Locus / Amplicon number / Primer name / Type / Primer sequence (5'-3')
PRL / 1 / OC001011-00105p / PCR / CCACAAATCTTCTACTCCACAAT
1 / OC001011-00108p / PCR / CAGCAAGAAGGCACACAATC
1 / OC001011-00104i / sequencing / TTTAAATTACCACATCCATCGG
1 / OC001011-00110i / sequencing / CAGAGAAACATGTACCTCTTTGC
1 / OC001011-00111i / sequencing / CCACCTGAGTCTCCCACATAG
2 / OC001011-00207p / PCR / AAAGCATATGTTTATTTCTTTTGATGT
2 / OC001011-00208p / PCR / GAGAGCACACACAGAAAGTAAGG
2 / OC001011-00202i / sequencing / TGTGAGTGCACATTCATGCT
2 / OC001011-00203i / sequencing / TTTCATAGTTGCTAGTGCCATGT
2 / OC001011-00205i / sequencing / CACTCTTCTATAGTCAAGTTAGATGCG
MGST3 / 1 / OC002011-00100p / PCR / AAGCCTGAACCAGTTTTACTCTCTAT
1 / OC002011-00101p / PCR / TGTCTGTACCATCCAGAGCTAGG
1 / OC002011-00102i / sequencing / GACTCTTGATTTGCAAAGTTTGGT
1 / OC002011-00103i / sequencing / AGCCTGTCTCATATCCTTGAAGT
1 / OC002011-00105i / sequencing / GAGGCGAGAGCTTCAACC
2 / OC002011-00200p / PCR / GTTTCTCCCGTGGTGTCAGT
2 / OC002011-00201p / PCR / CTCTTTAGTAGGAATCTGGATCGG
2 / OC002011-00202i / sequencing / ACGTCTACTTGTAGATTGCAGCAC
2 / OC002011-00203i / sequencing / ATGCAGAGCAACCAGGACT
2 / OC002011-00204i / sequencing / GAGAAGAGAGGGACACTTAGGATG
2 / OC002011-00205i / sequencing / ACCAAACTTTGCAAATCAAGAGTC
* / OC002011-00206i / sequencing / aggttatgacatacaaagca
* / OC002011-00207i / sequencing / gctgtagtgatgagttttga
* / OC002011-00208i / sequencing / tagtattggtgcagcatgag
T / 1 / OC003011-00200p / PCR / TGTGGTCATGTGTGTCATGC
1 / OC003011-00201p / PCR / GGAGTTTAGGGAGCAGACGG
1 / OC003011-00202i / sequencing / GAGTCAGCCGATGCCAGT
1 / OC003011-00203i / sequencing / CTGTGTCCTCTGTGCCTTTCTC
1 / OC003011-00205i / sequencing / GCTGCAGCGATTTTCTGG
2 / OC003011-00304i / sequencing / CCCATTCAAATGCTAATGGC
2 / OC003011-00307p / PCR / AGAAGATGGCCTTGTTCCA
2 / OC003011-00308p / PCR / TGCAAACTCAAAGGGAACAGA
2 / OC003011-00312i / sequencing / GTCCTGTGGTCCCTCCTGT
2 / OC003011-00313i / sequencing / AGTTCAGGGTCATCTGTGGC
2 / OC003011-00319i / sequencing / GCGAAAGAGAGTTCAGGGTCAT
* / OC003011-00320i / sequencing / CGATGCCAGTCCATGTCCTGAC
* / OC003011-00321i / sequencing / GCAGCCTGGTGGGCTCAGGCTG
* / OC003011-00322i / sequencing / GTGGGGRAAGGGGCTCTACC
CYTC / 1 / OC004011-00100p / PCR / GTGTTTGGCGCCTTAGTCAT
1 / OC004011-00101p / PCR / CAGAACTGCCACCCACAAG
1 / OC004011-00102i / sequencing / GGAGTTCGGCTGAGTCACG
1 / OC004011-00103i / sequencing / TGGCCTACAGCACCTCACTC
1 / OC004011-00105i / sequencing / CCCAGTCCCTCTCACGGAT
2 / OC004011-00300p / PCR / GGTCTGGGTGCGTCTGTC
2 / OC004011-00301p / PCR / CTCCCAATAGGGTGTCTCCTG
2 / OC004011-00302i / sequencing / CAGTGGGAGCTGTTCGTTAAA
2 / OC004011-00303i / sequencing / TTAAGAGGAAACGCAAGAGGG
2 / OC004011-00304i / sequencing / GGCTGTCACATGAGAGCG
* / OC004011-00305i / sequencing / TTCTGAACACTTCTTTYTGC
* / OC004011-00306i / sequencing / ATAGGGAGAGGAARGGGTG
* / OC004011-00307i / sequencing / TCTTACCTCCCTAACGCGCGC
* / OC004011-00308i / sequencing / GACAGCCTGAGGATCTGCT
* / OC004011-00309i / sequencing / CCACTCTGTAACCMCCTG
* / OC004011-00310i / sequencing / CAGGGGCAGGCAAACAGTT
UD14 / 1 / OC005011-00300p / PCR / GGAATCAGAGGAGAAAACTCAGAA
1 / OC005011-00301p / PCR / ACTGCAGGAAATCCAGAGTCAC
1 / OC005011-00302i / sequencing / AGTAGCAAGAGCAGTTGTCCAAA
1 / OC005011-00303i / sequencing / AGCAGAGTGAAAGGATTTGTTACTAA
1 / OC005011-00305i / sequencing / CCCAAAGGTGCTCTGTACTTTC
2 / OC005011-00400p / PCR / CCGAGAGCTGCTGGTCTG
2 / OC005011-00401p / PCR / AGCCATGACTAAGCAATCCAGTA
2 / OC005011-00402i / sequencing / CGTGTTCATGATGCGAGTCC
2 / OC005011-00403i / sequencing / GATCTACACTCAAAATCCATTGTGAA
2 / OC005011-00404i / sequencing / CGGAAGTGGTAGTGGAGAGG
* / OC005011-00405i / sequencing / TTGGGAAGRGCAAGCAAT
* / OC005011-00406i / sequencing / CAGTTTCAGGGCCCCAGC
ATP12A / 1 / OC006031-00100p / PCR / TTGTGCATATCCTCCCTTATACTTT
1 / OC006031-00101p / PCR / CTGGAGAAAGTCCCAAGAAATATG
1 / OC006031-00102i / sequencing / CCTCTATGCACCTGTGAATGTC
1 / OC006031-00103i / sequencing / TATTTAATGCTGATAGCCAGCAAG
1 / OC006031-00104i / sequencing / TGTGAATGCTATGTAAATAGGTGTTG
2 / OC006031-00200p / PCR / CCATAAGGTCCCTCCTTGATAGTA
2 / OC006031-00201p / PCR / AAAGCAAACTGGAGTGAGACATC
2 / OC006031-00202i / sequencing / CAGTTACAGACAGAGAGAAGGCAA
2 / OC006031-00203i / sequencing / GGAAGCCCTGGAATAAGCTC
2 / OC006031-00205i / sequencing / CCTAATTGTGTTGCCAGCTACATA
STAG1 / 1 / OC007011-00500p / PCR / TAAGCAATGTCAAGGAGCATTTTAT
1 / OC007011-00501p / PCR / TGTTGTAAGAAACAGATTTTGAGCA
1 / OC007011-00502i / sequencing / GTTAGCTTGCCAATACAGAAAACAC
1 / OC007011-00503i / sequencing / AAGGAGAAGCATTAGGTTAATATAGGG
1 / OC007011-00505i / sequencing / TGCATAATATACAGTTTTGCTTTAACC
2 / OC007011-00600p / PCR / TGCACATAGTCTTTGAAGCAGAG
2 / OC007011-00601p / PCR / TGAGTATCTTTCTCATTCGGAAAAC
2 / OC007011-00602i / sequencing / CCCAAGACTTGTCCTGCAAA
2 / OC007011-00603i / sequencing / CTTGTTGGAATCAGTTGCATTTT
2 / OC007011-00604i / sequencing / CAGCTCAAAGATATAGAAAGAAAGCAG
* / OC007011-00605i / sequencing / CCAAAGACGATAATCATATC
* / OC007011-00606i / sequencing / TCACTTTGCAGGACAAGTCTT
* / OC007011-00607i / sequencing / CCAGTGTAAATATAACTCAC
* / OC007011-00608i / sequencing / AGAAGCATTAGGTTAATATA
LUM / 1 / OC008011-00500p / PCR / GGACGGTTTGGGACATCTTT
1 / OC008011-00501p / PCR / TCCCAGATCTTATCATGGTACCTATTT
1 / OC008011-00502i / sequencing / TTTTCCATTTTCTTGCTGCC
1 / OC008011-00503i / sequencing / TGAGCTGAAATTTTACCTCTGCC
1 / OC008011-00504i / sequencing / CAAAACTCACCATGTGGCAA
2 / OC008011-00600p / PCR / CTCTGTTTCCATGACAATCAGCTA
2 / OC008011-00601p / PCR / ACTTTAATGGAAACCCAATCACAC
2 / OC008011-00602i / sequencing / GGGACAGAAAACATAGTACCTAGCAC
2 / OC008011-00603i / sequencing / CAATTTTATGCATGATTATTATCCTGA
2 / OC008011-00605i / sequencing / CCCAACCCTCAAGAAGTTTCA
* / OC008011-00606i / sequencing / GAAATTTAACATCTGTATT
* / OC008011-00607i / sequencing / ACTATGTCTGACCAGAYGT
* / OC008011-00608i / sequencing / CAGGATAATAATCWTGCATA
* / OC008011-00609i / sequencing / CACATTAGGAAAATCTGTGAT
EXT1 / 1 / OC009011-00700p / PCR / CTTATTTTATAAGCCGGAGAATGGG
1 / OC009011-00701p / PCR / GCAAGTATAAACTCAAAGGCCTCTTC
1 / OC009011-00702i / sequencing / TGAAGCTAACGTCATCACTTTCG
1 / OC009011-00703i / sequencing / TTTTATGCATCCCACACTCTAATTT
1 / OC009011-00704i / sequencing / TTTGCACTGAGATTACACTGAAGTATT
2 / OC009011-00800p / PCR / AGCAACAGTATCAACAAATGCTTC
2 / OC009011-00801p / PCR / GGAATTTTACCAAAGAACATGTCTG
2 / OC009011-00802i / sequencing / TTTGTTTCCTGTTACAGTGTTGATTA
2 / OC009011-00803i / sequencing / CGACTTTGGAGTCAGAGTACAGAA
2 / OC009011-00804i / sequencing / CGAGATGGTTTCCATTGTTCC
* / OC009011-00805i / sequencing / TGCAACTCAAACAGGACATAA
TIAM1 / 1 / OC010021-00100p / PCR / AGGAACCAAGCCACAAACATAC
1 / OC010021-00101p / PCR / TGTTCTTGAGACTGAAGTAGGCA
1 / OC010021-00103i / sequencing / GCTGTAGCTTACCTTTCCCG
1 / OC010021-00104i / sequencing / ACCCAACACACCTACCCTC
1 / OC010021-00105i / sequencing / TGGCATGAGCAGATGTTCAG
2 / OC010021-00200p / PCR / GTTCACCTCCATCATACGTAAACA
2 / OC010021-00201p / PCR / AAAGAGGGAAAGGGAGAAGAGTT
2 / OC010021-00202i / sequencing / ACAAAGCCAGACATGAAGCAAG
2 / OC010021-00203i / sequencing / CTTCTGGGTATTTGGGACATCT
2 / OC010021-00204i / sequencing / GCAATCAGCTTTAAGGACCC
*Additional primers to obtain sequence in some individuals because of multiple indel polymorphisms, allele specific PCR and allele specific sequencing.
Supplementary Table 2- Linkage disequilibrium test of postdivergence gene flow
O. c. algirus / O. c. cuniculus
Locus / Obs.a / Sim.b / pc / Obs.a / Sim.b / pc
Run 1 / ATP12A / 0.085 / 0.011 / 0.202 / 0.067 / 0.028 / 0.225
CYTC / 0.477 / 0.042 / 0.045 / 0.083 / -0.003 / 0.250
MGST3 / 0.197 / 0.060 / 0.112 / -0.021 / 0.025 / 0.568
PRL / 0.660 / -0.080 / 0.000 / 0.239 / 0.000 / 0.023
STAG1 / NA / 0.732 / NA / NA / 0.672 / NA
EXT1 / -0.101 / 0.043 / 0.787 / 0.174 / -0.034 / 0.157
LUM / 0.056 / 0.033 / 0.287 / 0.131 / 0.021 / 0.128
T / 0.042 / -0.001 / 0.372 / 0.111 / 0.018 / 0.117
TIAM1 / 0.059 / 0.015 / 0.234 / 0.110 / 0.020 / 0.170
UD14 / 0.364 / 0.024 / 0.021 / 0.065 / 0.013 / 0.266
Meand / 0.204 / 0.066 / 0.046 / 0.107 / 0.047 / 0.159
Run 2 / ATP12A / 0.753 / 0.135 / 0.015 / -0.333 / 0.113 / 0.994
CYTC / 0.235 / 0.197 / 0.328 / -0.110 / 0.164 / 0.895
MGST3 / 0.185 / 0.129 / 0.305 / 0.316 / 0.100 / 0.132
PRL / 0.945 / 0.107 / 0.003 / 0.378 / 0.084 / 0.044
STAG1 / NA / 0.328 / NA / NA / 0.291 / Na
EXT1 / 0.415 / 0.207 / 0.177 / 0.950 / 0.175 / 0.037
LUM / 0.343 / 0.095 / 0.059 / 0.277 / 0.078 / 0.093
T / 0.271 / 0.076 / 0.036 / 0.227 / 0.062 / 0.066
TIAM1 / 0.355 / 0.082 / 0.038 / 0.424 / 0.063 / 0.021
UD14 / 0.069 / 0.074 / 0.489 / 0.129 / 0.062 / 0.241
Meand / 0.397 / 0.136 / 0.023 / 0.251 / 0.113 / 0.060
Run 3 / ATP12A / 1.250 / 0.002 / 0.000 / 0.648 / -0.001 / 0.000
CYTC / 0.306 / 0.023 / 0.114 / 0.743 / 0.035 / 0.023
MGST3 / 0.055 / 0.018 / 0.289 / 0.047 / 0.009 / 0.333
PRL / 0.747 / 0.070 / 0.021 / 0.462 / 0.038 / 0.021
STAG1 / NA / 0.671 / NA / NA / 0.593 / NA
EXT1 / 0.459 / 0.029 / 0.023 / 0.319 / 0.041 / 0.163
LUM / 0.577 / 0.029 / 0.000 / 0.326 / 0.029 / 0.000
T / 0.274 / 0.038 / 0.020 / 0.017 / 0.007 / 0.388
TIAM1 / 0.165 / 0.029 / 0.063 / NA / 0.016 / NA
UD14 / 0.272 / 0.040 / 0.061 / 0.046 / 0.042 / 0.388
Meand / 0.456 / 0.070 / 0.000 / 0.326 / 0.057 / 0.000
a Observed values of x.
b Simulated values of x.
c Estimated probability of observing a simulated value higher than the observed value of x. Significant results (P < 0.05) are in bold.
dMean and standard deviation are based on all loci for which the observed x could be calculated.
NA Observed values are shown if x was calculated for at least four pairs of sites
Supplementary Figure 1- Polymorphisms for the 10 autosomal loci: (a) ATP12A, (b) CYTC, (c) MGST3, (d) PRL, (e) STAG1, (f) EXT1, (g) LUM, (h) T, (i) TIAM1, (j) UD14. Numbers in the columns indicate the position of the polymorphism in the alignment. Each row represents one haplotype inferred with the software PHASE. Names in the rows indicate the population, the number of the individual and the two haplotypes inferred from each individual (A or B). The rabbit genomic sequence was used as reference sequence. Dots and letters (A, C, G and T) represent homology and nucleotide differences from the reference sequence, respectively. N’s represent missing data. Indels were excluded.
(a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
(i)
(j)