3 II 21.88 6.25 21.88 20.00 14.29 14.81 54.17 54.17 48.15 45.83 40.00 29.17 66.67 62.50 58.33 54.17 70.Ability to discriminate (character) ( )II 25.00 15.63 34.38 32.00 32.14 14.81 58.33 58.33 59.26 41.67 32.00 33.33 62.50 62.50 62.50 50.00 70.32 32 32 25 28 27 24 24 27 24 25 24 24 24 24 2437.50 25.00 40.63 60.00 39.29 14.81 66.67 75.00 62.96 58.33 60.00 45.83 75.00 66.67 75.00 58.33 75.43.75 31.25 50.00 48.00 35.71 14.81 70.83 62.50 62.96 54.17 48.00 45.83 70.83 66.67 66.67 58.33 75.34.38 18.75 40.63 40.00 25.00 14.81 -Species represented by multiple individuals. The percentage of the species with higher minimum interspecific distance than maximum intraspecific distance (species barcoding gap) amongstudied species. Column I: the percentage of the get WP1066 monophyletic clusters of individuals belonging to the same morphological species among studied species. Column II: the corresponding number for the monophyletic clusters with 70 bootstrap values in ML and 0.95 posterior probabilities in BI. ML, maximumlikelihood method; BI, Bayesian-inference method.The percentage of the species that could be identified by diagnostic characters among studied species. The analyses did not include multilocus combinations. doi:10.1371/journal.pone.0125574.tfamily level and the genus level (Table 3 and S3 Table). In addition, ITS performed better than both ITS1 and ITS2 at the family level, as it did for Illicium (Table 3 and S3 Table). According to the data from the genera Schisandra and Kadsura, ITS1 performed as well as ITS (S3 Table). The multi-locus combinations, ITS+matK, ITS+trnH-psbA+matK, ITS+matK+rbcL, and ITS +trnH-psbA+matK+rbcL, performed better than others at the family level, as they did for Schisandra and Kadsura (Table 3 and S3 Table). The combinations ITS+trnH-psbA and ITS+trnHpsbA +rbcL also performed as well as the former ones for Illicium (S3 Table).Tree-based identificationThe ML Belinostat site phylogenetic tree of the combination of ITS+trnH-psbA+matK+rbcL is presented in Fig 3, and all the other phylogenetic trees are shown in S1 and S2 Figs. Among four commonly used barcoding loci, rbcL had the lowest discriminatory power at both the family level and the genus level (Table 3 and S3 Table). ITS showed the highest level of discrimination for the family as a whole and for Illicium alone (Table 3 and S3 Table). In comparison, trnH-psbA showed relatively better performance than the other three loci for Schisandra and Kadsura (Table 3 and S3 Table). In addition, ITS displayed higher species-resolving power than both ITS1 and ITS2 for the family as a whole and for Illicium alone (Table 3 and S3 Table). According to thePLOS ONE | DOI:10.1371/journal.pone.0125574 May 4,9 /DNA Barcoding for SchisandraceaePLOS ONE | DOI:10.1371/journal.pone.0125574 May 4,10 /DNA Barcoding for SchisandraceaeFig 3. Schisandraceae ML phylogenetic tree based on the combination of ITS, trnH-psbA, matK, and rbcL. The tree included 24 species from three genera of Schisandraceae, Schisandra, Kadsura, and Illicium. The species Austrobaileya scandens was the outgroup for the analysis. All loci were available for all individuals of Schisandraceae species in the tree. Numbers above the branches represent bootstrap values for monophyletic species with 70 bootstrap values in ML and 0.95 posterior probabilities in BI. The asterisk indicates the bootstrap value or posterior probability lower than the threshold. ML, maximum-likelihood method; BI, Bayesian-inference method. The two clusters for t.3 II 21.88 6.25 21.88 20.00 14.29 14.81 54.17 54.17 48.15 45.83 40.00 29.17 66.67 62.50 58.33 54.17 70.Ability to discriminate (character) ( )II 25.00 15.63 34.38 32.00 32.14 14.81 58.33 58.33 59.26 41.67 32.00 33.33 62.50 62.50 62.50 50.00 70.32 32 32 25 28 27 24 24 27 24 25 24 24 24 24 2437.50 25.00 40.63 60.00 39.29 14.81 66.67 75.00 62.96 58.33 60.00 45.83 75.00 66.67 75.00 58.33 75.43.75 31.25 50.00 48.00 35.71 14.81 70.83 62.50 62.96 54.17 48.00 45.83 70.83 66.67 66.67 58.33 75.34.38 18.75 40.63 40.00 25.00 14.81 -Species represented by multiple individuals. The percentage of the species with higher minimum interspecific distance than maximum intraspecific distance (species barcoding gap) amongstudied species. Column I: the percentage of the monophyletic clusters of individuals belonging to the same morphological species among studied species. Column II: the corresponding number for the monophyletic clusters with 70 bootstrap values in ML and 0.95 posterior probabilities in BI. ML, maximumlikelihood method; BI, Bayesian-inference method.The percentage of the species that could be identified by diagnostic characters among studied species. The analyses did not include multilocus combinations. doi:10.1371/journal.pone.0125574.tfamily level and the genus level (Table 3 and S3 Table). In addition, ITS performed better than both ITS1 and ITS2 at the family level, as it did for Illicium (Table 3 and S3 Table). According to the data from the genera Schisandra and Kadsura, ITS1 performed as well as ITS (S3 Table). The multi-locus combinations, ITS+matK, ITS+trnH-psbA+matK, ITS+matK+rbcL, and ITS +trnH-psbA+matK+rbcL, performed better than others at the family level, as they did for Schisandra and Kadsura (Table 3 and S3 Table). The combinations ITS+trnH-psbA and ITS+trnHpsbA +rbcL also performed as well as the former ones for Illicium (S3 Table).Tree-based identificationThe ML phylogenetic tree of the combination of ITS+trnH-psbA+matK+rbcL is presented in Fig 3, and all the other phylogenetic trees are shown in S1 and S2 Figs. Among four commonly used barcoding loci, rbcL had the lowest discriminatory power at both the family level and the genus level (Table 3 and S3 Table). ITS showed the highest level of discrimination for the family as a whole and for Illicium alone (Table 3 and S3 Table). In comparison, trnH-psbA showed relatively better performance than the other three loci for Schisandra and Kadsura (Table 3 and S3 Table). In addition, ITS displayed higher species-resolving power than both ITS1 and ITS2 for the family as a whole and for Illicium alone (Table 3 and S3 Table). According to thePLOS ONE | DOI:10.1371/journal.pone.0125574 May 4,9 /DNA Barcoding for SchisandraceaePLOS ONE | DOI:10.1371/journal.pone.0125574 May 4,10 /DNA Barcoding for SchisandraceaeFig 3. Schisandraceae ML phylogenetic tree based on the combination of ITS, trnH-psbA, matK, and rbcL. The tree included 24 species from three genera of Schisandraceae, Schisandra, Kadsura, and Illicium. The species Austrobaileya scandens was the outgroup for the analysis. All loci were available for all individuals of Schisandraceae species in the tree. Numbers above the branches represent bootstrap values for monophyletic species with 70 bootstrap values in ML and 0.95 posterior probabilities in BI. The asterisk indicates the bootstrap value or posterior probability lower than the threshold. ML, maximum-likelihood method; BI, Bayesian-inference method. The two clusters for t.
