Table 2.

Levels of polymorphism within species of house mice, and divergence between these species and Mus caroli

Locus (chromosome)	Species	N^†	L (bp)^‡	S^§	π (%)^¶	Θ (%)^¶	Tajima's D^†^†	Fu and Li's D^†^†	Dxy^‡‡
Chrng (1)	M. domesticus	92	2218	30	0.284	0.266	0.211	−0.038	3.382
	M. musculus	108	2214	19	0.046	0.163	−2.050^**	−2.157^*	3.526
	M. castaneus	62	2124	62	0.671	0.622	0.270	0.391	3.471
Med19 (2)	M. domesticus	102	1699	13	0.048	0.147	−1.808^*	−2.792^**	5.489
	M. musculus	84	1658	7	0.135	0.084	1.443	−0.562	5.592
	M. castaneus	76	1679	15	0.056	0.182	−1.990^**	−1.047	5.494
Prpf3 (3)	M. domesticus	108	2423	21	0.071	0.165	−1.641^*	−3.226^**	2.380
	M. musculus	108	2399	29	0.062	0.230	−2.194	−2.395	2.441
	M. castaneus	100	2430	34	0.126	0.270	−1.640^*	−3.384^**	2.250
Clcn6 (4)	M. domesticus	104	2028	29	0.216	0.274	−0.645	1.305	3.745
	M. musculus	106	2012	46	0.547	0.437	0.791	0.731	3.833
	M. castaneus	92	1986	62	0.763	0.613	0.794	0.634	3.747
Average of autosomal loci	M. domesticus	102	2092	23	0.155	0.213			3.749
	M. musculus	102	2071	25	0.198	0.229			3.848
	M. castaneus	83	2055	43	0.404	0.422			3.741
G6pdx (X)	M. domesticus	56	2386	5	0.060	0.046	0.769	−0.923	2.591
	M. musculus	59	2386	5	0.026	0.045	−1.012	−2.981^**	2.617
	M. castaneus	43	2354	23	0.174	0.226	−0.755	−0.242	2.679
Ocrl (X)	M. domesticus	55	2123	17	0.122	0.175	−0.933	−1.997^*	3.477
	M. musculus	55	2100	8	0.017	0.083	−2.128^**	−3.245^**	3.341
	M. castaneus	30	1983	32	0.336	0.407	−0.634	−0.227	3.538
Average of X-linked loci	M. domesticus	56	2255	11	0.091	0.111			3.034
	M. musculus	57	2243	7	0.022	0.064			2.979
	M. castaneus	37	2169	28	0.255	0.317			3.109
Jarid1d (Y)	M. domesticus	52	2329	4	0.034	0.038	−0.247	−0.131	4.740
	M. musculus	36	2335	3	0.023	0.031	−0.544	−1.644	4.882
	M. castaneus	28	2315	13	0.185	0.144	0.948	−0.320	4.904
control region (mtDNA)	M. domesticus	67	889	37	0.563	0.872	−1.154	0.483	12.631
	M. musculus	138	889	26	0.378	0.532	−0.836	−0.949	11.735
	M. castaneus	80	889	44	0.712	0.999	−0.928	0.476	12.134

^†

Number of chromosomes;

^‡

Average sequence length;

^§

Number of polymorphic nucleotide sites;

^¶

π and θ are estimators of the population mutation parameter; see Materials and methods;

^††*

P < 0.05,

^**

P < 0.01;

^‡‡

Dxy is the average pairwise divergence per site compared to M. caroli (Nei 1987).