Gains in job execution time (speed-up) for the example data when running on variable number of processors on two computer architectures.

<p>(a) a Windows 7 laptop PC equipped with a Core i7 2.2GHz quad core processor with 8Gb of RAM and (b) an Apple workstation equipped with an Intel Xeon 2.26GHz double quad core processor with 16GB of RAM. Maximum speed-up is represented by the dashed line (y = x).</p

Scenario 5 –Differences in growth and mortality between salmon of farm and wild origin are doubled.

<p>Sum of genetic effects and size of spawners population. The vertical dotted line marks the stop of the introgression phase and the beginning of the recovery phase. The initial settling phase is not shown in the figure.</p

Scenario 1—The evolution of the heritability of the fork length (i.e. activity trait in Eq. 11) in the simulated population.

<p>The figures show the average values of 10 independent runs over the 100 monitoring years. The population was initialised as composed of farm individuals (average frequency of allele ‘1’ ≈0.1, S^Φ≈0.1), and subjected to a simulated immigration of spawners of wild origin (strayers from other rivers, average frequency of allele ‘1’ ≈0.8, S^Φ≈0.8, see Section 2.4.6) equal to 5% of the overall number of returners.</p

Scenario 1 –Egg density.

<p>Statistical measures of simulated egg densities per m². The tables report the averages and standard deviations over 100 years, averaged over 10 independent runs of the model. The overall minimum and maximum values over the 100 years and 10 independent runs are also reported. The results are compared with averages of estimated egg densities in the Os river in the 1989–2010 period (Rådgivende Biologer AS, 2012).</p><p>Scenario 1 –Egg density.</p

Scenario 2—Plots b)-d) show, for each set of genes (embryonic, juvenile, adult), the evolution of the alleles for a number of sample loci during the 200 evolution years.

<p>The figures show the average allelic values of the population, averaged over 10 independent runs. A value of ‘1’ means that only the ‘wild’ allele is present, a value of ‘0’ means that only the farm allele is present. Plot a) shows the overall genotypic effect (S^Φ, Eq. A.2 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138444#pone.0138444.s001" target="_blank">S1 File</a>) on the traits of the three main phases (embryonic, juvenile, adult). The population was initialised as composed of farm individuals (average frequency of allele ‘1’ ≈0.1, S^Φ≈0.1), and subjected to a simulated immigration of spawners of wild origin (strayers from other rivers, average frequency of allele ‘1’ ≈0.8, S^Φ≈0.8, see Section 2.4.6) equal to 5% of the overall number of returners.</p

Scenario 3 –Standard parameter setting.

<p>Sum of genetic effects and size of spawners population. The vertical dotted line marks the stop of the introgression phase and the beginning of the recovery phase. The initial settling phase is not shown in the figure.</p

Scenario 1—Juvenile and adult growth.

<p>The theoretical curves for density-dependent juvenile growth (default settings as in Table B in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138444#pone.0138444.s002" target="_blank">S2 File</a>) are plotted together with the results of the simulations. Figs a)-c) show the average fork length of parr at end of the growth season (31-October) against the density on 01-May (alevin emergence). The theoretical curves for adult growth (default settings as in Table B in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138444#pone.0138444.s002" target="_blank">S2 File</a>) are plotted together with the results of the simulations. Fig d) shows the average size per year class on 31-September (before spawners return to freshwater) against the size on 01-May (migration of smolts to sea). The Figs show the average values of 10 independent runs, and plot the distribution of the results over the 100 monitoring years.</p

Scenario 1—Demographics of spawners population.

<p>Population size information is broken down per age groups. The table reports the averages and standard deviations over 100 years, averaged over 10 independent runs of the model. The overall minimum and maximum values over the 100 years and 10 independent runs are also reported. The results are compared with statistical measures of population surveys carried out in the Os river in the period 1992–2008 (Rådgivende Biologer AS, 2012).</p><p>Scenario 1—Demographics of spawners population.</p

Scenario 2—The evolution of the heritability of the fork length in the simulated population.

<p>The figures show the average values of 10 independent runs over the 200 evolution years. The population was initialised as composed of farm individuals (average frequency of allele ‘1’ ≈0.1), and subjected to a simulated immigration of spawners of wild origin (strayers from other rivers, Section 2.4.6) equal to 5% of the overall number of returners.</p

Scenario 1 –Average parr fork length.

<p>Statistical measures (model) of parr fork lengths (mm) in May (alevin emergence) and at the end of the growth season. Size data are broken down per life phases and age groups. The tables report the averages and standard deviations over 100 years, averaged over 10 independent runs of the model. The overall minimum and maximum values over the 100 years and 10 independent runs are also reported. The results are compared with those of the 2010 survey in the Os river (Rådgivende Biologer AS, 2012).</p><p>Scenario 1 –Average parr fork length.</p