plants by occluding the pitchers with cotton. Treatments were applied in a 2 × 2 factorial design in order to isolate the hypothesized defensive benefits from nutritional ones. We recorded visitation by ants, the mean number of ants captured, foliar nitrogen content, plant growth and size, and levels of herbivory by the pitcher plant mining moth Exyra semicrocea. Changes in ant visitation and prey capture significantly affected nitrogen content, plant height, and the number of pitchers per plant. Increased ant visitation independent of prey capture reduced herbivory and pitcher mortality, and increased the number of pitchers per plant. Results from this study show that the hooded pitcher plant derives a double benefit from attracting potential prey that are also capable of providing defense against herbivory.     

Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection

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Expanding the Proteome of an RNA Virus by Phosphorylation of an Intrinsically Disordered Viral Protein

The human proteome contains myriad intrinsically disordered proteins. Within intrinsically disordered proteins, polyproline-II motifs are often located near sites of phosphorylation. We have used an unconventional experimental paradigm to discover that phosphorylation by protein kinase A (PKA) occurs in the intrinsically disordered domain of hepatitis C virus non-structural protein 5A (NS5A) on Thr-2332 near one of its polyproline-II motifs. Phosphorylation shifts the conformational ensemble of the NS5A intrinsically disordered domain to a state that permits detection of the polyproline motif by using ¹⁵N-, ¹³C-based multidimensional NMR spectroscopy. PKA-dependent proline resonances were lost in the presence of the Src homology 3 domain of c-Src, consistent with formation of a complex. Changing Thr-2332 to alanine in hepatitis C virus genotype 1b reduced the steady-state level of RNA by 10-fold; this change was lethal for genotype 2a. The lethal phenotype could be rescued by changing Thr-2332 to glutamic acid, a phosphomimetic substitution. Immunofluorescence and transmission electron microscopy showed that the inability to produce Thr(P)-2332-NS5A caused loss of integrity of the virus-induced membranous web/replication organelle. An even more extreme phenotype was observed in the presence of small molecule inhibitors of PKA. We conclude that the PKA-phosphorylated form of NS5A exhibits unique structure and function relative to the unphosphorylated protein. We suggest that post-translational modification of viral proteins containing intrinsic disorder may be a general mechanism to expand the viral proteome without a corresponding expansion of the genome.