Lepais et al Plos ONE North African alder microsatellite data

Microsatellite genotype file including individuals mane (ID), country and population of origin, and allele names at 11 microsatellites

Regional genetic structure of <i>A. glutinosa</i> as inferred by Structure (A, B and C) and DAPC (D, E and F).

<p>Results from the population genetics model-based Bayesian clustering method implemented in Structure: (A) variation of the likelihood of the data across a range of number of clusters K; (B) neighbour joining tree computed using the genetic distance (allele frequency divergence) between clusters; (C) histogram of individual assignment to clusters where each individual is represented by a thin vertical bar partitioned into several coloured segments proportionally to its membership of a given cluster (admixture coefficient). Results from the multivariate statistics based clustering method implemented in DAPC: (D) variation of the Bayesian Information Criterion (BIC) of the k-means clustering algorithm across a range of number of clusters K; (E) neighbour joining tree computed using the DAPC distance between centroids of the clusters; (F) histogram of individual assignment to clusters where each individual is represented by a thin vertical bar partitioned into several coloured segments proportionally to its membership of a given cluster (admixture coefficient). All graphs were plotted in R v.2.12.0 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075029#pone.0075029-R1" target="_blank">[36]</a>.</p

Demographic parameter posterior densities: contemporary (A) and ancestral effective population sizes (B), divergence times (C).

<p>Estimates resulted from the most-likely scenario 5 (Fig. 3) of population history of <i>A. glutinosa</i> estimated in diyabc <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075029#pone.0075029-Cornuet2" target="_blank">[51]</a> based on genotyping of 96 individuals from three genetically distinct isolated populations of Morocco (BOU), Tunisia (TIT) and Scotland (PGM). See Fig. 1 and Fig. 3 for details. Divergence times are expressed in generations and effective population sizes in number of diploid genomes.</p

Distribution area (A) and sampling locations (B and C) of <i>A. glutinosa</i>.

<p>Small grey squares represent fragmented distribution at the distribution area margin while grey area represent more continuous distribution according to data compiled and released by the EUFORGEN Network. Population codes refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075029#pone-0075029-t001" target="_blank">Table 1</a>.</p

Characteristics of prior and posterior distributions of demographic parameters of population history of <i>A. glutinosa</i> estimated under the most-likely of seven tested scenarios by means of Approximate Bayesian Computation in diyabc[51].

#<p>Details of demographic scenarios tested and estimated parameters are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075029#pone-0075029-g003" target="_blank">Fig. 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075029#pone-0075029-g004" target="_blank">Fig. 4</a>. N1, N2, N3a and N3b, Ne, Ns refer to effective population sizes in number of diploid genomes respectively of standing populations from Morocco (BOU), Tunisia (TIT) and Scotland (PGM) and from ancestral populations from which they have diverged as modelled in the most-likely of the seven tested scenarios (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075029#pone-0075029-g003" target="_blank">Fig. 3</a>). t1, t2, t3a and t3b: divergence time of the standing populations from the ancestral populations in generations (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075029#pone-0075029-g003" target="_blank">Fig. 3</a>). Q_0.05 and Q_0.95∶5% and 95% quantiles.</p

Representation of seven tested scenarios of past population history of north-African <i>A. glutinosa</i>.

<p>Scenarios were tested by means of Approximate Bayesian Computation (ABC) in diyabc <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075029#pone.0075029-Cornuet2" target="_blank">[51]</a> and based on genotyping of 96 individuals at 11 microsatellite markers sampled in three populations from Morocco (BOU, of effective size N1), Tunisia (TIT, of effective size N2) and Scotland (PGM, of effective size N3) representative of the regional genetic structure and identified as genetically distinct with no admixture in structure (Fig. 2). Ne and Ns refer to effective size of ancestral populations and t, t3a,b, t2, t1 to divergence times. Posterior probabilities (<i>P</i>) of the scenarios and 95% confidence intervals of <i>P</i> (in brackets) were obtained by means of simulations. 7.10³ out of 70.10⁶ simulations closest to the real genetic dataset were subjected to a weighted polychotomous logistic regression to estimate P <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075029#pone.0075029-Cornuet1" target="_blank">[33]</a>.</p