Phylogeography of Limia vittata (Cyprinodontiformes: Poeciliidae): geographical distribution of mitochondrial haplotypes is comparable to other Cuban poeciliids
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This is the supplementary material associated with the article "Phylogeography of <em>Limia vittata</em> (Cyprinodontiformes: Poeciliidae): geographical distribution of mitochondrial haplotypes is comparable to other Cuban poeciliids", published by the Biological Journal of the Linnean Society (https://doi.org/10.1093/biolinnean/blad040). The following documents (pdf format) are included: <strong>Supporting Information 1 </strong> <strong>Table S1.</strong> Sampling size (n) and haplotype (<em>COI</em>+<em>CR</em>) information for each sampling locality of <em>L. vittata</em> included in this study. Numbers correspond to those indicated in Figure 1. A star (*) represents a new locality record for <em>L. vittata</em>. ANC: acronym of the Acuario Nacional de Cuba Collection, La Habana, Cuba. <strong>Supporting Information 2</strong> <strong>Table S1.</strong> Prior distribution of parameters used for the analysis of the <em>L. vittata</em> data based on the ABC approach using DIYABC v.2.1.0 (Cornuet <em>et al</em>., 2014). Time is in generations. W-PR: Western Pinar del Río population, W-C: Western-Central population, C-E: Central-Eastern population. <strong>Table S2.</strong> Summary statistics between <em>L. vittata</em> haplogroups for each scenario based on 3 × 10<sup>6</sup> simulated datasets. NHA: number of alleles, NSS: number of segregating sites, MPD: mean of pairwise differences, VPD: variance of pairwise differences, MP2: mean pairwise differences within samples, MPB: mean pairwise differences between samples, HST: F<sub><em>ST</em></sub> between samples. <strong>Table S3.</strong> Posterior distributions of the parameters based on scenario B for <em>L. vittata</em>. Data were obtained from 1% of the simulated dataset (1 × 10<sup>6</sup>). Time is in generations. W-PR: Western Pinar del Río population, W-C: Western-Central population, C-E: Central-Eastern population. RMAE: relative median of absolute error. <strong>Figure S1.</strong> PCA of the summary statistics of the observed dataset and the dataset generated from the prior distribution of parameters to evaluate the three biogeographic scenarios explaining the current distribution of <em>L. vittata</em>. The analysis was performed using DIYABC v.2.1.0 (Cornuet <em>et al.</em>, 2014). <strong>Figure S2.</strong> Posterior probability of the biogeographic scenarios tested to explain the current distribution of <em>L. vittata</em>. Logistic regression was used to compute the posterior probability using the ABC approach as implemented in DIYABC v.2.1.0 (Cornuet <em>et al.</em>, 2014). <strong>Supporting Information 3</strong> <strong>Figure S1.</strong> Bayesian tree depicting the relationships of 160 partial <em>COI</em>+<em>CR</em> sequences of <em>L. vittata</em>. The red dots depict samples from eastern localities (Yateras, Sabanalamar, and Yacabo Abajo) sharing the W-C haplogroups (H9 and H10). Bootstrap support (≥ 93) and Bayesian posterior probabilities (≥ 0.95) are shown for the main clades. <strong>Supporting Information 4</strong> <strong>Figure S1.</strong> Mismatch distribution of pairwise haplotype differences from partial <em>COI</em> and <em>CR</em> sequences for the three haplogroups recovered in <em>L. vittata</em>. Dashed lines represent the distribution of the observed pairwise nucleotide differences, whereas solid lines represent the values expected after a population growth or decline model. <strong>Supporting Information 5</strong> <strong>Figure S1.</strong> Maximum Likelihood tree and haplotype network of <em>Girardinus falcatus</em>, <em>Girardinus metallicus,</em> and the <em>Gambusia punctata</em> species complex based on <em>cytb</em> partial sequences. Each colour represents a geographic region in Cuba. Green: westernmost Cuba, blue: western Cuba, orange: central Cuba, red: eastern Cuba. Numbers on tree branches are bootstrap values ≥ 95% and hatch marks on the networks are the number of mutations. n: number of individuals, H: number of haplotypes, <em>h</em>: haplotype diversity, π: nucleotide diversity, SD: standard deviation. <strong>Table S1.</strong> Sampling size (n), GenBank accession numbers, and studies that made available the sequences of cytochrome <em>b</em> used for the phylogeographic comparisons of the different poeciliids in Cuba.
