EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics.

BACKGROUND: Branch-length parameters are a central component of phylogenetic models and of intrinsic biological interest. Default branch-length priors in some Bayesian phylogenetic software can be unintentionally informative and lead to branch- and tree-length estimates that are unreasonable. Alternatively, priors may be uninformative, but lead to diffuse posterior estimates. Despite the widespread availability of relevant datasets from other groups, biologists rarely leverage outside information to specify branch-length priors that are specific to the analysis they are conducting. RESULTS: We developed the software package EmpPrior to facilitate the collection and incorporation of relevant, outside information when setting branch-length priors for phylogenetics. EmpPrior efficiently queries TreeBASE to find data that are similar to focal data, in terms of taxonomic and genetic sampling, and uses them to inform branch-length priors for the focal analysis. EmpPrior consists of two components: EmpPrior-search, written in Java to query TreeBASE, and EmpPrior-fit, written in R to parameterize branch-length distributions. In an example analysis, we show how the use of relevant, outside data is made possible by EmpPrior and improves tree-length estimates from a focal dataset. CONCLUSION: EmpPrior is easy to use, fast, and improves both the accuracy and precision of branch-length estimates in many circumstances. While EmpPrior's focus is on branch lengths, the strategy it employs could easily be extended to address other prior parameterization problems in phylogenetics.

Deflating trees: improving Bayesian branch-length estimates using informed priors.

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.

Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster.

Stochastic models of sequence evolution have been developed to reflect many biologically important processes, allowing for accurate phylogenetic reconstruction when an appropriate model is selected. However, commonly used models do not incorporate several potentially important biological processes. Spurious phylogenetic inference may result if these processes play an important role in the evolution of a dataset yet are not incorporated into assumed models. Few studies have attempted to assess the relative importance of multiple processes in producing spurious inferences. The application of phylogenetic methods to infer the source of HIV-1 transmission clusters depends upon accurate phylogenetic results, yet there are several relevant unmodeled biological processes (e.g., recombination and convergence) that may cause complications. Here, through analyses of HIV-1 env sequences from a small, forensically important transmission cluster, we tease apart the impact of these processes and present evidence suggesting that convergent evolution and high rates of insertions and deletions (causing alignment uncertainty) led to spurious phylogenetic signal with forensic relevance. Previous analyses show paraphyly of HIV-1 lineages sampled from an individual who, based on non-phylogenetic evidence, had never acted as a source of infection for others in this transmission cluster. If true, this pattern calls into question assumptions underlying phylogenetic approaches to source and recipient identification. By systematically assessing the contribution of different unmodeled processes, we demonstrate that removal of sites likely influenced by strong positive selection both reduces the alignment-wide signal supporting paraphyly of viruses sampled from this individual and eliminates support for the effects of recombination. Additionally, the removal of ambiguously aligned sites alters strongly supported relationships among viruses sampled from different individuals. These observations highlight the need to jointly consider multiple unmodeled evolutionary processes and motivate a phylogenomic perspective when inferring viral transmission histories.

Populations at risk: conservation genetics of kangaroo mice (Microdipodops) of the Great Basin Desert.

The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mice are ecological specialists found within the Great Basin Desert and are potentially ideal organisms for assessing ecosystem health and inferring the biogeographic history of this vulnerable region. Herein, newly acquired nuclear-encoded microsatellite loci were utilized to assess patterns of variation within and among spatially discrete groups of kangaroo mice and to evaluate gene flow, demographic trends, and genetic integrity. Results confirm that there are at least three genetically distinct units within M. megacephalus and two such units within M. pallidus. The three units of M. megacephalus appear to have different demographic histories, with effectively no gene flow among them since their divergence. Similarly, the two units of M. pallidus also appear to have experienced different demographic histories, with effectively no gene exchange. Contemporary effective population sizes of all groups within Microdipodops appear to be low (<500), suggesting that each genetic lineage may have difficulty coping with changing environmental pressures and hence may be at risk of extirpation. Results of this study indicate that each Microdipodops group should be recognized, and therefore managed, as a separate unit in an effort to conserve these highly specialized taxa that contribute to the diversity of the Great Basin Desert ecosystem. The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Herein, newly acquired nuclear-encoded microsatellite loci were utilized to assess patterns of variation within and among spatially discrete groups of the dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mouse, and to evaluate gene flow, demographic trends, and genetic integrity. Results of this study indicate that each Microdipodops group should be recognized, and therefore managed, as a separate unit in an effort to conserve these highly specialized taxa that contribute to the diversity of the Great Basin Desert ecosystem (photo credit J. C. Hafner).