Computational protocol: Prevalence of blood parasites in seabirds - a review

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Protocol publication

[…] We constructed a phylogenetic tree using published information on phylogenetic associations among the species of our study, in particular for Neoaves [,], for Sphenisciformes [], for Procellariiformes [-], for Phaethontidae [], for Pelecaniformes [-] and for Charadriiformes [-].Because we used information from different sources and the branch lengths were not specified in all studies we used to reconstruct the phylogeny, we conducted all analyses with a tree of equal branch lengths, which assumes a punctuational model of evolution []. The software MESQUITE [] was used to construct the phylogenetic tree (see tree topology in Figure ). [...] We included all available data (from blood smears and PCR data) for each species with at least 15 sampled individuals. Parasite prevalences were arsin-square root transformed, while the variables body mass, clutch size, incubation and nestling period were log10-transformed. To control for allometric effects on parasite prevalence, average adult body mass for the species (obtained from the literature) was included in all analyses as a predictor variable. Evolutionary models were tested by Generalized Least Squares models fitted by REML, incorporating phylogenetic information with a Brownian motion correlation structure, and method (smears vs. PCR) as a variable. Model selection was based on Akaike's information criterion (AIC). All analyses were repeated using parasite prevalence as a categorical variable (presence/absence) in phylogenetically informed Generalized Estimating Equations (GEE) models []. To estimate parameters of character evolution and the proportion of variance in parasite prevalence explained by phylogenetic associations among species, we computed phylogenetic autorregressions and calculated Moran's autocorrelation Index []. We used R 2.11.1 (R Development Core Team 2010) and the package "ape" [] for the analyses. […]

Pipeline specifications

Software tools Mesquite, APE
Application Phylogenetics