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.
Department of Genetics and Physiology, University of Oulu, Finland; marko.mutanen@oulu.fi.
Marko
M
Mutanen
Department of Ecology, University of Oulu, Finland.
Sami M
SM
Kivelä
Naturalis Biodiversity Center, Leiden, The Netherlands.
Rutger A
RA
Vos
Naturalis Biodiversity Center, Leiden, The Netherlands.
Camiel
C
Doorenweerd
Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.
Sujeevan
S
Ratnasingham
SNSB - Bavarian State Collection of Zoology, Munich, Germany.
Axel
A
Hausmann
Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria.
Peter
P
Huemer
Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.|Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
Vlad
V
Dincă
Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
Erik J
EJ
van Nieukerken
INRA, UR633 Zoologie Forestière, 45075 Orléans, France.|Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France.
Carlos
C
Lopez-Vaamonde
Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
Roger
R
Vila
Natural History Museum University of Oslo, Norway.
Leif
L
Aarvik
Centre d'Écologie Fonctionnelle et Évolutive, UMR 5175 CNRS / University of Montpellier / University of Montpellier 3 / EPHE / SupAgro Montpellier / INRA / IRD, 1919 Route de Mende, 34293 Montpellier Cedex 5, France.
Thibaud
T
Decaëns
Crimean Federal University, Simferopol, Crimea.
Konstantin A
KA
Efetov
Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.
Paul D N
PD
Hebert
Natural History Museum University of Oslo, Norway.
Arild
A
Johnsen
Zoologisk Museum, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark.
Ole
O
Karsholt
Department of Genetics and Physiology, University of Oulu, Finland.
Mikko
M
Pentinsaari
Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Paris, France.
Rodolphe
R
Rougerie
SNSB - Bavarian State Collection of Zoology, Munich, Germany.
Andreas
A
Segerer
Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria.
Gerhard
G
Tarmann
Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.|Ottawa Plant Laboratory, Canadian Food Inspection Agency, Canada.
Reza
R
Zahiri
Department of Zoology, University of Oxford, UK.
H Charles J
HC
Godfray
D000818:Animals; D015982:Bias; D002965:Classification / Q000379:methods*; D058893:DNA Barcoding, Taxonomic; D004272:DNA, Mitochondrial; D050259:Genes, Mitochondrial; D007915:Lepidoptera / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny
D004272:DNA, Mitochondrial
DNA barcoding; Lepidoptera; gene tree; mitochondrial COI; mitochondrial cox1; paraphyly; polyphyly; species delimitation; species monophyly