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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ftmdpi:oai:mdpi.com:/2073-4425/14/4/935/ 2023-08-20T04:02:28+02:00 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 Mariano Martínez Lars Harms Doris Abele Christoph Held agris 2023-04-18 application/pdf https://doi.org/10.3390/genes14040935 EN eng Multidisciplinary Digital Publishing Institute Population and Evolutionary Genetics and Genomics https://dx.doi.org/10.3390/genes14040935 https://creativecommons.org/licenses/by/4.0/ Genes; Volume 14; Issue 4; Pages: 935 mitochondrial heteroplasmy amplification bias mitochondrial DNA DNA barcoding Text 2023 ftmdpi https://doi.org/10.3390/genes14040935 2023-08-01T09:44:31Z 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. Text Antarc* Antarctic Antarctica Drake Passage MDPI Open Access Publishing Antarctic Drake Passage The Antarctic Genes 14 4 935 |
institution |
Open Polar |
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MDPI Open Access Publishing |
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ftmdpi |
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English |
topic |
mitochondrial heteroplasmy amplification bias mitochondrial DNA DNA barcoding |
spellingShingle |
mitochondrial heteroplasmy amplification bias mitochondrial DNA DNA barcoding Mariano Martínez Lars Harms Doris Abele Christoph Held 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_facet |
mitochondrial heteroplasmy amplification bias mitochondrial DNA DNA barcoding |
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. |
format |
Text |
author |
Mariano Martínez Lars Harms Doris Abele Christoph Held |
author_facet |
Mariano Martínez Lars Harms Doris Abele Christoph Held |
author_sort |
Mariano Martínez |
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_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_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_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 |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2023 |
url |
https://doi.org/10.3390/genes14040935 |
op_coverage |
agris |
geographic |
Antarctic Drake Passage The Antarctic |
geographic_facet |
Antarctic Drake Passage The Antarctic |
genre |
Antarc* Antarctic Antarctica Drake Passage |
genre_facet |
Antarc* Antarctic Antarctica Drake Passage |
op_source |
Genes; Volume 14; Issue 4; Pages: 935 |
op_relation |
Population and Evolutionary Genetics and Genomics https://dx.doi.org/10.3390/genes14040935 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/genes14040935 |
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Genes |
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14 |
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4 |
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935 |
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1774712940303220736 |