Table 1 Symbols used in the model description
ParameterDescription
Embedded Image = [dijs]Data composed of counts for each SNP j within pool i of type s ∈ {0, 1}
i = 1, … , NIndex and no. pools
j = 1, … , MIndex and no. SNPs
k = 1, … , KIndex and no. lineages
ℒ = [lkj]Lineages composed by state of SNP j in lineage k
Embedded ImagePhylogeny
τ, {tb}Topology and branch lengths for Embedded Image
TThe total branch length of Embedded Image
λProbability of a phylogenetic SNP
Embedded Image Embedded ImagePhylogenetic and null SNP sets defined by Embedded Image
Embedded ImagePartition of SNPs into phylogenetic and null components
Embedded Image = [sik]Pool composition specified by pool proportion for pool i and lineage k
pijThe uncorrected reference allele frequency for SNP j in pool i
ηSNP error rate
Embedded ImageThe corrected reference allele frequency for SNP j in pool i
ξMutation rate
ψMixing rate in the island coalescent simulations