TABLE 1.

Nucleotide differences (π ± SD) of linked and unlinked loci to the SDL

	Recombination rate (cM/Mb)	Distance to 3′-end of csd (kb)	Fragments	Length (bp)	Polymorphic sites	π ± SD
Loci linked to SDL
Ex2/3		−7.3	14	456	27	0.0200 ± 0.0064
Ex4/5		−4.7	14	201	10	0.0135 ± 0.0099
Ex6/7		−0.5	14	288	51	0.0918 ± 0.021
KF22	50	1.5	3	372	13	0.0233 ± 0.0074
KF2	50	2	4	294	7	0.0136 ± 0.0038
HF63	25	12	8	298	8	0.0108 ± 0.0029
DF33	10	28	5	268	4	0.0067 ± 0.0023
DF37	10	45	7	338	2	0.0017 ± 0.0007
Loci unlinked to SDL	Recombination rate (cM/Mb)		Fragments	Length (bp)	Polymorphic sites	π ± SD
RR22	0		7	473	2	0.0012 ± 0.0008
RR25	7		7	503	4	0.0023 ± 0.0006
RR8	12		10	325	7	0.0092 ± 0.0024
RR9	19		9	699	9	0.0045 ± 0.0017
RR23	22		10	783	14	0.0062 ± 0.0012
RR19	25		10	532	2	0.0016 ± 0.0003
RR21	34		10	622	11	0.0045 ± 0.0012
RR17	51		9	482	4	0.0024 ± 0.0006
RR28	52		10	485	20	0.0173 ± 0.0021
RR7	56		10	416	14	0.0095 ± 0.0025
RR11	53		10	590	10	0.0051 ± 0.0007
RR14	72		10	884	7	0.0027 ± 0.0004
Average nucleotide diversity of unlinked loci						0.0055 ± 0.0044

The number of polymorphic sites and π are obtained from the sequence alignment that exclude gaps and a chromosome sample of up to 10 sequences (see text). Synonymous sites of the csd coding sequence were used for calculations at Ex2/3, Ex4/5, and Ex6/7 and distances are calculated from the 3′-end of csd. Recombination rates for loci linked to SDL are based on mapping data (see Figure 1). For loci unlinked to SDL, recombination rates were estimated in 125-kb windows by a genomewide analysis of the honeybee sequence assembly 2.1. Putatively neutral loci were chosen on the basis of the region corresponding to those windows in the annotated genome.