Table 1.
Summary statistics for the 1143 species of Welsh flora DNA barcoded using rbcL and matK.
Table 2.
Recoverability of DNA barcodes from herbarium and fresh material for rbcL and matK.
Table 3.
Sequence quality of DNA barcodes from herbarium and fresh material for rbcL and matK.
Figure 1.
Effect of herbarium specimen age on recoverability (%).
Using 3607 herbarium specimens ranging in age from 1899–2008, samples were divided into 11 age classes and Spearman rank correlation used to test for a relationship between age class and recoverability (%) using the DNA barcode loci, rbcL and matK.
Figure 2.
Recoverability of the orders of flowering plants and conifers found within Wales using herbarium and fresh material.
Recoverability (%) of rbcL and matK across the 34 orders of seed plants found within the Welsh flora. Results are based on 3637 herbarium and 635 freshly collected specimens. White cells denote orders for which fresh specimens were not collected.
Table 4.
Interspecific and intraspecific divergence for rbcL and matK.
Figure 3.
Ability of the DNA barcode markers rbcL and matK to discriminate the Welsh flora.
Discrimination (%) at species, genus and family level for rbcL, matK and both markers combined using monophyletic groups in Neighbour-Joining trees (Tree), BLASTn searches (BLAST) and barcode gap analysis using pairwise (Barcode gap pairwise) and multiple alignments (Barcode gap multiple). Species level discrimination for monophyletic groups in Neighbour-Joining trees is divided into bootstrap support values of ‘any’, >50% and >70% based on 1000 bootstrap replicates. Discrimination uses 808 species for which multiple individuals were DNA barcoded for both rbcL and matK. Species with single sequences were included in the analyses as sources of discrimination failure. For a complete list of which species can be discriminated using the different methods see Dataset S3.
Figure 4.
Species discrimination for the orders of flowering plants and conifers found within Wales.
Species discrimination (%) for rbcL, matK and both combined across the 34 orders of flowering plants and conifers found within the Welsh flora. Discrimination is assessed using three methods; barcode gap using multiple alignments (Barcode gap), monophyletic groups in Neighbour-Joining trees (Tree) and BLASTn searches (BLAST). To allow for comparison across the markers and methods 808 species for which multiple individuals were sequenced for both rbcL and matK were used, but species with single sequences were included as a source of discrimination failure. The number of species per order in the Welsh flora (out of the 808) is shown in brackets next to the order name. Pearson correlation coefficients and associated p-values for the relationship between the number of species per order and % species discrimination success are shown.
Table 5.
Testing the ability of the Welsh flora DNA barcode database to identify sequences downloaded from GenBank.
Figure 5.
Species discrimination success (%) at different spatial scales across Wales.
Species discrimination for Wales at the 10×10 km level and for 3 vice-counties at the 2×2 km level for A) rbcL B) matK and C) combined. This uses 891,756 plant species records from the Botanical Society of the British Isles. Species discrimination for each square is determined by taking the species list for that square and conducting barcode gap analysis (using multiple alignments).