He individuals of Schisandra rubriflora and S. grandiflora are labeled by different colors, red and blue, corresponding to the different sampling points (Cluster I: red, the southern Hengduan Mountains region; Cluster II: blue, the other sampling PP58 site regions). doi:10.1371/journal.pone.0125574.gdata from the genera Schisandra and Kadsura, ITS1 and ITS performed equally well (S3 Table). In contrast, the performance of ITS2 was the worst at both the family level and the genus level (Table 3 and S3 Table). Under the ML method, the best multi-locus combination for species discrimination was ITS+trnH-psbA+matK+rbcL, which showed visibly higher discriminatory power than four commonly used barcoding loci, for the family as a whole and for Schisandra and Kadsura (Table 3 and S3 Table). In comparison, for Illicium, there were multiple best multi-locus combinations for species discrimination: ITS+order PP58 trnH-psbA, ITS+trnH-psbA+matK, ITS+trnH-psbA+rbcL, and ITS+trnH-psbA+matK+rbcL (S3 Table). The results of BI analyses were similar to those 1471-2474-14-48 of ML analyses, except for one more best combination for species discrimination, ITS+matK+rbcL, which performed as well as ITS+trnH-psbA+matK+rbcL for Schisandra and Kadsura (S3 Table). Most of the four commonly used barcoding loci could only identify half or less than half of the sampled species at both the family level and the genus level, and the bootstrap re-sampling further reduced the already low identification success rates (Table 3 and S3 Table). Thus, bootstrap values were only used as a reference and not as a criterion in this study. According to the calculation of highly supported monophyletic clusters, the best combination for species discrimination was ITS+trnH-psbA+matK+rbcL for the family as a whole and for Schisandra and Kadsura (Table 3 and S3 Table). In comparison, ITS+trnH-psbA, ITS+trnH-psbA+matK, ITS +trnH-psbA+rbcL, and ITS+trnH-psbA+matK+rbcL worked equally well for Illicium (S3 Table).Similarity-based identificationThe results of the similarity-based method at the family level and the genus level performed in TAXONDNA are shown in Table 4 and S4 Table, respectively. Among the single loci, trnHpsbA had the highest successful identification rate (62.26 for the whole family, 50.00 for Schisandra and Kadsura, 84.21 for Illicium), and rbcL had the lowest successful identification rate (21.23 for the whole family, 29.72 for Schisandra and Kadsura, 5.12 for Illicium), under the `best match’ method at both the family level and the genus level (Table 4 and S4 Table). The results of the `best close match’ method was similar with that of the `best match’ method, except that ITS performed better than other single loci for Illicium (S4 Table). Among ITS, ITS1, and ITS2, the rank order for the correct identification was ITS, ITS1, and ITS2 under the similarity-based method for the family as a whole and for Schisandra and Kadsura, while the rank was ITS, ITS2, and ITS1 for jir.2010.0097 Illicium (Table 4 and S4 Table). Most of the multilocus combinations displayed higher successful identification rates than single loci under the similarity-based method at both the family level and the genus level (Table 4 and S4 Table). The combination of ITS+trnH-psbA+matK+rbcL had the highest percentage of correct identifications (86.86 for the whole family, 80.59 for Schisandra and Kadsura, 100 for Illicium) under the `best match’ method for the family as a whole and for Schisandra and Kadsura (Table 4 and S4 Table). In comparison,.He individuals of Schisandra rubriflora and S. grandiflora are labeled by different colors, red and blue, corresponding to the different sampling points (Cluster I: red, the southern Hengduan Mountains region; Cluster II: blue, the other sampling regions). doi:10.1371/journal.pone.0125574.gdata from the genera Schisandra and Kadsura, ITS1 and ITS performed equally well (S3 Table). In contrast, the performance of ITS2 was the worst at both the family level and the genus level (Table 3 and S3 Table). Under the ML method, the best multi-locus combination for species discrimination was ITS+trnH-psbA+matK+rbcL, which showed visibly higher discriminatory power than four commonly used barcoding loci, for the family as a whole and for Schisandra and Kadsura (Table 3 and S3 Table). In comparison, for Illicium, there were multiple best multi-locus combinations for species discrimination: ITS+trnH-psbA, ITS+trnH-psbA+matK, ITS+trnH-psbA+rbcL, and ITS+trnH-psbA+matK+rbcL (S3 Table). The results of BI analyses were similar to those 1471-2474-14-48 of ML analyses, except for one more best combination for species discrimination, ITS+matK+rbcL, which performed as well as ITS+trnH-psbA+matK+rbcL for Schisandra and Kadsura (S3 Table). Most of the four commonly used barcoding loci could only identify half or less than half of the sampled species at both the family level and the genus level, and the bootstrap re-sampling further reduced the already low identification success rates (Table 3 and S3 Table). Thus, bootstrap values were only used as a reference and not as a criterion in this study. According to the calculation of highly supported monophyletic clusters, the best combination for species discrimination was ITS+trnH-psbA+matK+rbcL for the family as a whole and for Schisandra and Kadsura (Table 3 and S3 Table). In comparison, ITS+trnH-psbA, ITS+trnH-psbA+matK, ITS +trnH-psbA+rbcL, and ITS+trnH-psbA+matK+rbcL worked equally well for Illicium (S3 Table).Similarity-based identificationThe results of the similarity-based method at the family level and the genus level performed in TAXONDNA are shown in Table 4 and S4 Table, respectively. Among the single loci, trnHpsbA had the highest successful identification rate (62.26 for the whole family, 50.00 for Schisandra and Kadsura, 84.21 for Illicium), and rbcL had the lowest successful identification rate (21.23 for the whole family, 29.72 for Schisandra and Kadsura, 5.12 for Illicium), under the `best match’ method at both the family level and the genus level (Table 4 and S4 Table). The results of the `best close match’ method was similar with that of the `best match’ method, except that ITS performed better than other single loci for Illicium (S4 Table). Among ITS, ITS1, and ITS2, the rank order for the correct identification was ITS, ITS1, and ITS2 under the similarity-based method for the family as a whole and for Schisandra and Kadsura, while the rank was ITS, ITS2, and ITS1 for jir.2010.0097 Illicium (Table 4 and S4 Table). Most of the multilocus combinations displayed higher successful identification rates than single loci under the similarity-based method at both the family level and the genus level (Table 4 and S4 Table). The combination of ITS+trnH-psbA+matK+rbcL had the highest percentage of correct identifications (86.86 for the whole family, 80.59 for Schisandra and Kadsura, 100 for Illicium) under the `best match’ method for the family as a whole and for Schisandra and Kadsura (Table 4 and S4 Table). In comparison,.
