Table 1.

12 types of genotype transitions that SIEVE is able to identify, with their interpretation as mutation events. The genotype transitions correspond to possible changes of genotypes on a branch from the parent node to the child node. If any of these events occurs on independent branches of the phylogenetic tree, it is also considered as a parallel evolution event. For detailed explanations of the mutation events, see the “Methods” section

Genotype transition	Mutation event
$0/0\to 0/1$	Single mutation
$0/0\to 1/1$	Homozygous coincident double mutation
$0/0\to 1/1^{\prime }$	Heterozygous coincident double mutation
$0/1\to 0/0$	Single back mutation
$1/1\to 0/1$	Single back mutation
$1/1^{\prime }\to 0/1$	Single back mutation
$1/1\to 0/0$	Double back mutation
$1/1^{\prime }\to 0/0$	Double back mutation
$0/1\to 1/1$	Homozygous single mutation addition
$0/1\to 1/1^{\prime }$	Heterozygous single mutation addition
$1/1^{\prime }\to 1/1$	Homozygous substitute single mutation
$1/1\to 1/1^{\prime }$	Heterozygous substitute single mutation