Molecular Markers Allow to Remove Introgressed Genetic Background: A Simulation Study

<div><p>The maintenance of genetically differentiated populations can be important for several reasons (whether for wild species or domestic breeds of economic interest). When those populations are introgressed by foreign individuals, methods to eliminate the exogenous alleles can be implemented to recover the native genetic background. This study used computer simulations to explore the usefulness of several molecular based diagnostic approaches to recover of a native population after suffering an introgression event where some exogenous alleles were admixed for a few generations. To remove the exogenous alleles, different types of molecular markers were used in order to decide which of the available individuals contributed descendants to next generation and their number of offspring. Recovery was most efficient using <em>diagnostic</em> markers (i.e., with private alleles) and least efficient when using alleles present in both native and exogenous populations at different frequencies. The increased inbreeding was a side-effect of the management strategy. Both values (% of native alleles and inbreeding) were largely dependent on the amount of exogenous individuals entering the population and the number of generations of admixture that occurred prior to management.</p> </div

Results obtained for Native Representation (<i>NR</i>) and inbreeding coefficient (<i>F</i>) after managing during 10 generations with 20 markers of each type (<i>N</i> = 100, admixture period of 5 generations) under the different inbreeding control strategies (<i>NR</i> errors ranging between 0.003 and 0.016, <i>F</i> errors between 0.001 and 0.015).

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049409#s3" target="_blank">Results</a> obtained for Native Representation (<i>NR</i>) and inbreeding coefficient (<i>F</i>) after managing during 10 generations with 20 markers of each type (<i>N</i> = 100, admixture period of 5 generations) under the different inbreeding control strategies (<i>NR</i> errors ranging between 0.003 and 0.016, <i>F</i> errors between 0.001 and 0.015).</p

Inbreeding coefficient under the different management strategies (<i>N</i> = 100).

<p>Values shown are those obtained at the 10^th generation of management. Upper panel: <i>Diagnostic</i> markers, Medium panel: <i>Diagnostic-like</i> markers, Lower panel: <i>Non-Diagnostic</i> markers a) one generation of admixture b) three generations of admixture, c) five generations of admixture. Vertical bars represent the 95% percentiles.</p

Results obtained for Native Representation (<i>NR</i>) and inbreeding coefficient (<i>F</i>) after managing during 10 generations with 20 <i>diagnostic-like</i> markers with different <i>native allele</i> frequencies (admixture period of 5 generations).

<p>In all cases the frequency of the <i>native allele</i> in the foreign population was 0.5.</p

Native representation under the different management strategies (<i>N</i> = 100).

<p>Values shown are those obtained at the 10^th generation of management. Upper panel: <i>Diagnostic</i> markers, Medium panel: <i>Diagnostic-like</i> markers, Lower panel: <i>Non-Diagnostic</i> markers. a) one generation of admixture b) three generations of admixture, c) five generations of admixture. Vertical bars represent the 95% percentiles.</p

Dryad_data.tar

Four sets of genotypes used for population management, for populations of 1000 diploid individuals with 20 chromosomes of 1 Morgan each. For S=100 (1000), each chromosome has 2000 neutral loci, 100 (1000) selected loci and 1000 markers. Each row is one individual, and within row the two alleles per position

Rates of change in inbreeding, molecular homozygosity, coancestry and molecular similarity per year (Δ<i>F</i>_(y), Δ<i>H</i>_(y), Δ<i>f</i>_(y) and Δ<i>S</i>_(y)), respectively, and per generation (Δ<i>F</i>, Δ<i>H</i>, Δ<i>f</i> and Δ<i>S</i>) using different sources of information, and estimates of effective population sizes obtained from Δ<i>F</i> (<i>N_e</i>_<i>F</i>), Δ<i>H</i> (<i>N_e</i>_<i>H</i>), Δ<i>f</i> (<i>N_e</i>_<i>f</i>) and from Δ<i>S</i> (<i>N_e</i>_<i>S</i>).

<p>Rates of change in inbreeding, molecular homozygosity, coancestry and molecular similarity per year (Δ<i>F</i>_(y), Δ<i>H</i>_(y), Δ<i>f</i>_(y) and Δ<i>S</i>_(y)), respectively, and per generation (Δ<i>F</i>, Δ<i>H</i>, Δ<i>f</i> and Δ<i>S</i>) using different sources of information, and estimates of effective population sizes obtained from Δ<i>F</i> (<i>N_e</i>_<i>F</i>), Δ<i>H</i> (<i>N_e</i>_<i>H</i>), Δ<i>f</i> (<i>N_e</i>_<i>f</i>) and from Δ<i>S</i> (<i>N_e</i>_<i>S</i>).</p

Intercept (<i>a</i>), regression coefficient (<i>b</i>) and correlation (<i>R</i>) between different estimates.

<p><i>F</i>_<i>PED</i>: pedigree-based inbreeding; <i>F</i>_<i>ROH</i>: inbreeding based on ROHs; <i>H</i>_<i>SNP</i>: SNP-by-SNP based homozygosity; <i>f</i>_<i>PED</i>: pedigree-based coancestry; <i>f</i>_<i>SEG</i>: coancestry based on IBD segments; <i>S</i>_<i>SNP</i>: SNP-by-SNP based similarity</p><p>Intercept (<i>a</i>), regression coefficient (<i>b</i>) and correlation (<i>R</i>) between different estimates.</p

Distribution of genotyped animals by year of birth.

<p>Distribution of genotyped animals by year of birth.</p