G3/2017/044198

Deer31_QC.RData is the genotype and sex data in R/GenABEL format for all deer after basic quality control.

Pseudoautosomal_SNPs.txt is a list of all SNPs in the pseudoautosomal region on the X chromosome.

Pedigree_16-05-02.recoded.txt is the raw pedigree data.

Table S1: Rum red deer (\textit{Cervus elaphus}) linkage map after Build 5. Column headers are as follows: SNP.Name = SNP Name, BTA.Chr = cattle chromosome, BTA.Position = cattle base pair position (BTA UMD v3.0), CEL.LG = Deer linkage group, CEL.Order = Marker order on deer linkage group, cMPosition.SexAveraged = sex-averaged linkage map position (cM), cMPosition.Female = female linkage map position (cM), cMPosition.Male = male linkage map position (cM), Skeleton.SNP = indicates if SNP is included in the skeleton map (see main text), PAR = indicates if SNP is in the pseudoautosomal region, Estimated.Mb.Position = the estimated genomic position on the deer genome (see methods), inf.mei = number of informative meioses, inf.mei.PK = number of informative meioses where grandparental phase was known, tot\_f = number of informative meioses in females, tot\_m = number of informative meioses in males, pk\_f = number of informative meioses in females with phase known, pk\_f = number of informative meioses in males with phase known, A1 = major reference allele, A2 = minor reference allele, CallRate = SNP call rate in original dataset (N$_{IDS}$ = 2361), Q.2 = minor allele frequency, PseudoAutosomalSNP = indicates if sex-linked SNPs (CEL34) are in the pseudoautosomal region.

Table S2: Data for Figure S5, comparison of map positions between Cattle (bp, build vUMD 3.0), Deer (cM, Build 5) and Sheep (bp, build Oar\_v3.1) for the X chromosome. Window.Start = cM position of the start of the window of most likely position, Window.Stop = cM position of the end of the window, CEL.LG = Deer linkage group identifier, SNP.Start = First mapped SNP at the start cM position, SNP.Stop = Last mapped SNP at the end cM position, chunk = chunk identifier, SNP.Start.Of.Chromosome = Indicates if the most likely position is at the beginning of the chromosome, SNP.End.Of.Chromosome = Indicates if the most likely position is at the end of the chromosome, Unmap.SNP.vec = Vector of SNPs within the unmapped chunk.

Table S3: Probabilities of crossing over within 1Mb windows in males and females.Column headers are as follows: CEL.LG = Deer linkage group identifier, Window = Window order, Start = Mb position of the start of the window, Stop = Mb position of the end of the window, Locus.Count & Number of loci within the window, Mean.Inf.Count = Mean number of informative loci, cM = Sex-averaged recombination rate, cM.Male = Male recombination rate, cM.Female = Female recombination rate, Window.To.End = Window order from the other end of the chromosomes, FM.Rate = Ratio of female to male recombination rate, adj.cM = Sex-averaged recombination rate adjusted for chromosome size, adj.cM.Male & Male recombination rate adjusted for chromosome size, adj.cM.Female = Female recombination rate adjusted for chromosome size, adj.FM.Rate = Ratio of female to male recombination rate adjusted for chromosome size.

Table S4: Probabilities of crossing over within 1Mb windows in males and females. Column headers are as follows: CEL.LG & Deer linkage group identifier, Window = Window order, Start = Mb position of the start of the window, Stop = Mb position of the end of the window, Locus.Count = Number of loci within the window, Mean.Inf.Count = Mean number of informative loci, cM = Sex-averaged recombination rate, cM.Male = Male recombination rate, cM.Female = Female recombination rate, Window.To.End = Window order from the other end of the chromosomes, FM.Rate = Ratio of female to male recombination rate, adj.cM = Sex-averaged recombination rate adjusted for chromosome size, adj.cM.Male = Male recombination rate adjusted for chromosome size, adj.cM.Female = Female recombination rate adjusted for chromosome size, adj.FM.Rate = Ratio of female to male recombination rate adjusted for chromosome size.

Table S5: BLAST results for SNP flanking sequences in the Deer against the Sheep (Oar\_v3.1) and Cattle (Btau\_4.6.1) genomes in order to determine lineage of origin. Column headers are as follows: Locus\_Name = SNP ID, Species = Reference sequence, Ovis or Bos for sheep and cattle, respectively., bit = Bit score of local alignment., Chr = Reference species chromosome., PCmatch = Percentage match between query and reference sequences., matches = Number of matching bases between query and reference sequences., mismatches = Number of mismatching bases between query and reference sequences., gaps = Number of gaps between query and reference sequences., SeqStart = Query sequence start position., SeqSto = Query sequence stop position., ChrStart = Reference sequence start position., ChrStop = Reference sequence stop position., eval = Expect value (E): the number of hits one can expect to see by chance when searching a database of a particular size., Ncount = Number of unknown bases in the deer query sequence., Informative.Length = Number of known bases in the deer query sequence., PCmatch.Full = Percentage of matches at known bases., Count = Number of independent hits for the query sequence., BTA3Chr = Chromosome on cattle genome version vUMD3.0., BTA3Position = Position on cattle genome version vUMD3.0., CEL.LG = Deer linkage group., cMPosition.run5 = Deer build 5 centimorgan position.

Table S6: Raw data and results for binomial tests for the transmission distortion analysis. Alleles were assigned as A or B as the first and second reference allele in the GenABEL files. Column headers are as follows: A.Count & Number of A alleles transmitted from FID to offspring, SNP.Name = SNP ID, Parent = Indicates if FID was the father or mother, Geno.Count = Number of informative transmissions, P.val = P-value from the exact binomial test, CEL.order = The order of SNPs on the linkage group, CEL.LG = Linkage group, Fission = The fission/fusion history of the chromosomes, cMPosition.run5 = Deer build 5 centimorgan position., Dummy.Position = The estimated genomic position on the deer genome, Bin = 1Mb Window in which the SNP falls.