Table S1 Location and environmental characteristics of five Taxus baccata populations studied in the Iberian Peninsula.

Table S2 List of primers used to sequence five taxol-related genes in Taxus baccata.

Table S3 Parameter prior distributions for the Bayesian analysis performed with OmegaMap v.0.5, to estimate the ratio of non-synonymous to synonymous substitutions (dn/ds  =  ω) along the functional regions of four taxol-related genes.

Table S4 Observed and expected values of segregating sites within Taxus baccata (S) and between Taxus baccata and the outgroup species (D) for multilocus Hudson–Kreitman–Aguadé (HKA) tests for all/non-synonymous/synonymous/non-coding sites performed with all loci, and P values of the HKA test performed with all combinations of four out of five loci.

Table S5 Nucleotide diversity, and polymorphism and divergence neutrality tests in coding functional parts of five taxol-related genes.

Table S6 Parameter priors and posteriors of demographic inference performed with the Approximate Bayesian Computation (ABC) approach of DIYABC for each population of Taxus baccata and for the whole sample.

Table S7 Neutrality tests per gene calculated for each population and the whole sample, considering different recombination (ρ) values.

Table S8 Correspondence between sequence accession number (EMBL/GenBank Data Libraries) and individual samples.

Fig. S1 Bayesian clustering analysis of Taxus baccata individuals (vertical bars) from five populations of the Iberian Peninsula. The relative length of different colours represents the posterior probability of each individual to belong to each of two (a) and five (b) different gene pools, respectively.

Fig. S2 Maximal mean posterior probability across replicates (a) and statistic based on the second rate of change in log probability of data (b) according to Evanno et al. (2005) approach to identify the optimal number of gene pools, K, in the Bayesian clustering analysis performed by Structure. Five runs were performed for each value of K from 1 to 10.

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