Table 2 Nucleotide diversity in various rodent colonies
SpeciesπNumber of IndividualsBreeding SchemeRegion of Genome for Which π Was EvaluatedApproximate Number of Bases SurveyedCitation
M. unguiculatus0.005924Outbred colonyNear autosomal restriction sites (GBS)2,200,000This article
M. musculus subsp.a0.028969Collaborative CrossWhole genome sequencing2,300,000,000Srivastava et al. (2017)
M. musculus subsp.0.00558Eight inbred strainsAutosomal genes (Sanger)14,000Salcedo et al. (2007)
M. musculus domesticus0.010264Wild caughtAutosomal genes (Sanger)15,000Salcedo et al. (2007)
M. musculus musculus0.005426Wild caughtAutosomal genes (Sanger)15,000Salcedo et al. (2007)
Peromyscus maniculatusb0.000613Outbred colonyNear restriction sites (ddRAD)400,000Weber et al. (2013)
P. polionotusb0.00101Outbred colonyNear restriction sites (ddRAD)400,000Weber et al. (2013)
Phodopus campbellic0.000614Outbred colonyNear restriction sites (ddRAD)1,300,000J. Good, personal communication
P. sungorusc0.000211Outbred colonyNear restriction sites (ddRAD)1,400,000J. Good, personal communication
R. norvegicus0.0015–0.00299696 inbred strainsCEL I-based SNP detection5,800,000Smits et al. (2004)
R. norvegicus0.002258Wild caughtAutosomal genes (Sanger)10,000Ness et al. (2012)
  • a Based on mean value of 69 Collaborative Cross individuals. Data from the column titled “% het (autosomes) in sequenced sample” in table S2 of Srivastava et al. (2017). Approximate number of bases surveyed is based on a genome size of 2.7 GB divided by the mean “% coverage at 15×.”

  • b The Peromyscus animals evaluated here are the BW and PO strains originating with the Peromyscus stock center, bred at Harvard University in the Hoekstra laboratory, and sequenced by Weber et al. (2013).

  • c The Phodopus animals evaluated here are from the Good laboratory at the University of Montana described in Brekke and Good (2014).