Abstract
To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.
Highlights
To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD)
A two-locus combination of rbcL + matK from the chloroplast region has been approved as a core DNA barcode to identify land plants, which achieves a rate of 72% correct species level identification based on a data set of 550 species representing the major lineages of land plants[12]
To the best of our knowledge, the present study comprehensively reported a general performance of the suggested two-locus core DNA barcode of land plants on tree species discrimination, and the improvements when adding a complementary DNA barcode using a monophyly-based method (i.e., GARLI), utilizing large data sets from 13 CTFS-ForestGEO FDPs ranging from tropics to temperate zones
Summary
To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities. A two-locus combination of rbcL + matK from the chloroplast region has been approved as a core DNA barcode to identify land plants, which achieves a rate of 72% correct species level identification based on a data set of 550 species representing the major lineages of land plants (including 445 angiosperm, 38 gymnosperm, and 67 cryptogam species)[12]. To the best of our knowledge, the present study comprehensively reported a general performance of the suggested two-locus core DNA barcode of land plants on tree species discrimination, and the improvements when adding a complementary DNA barcode (i.e., trnH-psbA spacer region) using a monophyly-based method (i.e., GARLI), utilizing large data sets from 13 CTFS-ForestGEO FDPs ranging from tropics to temperate zones. We predicted that the accuracy of correct species discriminations using plant DNA barcodes was mainly determined by the ratios of closely-related taxa (i.e., S/G ratio and Gm/Gt ratio) in global FDPs
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