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Excluding spatial sampling bias does not eliminate oversplitting in DNA‐based species delimitation analyses

DNA barcoding and DNA‐based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affects the accuracy and performance of DNA barcoding. Performance of complex DNA‐based species delimitation is to be...

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Autores principales: Lukic, Daniel, Eberle, Jonas, Thormann, Jana, Holzschuh, Carolus, Ahrens, Dirk
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8328443/
https://www.ncbi.nlm.nih.gov/pubmed/34367578
http://dx.doi.org/10.1002/ece3.7836
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author Lukic, Daniel
Eberle, Jonas
Thormann, Jana
Holzschuh, Carolus
Ahrens, Dirk
author_facet Lukic, Daniel
Eberle, Jonas
Thormann, Jana
Holzschuh, Carolus
Ahrens, Dirk
author_sort Lukic, Daniel
collection PubMed
description DNA barcoding and DNA‐based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affects the accuracy and performance of DNA barcoding. Performance of complex DNA‐based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical dataset sampled from a single locality in a Southeast‐Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivorous chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA‐based and morphology‐based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analyzed for a total of 186 individuals of 56 morphospecies. Tree‐based and distance‐based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. Poisson tree process (PTP) and statistical parsimony network analysis (TCS) prevailingly over‐splitted morphospecies, while 3% clustering and Automatic Barcode Gap Discovery (ABGD) also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs have to be explained by historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.
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spelling pubmed-83284432021-08-06 Excluding spatial sampling bias does not eliminate oversplitting in DNA‐based species delimitation analyses Lukic, Daniel Eberle, Jonas Thormann, Jana Holzschuh, Carolus Ahrens, Dirk Ecol Evol Original Research DNA barcoding and DNA‐based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affects the accuracy and performance of DNA barcoding. Performance of complex DNA‐based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical dataset sampled from a single locality in a Southeast‐Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivorous chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA‐based and morphology‐based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analyzed for a total of 186 individuals of 56 morphospecies. Tree‐based and distance‐based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. Poisson tree process (PTP) and statistical parsimony network analysis (TCS) prevailingly over‐splitted morphospecies, while 3% clustering and Automatic Barcode Gap Discovery (ABGD) also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs have to be explained by historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation. John Wiley and Sons Inc. 2021-07-02 /pmc/articles/PMC8328443/ /pubmed/34367578 http://dx.doi.org/10.1002/ece3.7836 Text en © 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Lukic, Daniel
Eberle, Jonas
Thormann, Jana
Holzschuh, Carolus
Ahrens, Dirk
Excluding spatial sampling bias does not eliminate oversplitting in DNA‐based species delimitation analyses
title Excluding spatial sampling bias does not eliminate oversplitting in DNA‐based species delimitation analyses
title_full Excluding spatial sampling bias does not eliminate oversplitting in DNA‐based species delimitation analyses
title_fullStr Excluding spatial sampling bias does not eliminate oversplitting in DNA‐based species delimitation analyses
title_full_unstemmed Excluding spatial sampling bias does not eliminate oversplitting in DNA‐based species delimitation analyses
title_short Excluding spatial sampling bias does not eliminate oversplitting in DNA‐based species delimitation analyses
title_sort excluding spatial sampling bias does not eliminate oversplitting in dna‐based species delimitation analyses
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8328443/
https://www.ncbi.nlm.nih.gov/pubmed/34367578
http://dx.doi.org/10.1002/ece3.7836
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