Application to oriole niche evolution
Large numbers of occurrence points were available for this genus, thanks to recent advances in biodiversity informatics and citizen-science initatives regarding bird distributions (Supplement 7 Table 1, Supplements 8 and 9). Coding knowledge of known niche characteristics of each oriole species (Supplementary Figures 2 and 3) yielded niche estimates for some species that were completely characterized with respect to M . That is, estimates of suitable conditions were contained completely within the environments available in M , and did not appear truncated for the following species: Icterus fuertesi with regard to temperature and precipitation, andIcterus graceannae and Icterus galbula with regard to precipitation (Supplement 7 Figures 2 and 3). The remaining species had niche axes that were flanked by unknown maxima and/or minima.
Evolutionary rate estimates for the two niche dimensions showed conflicting patterns. For annual precipitation, σ2estimates based on traditional coding were an order of magnitude higher than our bin-based coding method, consistent with the pattern shown in Saupe et al (2017) and our bin-based coding simulation. In contrast, for mean annual temperature, traditional coding methods yielded an estimated σ2 value lower (but still within an order of magnitude) than the σ2 estimated from our bin-based coding method (Supplement 7 Table 2).
In general, our reconstructions of the evolutionary history of species’ fundamental niche in the genus Icterus indicated evolutionary stability (Figs. 5 and 6; Supplement 7 Tables 3-6, Supplement 12). For temperature, both methods reconstructed a conserved mean annual temperature niche, although it was much broader for maximum likelihood (21 to 26ºC) than parsimony (24 to 25ºC). For precipitation, maximum likelihood reconstructed a core certain conserved annual precipitation niche of 71 to 240 mm. Parsimony-based reconstructions suggested far less certainty in inferred ancestral character states than maximum likelihood, and recovered no core conserved fundamental niche for precipitation. Furthermore, reconstructions based on traditional coding methods fell within the breadth of the fundamental niches reconstructed using maximum likelihood at every node for both environmental variables (Supplement 7 Tables 4 and 6), whereas reconstructions based on maximum parsimony inferred unknown character states bins containing the values based on traditional coding at only four of 33 nodes for mean annual temperature and 30 of 33 nodes for annual precipitation (Supplement 7 Tables 3 and 5).