Detect and exploit hidden structure in fatty acid signature data
Abstract Estimates of predator diet composition are essential to our understanding of their ecology. Although several methods of estimating diet are practiced, methods based on biomarkers have become increasingly common. Quantitative fatty acid signature analysis (QFASA) is a popular method that con...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Wiley
2017-07-01
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| Series: | Ecosphere |
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| Online Access: | https://doi.org/10.1002/ecs2.1896 |
| _version_ | 1811167094396420096 |
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| author | Jeffrey F. Bromaghin Suzanne M. Budge Gregory W. Thiemann |
| author_facet | Jeffrey F. Bromaghin Suzanne M. Budge Gregory W. Thiemann |
| author_sort | Jeffrey F. Bromaghin |
| collection | DOAJ |
| description | Abstract Estimates of predator diet composition are essential to our understanding of their ecology. Although several methods of estimating diet are practiced, methods based on biomarkers have become increasingly common. Quantitative fatty acid signature analysis (QFASA) is a popular method that continues to be refined and extended. Quantitative fatty acid signature analysis is based on differences in the signatures of prey types, often species, which are recognized and designated by investigators. Similarly, predator signatures may be structured by known factors such as sex or age class, and the season or region of sample collection. The recognized structure in signature data inherently influences QFASA results in important and typically beneficial ways. However, predator and prey signatures may contain additional, hidden structure that investigators either choose not to incorporate into an analysis or of which they are unaware, being caused by unknown ecological mechanisms. Hidden structure also influences QFASA results, most often negatively. We developed a new method to explore signature data for hidden structure, called divisive magnetic clustering (DIMAC). Our DIMAC approach is based on the same distance measure used in diet estimation, closely linking methods of data exploration and parameter estimation, and it does not require data transformation or distributional assumptions, as do many multivariate ordination methods in common use. We investigated the potential benefits of the DIMAC method to detect and subsequently exploit hidden structure in signature data using two prey signature libraries with quite different characteristics. We found that the existence of hidden structure in prey signatures can increase the confusion between prey types and thereby reduce the accuracy and precision of QFASA diet estimates. Conversely, the detection and exploitation of hidden structure represent a potential opportunity to improve predator diet estimates and may lead to new insights into the ecology of either predator or prey. The DIMAC algorithm is implemented in the R diet estimation package qfasar. |
| first_indexed | 2024-04-10T16:03:22Z |
| format | Article |
| id | doaj.art-2bec5b80348d443396bcbbcfd0130831 |
| institution | Directory Open Access Journal |
| issn | 2150-8925 |
| language | English |
| last_indexed | 2024-04-10T16:03:22Z |
| publishDate | 2017-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecosphere |
| spelling | doaj.art-2bec5b80348d443396bcbbcfd01308312023-02-10T07:33:12ZengWileyEcosphere2150-89252017-07-0187n/an/a10.1002/ecs2.1896Detect and exploit hidden structure in fatty acid signature dataJeffrey F. Bromaghin0Suzanne M. Budge1Gregory W. Thiemann2Alaska Science Center U.S. Geological Survey 4210 University Drive Anchorage Alaska 99508 USAProcess Engineering and Applied Science Dalhousie University Halifax Nova Scotia B3H 4R2 CanadaFaculty of Environmental Studies York University 4700 Keele Street Toronto Ontario M3J 1P3 CanadaAbstract Estimates of predator diet composition are essential to our understanding of their ecology. Although several methods of estimating diet are practiced, methods based on biomarkers have become increasingly common. Quantitative fatty acid signature analysis (QFASA) is a popular method that continues to be refined and extended. Quantitative fatty acid signature analysis is based on differences in the signatures of prey types, often species, which are recognized and designated by investigators. Similarly, predator signatures may be structured by known factors such as sex or age class, and the season or region of sample collection. The recognized structure in signature data inherently influences QFASA results in important and typically beneficial ways. However, predator and prey signatures may contain additional, hidden structure that investigators either choose not to incorporate into an analysis or of which they are unaware, being caused by unknown ecological mechanisms. Hidden structure also influences QFASA results, most often negatively. We developed a new method to explore signature data for hidden structure, called divisive magnetic clustering (DIMAC). Our DIMAC approach is based on the same distance measure used in diet estimation, closely linking methods of data exploration and parameter estimation, and it does not require data transformation or distributional assumptions, as do many multivariate ordination methods in common use. We investigated the potential benefits of the DIMAC method to detect and subsequently exploit hidden structure in signature data using two prey signature libraries with quite different characteristics. We found that the existence of hidden structure in prey signatures can increase the confusion between prey types and thereby reduce the accuracy and precision of QFASA diet estimates. Conversely, the detection and exploitation of hidden structure represent a potential opportunity to improve predator diet estimates and may lead to new insights into the ecology of either predator or prey. The DIMAC algorithm is implemented in the R diet estimation package qfasar.https://doi.org/10.1002/ecs2.1896clusteringdiet estimationdistance measuredivisive magnetic clustering (DIMAC)nonparametricqfasar |
| spellingShingle | Jeffrey F. Bromaghin Suzanne M. Budge Gregory W. Thiemann Detect and exploit hidden structure in fatty acid signature data Ecosphere clustering diet estimation distance measure divisive magnetic clustering (DIMAC) nonparametric qfasar |
| title | Detect and exploit hidden structure in fatty acid signature data |
| title_full | Detect and exploit hidden structure in fatty acid signature data |
| title_fullStr | Detect and exploit hidden structure in fatty acid signature data |
| title_full_unstemmed | Detect and exploit hidden structure in fatty acid signature data |
| title_short | Detect and exploit hidden structure in fatty acid signature data |
| title_sort | detect and exploit hidden structure in fatty acid signature data |
| topic | clustering diet estimation distance measure divisive magnetic clustering (DIMAC) nonparametric qfasar |
| url | https://doi.org/10.1002/ecs2.1896 |
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