Table 1 QTL identified with the combined analysis and their inferred phylogenetic partitions
PhenotypeChr.Position (cM)LOD scorePosition (Mb)1.5 LOD int. (Mb)PartitionPosterior probability
Amorphous sperm head266.04.70168.3131.9–178.7C|MD1.00
5a50.03.95120.588.3–135.7D|MC0.94
92.07.7313.33.1–30.2C|MD1.00
X20.011.4660.846.9–95.2D|MC0.97
PAR4.0c3.87C|MD0.99
Distal bent tail316.05.5842.316.2–67.9M|CD1.00
572.08.64147.3133.7–148.4M|CD1.00
X23.08.6867.756.2–93.3M|CD1.00
Headless/tailless150.03.9616.516.5–46.7M|CD0.96
X23.010.1067.751.5–97.1D|MC0.99
PAR0.03.95C|MD0.98
Proximal bent tail108.04.8648.533.8–81.9M|CD0.97
X31.510.0590.856.2–97.1M|CD0.98
Xb58.03.36146.995.2–62.9C|MD
Testis weight228.68.2980.669.7–08.3D|MC1.00
447.111.51108.957.8–114.3D|MC0.98
1016.07.2167.858.3–88.1M|CD0.94
PAR2.04.51C|MD0.99
Sperm density1713.56.0229.93.1–64.8M|CD1.00
X4.04.2220.710.2–56.2D|MC0.92
Xb56.03.82142.486.6–162.9C|MD
PAR2.06.06C|MD1.00
Sperm head PC12b76.04.00177.0143.8–179.0C|MD
14a 46.010.2696.889.4–104.1M|CD1.00
19a 30.017.9439.133.2–44.9M|CD1.00
Xb12.04.1841.910.2–162.9C|MD
X20.085.3260.851.5–65.5M|CD1.00
PAR6.08.52C|MDd0.93
Sperm head PC2X18.010.8056.245.1–70.3D|MC1.00
PAR0.08.35C|MD0.51
Seminiferous tubule area226.07.2576.357.7–102.4C|MD0.99
851.14.33125.0113.0–130.8C|MD0.96
16a 24.44.0997.290.4–97.2D|MC0.93
1826.04.6268.357.8–73.4M|CD0.97
X65.24.46162.9142.4–162.9C|MD1.00
PAR0.08.29C|MD1.00
Total abnormal sperm564.04.96137.7123.6–148.4M|CD0.75
154.04.6628.616.5–68.7M|CD0.99
X34.015.9893.356.2–99.1D|MC1.00
PAR0.05.44C|MD1.00
  • Posterior probabilities of the partitions were calculated using the approximate Bayes procedure in Broman et al. (2012). D|MC, M|CD, and C|MD describe the domesticus|musculus,castaneus; musculus|castaneus,domesticus; and castaneus|musculus,domesticus partitions, respectively. PAR, pseudoautosomal region.

  • a QTL newly identified by the combined analysis.

  • b QTL detected in separate analyses of the two crosses but not detected by the combined analysis.

  • c PAR genetic positions are relative to the beginning of the region, not the X chromosome.

  • d Sperm morphology PC1 assigned to D|MC in PhyloQTL, but likely in error due to the high LOD score of QTL on the X in the musculus × domesticus cross (see text).