Estimated F_ST values on complete dataset.

<p>Estimated F_ST values on complete dataset.</p

Estimated F_ST values changed allele frequency distributions, n = 50, k = 1000.

<p>Estimated F_ST values changed allele frequency distributions, n = 50, k = 1000.</p

Effect of increasing sample sizes.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042649#s2" target="_blank">Results</a> are shown for the simulations where allele frequencies were equally distributed from 0.05 to 0.95. The number of markers was fixed at k = 100 (left column) and k = 1,000 (right column). Each row contains a different level of genetic differentiation (F_ST = 0, 0.01, 0.05, 0.1, 0.2, 0.4). The results (average F_ST and 95% CI) of each estimator are depicted in the different graphs: F_ST^W (blue circles), F_ST^C&W (purple squares) and F_ST^R (green triangles). The dashed red line indicates the actual F_ST for the simulated population.</p

Effect of increasing the number of markers.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042649#s2" target="_blank">Results</a> are shown for the simulations where allele frequencies were equally distributed from 0.05 to 0.95. The number of individuals was fixed at n = 4 (left column) and n = 20 (right column). Each row contains (like in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042649#pone-0042649-g001" target="_blank">Figure 1</a>) a different level of genetic differentiation (F_ST = 0, 0.01, 0.05, 0.1, 0.2, 0.4). The results (average F_ST and 95% CI) of each estimator are depicted in the different graphs: F_ST^W (blue circles), F_ST^C&W (purple squares) and F_ST^R (green triangles). The dashed red line indicates the actual F_ST for the simulated population.</p

Full SNP dataset

Provided is the SNP dataset file for guppies distributed across northen trinidad

Pigment cell types of the guppy.

<p>Xanthophores (X), melanophores (M) and iridophores (I) on the dorsal side of a guppy female shown under incident light. Leucophores could not be identified. Scale bar: 200 µm.</p

Ultrastructure of Cumaná blue spot.

<p>(A,B) TEM images of Cumaná blue spot. An image of the blue spot taken under incident light conditions is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085647#pone-0085647-g002" target="_blank">Figure 2B</a> (trait 2). Dermal iridophores and hypodermal iridophores and melanophores contribute to the spot. The epidermis was detached during sample preparation in (A). D, dermis; H, hypodermis; MU, muscle; S, scale; SP, stratum spongiosum of dermis. For other abbreviations see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085647#pone-0085647-g003" target="_blank">Figure 3</a>. Individual from which image (A) was taken was post-fixed with osmium tetroxide. Scale bars: 5 µm.</p

Grid references of catching sites.

<p>Grid references of sites used to catch fish for the re-sampling of the Turure, behavioural and mesocosm experiments. The drainage system each river belongs to is indicated.</p

Primer sequences.

<p>Sequences of forward and reverse primer for each marker that produced clear results in pure Guanapo and Oropuche fish. The linkage group of all markers and the number of resulting SNPs per marker are shown. (Sequences from: <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038404#pone.0038404-Magurran2" target="_blank">[31]</a>, Data supplement no 2 & 3).</p

Phenotypes of male Cumaná, Quare6, and Maculatus guppies.

<p>(A,C,E) Lateral aspects of adult males taken under incident light conditions. White rectangles indicate details enlarged in (B,D,F) and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085647#pone-0085647-g006" target="_blank">Figures 6</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085647#pone-0085647-g007" target="_blank">7</a>. Traits are labeled with numbers according to their appearance in the text: 1, Cumaná black and orange ornaments on the dorsal fin; 2, Cumaná blue iridescent spot; 3, Cumaná ventral black margin of the caudal peduncle; 4, Cumaná orange-black lining of the tail fin; 5, Quare6 tail fin color pattern; 6, central black spot; 7, central orange spot; 8, Quare6 posterior black spot on caudal peduncle; 9, Maculatus black spot and whitish ornaments on the dorsal fin. We investigated the ultrastructure of traits 2, 4 (orange part), 5, 6, 7, 8, and 9 (whitish part). Scale bars: (A,C,E) 0.5 cm; (B,D,F) 500 µm.</p