Online Appendix 4

R code employed to conduct analyse

Online Appendix 3

Morphological measurements and geographic provenance of male specimens of Geospiza ground-finches employed in analyses

Supplementary Material

Supplementary figures and online appendices 1 and 2

Haplotype networks showing that no alleles are shared between populations of <i>A. floriceps</i> in any of the genes analyzed.

<p>Blue corresponds to <i>A. f. floriceps</i> and red to <i>A. f. berlepschi</i>. Circle size is proportional to the number of individuals with each haplotype; hatches indicate mutational steps. (a) ND2, (b) ND4, (c) Bfib7 and (d) ODC.</p

Model of potential distribution constructed based on localities of <i>A. f. berlepschi</i> projected onto the region where <i>A. f. floriceps</i> occurs (indicated by a blue shape; (a)).

<p>Model of potential distribution constructed based on localities of <i>A. f. floriceps</i> projected onto the region where <i>A. f. berlepschi</i> occurs (indicated by a red shape; (b)). Red and blue dots indicate localities used to build the models for <i>A. f. berlepschi</i> and <i>A. f. floriceps,</i> respectively. Darker colors denote areas of greater climatic suitability in a continuous scale (i.e., no cutoff threshold was established in Maxent). Note that localities of each population have low suitability according to the model constructed with data from the other population, indicating niche divergence.</p

Genetic Differentiation, Niche Divergence, and the Origin and Maintenance of the Disjunct Distribution in the Blossomcrown <i>Anthocephala floriceps</i> (Trochilidae)

<div><p>Studies of the origin and maintenance of disjunct distributions are of special interest in biogeography. Disjunct distributions can arise following extinction of intermediate populations of a formerly continuous range and later maintained by climatic specialization. We tested hypotheses about how the currently disjunct distribution of the Blossomcrown (<i>Anthocephala floriceps</i>), a hummingbird species endemic to Colombia, arose and how is it maintained. By combining molecular data and models of potential historical distributions we evaluated: (1) the timing of separation between the two populations of the species, (2) whether the disjunct distribution could have arisen as a result of fragmentation of a formerly widespread range due to climatic changes, and (3) if the disjunct distribution might be currently maintained by specialization of each population to different climatic conditions. We found that the two populations are reciprocally monophyletic for mitochondrial and nuclear loci, and that their divergence occurred ca. 1.4 million years before present (95% credibility interval 0.7–2.1 mybp). Distribution models based on environmental data show that climate has likely not been suitable for a fully continuous range over the past 130,000 years, but the potential distribution 6,000 ybp was considerably larger than at present. Tests of climatic divergence suggest that significant niche divergence between populations is a likely explanation for the maintenance of their disjunct ranges. However, based on climate the current range of <i>A. floriceps</i> could potentially be much larger than it currently is, suggesting other ecological or historical factors have influenced it. Our results showing that the distribution of <i>A. floriceps</i> has been discontinous for a long period of time and that populations exhibit different climatic niches have taxonomic and conservation implications.</p></div

Divergence on niche axes between populations of <i>A. floriceps.</i>

<p>Instances of significant niche divergence (D) or conservatism (C) are shown in bold (t-test; p<0.05). Values in parentheses represent the 95% confidence intervals of the null distributions based on background divergence between the geographic ranges of each population. For each niche axis, the top four environmental variables loading on it are shown (asterisks indicate opposite sign). bio3 = isothermality, bio6 = minimum temperature of coldest month, bio10 = mean temperature of warmest quarter, bio 11 = mean temperature of coldest quarter, bio12 = annual precipitation, bio13 = precipitation of wettest month, bio14 = precipitation of driest month, bio15 = precipitation seasonality, bio16 = precipitation of wettest quarter, bio17 = precipitation of driest quarter, bio18 = precipitation of warmest quarter. For full results of principal components analysis see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108345#pone.0108345.s001" target="_blank">Fig. S1</a>.</p><p>Divergence on niche axes between populations of <i>A. floriceps.</i></p

Current distribution of the Blossomcrown (<i>Anthocephala floricep</i>s).

<p>The blue area corresponds to <i>A. f. floriceps</i> from the Sierra Nevada de Santa Marta and the red to <i>A. f. berlepschi</i> from the Andes. The locations of different montane regions mentioned in the text are indicated.</p

Potential distributions for <i>A. floriceps</i> predicted using climatic data in Maxent.

<p>Models are shown for climatic conditions of (a) the present, (b) 6,000 ybp, (c) 21,000 ybp and (d) 130,000 ybp. Dots on the present distribution map indicate localities used to build the models. Darker colors denote areas of greater climatic suitability; areas in white are below the minimum suitability threshold and are therefore considered to be unsuitable.</p

Divergence-time estimates (mya) between populations of <i>A. floriceps</i> and outgroups, based on two mitochondrial genes using a Bayesian relaxed molecular-clock analysis.

<p>Node bars indicate 95% credibility intervals on node ages; scale bar shows time in million years. Values on each clade indicate posterior probabilities when greater than 0.7. Symbols indicate individuals having identical sequences in <i>A. f. floriceps</i> (*) and <i>A. f. berlepschi</i> (¶).</p