DOI: 10.5061/dryad.k3mr1
title: Data from: Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera

description: The proliferation of DNA data is revolutionizing all fields of systematic
 research. DNA barcode sequences, now available for millions of specimens
 and several hundred thousand species, are increasingly used in algorithmic
 species delimitations. This is complicated by occasional incongruences
 between species and gene genealogies, as indicated by situations where
 conspecific individuals do not form a monophyletic cluster in a gene tree.
 In two previous reviews, non-monophyly has been reported as being common
 in mitochondrial DNA gene trees. We developed a novel web service
 “Monophylizer” to detect non-monophyly in phylogenetic trees and used it
 to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1)
 barcode sequence data from 4977 species and 41,583 specimens of European
 Lepidoptera, the largest data set of DNA barcodes analyzed from this
 regard. Particular attention was paid to accurate species identification
 to ensure data integrity. We investigated the effects of tree-building
 method, sampling effort, and other methodological issues, all of which can
 influence estimates of non-monophyly. We found a 12% incidence of
 non-monophyly, a value significantly lower than that observed in previous
 studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded
 almost equal numbers of non-monophyletic species, but 24.1% of these cases
 of non-monophyly were only found by one of these methods. Non-monophyletic
 species tend to show either low genetic distances to their nearest
 neighbors or exceptionally high levels of intraspecific variability. Cases
 of polyphyly in COI trees arising as a result of deep intraspecific
 divergence are negligible, as the detected cases reflected
 misidentifications or methodological errors. Taking into consideration
 variation in sampling effort, we estimate that the true incidence of
 non-monophyly is ∼23%, but with operational factors still being included.
 Within the operational factors, we separately assessed the frequency of
 taxonomic limitations (presence of overlooked cryptic and oversplit
 species) and identification uncertainties. We observed that operational
 factors are potentially present in more than half (58.6%) of the detected
 cases of non-monophyly. Furthermore, we observed that in about 20% of
 non-monophyletic species and entangled species, the lineages involved are
 either allopatric or parapatric—conditions where species delimitation is
 inherently subjective and particularly dependent on the species concept
 that has been adopted. These observations suggest that species-level
 non-monophyly in COI gene trees is less common than previously supposed,
 with many cases reflecting misidentifications, the subjectivity of species
 delimitation or other operational factors.
description: Supplementary figure
 1ROC
 (i.e. receiver operating characteristic) curve (thick continuous line)
 from the leave-one-family-out cross-validation analysis. Area under the
 ROC curve is 0.988, which can be interpreted as the probability that the
 model under investigation will score a randomly sampled positive
 (non-monophyletic) sample higher than a randomly drawn negative
 (monophyletic) sample. The dashed line is a reference that would be
 expected if the model classifies cases randomly.Supplementary Table
 1Species found
 non-monophyletic in ML trees, with information of type of non-monophyly,
 entangled species, K2P intraspecific variation, geographic relationship to
 the entangled species, possible oversplitting of species, presence of
 cryptic species and identification difficulties. Other remarks are shown
 in the last column.Supplementary table
 1.xlsxML
 treesMaximum Likelihood trees
 used in the study (Newick format).NJ
 treesNeighbor-Joining trees
 in in the study (Newick format).NJ_p_treesNeighbor-Joining trees calculated under p-distance model of nucleotide substitution.Data from: Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European LepidopteraCollection localities in .klm format (viewable with Google Earth).BOLD_Interactive_Map_-_DS-MARKALL.kml