DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits
Abstract Background Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate “species” diversity for a taxon, without a well-developed taxonomy and/or an extensive reference...
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ftbiomed:oai:biomedcentral.com:1472-6785-12-24 2023-05-15T15:55:05+02:00 DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits Renaud, Anaïs K Savage, Jade Adamowicz, Sarah J 2012-11-23 http://www.biomedcentral.com/1472-6785/12/24 en eng BioMed Central Ltd. http://www.biomedcentral.com/1472-6785/12/24 Copyright 2012 Renaud et al.; licensee BioMed Central Ltd. Insects Muscid flies Churchill Manitoba Barcoding biotas Cytochrome c oxidase subunit 1 COI DNA barcoding Clustering-based method Threshold-based method Research article 2012 ftbiomed 2013-01-06T01:01:26Z Abstract Background Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate “species” diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues. Results Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected. Conclusions Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon. Article in Journal/Newspaper Churchill BioMed Central |
institution |
Open Polar |
collection |
BioMed Central |
op_collection_id |
ftbiomed |
language |
English |
topic |
Insects Muscid flies Churchill Manitoba Barcoding biotas Cytochrome c oxidase subunit 1 COI DNA barcoding Clustering-based method Threshold-based method |
spellingShingle |
Insects Muscid flies Churchill Manitoba Barcoding biotas Cytochrome c oxidase subunit 1 COI DNA barcoding Clustering-based method Threshold-based method Renaud, Anaïs K Savage, Jade Adamowicz, Sarah J DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits |
topic_facet |
Insects Muscid flies Churchill Manitoba Barcoding biotas Cytochrome c oxidase subunit 1 COI DNA barcoding Clustering-based method Threshold-based method |
description |
Abstract Background Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate “species” diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues. Results Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected. Conclusions Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon. |
format |
Article in Journal/Newspaper |
author |
Renaud, Anaïs K Savage, Jade Adamowicz, Sarah J |
author_facet |
Renaud, Anaïs K Savage, Jade Adamowicz, Sarah J |
author_sort |
Renaud, Anaïs K |
title |
DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits |
title_short |
DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits |
title_full |
DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits |
title_fullStr |
DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits |
title_full_unstemmed |
DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits |
title_sort |
dna barcoding of northern nearctic muscidae (diptera) reveals high correspondence between morphological and molecular species limits |
publisher |
BioMed Central Ltd. |
publishDate |
2012 |
url |
http://www.biomedcentral.com/1472-6785/12/24 |
genre |
Churchill |
genre_facet |
Churchill |
op_relation |
http://www.biomedcentral.com/1472-6785/12/24 |
op_rights |
Copyright 2012 Renaud et al.; licensee BioMed Central Ltd. |
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1766390429430841344 |