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).