Additional file 2: of The genomic impact of historical hybridization with massive mitochondrial DNA introgression

Figure S1. Distribution of differential levels of average introgression between the five northern and five southern individuals across the 1000 simulations of mitochondrial introgression. Figure S2. Power and false discovery rate of the relative node depth method for inferring introgression. Figure S3. Empirical distribution of nuclear introgression frequencies inferred with RND. Figure S4. Introgression frequency distribution of mitonuc and background genes. Figure S5. Variation of the proportion of introgression across individuals for autosomes and the X chromosome. Figure S6. Correlation between prevalence of introgression (estimated with the ELAI method) and relative distance to the centromere for all chromosomes. Figure S7. Correlation between prevalence of introgression (estimated with the ELAI method) and relative distance to a the centromere and b the chromosome center for each chromosome category. Figure S8. Correlation between introgression tract size and geography. Figure S9. Expected introgression frequency distribution in a sample of ten L. granatensis individuals with the same geographic origin as the ten samples used in this study, considering empirical mtDNA introgression frequencies. (PDF 1177 kb

Additional file 1: of The genomic impact of historical hybridization with massive mitochondrial DNA introgression

Table S1. Basic information of specimens sequenced in this study. Table S2. ELAI’s Power for inferring introgression according to our simulations of artificial introgression. Table S3. Demographic inferences from IBS tracts. Table S4. List of nuclear genes overlapping regions with outlier introgression frequencies. Table S5. Gene Ontology functional enrichment analyses of genes overlapping regions with outlier frequencies of introgression. Table S6. Summary of GO functional categories significantly enriched in the set of genes with outlier introgression frequencies. Table S7. Nonsynonymous mutations detected within 123 high frequency introgression genes and their potential functional impact inferred using SIFT. Table S8. List of mitonuc genes with outlier frequencies of introgression. Table S9. List of mitonuc genes with geographic patterns similar to that of mtDNA. Table S10. Nonsynonymous mutations detected within mitonuc gene candidates to have co-introgressed with mitochondrial. Table S11. Classification of chromosomes according to centromere position. (XLSX 58 kb

Melo_Ferreira_et_al_HPRT1_complete

Final alignment of HPRT1 sequences used in this work. Data is phased - alternative alleles in females are indicated by a and b. A polymorphic poly-T of undetermined length was removed

Melo_Ferreira_et_al_PHKA2_complete

Final alignment of PHKA2 sequences used in this work. Data is phased - alternative alleles in females are indicated by a and b

Melo_Ferreira_et_al_MSN_complete

Final alignment of MSN sequences used in this work. Data is phased - alternative alleles in females are indicated by a and b

Melo-Ferreira_et_al_Genotypes

Genotypes of 6 microsatellite loci (Sat2, Sat8, Sat12, INRACCDDv358, Lsa2, Sol30Le) from a total of 342 specimens from three species: Lepus granatensis, Lepus europaeus and Lepus timidus. Population code and number are indicated in the second and third column respectively

Simplified triplet protein variants of the <i>Prdm9</i> ZnF array in wild mice.

<p>Sequence identifiers are highlighted with colors as in the phylogenetic tree of DNA alleles in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g002" target="_blank">Fig. 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g003" target="_blank">3</a>. Alleles of laboratory strains previously sequenced are identified as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone.0085021-Parvanov1" target="_blank">[12]</a>. Each ZnF is simplified to the three most variable codons −1, 3 and 6, and separated with a dash from the next ZnF. Sequences start at the first functional C2H2 ZnF (the second repeat) and end at the last carboxy-terminal ZnF of the protein. A few remarkable stretches of zinc fingers are highlighted: some are shared between most <i>M. musculus</i> protein variants (QNK-QDQ, red), some are shared between the twin species <i>spicilegus</i> and <i>macedonicus</i> (QNQ-ANK-**Q-QDQ, purple), some are shared between <i>castaneus</i> and <i>musculus</i> alleles (ANQ-ESK, yellow) and some others are specific or enriched in each of <i>domesticus</i> (QHQ-QDK, dark blue; AVQ-AVQ, light blue), <i>castaneus</i> (VVQ, green), <i>M. spretus</i> (ADK-VNQ; QNQ-ADK, grey); <i>M. macedonicus</i> (QHK-QNQ, purple) and <i>M. spicilegus</i> (QNQ-ADK, grey) groups of alleles.</p

Predicted DNA binding sites of mouse <i>Prdm9</i> ZnF alleles and dispersed repeats.

<p>(A) Distribution among <i>Prdm9</i> alleles of the proportion of the coverage of hits of the predicted recognized DNA motifs that fall in dispersed repeated sequences, as annotated on the reference mouse genome. (B) Absolute proportion of hit coverage falling in a given repeat family for each of the sequenced allele. Red cross: expected proportion if hit coverage was proportional to the coverage of the family in the genome. Red circles: median, first and third quartile of the distribution across alleles. Note the log scales. (C) Projection of the alleles on the first two axes of the Principal Component Analysis on the relative proportion of hits of each allele in the different repeated families. Symbol colors refer to lineage colors as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g002" target="_blank">Fig. 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g003" target="_blank">3</a>. Symbol shapes are arbitrary. PC1 absorbs 35% of the variance, and PC2 13%.</p

Inferred phylogeny of the <i>Prdm9</i> ZnF domain alleles.

<p>Taxon names on the branches include allele number, followed by the number of observations, then by taxon code (abbreviation of species name), country code, locality name and number of ZnF repeats. Numbers at the nodes indicate the level of confidence of the node (only values >0.5 reported).</p

Melo_Ferreira_et_al_SMCX_complete

Final alignment of SMCX sequences used in this work. Data is phased - alternative alleles in females are indicated by a and b