. 2008 Jul;179(3):1455–1468. doi: 10.1534/genetics.108.088229

TABLE 3.

Population genetic analysis of 12 loci located within and outside the region rearranged between ZAL2 and ZAL2^m chromosomes

Locus	C20orf74^a	THADA^a	MAP3K4^a	ESR1^a	VIP^a	REPS1^a	TRMT11^a	CGA^a	FAM83B^a	Combined results for all loci within the rearrangement^b	SUPT3H^c	ARHGAP21^d	ANKIB1^d
Z. albicollis intraspecific data
Total sequence length (noncoding and synonymous positions)	754 (754)	1146 (746.6)	355 (83.8)	1136 (918.7)	733 (667.5)	1243 (1207.2)	1168 (1157.7)	1045 (967.3)	391 (83.4)	7971 (6586.2)	686 (607.5)	774 (647.7)	801 (801)
Segregating sites, S	9	20	1	11	5	17	14	13	5	95	13	14	9
WS birds average heterozygosity^e	0.5741	0.7667	1.0000	0.8485	1.0000	0.9902	0.8929	0.6282	1.0000	0.8246	0.1026	0.1429	0.1667
TS birds average heterozygosity^e	0.1111	0.0500	0	0.0227	0	0	0.0357	0.1731	0	0.0526	0.1731	0.1071	0.1944
Nucleotide diversity, π^f	0.0036	0.0086	0.0053	0.0046	0.0033	0.0063	0.0052	0.0054	0.0159	0.0055	0.0038	0.0030	0.0018
Tajima's D	0.22	1.03	1.03	1.82	1.74	2.16*	1.92	1.52	1.74	1.75	−1.50	−1.87*	−1.51
Fu and Li's D*	−0.17	0.25	0.65	1.44*	1.19	1.55**	1.50**	1.10	1.19	1.21	−2.47*	−1.75	−1.72
Fu and Li's F*	−0.07	0.56	0.86	1.79**	1.55	2.00**	1.88**	1.42	1.55	1.60	−2.54	−2.07	−1.92
ZAL2/2^m genetic differentiation^g
ZAL2 nucleotide diversity, π₂^f	0.0009	0.0004	0	0.0006	0	0.0001	0.0007	0.0035	0	0.0009	0.0027	—	—
ZAL2^m nucleotide diversity, π_2m^f	0	0	0	0.0009	0	0	0	0.0003	0	0.0002	0.0033	—	—
Shared polymorphisms	0	0	0	1	0	0	0	0	0	1	3	—	—
Fixed differences between arrangement	5	14	1	9	5	16	12	4	5	71	0	—	—
Average nucleotide substitutions per site, d_xy^f	0.0071	0.0188	0.0119	0.0097	0.0075	0.0140	0.0110	0.0081	0.0360	0.0114	0.0033	—	—
F_ST	0.91***	0.97***	1***	0.94***	1***	0.99***	0.96***	0.70***	1***	0.94***	0.11	—	—

*P < 0.05, **P < 0.02, ***P < 0.001.

Loci that map within the region rearranged between ZAL2 and ZAL2^m.

The results obtained after concatenating the sequences of the nine loci included within the region rearranged between ZAL2 and ZAL2^m chromosomes (underlined).

The locus linked to ZAL2 and ZAL2^m but outside of the rearranged region.

Loci that map to ZAL1.

Heterozygosity was calculated independently for the WS (ZAL2/ZAL2^m heterokaryotypes) and TS (ZAL2/ZAL2 homokaryotypes) groups as the average fraction of heterozygotes per segregating position.

The nucleotide diversity (π) and the average number of nucleotide substitutions per site between arrangements (d_xy) were calculated considering only noncoding and synonymous positions.

For the calculation of genetic differentiation measures between ZAL2 and ZAL2^m, haplotypes were estimated with the Phase program and only positions that could be reliably assigned to a particular haplotype were included in the analysis.