Total evidence tree with highlighted phylogeographic structure.

<p>Letter codes next to the species symbol denote the geographical region of each sample. OCC: Sierra Madre Occidental; NRM: Northern Rocky Mountains; SRM: Southern Rocky Mountains; SI; Sky Islands; C: Contact zone comprised of the Sierra Madre Oriental and Trans-Mexican Volcanic Belt (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078228#pone-0078228-g002" target="_blank">Fig. 2</a>). Species key: Δ <i>Pinus ayacahuite</i>; * <i>Pinus strobiformis</i>; • <i>Pinus flexilis</i>; ▪ <i>Pinus strobus</i>; ◊ <i>Pinus lambertiana</i>.</p

Alignment of mitochondrial sequences

Second intron of the nad5 mitochondrial gene

Histograms of the background (random) distribution of <i>I</i> values (niche similarity statistic) of pairwise species comparisons (A-C) after 100 replicates, which corresponds to a p>0.01.

<p>Observed <i>I</i> values for each pairwise comparison are indicated by the vertical line.</p

Ecological Niche Models for the present conditions.

<p>(A) Colours represent the range of <i>P. flexilis</i> (green), <i>P. strobiformis</i> (yellow) and <i>P. ayacahuite</i> (cyan), with range overlaps shown in magenta. Zoom to the contact zone; (B) of the TMVB and SMOR with presence sites for <i>P. ayacahuite</i> Δ and <i>P. strobiformis</i> *.</p

Genetic diversity and genetic differentiation within and between species.

<p>Numbers in bold indicate statistically significant values at 99% confidence level.</p><p><i>n</i>: number of sequences; <i>h</i>: number of haplotypes; <i>S</i>: segregating sites; <i>H</i>_D: haplotype diversity; π: nucleotide diversity; θ_W: Watterson estimate for population mutation rate; <i>H</i>_ST: haplotype population differentiation; <i>F</i>_ST: genetic differentiation; <i>S</i>_nn: nearest neighbour statistic.</p

Environmental characterisation of the species complex.

<p>(A) Principal component analysis (PCA) of climatic variables for each species and over the entire climate availability (grey dots). The contribution of each component to the total variation is denoted in each axis. Arrows indicate the variables with a higher factor loadings for each component: Bio1: Annual Mean Temperature; Bio2: Mean Diurnal Range; Bio3: Isothermality; Bio5: Max. Temperature of Warmest Month; Bio6: Min. Temperature of Coldest Month; Bio7: Temperature Annual Range; Bio12: Annual Precipitation; Bio14: Precipitation of Driest Month. (B) Canonical analysis of the 3 principal components for the 3 species. Circles represent 95% confidence intervals.</p

Sequence Key for populations

This file has the identification keys for all sequences in the mitochondrial and chloroplast alignments

Bayesian genealogical reconstruction using different combinations of data.

<p>(A) Mitochondrial and chloroplast intergenic sequences; (B) Sequence data plus chloroplast microsatellites (cpSSR) coded as binary data; (C) Agglomerative nested cluster analysis of environmental information (principal components, C: contact zone; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078228#pone-0078228-g001" target="_blank">Figs. 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078228#pone-0078228-g002" target="_blank">2</a>); (D) Dated multilocus genealogy. Species key: Δ <i>Pinus ayacahuite</i>; * <i>Pinus strobiformis</i>; + <i>Pinus flexilis</i>; <i>▪ Pinus strobus</i>; ◊ <i>Pinus lambertiana</i>.</p

Phylogeny of <i>pvr2/eIF4E1</i> nucleotide sequence haplotypes and pvr2/eIF4E1-VPg:PVY interactions.

<p>The presented phylogeny was reconstructed by the NJ method using <i>pvr2/eIF4E1</i>, coding sequences. Bootstrap values (1000 replicates) are indicated on the nodes. A to Q are <i>pvr2/eIF4E1</i> haplotypes identified in chiltepin populations <i>pvr1</i>⁺ and <i>pvr2</i>⁺ to <i>pvr2</i>²⁵ denote <i>pvr2/eIF4E1</i> alleles deduced from the <i>pvr2/eIF4E1</i> coding sequences; <i>pot1</i>⁺: <i>Potyvirus</i> susceptibility allele from tomato (<i>Solanum lycopersicum</i>, accession number AY723733). pvr2/eIF4E1-VPg:PVY interactions were evaluated by yeast two-hybrid assays. Yeast growth (%) indicates the percentage of the yeast growth on the selective medium (-LWH) compared to the reference yeast colonies co-transformed with pGADT7::<i>pvr2</i>⁺ and pGBKT7::VPg-PVY; standard errors were obtained after 3 replicates of the yeast two-hybrid assays in which 3 independent colonies for each pvr2/eIF4E1-VPg:PVY combination were randomly selected.</p

Tajima’s D (<i>D</i>_<i>T</i>) values across the <i>pvr2/eIF4E1</i> coding sequences of all (A), wild (B) and cultivated (C) chiltepin populations.

<p>The green areas indicate the maximum of <i>D</i>_<i>T</i> values. I and II delimit the protein regions I and II involved in potyvirus resistance (as described in [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006214#pgen.1006214.ref023" target="_blank">23</a>]).</p