Table 1.

Number of SNPs Identified and Filtered for Different Data Sets.

Data Set	Number of Unfiltered SNPs	Number of SNPs Removed due to Linkage	Number of SNPs Removed That Were Not in HWE	Number of Nonneutral SNPs Removed	Number of SNPs Removed Mapping to Z Chromosome	Number of Transitions Removed	Number of SNPs Retained	Number of SNPs with No Missing Data
Pellorneum capistratum
Data set I: all SNPs obtained after mapping to Mixornis gularis genome	82,468	24,025	1,904	82	1,246	NA	54,906	54,906
Data set II: only transversions obtained after mapping to M. gularis genome	82,468	24,025	1,904	82	1,246	37,690	17,216	17,216
Data set III: single random SNP per target locus	960	NA	30	12	35	NA	883	883
Data set IV: only transversions obtained after mapping to Parus major genome	208,186	67,451	3,357	1,130	1,470	96,315	38,463	10,848
Pellorneum malaccense
Data set I: all SNPs obtained after mapping to M. gularis genome	57,300	21,595	440	240	1,317	NA	33,708	33,708
Data set II: only transversions obtained after mapping to M. gularis genome	57,300	21,595	440	240	1,317	22,558	11,150	11,150
Data set III: single random SNP per target locus	958	NA	17	2	44	NA	895	895
Data set IV: only transversions obtained after mapping to Parus major genome	198,711	83,460	749	1,490	1,491	78,786	32,735	6,091

Note.—HWE, Hardy–Weinberg equilibrium; NA, not applicable.