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reflected errors or outdated taxonomic arrangements.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.