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Pipeline publication

[…] , Australia‐New Guinea, New Zealand, and Chatham Islands); (5) a multi‐peak OU model (OUMniche) with separate random‐walk variances for each one of the five foraging niche categories (“canopy,” “low trees,” “trunks,” “shrubs,” and “ground”) and one global selection parameter (α); and (6) a multi‐peak OU model (OUMSURFACE) with separate random‐walk variances for each one of the adaptive peaks identified using SURFACE (see Section ). To deal with phylogenetic uncertainty, the BM, EB, and OU1 models were run across a sample of 100 trees obtained from the posterior distribution of the Bayesian analysis. For the multi‐peak (OUM) models, we first built stochastic character‐mapped reconstructions (SIMMAP; Bollback, ) of (1) foraging niche categories, (2) regions, and (3) adaptive peaks estimated by SURFACE, for each of the 100 trees sampled from the posterior distribution, using phytools (Revell, ). Models were implemented using the R packages geiger (Harmon, Weir, Brock, Glor, & Challenger, ) and OUwie (Beaulieu & O'Meara, ) and compared by means of the sample size‐corrected Akaike's Information Criterion (AICc)., We used Mantel tests to determine whether more similar species are those that (1) are closely related; (2) are more geographically close; (3) do not exhibit range overlap; and/or (4) share climatic conditions. To this end, we first produced matrices representing the phylogenetic, morphological, climatic, and geographic distances between all pairs of species. The phylogenetic matrix represents the patristic distance between each pair of species in the phylogeny depicted in Marki et al. (). Patristic distances wer […]

Pipeline specifications

Software tools SIMMAP, Phytools, GEIGER