Nuclear and chloroplast microsatellite genotypes of open-pollinated seeds and naturally established seedlings in Pinus pinaster at Fuencaliente (Ciudad Real, Spain)

One line per combined nuclear-chloroplast individual genotype, comprising 12 nSSR diploid loci and 6 cpSSR haploid regions. For nSSR, the two alleles at each locus are listed in consecutive columns. Missing data coded with zeros. Samples collected in the field. DNA extracted with Invisorb DNA Plant HTS 96 Kit. Electrophoresis of amplified products with LI-COR 4300 DNA Analyzer for cpSSRs, and 3130xL and 3500 Genetic Analyzers (Applied Biosystems) for nSSRs. Fragment size determination through visual inspection using external size markers and reference samples with known allele size for cpSSR, and internal size standard and GeneMapper software (Applied Biosystems) for nSSR. The reference adult genotypes used in the study are available at http://dx.doi.org/10.5061/dryad.pq6hg

Nuclear and chloroplast microsatellite genotypes of open-pollinated seeds and naturally established seedlings in Pinus sylvestris at Sierra Nevada (Granada, Spain)

One line per combined nuclear-chloroplast individual genotype, comprising 10 nSSR diploid loci and 7 cpSSR haploid regions. For nSSR, the two alleles at each locus are listed in consecutive columns. Missing data coded with zeros. Samples collected in the field. DNA extracted with Invisorb DNA Plant HTS 96 Kit. Electrophoresis of amplified products with LI-COR 4300 DNA Analyzer for cpSSRs, and 3130xL and 3500 Genetic Analyzers (Applied Biosystems) for nSSRs. Fragment size determination through visual inspection using external size markers and reference samples with known allele size for cpSSR, and internal size standard and GeneMapper software (Applied Biosystems) for nSSR. The reference adult genotypes used in the study are available at http://dx.doi.org/10.5061/dryad.pq6h

Symphonia_globulifera_nSSR_data

Symphonia_globulifera_nSSR_dat

Graphical representation of two evolutionary scenarios tested using coalescent simulations.

<p>A) population divergence scenario, B) constant population size scenario.</p

Diversity patterns at the <i>trnC-ycf6</i> region in 14 Afrotropical tree taxa.

<p><i>N</i>, sample size; <i>pops</i>, number of sampling locations; <i>L_tot</i>, total length of alignment; <i>L</i>, length of alignment excluding gaps and missing data; <i>S(singl.)</i>, total number of single nucleotide mutations (number of singletons); <i>inv.</i>, number of inversions; <i>indel</i>, number of insertions/deletions; <i>SSR</i>, number of simple sequence repeats; <i>haps</i>, number of haplotypes; <i>Hd</i>, haplotype diversity; <i>π_T</i> and <i>θ_W</i>, estimates of nucleotide diversity x 10³; <i>h</i> and <i>v</i>, genetic diversity based on ordered or unordered alleles; nc, not calculated. For details see materials and methods.</p

Diversity estimates in 14 Afrotropical tree taxa under two evolutionary scenarios.

<p><i>N</i>, sample size; <i>h(SE)</i>, gene diversity and its standard error; <i>Nhap</i>, number of haplotypes; <i>Ar</i>, rarefied haplotype richness in a random sample of 3 sequences in dataset 1 or 18 sequences in dataset 2; <i>Npriv</i>, number of private haplotypes; <i>Arpriv</i>, rarefied private haplotypic richness; nc, not calculated.</p

Simulation results showing summary statistics and the expected proportion of significant differentiation tests under divergence or constant population size scenarios for simulated deme sizes, <i>N</i>, and mutation rates, <i>µ</i>, and their comparison to observed data from dataset 1.

<p>Averages over 100 independent simulations are shown, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084307#pone-0084307-g004" target="_blank">Figure 4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084307#pone.0084307.s004" target="_blank">Table S4</a>.</p><p>^a The fraction of samples with significant <i>F</i>_ST considers the proportion of 1-sided tests with <i>P</i><0.05.</p

Two physioclimatic features of the Lower Guinea region that led to the formulation of alternative evolutionary scenarios for Afrotropical tree taxa.

<p>A) The W-E environmental gradient, B) the N-S seasonal inversion, illustrated by the difference of January and July precipitation (mm).</p

Analysis of variance in 14 Afrotropical tree taxa under two evolutionary scenarios.

<p><i>F</i> values and significance levels are given: *, P<0.05; **, P<0.01; ***, P<0.001. <i>Nhap</i>, number of haplotypes; <i>Npriv</i>, number of private haplotypes; <i>Ar₃</i>, haplotype richness in a random sample of 3 sequences; genetic diversity with unordered (<i>h</i>) or ordered haplotypes (<i>v</i>); <i>N</i>, sample size.</p

Tests of population expansion and patterns of isolation by distance in 14 Afrotropical tree taxa.

<p><i>blog</i>(<i>F</i>_ij) and <i>P</i>(IBD_<i>F</i>_ij), slope and test of isolation by distance; <i>blog</i>(<i>N</i>_ij) and <i>P</i>(IBD_<i>N</i>_ij) slope and test of isolation by distance using ordered alleles; <i>P</i>(blog(<i>N</i>_ij)N_ijperm.)), test for phylogeographic structure. For details, see materials and methods. +, <i>P</i><0.1; *, <i>P</i><0.05; **, <i>P</i><0.01; ***, <i>P</i><0.00; ns, not significant; nc, not calculated.</p