men12257-sup-0001-AppendixS1.pdfapplication/PDF100KAppendix S1 (A) List of species barcoded, including those where we suggest a taxonomic update, and also including to genus level only identified specimens. In parentheses number of individuals, an ‘e’ marks species for which individuals where used from outside the Mediterranean region. Taxa with potential candidate species or recovered synonyms are marked with an '*'. Alien taxa in the Mediterranean BH are marked with an ‘$’; (B) list of Mediterranean freshwater fish species for which no material could be acquired; (Ex) indicates that the species is probably extinct; (F) indicates the failure or poor quality of COI PCR amplification; (C) list of Mediterranean freshwater fish species for which COI sequences were obtained from NCBI GenBank with their respective accession numbers; (D) DNA barcoding studies that contributed materials to the study.
men12257-sup-0002-AppendixS2.pdfapplication/PDF288KAppendix S2 (A) Methodological details for DNA extraction, PCR and molecular data analysis; (B) best-fit and other GMYC models within delta AICc = 0.99 ranked by increasing delta AICc; weights: Akaike weight given to the model in the averaged parameter estimates below; method: single- or multiple-threshold GMYC model.
men12257-sup-0003-FigS1.pdfapplication/PDF1520KFig. S1 Collection of the maximum-likelihood trees obtained from the different data partitions (see Methods), with details for calculation given for each tree.
men12257-sup-0004-FigS2.pdfapplication/PDF56KFig. S2 (A) For each IUCN category (LC, least concern; NT, near threatened; VU, vulnerable; EN, endangered; CR, critically endangered; number of species in parentheses), the 25–75 per cent quartiles of the EDGE scores are drawn as box, the medians given as horizontal line. Whiskers show largest and smallest data points <1.5 times the box height from the box. Outliers (stars) are values further than three times the box height from the box, values outside the inner fences are shown as circles; (B) top 10 species listed according to decreasing EDGE score and according to decreasing ED (evolutionary distinctiveness) with their respective IUCN classification. Outliers with respect to IUCN category combined with EDGE score are marked with an (*). Only endemic species without closely related congeneric species outside the Mediterranean are considered.
men12257-sup-0005-TableS1.xlsapplication/msexcel587KTable S1 Excel spreadsheet with the name and sampling details for all newly generated individuals included in this study, museum or field accession numbers for specimens, and GenBank accession number for their DNA sequence.
men12257-sup-0006-TableS2.pdfapplication/PDF265KTable S2 (A) List of proposed updated taxonomy and, where applicable, mean K2P distances to former synonyms, and to nearest neighbour species if different; (B) commented lists of individuals identified as hybrids in the field with their respective putative parental species and number of individuals given in parentheses; (C) species or populations with haplotype-sharing indicating the need for more systematic research; (D) divergent lineages indicating introgressions and/or the need for more systematic research.

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