Estimation of population size history in four cattle breeds using ABC.

<p>Angus (<i>n</i> = 25 animals), Fleckvieh (<i>n</i> = 25), Holstein (<i>n</i> = 25) and Jersey (<i>n</i> = 15). Estimations were obtained independently in each breed, based on whole genome NGS data from sampled animals. Summary statistics considered in the ABC analysis were (i) the AFS and (ii) the average zygotic LD for several distance bins. These statistics were computed using SNPs with a MAF above 20%. Other parameter settings are the same as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005877#pgen.1005877.g005" target="_blank">Fig 5</a>.</p

Estimation of population size history using MSMC with two haplotypes in five different simulated scenarios.

<p>For each scenario, the five PODs considered for MSMC estimation were the same as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005877#pgen.1005877.g003" target="_blank">Fig 3</a>. The expected TMRCA shown here is also the same as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005877#pgen.1005877.g003" target="_blank">Fig 3</a>, it corresponds to samples of 50 haploid sequences.</p

Accuracy of ABC estimation and relative importance of the summary statistics.

<p>Prediction error for the estimated population size in each time window (left) and standard deviation of this error (right), evaluated from 2,000 random population size histories. Summary statistics considered in the ABC analysis included different combinations of (i) the AFS (possibly without the overall proportion of SNPs) and (ii) the average zygotic LD for several distance bins. These statistics were computed from <i>n</i> = 25 diploid individuals, using all SNPs for AFS statistics and only those with a MAF above 20% for LD statistics. The posterior distribution of each parameter was obtained by neural network regression [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005877#pgen.1005877.ref032" target="_blank">32</a>], with a tolerance rate of 0.005. Population size point estimates correspond to the median of the posterior distribution. The prediction errors were scaled in order that point estimates obtained from the prior distribution would result in a prediction error of 1.</p

Influence of phasing and sequencing errors on ABC estimation.

<p>Estimation of population size history in the Holstein cattle breed using ABC, based on whole genome NGS data from <i>n</i> = 25 animals. Summary statistics considered in the ABC analysis were (i) the AFS and (ii) the average LD for several distance bins. LD statistics were computed either from haplotypes or from genotypes, using SNPs with a MAF above 20%. AFS statistics were computed using either all SNPs or SNPs with a MAF above 10 or 20%. The posterior distribution of each parameter was obtained by neural network regression [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005877#pgen.1005877.ref032" target="_blank">32</a>], with a tolerance rate of 0.005. Population size point estimates were obtained from the median of the posterior distribution. Generation time was assumed to be five years.</p

Localization of selection signatures identified in 7 groups of populations.

<p>Candidate genes are indicated above their genomic localization. Only chromosomes harboring selection signatures are plotted.</p

Selection signatures in ancestral populations.

<p>SNP with significant FLK value at the 5% FDR level, with estimated allele frequencies in all ancestral groups. The number of genes included in each region (1Mb up-or-downstream the position) and the rank of candidate genes within the region is also provided. : signatures of selection previously identified <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103813#pone.0103813-Kijas2" target="_blank">[4]</a>.</p

Selection signatures in the 7 geographical groups.

<p>Regions identified with the hapFLK or FLK test, with the corresponding population group and most differentiated populations (except for the AFR group). Full names of groups and populations are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103813#pone-0103813-t001" target="_blank">Table 1</a>. The number of genes included in each region and the rank of candidate genes within the region is also provided. Overlapping regions detected in different population groups or with different tests are grouped within horizontal lines (in this case candidate genes are the same for all overlapping regions and are only reported in the first one). : signatures of selection previously identified <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103813#pone.0103813-Kijas2" target="_blank">[4]</a>. : this outlying region is not due to evolutionary processes (see details in the main text).</p

Additional file 1: of Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

Figure S1. p-values (in -log10 scale) obtained along the genome when applying FLK to generation 1 (yellow), 2 (green), 3 (blue), 4 (red) or 5 (black) of the selection experiment. Horizontal dotted lines indicate the 5% FDR threshold for each of these generations. Vertical black lines correspond to a change of chromosome, and the numbers below these lines provide the length of the finishing chromosome. (TIFF 1599 kb

Additional file 7: of Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

Table S2. Differential expressed genes within the most significant signatures of selection and QTL regions*. (DOCX 16 kb

Additional file 3: of Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

Figure S3. Evolution of haplotype cluster frequencies in region hapFLK-2c (Chromosome 2, from 24,502,152 to 33,353,778 bp). A: each panel corresponds to a population, from G0 (top) to G5plus (bottom). For one given genomic position (on the x-axis), each color band corresponds to one haplotype cluster, and the height of this band gives the cluster frequency. The selection scenario described in the text is based on cluster frequencies at the position of the strongest hapFLK signal, which is indicated by the vertical black line. B: Evolution of the light blue and light green cluster frequencies along generations. As discussed in the text, these clusters are the ones showing the strongest evidence of selection at this locus. (PNG 1608 kb