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Zanovello L, Girardi M, Marchesini A, Galla G, Casari S, Micheletti D, Endrizzi S, Fedrigotti C, Pedrini P, Bertorelle G, Hauffe HC. A validated protocol for eDNA-based monitoring of within-species genetic diversity in a pond-breeding amphibian. Sci Rep 2023; 13:4346. [PMID: 36928612 PMCID: PMC10020426 DOI: 10.1038/s41598-023-31410-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023] Open
Abstract
In light of the dramatic decline in amphibian biodiversity, new cost-efficient tools to rapidly monitor species abundance and population genetic diversity in space and time are urgently needed. It has been amply demonstrated that the use of environmental DNA (eDNA) for single-species detection and characterization of community composition can increase the precision of amphibian monitoring compared to traditional (observational) approaches. However, it has been suggested that the efficiency and accuracy of the eDNA approach could be further improved by more timely sampling; in addition, the quality of genetic diversity data derived from the same DNA has been confirmed in other vertebrate taxa, but not amphibians. Given the availability of previous tissue-based genetic data, here we use the common frog Rana temporaria Linnaeus, 1758 as our target species and an improved eDNA protocol to: (i) investigate differences in species detection between three developmental stages in various freshwater environments; and (ii) study the diversity of mitochondrial DNA (mtDNA) haplotypes detected in eDNA (water) samples, by amplifying a specific fragment of the COI gene (331 base pairs, bp) commonly used as a barcode. Our protocol proved to be a reliable tool for monitoring population genetic diversity of this species, and could be a valuable addition to amphibian conservation and wetland management.
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Affiliation(s)
- Lucia Zanovello
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
- Conservation Biology Unit, MUSE - Science Museum Trento, Trento, Italy
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Matteo Girardi
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Alexis Marchesini
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino, Florence, Italy
| | - Giulio Galla
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Stefano Casari
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Diego Micheletti
- Computational Biology Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Sonia Endrizzi
- Conservation Biology Unit, MUSE - Science Museum Trento, Trento, Italy
| | - Chiara Fedrigotti
- Conservation Biology Unit, MUSE - Science Museum Trento, Trento, Italy
| | - Paolo Pedrini
- Conservation Biology Unit, MUSE - Science Museum Trento, Trento, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy.
- National Biodiversity Future Center, S.c.a.r.l., Palermo, Italy.
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Dauphin B, Rellstab C, Wüest RO, Karger DN, Holderegger R, Gugerli F, Manel S. Re-thinking the environment in landscape genomics. Trends Ecol Evol 2023; 38:261-274. [PMID: 36402651 DOI: 10.1016/j.tree.2022.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/19/2022]
Abstract
Detecting the extrinsic selective pressures shaping genomic variation is critical for a better understanding of adaptation and for forecasting evolutionary responses of natural populations to changing environmental conditions. With increasing availability of geo-referenced environmental data, landscape genomics provides unprecedented insights into how genomic variation and underlying gene functions affect traits potentially under selection. Yet, the robustness of genotype-environment associations used in landscape genomics remains tempered due to various limitations, including the characteristics of environmental data used, sampling designs employed, and statistical frameworks applied. Here, we argue that using complementary or new environmental data sources and well-informed sampling designs may help improve the detection of selective pressures underlying patterns of local adaptation in various organisms and environments.
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Affiliation(s)
- Benjamin Dauphin
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland.
| | | | - Rafael O Wüest
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Dirk N Karger
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Rolf Holderegger
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland; Institute of Integrative Biology (IBZ), ETH, Zurich, 8092 Zurich, Switzerland
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Stéphanie Manel
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland; CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, 34000 Montpellier, France; Institut Universitaire de France, Paris, France
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3
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O'Brien D, Laikre L, Hoban S, Bruford MW, Ekblom R, Fischer MC, Hall J, Hvilsom C, Hollingsworth PM, Kershaw F, Mittan CS, Mukassabi T, Ogden R, Segelbacher G, Shaw RE, Vernesi C, MacDonald AJ. Bringing together approaches to reporting on within species genetic diversity. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Linda Laikre
- Division of Population Genetics Department of Zoology Stockholm University Stockholm Sweden
| | - Sean Hoban
- Center for Tree Science Lisle Illinois USA
| | | | - Robert Ekblom
- Wildlife Analysis Unit Swedish Environmental Protection Agency Stockholm Sweden
| | | | | | | | | | | | - Cinnamon S. Mittan
- Ecology and Evolutionary Biology Program Michigan State University East Lansing Michigan USA
| | - Tarek A. Mukassabi
- University of Benghazi Department of Botany, Faculty of Sciences Benghazi Libya
| | - Rob Ogden
- Royal (DIck) School of Veterinary Studies and the Roslin Institute University of Edinburgh Edinburgh UK
| | - Gernot Segelbacher
- Wildlife Ecology and Management University Freiburg Freiburg im Breisgau Germany
| | - Robyn E. Shaw
- Environmental and Conservation Sciences Murdoch University Perth Australia
| | - Cristiano Vernesi
- Forest Ecology Unit Research and Innovation Centre ‐ Fondazione Edmund Mach San Michele all'Adige Italy
| | - Anna J. MacDonald
- Australian Antarctic Division Department of Agriculture, Water and the Environment Kingston Tasmania Australia
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4
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Loera-Sánchez M, Studer B, Kölliker R. A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species. Mol Ecol Resour 2021; 22:1725-1745. [PMID: 34918474 PMCID: PMC9305562 DOI: 10.1111/1755-0998.13577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Abstract
Grasslands are widespread and economically relevant ecosystems at the basis of sustainable roughage production. Plant genetic diversity (PGD; i.e., within‐species diversity) is related to many beneficial effects on the ecosystem functioning of grasslands. The monitoring of PGD in temperate grasslands is complicated by the multiplicity of species present and by a shortage of methods for large‐scale assessments. However, the continuous advancement of high‐throughput DNA sequencing approaches has improved the prospects of broad, multispecies PGD monitoring. Among them, amplicon sequencing stands out as a robust and cost‐effective method. Here, we report a set of 12 multispecies primer pairs that can be used for high‐throughput PGD assessments in multiple grassland plant species. The target loci were selected and tested in two phases: a “discovery phase” based on a sequence capture assay (611 nuclear loci assessed in 16 grassland plant species), which resulted in the selection of 11 loci; and a “validation phase”, in which the selected loci were targeted and sequenced using multispecies primers in test populations of Dactylis glomerata L., Lolium perenne L., Festuca pratensis Huds., Trifolium pratense L. and T. repens L. The multispecies amplicons had nucleotide diversities per species from 5.19 × 10−3 to 1.29 × 10−2, which is in the range of flowering‐related genes but slightly lower than pathogen resistance genes. We conclude that the methodology, the DNA sequence resources, and the primer pairs reported in this study provide the basis for large‐scale, multispecies PGD monitoring in grassland plants.
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Affiliation(s)
- Miguel Loera-Sánchez
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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