Summary of Temporal MHC studies including population demographic parameters important for generating temporal variation.

<p>‘Fluctuating <i>s</i>’ refers to studies which concluded that fluctuating selection may have increased temporal differentiation of immune genes relative to that of neutral markers. Studies that provided either direct evidence for changes in population size, or temporally unstable population structure, were considered to have a fluctuating census population size (‘Fluctuating <i>N_c</i>’). ‘Populations’ indicates the number of sampled populations and ‘Alleles’ indicates the total observed number of MHC alleles in the sampled metapopulation.</p

Temporal genetic differentiation (<i>G'_ST</i>) in simulated populations under various demographic and population genetic scenarios.

<p>Unless stated otherwise, populations are of constant effective population size <i>N_e</i> = 100, gene flow <i>Nm</i> = 1 from a source population with 85 distinct MHC alleles (<i>k</i> = 85), with alleles being maintained by symmetric overdominant selection with <i>s</i> = 0.2. Error bars indicate 5–95% confidence interval. (A) The coefficient of selection ranges between 0≤<i>s</i>≤0.5. (B) The number of MHC alleles in the source metapopulation ranges between 5≤<i>k</i>≤80 distinct alleles. (C) Upstream migration rate ranges between 0.2≤<i>Nm</i>≤10.0 individuals per generation. The dashed grey line represents inferred value for 3<i>Nm</i> (D) The effective population size ranges between 30≤<i>N_e</i>≤1000. (E) Migration (<i>Nm</i> = 1) is either every generation or seasonal (every third generation), into a constant (solid circles) or fluctuating (open circles) population of harmonic mean size <i>N_H</i> = 100. (F) The temporal genetic differentiation within the MN and LA populations over time (2001–2007) at microsatellite (closed symbols) and MHC loci (open symbols). These simulations use fixed parameter estimates from previous runs (panels A–E) combined with annually fluctuating census population size migration. Simulated (mean <i>G'_ST</i> (5–95% CI)) and the mean observed genetic differentiation (<i>G'_ST</i>) are represented by circles and crosses, respectively (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042119#pone.0042119.s001" target="_blank">Tables S1</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042119#pone.0042119.s002" target="_blank">S2</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042119#pone.0042119.s003" target="_blank">S3</a> for data).</p

Maximum clade credibility trees using the total alignment as well as fossil calibrations

Maximum clade credibility trees using the total alignment as well as fossil calibrations. Trees were inferred using BEAST v1.62. Estimated ages of divergence are depicted in bold and posterior probabilities in italic. Abbreviations, Sb: Sorghum bicolor, Ta1 and Ta2: Triticum aestivum, Bd: Brachypodium distachyon

Maximum clade credibility trees using the truncated alignment with no priors on divergence times.

Maximum clade credibility trees using the truncated alignment with no priors on divergence times. Trees were inferred using BEAST v1.62. Estimated ages of divergence are depicted in bold and posterior probabilities in italic. Abbreviations, Sb: Sorghum bicolor, Ta1 and Ta2: Triticum aestivum, Bd: Brachypodium distachyon

Maximum clade credibility trees using the total alignement with no priors on divergence times.

Maximum clade credibility trees using the total alignment with no priors on divergence times. Trees were inferred using BEAST v1.62. Estimated ages of divergence are depicted in bold and posterior probabilities in italic. Abbreviations, Sb: Sorghum bicolor, Ta1 and Ta2: Triticum aestivum, Bd: Brachypodium distachyon

Total alignment of Rp1 sequences from the 5 Poaceae genera used in this study.

This alignment was used to construct phylogenetic trees with and without calibration points and evaluate the incidence of recombination

Truncated alignment of Rp1 sequences from the 5 Poaceae genera used in this study.

This alignment was used to construct phylogenetic trees with and without calibration points and to test for a correlation between positively-selected amino-acids and the incidence of recombination

Effect of increasing the number of markers.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042649#s2" target="_blank">Results</a> are shown for the simulations where allele frequencies were equally distributed from 0.05 to 0.95. The number of individuals was fixed at n = 4 (left column) and n = 20 (right column). Each row contains (like in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042649#pone-0042649-g001" target="_blank">Figure 1</a>) a different level of genetic differentiation (F_ST = 0, 0.01, 0.05, 0.1, 0.2, 0.4). The results (average F_ST and 95% CI) of each estimator are depicted in the different graphs: F_ST^W (blue circles), F_ST^C&W (purple squares) and F_ST^R (green triangles). The dashed red line indicates the actual F_ST for the simulated population.</p

Estimated F_ST values changed allele frequency distributions, n = 50, k = 1000.

<p>Estimated F_ST values changed allele frequency distributions, n = 50, k = 1000.</p

Relationship between shoaling behaviour and parasite load.

<p>Nearest neighbour distance and parasite load for female (A) and male (B) guppies. Shown are the mean and standard deviation for both nearest neighbour distance and parasite load, averaged across the individuals within a tank.</p