Identification of selective sweeps in closely related populations of the house mouse based on microsatellite scans.
Genome scans of polymorphisms promise to provide insights into the patterns and frequencies of positive selection under natural conditions. The use of microsatellites as markers has the potential to focus on very recent events, since in contrast to SNPs, their high mutation rates should remove signatures of older events. We assess this concept here in a large-scale study. We have analyzed two population pairs of the house mouse, one pair of the subspecies Mus musculus domesticus and the other of M. m. musculus. A total of 915 microsatellite loci chosen to cover the whole genome were assessed in a prescreening procedure, followed by individual typing of candidate loci. Schlötterer's ratio statistics (lnRH) were applied to detect loci with significant deviations from patterns of neutral expectation. For eight loci from each population pair we have determined the size of the potential sweep window and applied a second statistical procedure (linked locus statistics). For the two population pairs, we find five and four significant sweep loci, respectively, with an average estimated window size of 120 kb. On the basis of the analysis of individual allele frequencies, it is possible to identify the most recent sweep, for which we estimate an onset of 400-600 years ago. Given the known population history for the French-German population pair, we infer that the average frequency of selective sweeps in these populations is higher than 1 in 100 generations across the whole genome. We discuss the implications for adaptation processes in natural populations.
Teschke
Meike
M
Department of Genetics, University of Cologne, 50674 Cologne, Germany.
Mukabayire
Odette
O
Wiehe
Thomas
T
Tautz
Diethard
D
D000818:Animals; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D005787:Gene Frequency; D005828:Genetics, Population; D016678:Genome; D051379:Mice; D018895:Microsatellite Repeats / Q000235:genetics*; D012641:Selection, Genetic; D013223:Statistics as Topic / Q000379:methods*
Genetics. 2008 Sep;180(1):341-57
18716326
Trends Genet. 2003 Jan;19(1):24-31
12493245
Genetics. 2000 Jun;155(2):909-19
10835409
Genome Res. 2005 Jun;15(6):790-9
15930491
Genetics. 2007 Apr;175(4):1911-21
17287527
Trends Genet. 2001 Sep;17(9):481-5
11525814
Nature. 2005 Oct 20;437(7062):1149-52
16237443
Genome Res. 2006 Jun;16(6):702-12
16687733
Nat Rev Genet. 2005 Feb;6(2):119-27
15716908
Mol Biol Evol. 2002 Jul;19(7):1143-53
12082133
Dev Biol. 2005 Jan 1;277(1):16-26
15572136
Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12949-54
12351680
Trends Genet. 2006 Aug;22(8):437-46
16808986
Genetics. 2007 Mar;175(3):1395-406
17194788
Philos Trans R Soc Lond B Biol Sci. 2005 Jul 29;360(1459):1411-25
16048784
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
9862982
Nature. 2004 Jun 3;429(6991):558-62
15175752
Philos Trans R Soc Lond B Biol Sci. 1988 Jul 6;319(1196):587-600
2905494
Heredity (Edinb). 2007 Jun;98(6):340-8
17473869
Genetics. 2003 Nov;165(3):1137-48
14668371
Genetics. 2007 Apr;175(4):1823-34
17237516
Heredity (Edinb). 2002 Nov;89(5):329-38
12399990
Mol Ecol. 2008 Jan;17(2):627-41
18179435
Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8748-53
12070344
Nature. 2002 Feb 28;415(6875):1022-4
11875568
Genetics. 2007 Jan;175(1):207-18
17057237
Genetics. 2002 Feb;160(2):753-63
11861576
Genetics. 2004 Jul;167(3):1513-24
15280259
Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5447-52
18381818
PLoS Biol. 2006 Nov;4(12):e395
17105354
Mol Biol Evol. 2006 Apr;23(4):790-7
16421176
Genetics. 1997 May;146(1):309-20
9136020
Genome Res. 2008 Jun;18(6):881-7
18356314
Development. 2007 Oct;134(19):3507-15
17728347
Mol Biol Evol. 2003 Jun;20(6):893-900
12717000