Mitochondrial Heteroplasmy and PCR Amplification Bias Lead to Wrong Species Delimitation with High Confidence in the South American and Antarctic Marine Bivalve <i>Aequiyoldia eightsii</i> Species Complex
The species delimitation of the marine bivalve species complex <i>Aequiyoldia eightsii</i> 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 cytochrom...
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| Format: | Article |
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MDPI AG
2023-04-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/4/935 |
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| author | Mariano Martínez Lars Harms Doris Abele Christoph Held |
| author_facet | Mariano Martínez Lars Harms Doris Abele Christoph Held |
| author_sort | Mariano Martínez |
| collection | DOAJ |
| description | The species delimitation of the marine bivalve species complex <i>Aequiyoldia eightsii</i> 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 (<i>COI</i>) 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. |
| first_indexed | 2024-03-11T04:59:36Z |
| format | Article |
| id | doaj.art-fcb25cd2838b4866931e79bf36c4ded9 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T04:59:36Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-fcb25cd2838b4866931e79bf36c4ded92023-11-17T19:24:41ZengMDPI AGGenes2073-44252023-04-0114493510.3390/genes14040935Mitochondrial Heteroplasmy and PCR Amplification Bias Lead to Wrong Species Delimitation with High Confidence in the South American and Antarctic Marine Bivalve <i>Aequiyoldia eightsii</i> Species ComplexMariano Martínez0Lars Harms1Doris Abele2Christoph Held3Functional Ecology, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, GermanyHelmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, GermanyFunctional Ecology, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, GermanyFunctional Ecology, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, GermanyThe species delimitation of the marine bivalve species complex <i>Aequiyoldia eightsii</i> 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 (<i>COI</i>) 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.https://www.mdpi.com/2073-4425/14/4/935mitochondrial heteroplasmyamplification biasmitochondrial DNADNA barcoding |
| spellingShingle | 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 <i>Aequiyoldia eightsii</i> Species Complex Genes mitochondrial heteroplasmy amplification bias mitochondrial DNA DNA barcoding |
| title | Mitochondrial Heteroplasmy and PCR Amplification Bias Lead to Wrong Species Delimitation with High Confidence in the South American and Antarctic Marine Bivalve <i>Aequiyoldia eightsii</i> 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 <i>Aequiyoldia eightsii</i> 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 <i>Aequiyoldia eightsii</i> 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 <i>Aequiyoldia eightsii</i> 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 <i>Aequiyoldia eightsii</i> 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 i aequiyoldia eightsii i species complex |
| topic | mitochondrial heteroplasmy amplification bias mitochondrial DNA DNA barcoding |
| url | https://www.mdpi.com/2073-4425/14/4/935 |
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