Oriole analyses
We followed our methodologies described above for bin-based characterization of species’ ecological niches, evolutionary rate calculations, and illustration of ancestral niche inference for understanding patterns of niche evolution across the Icterusphylogeny. Analyses focused on 34 New World oriole species (genusIcterus ), represented in a phylogenetic analysis by Powell et al. (2014). We used the single best ultrametric maximum likelihood tree from Powell et al. (2014; their Figure 4) inferred from mitochondrial and nuclear DNA sequences. Distributional data for each species were drawn from the Global Biodiversity Information Facility (www.gbif.org, download specified at https://www.gbif.org/occurrence/download/0000369-180730143533302), a large portion of which derived from eBird (Supplement 7 Table 1, Supplements 8 and 9). We removed all records lacking geographic coordinates, and inspected those remaining with respect to known ranges of species based on expert assessment by four knowledgeable ornithologists (authors CXX, HXX, OXX, and PXX), removing records that reflected errors or outdated taxonomic arrangements. Species-specific hypotheses of areas accessible to the species (M ) were developed based on the biotic attributes and biogeographic history of the clade (Barve et al. 2011; Elith et al. 2010). That is, the ornithologists inspected patterns of occurrences for each species and outlined accessible-area hypotheses based on known barriers to dispersal (i.e., oceans, high mountain ranges, the Amazon River, deserts). While this step remains subjective, it is crucial to a realistic representation of the environments that should be considered as within the species’ environmental potential (Phillips et al. 2009; Barve et al. 2011). We included explicit recognition of the parts of these profiles that are not observable (i.e. at the periphery of M ), and scored them as unknown. For mean annual temperature (Bio1 in WorldClim v.1.4; Hijmans et al. 2005), we used 32 equal-width, 1ºC bins (3-4º, 4-5º, … 34-35º) across the full range of temperature values represented across all species’M areas. For annual precipitation (Bio12 in WorldClim v1.4; Hijmans et al. 2005), we used 80 10 mm-width bins, to cover the range of precipitation values from 0 to 800 mm across all species’ Mareas. For comparison to more traditional methods of coding species’ niches, we calculated the median annual precipitation and median mean annual temperature values at species’ occurrence points. As with our simulated species, we characterized species’ niches using R; the code can be found in Supplement 10 and an HTML report for this script can be found in Supplement 11.
We estimated evolutionary rates and inferred the evolutionary history of oriole temperature and precipitation niches using both our bin-based characterization and the more traditional trait characterization, following the same methods used in our simulations. We also compared the results of our new ancestral niche reconstruction method to those obtained from a more traditional single-continuous-value maximum likelihood reconstruction under a Brownian motion model, as implemented in ape , using the median cell value of suitable area within M for each species. Code for analyses can be found in Supplement 12; annotated code with tables and figures provided as an HTML document in Supplement 13.