TABLE 4.

Linkage disequilibrium and recombination statistics for mainland zebra finches

Locus	D′ × d	r2 × d	ρ per site PHASEa	ρ per site PHASEb	ρ per site LDhat
005	−0.18**	−0.16**	0.009 (0.003–0.022)	0.011 (0.004–0.024)	0.098 (0.035–0.147)
035	−0.09**	−0.06*	0.028 (0.016–0.049)	0.030 (0.018–0.051)	0.127 (0.039–0.150)
175	−0.07*	−0.12**	0.006 (0.002–0.013)	0.007 (0.003–0.017)	0.005 (0.002–0.007)
276	−0.19**	−0.12**	0.058 (0.035–0.098)	0.058 (0.036–0.094)	0.108 (0.056–0.130)
319	−0.15**	−0.06*	0.212 (0.109–0.384)	0.199 (0.103–0.344)	0.193 (0.085–0.223)
359	−0.06*	−0.12**	0.050 (0.028–0.087)	0.051 (0.028–0.087)	0.029 (0.008–0.029)
365	−0.15**	−0.10*	0.012 (0.004–0.027)	0.014 (0.006–0.028)	0.003 (0.001–0.005)
		Mean (SE):	0.053 (0.010)	0.051 (0.010)	0.08 (0.010)

D′ × d and r² × d are correlation coefficients of two measures of LD with genetic distance. Significance values are the proportion of data sets simulated in LDhat that show correlation coefficients that are less than or equal to the observed values (*P < 0.05, **P < 0.01). In parentheses are the 10% and 90% quantiles from the posterior distribution. For LDhat, we assessed confidence by running simulations conditioned on the point estimates of ρ. In parentheses are 10% and 90% quantiles of the distribution of these conditioned estimates.

^aEstimates of the recombination parameter ρ = 4N_ec per site are given from PHASE using priors for ρ from humans (0.0004).

^bEstimates of the recombination parameter ρ = 4N_ec per site are given from PHASE using priors for ρ from blackbirds (0.0588).