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mec12514-sup-0001-AppendixS1-TableS1-S8-FigS1-S7.docWord document1509K

Appendix S1 Supplemental text, Tables, and Figures.

Table S1 A summary of diversity panels assembled for polymorphism discovery in 11 species of pines from subgenus Strobus.

Table S2 PCR primers for the 167 genes sequenced for 11 species of pines within subgenus Strobus.

Table S3 Annotation information for the 167 loci sequenced for 11 species of pine within subgenus Strobus.

Table S4 Site annotations for 167 genes sequenced for 11 species of pine within subgenus Strobus.

Table S5 Summary statistics for 167 genes sequenced for 11 species of pines within subgenus Strobus.

Table S6 Estimates of ωa from each method proposed by Eyre-Walker and Keightley (2009).

Table S7 Maximum likelihood parameter estimates for the single step population size change model where N1 is set to 100 (Eyre-Walker and Keightley 2009).

Table S8 Effects of population structure (K = 2) on the estimation of α and ωa.

Fig. S1 Unfolded site-frequency spectra for all, synonymous (syn), and nonsynonymous (nsyn) sites across 11 species of soft pines (subgenus Strobus) and the outgroup.

Fig. S2 Site-frequency spectra for the first six sample coverage classes (n ∈ {13,18}) for P. strobiformis reveals that the U-shaped spectra are not an artifact of re-scaling, as the U shape is apparent within coverage classes where the sample size is constant.

Fig. S3 The decay of intragenic linkage disequilibrium, as measured using squared allelic correlation coefficients (r2), with physical distance (bp) for 167 genes sequenced for 11 species of pines in subgenus Strobus.

Fig. S4 Summary of pairwise Kolmogorov–Smirnov tests for convergence among three independent runs of the Markov chain Monte Carlo (MCMC) algorithm used to estimate the distribution of deleterious fitness effects (DFE) and the proportion of adaptive substitutions (α) for 11 species of pines in subgenus Strobus.

Fig. S5 The distribution of deleterious fitness effects (DFE) and the proportion of adaptive substitutions (α) for 11 species of soft pines (subgenus Strobus) as inferred using method 1 of Eyre-Walker and Keightley (2009).

Fig. S6 Population structure and sampling frequency across populations affects the estimation of the proportion of adaptive substitutions (α) for 11 species of soft pines (subgenus Strobus).

Fig. S7 The effect of population structure on estimation of the proportion of adaptive substitutions (α) as assessed using simulations.

mec12514-sup-0002-TableS1-S8-FigS1-S7.docWord document1534K 
mec12514-sup-0003-AppendixS2.txtplain text document242KAppendix S2 GenBank accession numbers for all data, with accession numbers organized in tabular format by locus and individual.
mec12514-sup-0004-TextS2.txtplain text document242K 

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