Classification of results in breakpoint identification.

The criteria used in the classification are BPP support for alternative tree topologies in the breakpoint region, and number of aligned nucleotide positions (nt) over which the topology changes. Cases in which all breakpoints show abrupt change between very strongly supported topologies constitute Class A, and those in which all breakpoints show more-gradual change between moderately to strongly supported topologies constitute Class B. Class C groups individual cases showing a combination of abrupt and more-gradual BPP changes across breakpoints. Classes A–C represent positively identified recombination events, and precise breakpoints were inferred. Cases showing inconclusive support (BPP<0.50) at breakpoint regions, or uninterpretably complex patterns, were assigned to Class D, and those that show no change were classified as Class E. ‘N/A’ denotes not applicable.