Baylisascaris procyonis

Camp, Lauren E., Radke, Marc R., Shihabi, Danny M., Pagan, Christopher, Yang, Guangyou & Nadler, Steven A., 2018, Molecular phylogenetics and species-level systematics of Baylisascaris, International Journal for Parasitology: Parasites and Wildlife 7 (3), pp. 450-462 : 453-454

2.5. Species delimitation of B. procyonis and B. columnaris with BP&P

The program BP&P v3.3 (Bayesian Phylogenetics and Phylogeography; Yang, 2015) was used for species delimitation analysis of B. procyonis and B. columnaris . BP&P implements the multispecies coalescent model (MSC) to account for possible conflicts between gene trees and species trees as coalescent models accommodate independent evolutionary histories of different loci ( Caviedes-Solis et al., 2015). Two parameters are included in the MSC: Θ s are the population size parameters for ancestral and modern species, and τ s are species divergence times. In BP&P the population size parameter is assigned a gamma prior of G Θ (α, β) with a mean of α/β. The root age (τ 0) also has a gamma prior G τ 0 (α, β), while the other species divergence times have a Dirichlet prior. The shape parameter α determines how informative each prior is – values of α ∼2 represent diffuse (non-informative) priors; diffuse priors were used for this analysis. However, for B. procyonis and B. columnaris we predict a moderate effective population size and a shallow divergence time (the latter based on previously observed low sequence divergence), and therefore initial priors were chosen to reflect those conditions. Multiple combinations of parameters for the gamma priors were run in BP&P module A00 to test the sensitivity of posterior estimates for Θ and τ to the priors before running the species delimitation module A11 ( Yang, 2015). We chose three priors each for Θ and τ. For Θ, the priors represented a large population (G Θ (1.95, 30)), a moderate population (G Θ (1.95, 300)), and a small population (G Θ (1.95, 3000)). For τ, the priors represented a deep divergence (G τ 0 (2, 200)), a shallow divergence (G τ 0 (2, 2000)), and a very shallow divergence (G τ 0 (2, 20000)).

The A11 module in BP&P was used to test the hypothesis of separate species for specimens from raccoon ( B. procyonis ) and skunk ( B. columnaris ). This module allows species delimitation and species tree inference to be conducted jointly. Specimens from grizzly bears ( B. transfuga ) collected in Alberta, Canada were used as an outgroup. Sequence files used in the analyses contained five loci: mitochondrial (12S + cox2), ITS, msp, ard1, and hars1. In BP&P, two sequences from each potential species are used to estimate Θ s. Sequence data from two individuals of Baylisascaris from grizzly bears were not available for msp or ard1, so these loci only included sequence data for specimens from skunk and raccoon hosts. The prior for the number of species was three, with the assumption that specimens derived from a given host were the same species. All nine combinations of Θ and τ 0 priors were run for 5 × 10 5 generations, with a burn-in of 1 × 10 4, and a sample frequency of 5. Two independent runs were conducted for each combination of priors to assess convergence. Similar results from both runs demonstrate adequate chain mixing.