Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation
Abstract Age structure information of animal populations is fundamental to their conservation and management. In fisheries, age is routinely obtained by counting daily or annual increments in calcified structures (e.g., otoliths) which requires lethal sampling. Recently, DNA methylation has been sho...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-06-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-36773-2 |
| _version_ | 1797801459959463936 |
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| author | Benjamin Mayne Tom Espinoza David A. Crook Chloe Anderson Darren Korbie Jonathan C. Marshall Mark J. Kennard Doug J. Harding Gavin L. Butler Brien Roberts Josh Whiley Sharon Marshall |
| author_facet | Benjamin Mayne Tom Espinoza David A. Crook Chloe Anderson Darren Korbie Jonathan C. Marshall Mark J. Kennard Doug J. Harding Gavin L. Butler Brien Roberts Josh Whiley Sharon Marshall |
| author_sort | Benjamin Mayne |
| collection | DOAJ |
| description | Abstract Age structure information of animal populations is fundamental to their conservation and management. In fisheries, age is routinely obtained by counting daily or annual increments in calcified structures (e.g., otoliths) which requires lethal sampling. Recently, DNA methylation has been shown to estimate age using DNA extracted from fin tissue without the need to kill the fish. In this study we used conserved known age-associated sites from the zebrafish (Danio rerio) genome to predict the age of golden perch (Macquaria ambigua), a large-bodied native fish from eastern Australia. Individuals aged using validated otolith techniques from across the species’ distribution were used to calibrate three epigenetic clocks. One clock was calibrated using daily (daily clock) and another with annual (annual clock) otolith increment counts, respectively. A third used both daily and annual increments (universal clock). We found a high correlation between the otolith and epigenetic age (Pearson correlation > 0.94) across all clocks. The median absolute error was 2.4 days in the daily clock, 184.6 days in the annual clock, and 74.5 days in the universal clock. Our study demonstrates the emerging utility of epigenetic clocks as non-lethal and high-throughput tools for obtaining age estimates to support the management of fish populations and fisheries. |
| first_indexed | 2024-03-13T04:50:48Z |
| format | Article |
| id | doaj.art-b8cd107bb1654048bf8c4b84a01da791 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-13T04:50:48Z |
| publishDate | 2023-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-b8cd107bb1654048bf8c4b84a01da7912023-06-18T11:12:56ZengNature PortfolioScientific Reports2045-23222023-06-011311810.1038/s41598-023-36773-2Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylationBenjamin Mayne0Tom Espinoza1David A. Crook2Chloe Anderson3Darren Korbie4Jonathan C. Marshall5Mark J. Kennard6Doug J. Harding7Gavin L. Butler8Brien Roberts9Josh Whiley10Sharon Marshall11Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research CentreDepartment of Regional Development, Manufacturing and WaterDepartment of Primary Industries, Narrandera Fisheries CentreEnvironomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research CentreAustralian Institute for Bioengineering and Nanotechnology, The University of QueenslandQueensland Department of Environment and ScienceAustralian Rivers Institute and Griffith School of Environment and Science, Griffith UniversityDepartment of Regional Development, Manufacturing and WaterNSW Department of Primary Industries (Fisheries)Fisheries Division, Department of Industry, Tourism and TradeAustralian Rivers Institute and Griffith School of Environment and Science, Griffith UniversityDepartment of Regional Development, Manufacturing and WaterAbstract Age structure information of animal populations is fundamental to their conservation and management. In fisheries, age is routinely obtained by counting daily or annual increments in calcified structures (e.g., otoliths) which requires lethal sampling. Recently, DNA methylation has been shown to estimate age using DNA extracted from fin tissue without the need to kill the fish. In this study we used conserved known age-associated sites from the zebrafish (Danio rerio) genome to predict the age of golden perch (Macquaria ambigua), a large-bodied native fish from eastern Australia. Individuals aged using validated otolith techniques from across the species’ distribution were used to calibrate three epigenetic clocks. One clock was calibrated using daily (daily clock) and another with annual (annual clock) otolith increment counts, respectively. A third used both daily and annual increments (universal clock). We found a high correlation between the otolith and epigenetic age (Pearson correlation > 0.94) across all clocks. The median absolute error was 2.4 days in the daily clock, 184.6 days in the annual clock, and 74.5 days in the universal clock. Our study demonstrates the emerging utility of epigenetic clocks as non-lethal and high-throughput tools for obtaining age estimates to support the management of fish populations and fisheries.https://doi.org/10.1038/s41598-023-36773-2 |
| spellingShingle | Benjamin Mayne Tom Espinoza David A. Crook Chloe Anderson Darren Korbie Jonathan C. Marshall Mark J. Kennard Doug J. Harding Gavin L. Butler Brien Roberts Josh Whiley Sharon Marshall Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation Scientific Reports |
| title | Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation |
| title_full | Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation |
| title_fullStr | Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation |
| title_full_unstemmed | Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation |
| title_short | Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation |
| title_sort | accurate non destructive and high throughput age estimation for golden perch macquaria ambigua spp using dna methylation |
| url | https://doi.org/10.1038/s41598-023-36773-2 |
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