Table 3 Accuracies for barcoding in Longidoridae using SPIDER package and tree-based comparison for monophyly using Bayesian inference.

From: The utility of mtDNA and rDNA for barcoding and phylogeny of plant-parasitic nematodes from Longidoridae (Nematoda, Enoplea)

Dataset

Number of species

Number of sequences

Near Neighbour

Best Close Match1

Sequences with inter-intra < = 0

Optimal differences for barcoding2

MrBayes phylogeny3

False

True

Ambiguous

Correct

Incorrect

No id

Cytochrome oxidase 1

42

253

3

250 (99.9%)

0

189 (74.7%)

2

62

58 (22.9%)

6.36%

92.9% (39/42)

D2 and D3 expansion segments of the 28S4

111

560

24

536 (95.7%)

18

503 (89.8%)

19

20

138 (24.7%)

2.87%

90.1% (100/111)

D2 and D3 expansion segments of the 28S (excluding X. americanum-group)

88

384

11

373 (99.9%)

7

354 (92.2%)

6

17

37 (9.6%)

2.04%

100% (88/88)

  1. Accuracy is defined as the percentage of sequences correctly assigned to their species in the case of Near Neighbour and Best Close Match. For the tree-based method, the accuracy was expressed as the percentage of species with more than one sequence that grouped as monophyletic in their respective molecular marker tree. 1Threshold based criterion of 1%. 2Experimental script in SPIDER. 3Percentage of species monophyletic to the respective tree. 4 X. brevicolle species complex excluded from the analysis.
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