Data from: Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera

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.