Prior distributions can have a strong effect on the results of Bayesian analyses. However, no general consensus exists for how priors should be set in all circumstances. Branch-length priors are of particular interest for phylogenetics, because they affect many parameters and biologically relevant inferences have been shown to be sensitive to the chosen prior distribution. Here, we explore the use of outside information to set informed branch-length priors and compare inferences from these informed analyses to those using default settings. For both the commonly used exponential and the newly proposed compound Dirichlet prior distributions, the incorporation of relevant outside information improves inferences for data sets that have produced problematic branch- and tree-length estimates under default settings. We suggest that informed priors are worthy of further exploration for phylogenetics.

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Due to the desire to both shorten the length and reduce the size of clinical trials in human immunodeficiency virus (HIV) disease, the use of surrogate end points such as HIV-1 RNA is becoming increasingly standard. While these end points may be reasonable surrogates for the clinical effectiveness of drugs, a key point in their use as trial end points is the definition of a relevant duration of antiviral response. This definition is often complicated by the desire to perform interim reviews of ongoing laboratory end point trials. Unlike clinical end point trials, in which early clinical response is generally indicative of longer-term follow-up, it is yet to be determined whether short-term viral response adequately predicts the long-term durability of that response.

We report 17 novel microsatellite loci in the parasitic chewing louse Geomydoecus ewingi, a common parasite of the pocket gopher, Geomys breviceps . Thirty-three G. ewingi individuals from 1 geographic locality and 3 pocket gopher hosts (populations) were genotyped at each locus. The number of alleles per locus ranged from 3 to 13. Observed heterozygosity ranged from 0.182 to 0.788. Four to 6 loci per louse population fell outside of Hardy-Weinberg expectations (HWE) and examination of population structure also revealed substantial homozygote excess as well as significant structure among louse populations. These findings are likely the consequence of biological characteristics of the lice (low dispersal abilities, population bottlenecks, etc.), which can result in inbreeding. Notably, when all louse individuals were analyzed together as 1 population, a Wahlund effect was detected, supporting that louse populations are restricted to 1 host individual. The microsatellite markers characterized in this study will be useful in future studies exploring the population dynamics in host-parasite systems, potentially yielding a better understanding of the processes underlying symbiotic associations.

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