Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France
Biodiversity is facing an unprecedented crisis and substantial efforts are needed to conserve natural populations, especially in river ecosystems. The use of molecular tools to guide conservation practices in rivers has grown in popularity over the last decades, but the amount of precision and/or bi...
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| Language: | English |
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MDPI AG
2023-05-01
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| Series: | Diversity |
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| Online Access: | https://www.mdpi.com/1424-2818/15/5/681 |
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| author | Jérôme G. Prunier Charlotte Veyssière Géraldine Loot Simon Blanchet |
| author_facet | Jérôme G. Prunier Charlotte Veyssière Géraldine Loot Simon Blanchet |
| author_sort | Jérôme G. Prunier |
| collection | DOAJ |
| description | Biodiversity is facing an unprecedented crisis and substantial efforts are needed to conserve natural populations, especially in river ecosystems. The use of molecular tools to guide conservation practices in rivers has grown in popularity over the last decades, but the amount of precision and/or biological information that would be gained by switching from the traditional short tandem repeats (STRs) to the increasingly used single nucleotide polymorphisms (SNPs) is still debated. Here, we compared the usefulness of STRs and SNPs to study spatial patterns of genetic variability in two freshwater fish species (<i>Phoxinus dragarum</i> and <i>Gobio occitaniae</i>) in southern France. SNPs were obtained from a pool-seq procedure and mapped to new genome assemblies. They provided much more precise estimates of genetic diversity and genetic differentiation than STRs, but both markers allowed the detection of very similar genetic structures in each species, which could be useful for delineating conservation units. While both markers provided similar outcomes, there were two discrepancies in genetic structures that could, nonetheless, be explained by unrecorded stocking events. Overall, we demonstrated that SNPs are not unconditionally superior to STRs in the context of large-scale riverscape genetic conservation, and that the choice of marker should primarily be based on research questions and resources available. |
| first_indexed | 2024-03-11T03:47:19Z |
| format | Article |
| id | doaj.art-0401c318c08a4f74b6e69a00f4c128c9 |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-11T03:47:19Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diversity |
| spelling | doaj.art-0401c318c08a4f74b6e69a00f4c128c92023-11-18T01:06:32ZengMDPI AGDiversity1424-28182023-05-0115568110.3390/d15050681Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in FranceJérôme G. Prunier0Charlotte Veyssière1Géraldine Loot2Simon Blanchet3Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d’Ecologie Théorique et Expérimentale, UAR 2029, F-09200 Moulis, FranceCNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 Route de Narbonne, CEDEX 4, F-31062 Toulouse, FranceCNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 Route de Narbonne, CEDEX 4, F-31062 Toulouse, FranceCentre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d’Ecologie Théorique et Expérimentale, UAR 2029, F-09200 Moulis, FranceBiodiversity is facing an unprecedented crisis and substantial efforts are needed to conserve natural populations, especially in river ecosystems. The use of molecular tools to guide conservation practices in rivers has grown in popularity over the last decades, but the amount of precision and/or biological information that would be gained by switching from the traditional short tandem repeats (STRs) to the increasingly used single nucleotide polymorphisms (SNPs) is still debated. Here, we compared the usefulness of STRs and SNPs to study spatial patterns of genetic variability in two freshwater fish species (<i>Phoxinus dragarum</i> and <i>Gobio occitaniae</i>) in southern France. SNPs were obtained from a pool-seq procedure and mapped to new genome assemblies. They provided much more precise estimates of genetic diversity and genetic differentiation than STRs, but both markers allowed the detection of very similar genetic structures in each species, which could be useful for delineating conservation units. While both markers provided similar outcomes, there were two discrepancies in genetic structures that could, nonetheless, be explained by unrecorded stocking events. Overall, we demonstrated that SNPs are not unconditionally superior to STRs in the context of large-scale riverscape genetic conservation, and that the choice of marker should primarily be based on research questions and resources available.https://www.mdpi.com/1424-2818/15/5/681conservation geneticsgenetic diversitygenome assemblieshierarchical clusteringisolation-by-distancemicrosatellites |
| spellingShingle | Jérôme G. Prunier Charlotte Veyssière Géraldine Loot Simon Blanchet Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France Diversity conservation genetics genetic diversity genome assemblies hierarchical clustering isolation-by-distance microsatellites |
| title | Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France |
| title_full | Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France |
| title_fullStr | Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France |
| title_full_unstemmed | Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France |
| title_short | Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France |
| title_sort | comparing the utility of microsatellites and single nucleotide polymorphisms in conservation genetics insights from a study on two freshwater fish species in france |
| topic | conservation genetics genetic diversity genome assemblies hierarchical clustering isolation-by-distance microsatellites |
| url | https://www.mdpi.com/1424-2818/15/5/681 |
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