Table 3.

Breakpoint locations

	5' part	3' part	Entire alignment
Positions in reduced alignment	1–1821	2385–4045	1–4045
Corresponding positions in full alignment	1–2718	3927–6416	1–6416
Number of base/indel characters	2718/148	2490/150	6416/361
Substitution model	GTR + Γ	GTR + Γ	GTR + Γ

Locations of breakpoints between non-recombinant parts of the reduced 4045-bp alignment suggested by GARD, and corresponding positions in the longer alignment. Substitution models were suggested by MrModeltest AIC.