2024-03-28T08:06:01Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/1526002021-11-22T12:52:30Zcom_10261_9676com_10261_8col_10261_9677
DIGITAL.CSIC
author
Matunen, Marko
author
Dincă, Vlad
author
Vila, Roger
author
Godfray, H. Charles J.
funder
European Commission
funder
Genome Canada
funder
Government of Canada
funder
Bavarian State Ministry of Education, Science and the Arts
funder
Ministry of Finance (The Netherlands)
funder
Kone Foundation
funder
Finnish Cultural Foundation
funder
University of Oulu
funder
Ministerio de Economía y Competitividad (España)
funder
Conseil Régional de Haute Normandie
funder
University of Oslo
funder
Provincia autonoma di Bolzano - Alto Adige
funder
Federal Ministry of Science, Research and Economy (Austria)
funder
Stockholm University
2017-07-11T12:24:06Z
2017-07-11T12:24:06Z
2016-11
Systematic Biology 65(6): 1204-1040 (2016)
1063-5157
http://hdl.handle.net/10261/152600
10.1093/sysbio/syw044
1076-836X
http://dx.doi.org/10.13039/501100000780http://dx.doi.org/10.13039/100008762http://dx.doi.org/10.13039/501100000023http://dx.doi.org/10.13039/501100004563http://dx.doi.org/10.13039/501100005781http://dx.doi.org/10.13039/501100006196http://dx.doi.org/10.13039/501100003329http://dx.doi.org/10.13039/501100003191http://dx.doi.org/10.13039/501100005366http://dx.doi.org/10.13039/501100009244http://dx.doi.org/10.13039/501100003413
27288478
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.
eng
closedAccess
DNA barcoding
Gene tree
Lepidoptera
Mitochondrial COI
Mitochondrial cox1
Paraphyly
Polyphyly
Species delimitation
Species monophyly
Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera
artículo
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URL
https://digital.csic.es/bitstream/10261/152600/1/accesoRestringido.pdf
File
MD5
42637ae8545636bc41605c1740a9a84e
15753
application/pdf
accesoRestringido.pdf