Four datasets were prepared for the different analyses: Dataset I includes 18S, 28S, DUNUC3, Cox1 concatenated for Dugesia representatives and used Recurva and Schmidtea genera as outgroups, to root the Dugesia (Sluys et al., 2013). Dataset I (4,444 bp): 18S - 1 - 1,737 28S - 1,738 - 3,316 Dunuc3 - 3,317 - 3,688 Cox1 - 3,689 - 4,444 Dataset II includes 18S, 28S, Cox1, DUNUC3, DUNUC5, ITS-1 concatenated (no outgroup included), to obtain the phylogenetic trees and to carry out dating analyses. Dataset II (5,501 bp): 18S - 1 - 1,607 28S - 1,608 - 3,184 Cox1 - 3,185 - 3,934 Dunuc3 - 3,935 - 4,300 Dunuc5 - 4,301 - 4,622 ITS-1 - 4,623 - 5,501 Dataset III is constituted by 18S gene sequences from Catenulida and Rhabditophora (including Tricladida) representatives, and a chaetognath species as outgroup to run a dating analysis. Dataset IV, to run biogeographical analyses, was obtained by pruning dataset II to include only one representative per biogeographical region but including at least one representative per clade (species of Recurva and Schmidtea were used as outgroup representatives). See table 1 for dataset characteristics and tables S2 and S3 for a list of individuals/species included in each dataset. Table 1. Datasets’ characteristics. Supporting information Tables S2 and S3 show the individuals included in each analysis. 18S 28S ITS-1 Cox1 DUNUC3 DUNUC5 Dataset I Length (bp) 1,737 1,579 - 756 372 - Missing data (%) 14.2 14.0 - 12.2 8.4 - Total length (missing data) (bp, %) 4,444 (13.4) Total sequences 115 Dataset II Gene length (bp) 1,607 1,577 879 750 366 322 Missing data (%) 12.9 14.1 3.9 12.2 8.4 37.7 Total length (missing data) (bp, %) 5,501 (13.1) Total sequences 112 Dataset III Gene length (bp) 1,423 Missing data (%) 0 Total sequences 39 Dataset IV Gene length (bp) 1,701 1,494 569 744 341 318 Missing data (%) 14.1 12.8 5.5 8.4 9.4 36.6 Total length (missing data) (bp, %) 5,167 (12.9) Total sequences 60 Table S2. Summary list of the Dugesia and other Dugesiidae specimens included in each dataset. Dataset I Dataset II Dataset III Dataset IV Dugesia Dnot X X X Dazr1 X X Dazr2 X X X Dazr3 X X Dazr4 X X Dban X X Dben X X X Dbul X X Dcam1 X X X X Dcam2 X X Dpus X X X Dchi1 X X X Dchi2 X X X Daet X X X Dfra X X X Dger1 X X Dger2 X X Dcre1 X X X Dcre2 X X Dcre3 X X Dmal X X Dter X X X Daen X X X Deff X X Dpar X X Dsag1 X X X Dsag2 X X Dpsa X X Dpho X X X Deub X X X Dnai X X X Ddam X X X Dari X X X Dimp X X Dpol X X Dele X X X Darc X X X Dsic X X X Dtri X X X Dlef X X X Dltr X X Dind X X X Dino X X X Dpap X X X Dira1 X X X Dira2 X X Dira3 X X Disr1 X X X Disr2 X X X Dlig X X Dilv X X X Dmon X X Dbnz X X Dhep X X X Detr X X Dryu1 X X X Dryu2 X X Dryu3 X X Djap1 X X X Djap2 X X X Djap3 X X X Djap4 X X X Djap5 X X Dmad1 X X X Dgra X X X Dmad2 X X Dmad3 X X Dmad4 X X Dmad5 X X X Dmad6 X X X Dmad7 X X Dmad8 X X X Dgib X X X Dbif X X X Dmad9 X X X Dmad10 X X Dmad11 X X Dmad12 X X X Dmad13 X X Dsig X X Dmad14 X X Dmad15 X X X Dmad16 X X Dmad17 X X Dbat X X Dtub X X X Dmar1 X X X Dmar2 X X X Doma1 X X X Doma2 X X Drom1 X X Drom2 X X Dsao1 X X Dsao2 X X X Dser X X X Dafr X X X Dsaf X X Dibe1 X X X Dibe2 X X Dibe3 X X Dibe4 X X Dibe5 X X Dtwn1 X X Dtwn2 X X X Dtwn3 X X X Dtai X X X X Dtky1 X X X Dtky2 X X X Dtky3 X X Dtky4 X X Dara X X X Other Dugesiidae Recurva postrema X X X Schmidtea polychroa X X Schmidtea mediterranea X X Girardia tigrina X Table S3. Sequences of 18S ribosomal gene downloaded from GenBank to be included in Dataset III used in the first calibration analysis (Supplementary material Figure S4). Classification Accession Number Platyhelminthes Claus, 1887 Catenulida Meixner, 1924 Paracatenula galateia HQ231344 Rhabditophora Ehlers, 1985 Polycladida Lang, 1884 Stylochus zebra AF342801 Bothrioplanida Braun, 1881 Bothrioplana semperi AF051333 Neodermata Ehlers, 1985 Trematoda Rudolphi, 1808 Schistosoma mansoni SMU65657 Gyliauchen sp. GLHRRNA Paramphistomum cervi KJ459937 Lobatostoma manteri LBORNA Fascioloides magna EF534989 Cestoda Rudolphi, 1808 Gyrocotyle urna AJ228782 Diphyllobothrium pacificus DQ925310 Acanthobothrium parviuncinatum EF095250 Hymenolepis nana AY193875 Hymenolepis diminuta AF124475 Echinococcus granulosus GQ260092 Taenia hydatigena GQ260090 Taenia solium GQ260091 Taenia multiceps GQ260089 Monogenea Carus, 1863 Diclybothrium armatum KP796245 Haliotrema cromileptis EU541306 Tricladida Maricola Hallez, 1892 Procerodes dohrni JN009783 Ectoplana limuli D85088 Palombiella stephensoni DQ666008 Pentacoelum hispaniense JN009784 Cercyra hastata DQ665995 Sabussowia dioica JN009785 Continenticola Carranza et al., 1998 Dendrocoelidae Hallez, 1892 Dendrocoelum lacteum AJ312271 Baikalobia guttata Z99946 Planariidae Stimpson, 1857 Phagocata ullala AF013149 Polycelis nigra AF013151 Geoplanidae Stimpson, 1857 Diversibipalium multilineatum Pending Dugesiidae Ball, 1974 Girardia tigrina AF013156 Recurva postrema KF308691 Schmidtea polychroa AF014154 Chaetognatha Leuckart, 1854 Eukrohnia sp. AY922316