Speciation and evolution in the Gagea reticulata species complex (Tulipeae; Liliaceae)

► A novel method was introduced to reduce complexity among DNA sequence haplotypes. ► This bioinformatics tool revealed the ancestral migratory path of Gagea. ► This is the first record of three copies of malate synthase in a land plant. ► The genome multiplication event coincided with speciation. ► Patterns of hybridization/introgression between species were recovered.