Table 1. Rates of recombination relative to mutation for representative genomic regions in high-light and low-light adapted Prochlorococcus.

Region	Functional group	Sequences in alignment	Alignment length (bp)	κ	δ	ν	R/θ	ρ/θ	R/m
High-light adapted Prochlorococcus (HLII and HLVI clades)
nirA-moaA	nitrate	33	11428	3.32	4202	0.012	0.68	1.36	34.0
polA region*	core flanking	19	11554	3.72	8035	0.020	0.20	0.41	33.2
Low-light adapted Prochlorococcus (LLI clade)
moaB-narB	nitrate	17	11985	2.91	435	0.021	1.78	3.57	16.5
pyrG region†	core flanking	15	10080	2.81	964	0.029	2.17	4.34	59.7
ppk region‡	core flanking	15	11918	3.19	1056	0.031	0.93	1.85	30.3

* 3’ flanking region, containing polA, adjacent to the nitrate assimilation gene cluster in the HLII clade.

^† 5’ flanking region, containing pyrG, adjacent to the nitrate assimilation gene cluster in the LLI clade.

^‡ 3’ flanking region, containing ppk, adjacent to the nitrate assimilation gene cluster in the LLI clade.

κ, Transition/transversion rate ratio as estimated by PhyML under the HKY85 model.

δ, Mean length of DNA imported by homologous recombination.

ν, Divergence rate, per site, of DNA imported by homologous recombination.

R/θ, Per-site rate of initiation of recombination relative to the population mutation rate.

ρ/θ, Population recombination rate relative to the population mutation rate (ρ = 2R).

r/m, Relative impact of recombination versus mutation on the per-site substitution rate. Equal to (R/θ) × δ × ν.