DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China

Abstract

Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH-psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China. We tested the ability of DNA barcoding to distinguish species and as an alternative tool for correcting species misidentification. We also used the rbcL+matK+trnH-psbA+ITS loci to investigate the phylogenetic relationships of the species examined. Among the gene regions and their combinations, ITS was the most efficient for identifying species (57.5%) and genera (70%). DNA barcoding also had a positive role for correcting species misidentification (10.8%). Furthermore, based on the results of the phylogenetic analyses, Chinese Lauraceae species formed three supported monophyletic clades, with the Cryptocarya group strongly supported (PP = 1.00, BS = 100%) and the clade including the Persea group, Laureae and Cinnamomum also receiving strong support (PP = 1.00, BS = 98%), whereas the Caryodaphnopsis-Neocinnamomum received only moderate support (PP = 1.00 and BS = 85%). This study indicates that molecular barcoding can assist in screening difficult to identify families like Lauraceae, detecting errors of species identification, as well as helping to reconstruct phylogenetic relationships. DNA barcoding can thus help with large-scale biodiversity inventories and rare species conservation by improving accuracy, as well as reducing time and costs associated with species identification.

Fig 1. A schematic pipelines of conventional and molecular species identification analyses.

Fig 2. Species misidentification and resolution at the genus and species levels.

The NJ tree based on the combined barcodes rbcL+matK+trnH–psbA+ITS. The bootstrap values ≥ 50% are shown on the branches. The stars represent corrected individuals; brackets represent successfully identified species.

Fig 3. Species resolution at the genus and species levels for single regions and combinations.

Results based on BLAST and Neighbor-Joining Tree analyses of the samples (A: n ≥ 1; B: n ≥ 2).

Fig 4. Species resolution success at the genus and species levels for ITS.

Result based on Neighbor-Joining Tree analysis (n ≥ 2). The bootstrap values ≥ 50% are shown on the branches. Brackets represent successfully identified species.

Fig 5. Bayesian consensus tree based on rbcL+matK+trnH–psbA+ITS.

Bayesian posterior probabilities (≥ 0.9) / Bootstrap support values (≥ 50%) are shown above the branches. Abbreviations: Act. = Actinodaphne, Bei. = Beilschmiedia, Cin. = Cinnamomum, Car. = Caryodaphnopsis, Cry. = Cryptocarya, Ite. = Iteadaphne, Lin. = Lindera, Lit. = Litsea, Mac. = Machilus, Neoc. = Neocinnamomum, Neol. = Neolitsea, Pho. = Phoebe, Hyp. = Hypodaphnis, Hor. = Hortonia, Pal. = Palmeria, Peu. = Peumus, Gom. = Gomortega.