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DNA barcoding the native flowering plants and conifers of Wales.

de Vere N, Rich TC, Ford CR, Trinder SA, Long C, Moore CW, Satterthwaite D, Davies H, Allainguillaume J, Ronca S, Tatarinova T, Garbett H, Walker K, Wilkinson MJ - PLoS ONE (2012)

Bottom Line: We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences.These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers.Species discrimination can be further improved using spatially explicit sampling.

View Article: PubMed Central - PubMed

Affiliation: National Botanic Garden of Wales, Llanarthne, United Kingdom. natasha.devere@gardenofwales.org.uk

ABSTRACT
We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.

Show MeSH
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).
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pone-0037945-g005: 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).

Mentions: Reducing the spatial scale from the whole of Wales to smaller units of area improved the potential for species-level diagnosis by reducing the total number of candidate species being compared. Examining for the presence of a barcode gap (using a multiple alignment) at the 10×10 km level provided a mean species discrimination for rbcL of 71.6% (SD 3.7), matK of 81.0% (SD 3.0) and 81.6% (SD 2.7) for the combined markers. This further improves at the 2×2 km level to 89.4% (SD 9.2) for rbcL, 93.4% (SD 6.6) for matK and 93.3% (SD 6.5) for the combined markers (Fig. 5).


DNA barcoding the native flowering plants and conifers of Wales.

de Vere N, Rich TC, Ford CR, Trinder SA, Long C, Moore CW, Satterthwaite D, Davies H, Allainguillaume J, Ronca S, Tatarinova T, Garbett H, Walker K, Wilkinson MJ - PLoS ONE (2012)

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).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368937&req=5

pone-0037945-g005: 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).
Mentions: Reducing the spatial scale from the whole of Wales to smaller units of area improved the potential for species-level diagnosis by reducing the total number of candidate species being compared. Examining for the presence of a barcode gap (using a multiple alignment) at the 10×10 km level provided a mean species discrimination for rbcL of 71.6% (SD 3.7), matK of 81.0% (SD 3.0) and 81.6% (SD 2.7) for the combined markers. This further improves at the 2×2 km level to 89.4% (SD 9.2) for rbcL, 93.4% (SD 6.6) for matK and 93.3% (SD 6.5) for the combined markers (Fig. 5).

Bottom Line: We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences.These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers.Species discrimination can be further improved using spatially explicit sampling.

View Article: PubMed Central - PubMed

Affiliation: National Botanic Garden of Wales, Llanarthne, United Kingdom. natasha.devere@gardenofwales.org.uk

ABSTRACT
We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.

Show MeSH