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Integrating machine learning with otolith isoscapes: Reconstructing connectivity of a marine fish over four decades
Stable isotopes are an important tool to uncover animal migration. Geographic natal assignments often require categorizing the spatial domain through a nominal approach, which can introduce bias given the continuous nature of these tracers. Stable isotopes predicted over a spatial gradient (i.e., is...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10231828/ https://www.ncbi.nlm.nih.gov/pubmed/37256866 http://dx.doi.org/10.1371/journal.pone.0285702 |
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author | Arai, Kohma Castonguay, Martin Lyubchich, Vyacheslav Secor, David H. |
author_facet | Arai, Kohma Castonguay, Martin Lyubchich, Vyacheslav Secor, David H. |
author_sort | Arai, Kohma |
collection | PubMed |
description | Stable isotopes are an important tool to uncover animal migration. Geographic natal assignments often require categorizing the spatial domain through a nominal approach, which can introduce bias given the continuous nature of these tracers. Stable isotopes predicted over a spatial gradient (i.e., isoscapes) allow a probabilistic and continuous assignment of origin across space, although applications to marine organisms remain limited. We present a new framework that integrates nominal and continuous assignment approaches by (1) developing a machine-learning multi-model ensemble classifier using Bayesian model averaging (nominal); and (2) integrating nominal predictions with continuous isoscapes to estimate the probability of origin across the spatial domain (continuous). We applied this integrated framework to predict the geographic origin of the Northwest Atlantic mackerel (Scomber scombrus), a migratory pelagic fish comprised of northern and southern components that have distinct spawning sites off Canada (northern contingent) and the US (southern contingent), and seasonally overlap in the US fished regions. The nominal approach based on otolith carbon and oxygen stable isotopes (δ(13)C/δ(18)O) yielded high contingent classification accuracy (84.9%). Contingent assignment of unknown-origin samples revealed prevalent, yet highly varied contingent mixing levels (12.5–83.7%) within the US waters over four decades (1975–2019). Nominal predictions were integrated into mackerel-specific otolith oxygen isoscapes developed independently for Canadian and US waters. The combined approach identified geographic nursery hotspots in known spawning sites, but also detected geographic shifts over multi-decadal time scales. This framework can be applied to other marine species to understand migration and connectivity at a high spatial resolution, relevant to management of unit stocks in fisheries and other conservation assessments. |
format | Online Article Text |
id | pubmed-10231828 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-102318282023-06-01 Integrating machine learning with otolith isoscapes: Reconstructing connectivity of a marine fish over four decades Arai, Kohma Castonguay, Martin Lyubchich, Vyacheslav Secor, David H. PLoS One Research Article Stable isotopes are an important tool to uncover animal migration. Geographic natal assignments often require categorizing the spatial domain through a nominal approach, which can introduce bias given the continuous nature of these tracers. Stable isotopes predicted over a spatial gradient (i.e., isoscapes) allow a probabilistic and continuous assignment of origin across space, although applications to marine organisms remain limited. We present a new framework that integrates nominal and continuous assignment approaches by (1) developing a machine-learning multi-model ensemble classifier using Bayesian model averaging (nominal); and (2) integrating nominal predictions with continuous isoscapes to estimate the probability of origin across the spatial domain (continuous). We applied this integrated framework to predict the geographic origin of the Northwest Atlantic mackerel (Scomber scombrus), a migratory pelagic fish comprised of northern and southern components that have distinct spawning sites off Canada (northern contingent) and the US (southern contingent), and seasonally overlap in the US fished regions. The nominal approach based on otolith carbon and oxygen stable isotopes (δ(13)C/δ(18)O) yielded high contingent classification accuracy (84.9%). Contingent assignment of unknown-origin samples revealed prevalent, yet highly varied contingent mixing levels (12.5–83.7%) within the US waters over four decades (1975–2019). Nominal predictions were integrated into mackerel-specific otolith oxygen isoscapes developed independently for Canadian and US waters. The combined approach identified geographic nursery hotspots in known spawning sites, but also detected geographic shifts over multi-decadal time scales. This framework can be applied to other marine species to understand migration and connectivity at a high spatial resolution, relevant to management of unit stocks in fisheries and other conservation assessments. Public Library of Science 2023-05-31 /pmc/articles/PMC10231828/ /pubmed/37256866 http://dx.doi.org/10.1371/journal.pone.0285702 Text en © 2023 Arai et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Arai, Kohma Castonguay, Martin Lyubchich, Vyacheslav Secor, David H. Integrating machine learning with otolith isoscapes: Reconstructing connectivity of a marine fish over four decades |
title | Integrating machine learning with otolith isoscapes: Reconstructing connectivity of a marine fish over four decades |
title_full | Integrating machine learning with otolith isoscapes: Reconstructing connectivity of a marine fish over four decades |
title_fullStr | Integrating machine learning with otolith isoscapes: Reconstructing connectivity of a marine fish over four decades |
title_full_unstemmed | Integrating machine learning with otolith isoscapes: Reconstructing connectivity of a marine fish over four decades |
title_short | Integrating machine learning with otolith isoscapes: Reconstructing connectivity of a marine fish over four decades |
title_sort | integrating machine learning with otolith isoscapes: reconstructing connectivity of a marine fish over four decades |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10231828/ https://www.ncbi.nlm.nih.gov/pubmed/37256866 http://dx.doi.org/10.1371/journal.pone.0285702 |
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