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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2021
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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. |
format | Online Article Text |
id | pubmed-8328443 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
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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