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

Geographic distribution of groups of alleles in the house mouse.

<p>The shape of the symbols indicates subspecies (square, <i>M. m. domesticus</i>, circles <i>M. m. musculus</i>, triangles <i>M. m. castaneus</i>). Colors indicate lineages as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g003" target="_blank">Fig. 3</a>.</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

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

The C2H2 zinc finger domain of PRDM9.

<p>(A) PRDM9 contains several identified domains: an amino-terminal region which includes a Krüppel-associated box (KRAB) domain and an SSX repression domain (SSXRD); a PR/SET domain carrying methyltransferase activity, surrounded by a zinc knuckle and a zinc finger; and a long carboxy-terminal C2H2 zinc finger array. In this example, such as observed in the mouse laboratory strain C57BL/6, the array is composed of 12 zinc fingers. (B) Size distribution of the <i>Prdm9</i> ZnF arrays (number of ZnF repeats) genotyped in the three subspecies of the house mouse</p

Repeat copy number variability of <i>Mus</i> ZnF <i>Prdm9</i> and size heterozygosity.

<p>N: number of mice. NA: number of allele sizes. H: observed heterozygosity, He: Expected heterozygosity in panmictic population based on allele frequencies.</p

Details of phylogenic tree.

<p>The yellow (A), blue (B) and green (C) collapsed parts of the tree in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g002" target="_blank">Fig. 2</a> are expended and represent the different house mouse lineages. Taxon name encoding is as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone-0085021-g002" target="_blank">Fig. 2</a>.</p

Patterns of diversity of amino-acids –1, 3 and 6 of PRDM9 ZnFs across taxa, species and subspecies.

<p>Number of ZnFs units sequenced, number of <i>Prdm9</i> ZnF arrays sequenced and number of protein variants are indicated for each species or subspecies of Primates, <i>Muridae</i> and Equids. Variant amino-acids at each of the three positions −1, 3 and 6 of the PRDM9 ZnFs are shown for each group. Variants present in every allele sequenced are in bold case and variants found in less than 10% of ZnF units are in grey case (all in normal case when one allele is available). Some variants at position −1 and position 3 are shared by most species (highlighted in yellow), others are shared by one taxon (highlighted according to the colour of the taxon). Hs: <i>Homo sapiens</i>; Pp: <i>Pan paniscus</i> (bonobo); Pt: <i>Pan troglodytes</i> (chimpanzee); Ptt<i>: P. T. troglodytes</i>; Ptv: <i>P. T. verus</i>; Pts: <i>P. T. schweininfurthii</i>; Gg: <i>Gorilla gorilla</i>; Hol: <i>Holobylata</i>e; Nl: <i>Nomascus leucogenys</i> (Gibbon); Cerc: <i>Cercopithecidae</i>; Mm: <i>Macaca mulata</i> (Rhesus monkey); Calli: <i>Callitrichidae</i>; Cj: <i>Callithrix jacchus</i> (Ouistiti); Gal: <i>Galagidae</i>; Og: <i>Otolemur garnettii</i> (Lemur); Mm: <i>Mus musculus</i>; Mmd: <i>Mus musculus domesticus</i>; Mmm: <i>M. m. musculus</i>; Mmc: <i>M. m. castaneus</i>; Msp: <i>Mus spretus</i>; Mm/s: <i>Mus macedonicus</i> and <i>spicigelus</i>; Mpy: <i>Mus Pyromys platythrix</i>; Mfa: <i>Mus famulus</i>; As: <i>Apodemus sylvaticus</i>; Pl: <i>Peromyscus leucopus</i>; Rn: <i>Rattus norvegicus</i>; Ef: <i>Equus ferus</i>; Ea: <i>Equus asinus</i>; Eh: <i>Equus hippotigris</i>. Data was gathered for <i>Mus</i> ZnFs from this study, for <i>Homo sapiens</i> ZnFs from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone.0085021-Baudat3" target="_blank">[10]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone.0085021-Parvanov1" target="_blank">[12]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone.0085021-Berg1" target="_blank">[20]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone.0085021-Kong1" target="_blank">[23]</a> for <i>Pan</i> ZnFs from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone.0085021-Groeneveld1" target="_blank">[22]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone.0085021-Auton1" target="_blank">[79]</a>, for Equids from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085021#pone.0085021-Steiner1" target="_blank">[80]</a> and retrieved from GenBank for other individual alleles (Gg, Nl, Mm, Cj, Og, Apos, Perol, Rn).</p

Behavioural data

This file provides behavioural raw data (mate choice tests). In particular, it provides for each actor of the choice the individual IDs (sample_ID1 and sample_ID2), the subspecies of origin, the sex, the geographical origin (field "Sample"), the trapping site ID with its geographical coordinates (in degrees), the time spent sniffing each stimulus (musculus or domesticus urinary signals), and the difference in time spent sniffing the two stimuli

Genotyping_raw_data_for_HI_estimation

This file provides genotyping data of the 21 diagnostic markers (insertion/deletion polymorphisms of transposable elements, columns C to W) used to estimate the hybrid index of each individual used in this study. More information on the markers used and applied genotyping procedure can be found in Latour et al 2015 Proceeedings of the Royal Society of London