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Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex

The species delimitation of the marine bivalve species complex Aequiyoldia eightsii in South America and Antarctica is complicated by mitochondrial heteroplasmy and amplification bias in molecular barcoding. In this study, we compare different data sources (mitochondrial cytochrome c oxidase subunit...

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Main Author: Martínez, Mariano (author)
Other Authors: Harms, Lars (author), Abele, Doris (author), Held, Christoph (author)
Format: article
Language:English
Published: 2023
Subjects:
Mitochondrial heteroplasmy
Amplification bias
Mitochondrial DNA
DNA barcoding
Online Access:https://hdl.handle.net/20.500.12008/43279
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_version_ 1868890123357126656
author Martínez, Mariano
author2 Harms, Lars
Abele, Doris
Held, Christoph
author2_role author
author
author
author_browse Abele, Doris
Harms, Lars
Held, Christoph
Martínez, Mariano
author_facet Martínez, Mariano
Harms, Lars
Abele, Doris
Held, Christoph
author_role author
collection COLIBRI
dc.contributor.none.fl_str_mv Martínez Mariano, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Ecología y Ciencias Ambientales.
Harms Lars
Abele Doris
Held Christoph
dc.creator.none.fl_str_mv Martínez, Mariano
Harms, Lars
Abele, Doris
Held, Christoph
dc.date.none.fl_str_mv 2023
2024-04-01T14:00:54Z
2024-04-01T14:00:54Z
dc.format.none.fl_str_mv 15 h.
application/pdf
dc.identifier.none.fl_str_mv Martínez, M, Harms, L, Abele, D [y otros autores]. "Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex". Genes. [en línea] 2023, 14(4): 935. 15 h. DOI: 10.3390/genes14040935.
2073-4425
https://hdl.handle.net/20.500.12008/43279
10.3390/genes14040935
dc.language.none.fl_str_mv en
eng
dc.publisher.none.fl_str_mv MDPI
dc.relation.none.fl_str_mv Genes, 2023, 14(4): 935.
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
Licencia Creative Commons Atribución (CC - By 4.0)
dc.source.none.fl_str_mv reponame:COLIBRI
instname:Universidad de la República
instacron:Universidad de la República
dc.subject.none.fl_str_mv Mitochondrial heteroplasmy
Amplification bias
Mitochondrial DNA
DNA barcoding
dc.title.none.fl_str_mv Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex
dc.type.none.fl_str_mv Artículo
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
description The species delimitation of the marine bivalve species complex Aequiyoldia eightsii in South America and Antarctica is complicated by mitochondrial heteroplasmy and amplification bias in molecular barcoding. In this study, we compare different data sources (mitochondrial cytochrome c oxidase subunit I (COI) sequences; nuclear and mitochondrial SNPs). Whilst all the data suggest that populations on either side of the Drake Passage belong to different species, the picture is less clear within Antarctic populations, which harbor three distinct mitochondrial lineages (p-dist ≈ 6%) that coexist in populations and in a subset of individuals with heteroplasmy. Standard barcoding procedures lead to amplification bias favoring either haplotype unpredictably and thus overestimate the species richness with high confidence. However, nuclear SNPs show no differentiation akin to the trans-Drake comparison, suggesting that the Antarctic populations represent a single species. Their distinct haplotypes likely evolved during periods of temporary allopatry, whereas recombination eroded similar differentiation patterns in the nuclear genome after secondary contact. Our study highlights the importance of using multiple data sources and careful quality control measures to avoid bias and increase the accuracy of molecular species delimitation. We recommend an active search for mitochondrial heteroplasmy and haplotype-specific primers for amplification in DNA-barcoding studies.
eu_rights_str_mv openAccess
format article
id anni_8aeb00c699b6371c8a03ae6d605b952a
identifier_str_mv Martínez, M, Harms, L, Abele, D [y otros autores]. "Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex". Genes. [en línea] 2023, 14(4): 935. 15 h. DOI: 10.3390/genes14040935.
2073-4425
10.3390/genes14040935
instacron_str Universidad de la República
institution Universidad de la República
instname_str Universidad de la República
language eng
language_invalid_str_mv en
network_acronym_str anni
network_name_str oai-lr-anni
oai_identifier_str oai:colibri.udelar.edu.uy:20.500.12008/43279
publishDate 2023
publishDateSort 2023
publisher.none.fl_str_mv MDPI
reponame_str COLIBRI
repository.mail.fl_str_mv
repository.name.fl_str_mv
repository_id_str
rights_invalid_str_mv Licencia Creative Commons Atribución (CC - By 4.0)
spelling Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complexMartínez, MarianoHarms, LarsAbele, DorisHeld, ChristophMitochondrial heteroplasmyAmplification biasMitochondrial DNADNA barcodingThe species delimitation of the marine bivalve species complex Aequiyoldia eightsii in South America and Antarctica is complicated by mitochondrial heteroplasmy and amplification bias in molecular barcoding. In this study, we compare different data sources (mitochondrial cytochrome c oxidase subunit I (COI) sequences; nuclear and mitochondrial SNPs). Whilst all the data suggest that populations on either side of the Drake Passage belong to different species, the picture is less clear within Antarctic populations, which harbor three distinct mitochondrial lineages (p-dist ≈ 6%) that coexist in populations and in a subset of individuals with heteroplasmy. Standard barcoding procedures lead to amplification bias favoring either haplotype unpredictably and thus overestimate the species richness with high confidence. However, nuclear SNPs show no differentiation akin to the trans-Drake comparison, suggesting that the Antarctic populations represent a single species. Their distinct haplotypes likely evolved during periods of temporary allopatry, whereas recombination eroded similar differentiation patterns in the nuclear genome after secondary contact. Our study highlights the importance of using multiple data sources and careful quality control measures to avoid bias and increase the accuracy of molecular species delimitation. We recommend an active search for mitochondrial heteroplasmy and haplotype-specific primers for amplification in DNA-barcoding studies.ANII: POS_EXT_2015_122792MDPIMartínez Mariano, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Ecología y Ciencias Ambientales.Harms LarsAbele DorisHeld Christoph2024-04-01T14:00:54Z2024-04-01T14:00:54Z2023Artículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion15 h.application/pdfMartínez, M, Harms, L, Abele, D [y otros autores]. "Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex". Genes. [en línea] 2023, 14(4): 935. 15 h. DOI: 10.3390/genes14040935.2073-4425https://hdl.handle.net/20.500.12008/4327910.3390/genes14040935reponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaenengGenes, 2023, 14(4): 935.Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC - By 4.0)oai:colibri.udelar.edu.uy:20.500.12008/432792026-04-14T10:10:36Z
spellingShingle Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex
Martínez, Mariano
Mitochondrial heteroplasmy
Amplification bias
Mitochondrial DNA
DNA barcoding
status_str publishedVersion
title Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex
title_full Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex
title_fullStr Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex
title_full_unstemmed Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex
title_short Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex
title_sort Mitochondrial heteroplasmy and PCR amplification bias lead to wrong species delimitation with high confidence in the South American and Antarctic marine bivalve Aequiyoldia eightsii species complex
topic Mitochondrial heteroplasmy
Amplification bias
Mitochondrial DNA
DNA barcoding
url https://hdl.handle.net/20.500.12008/43279

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