Application of Shape Analyses to Recording Structures of Marine Organisms for Stock Discrimination and Taxonomic Purposes

Morphometric analysis of biogenic recording structures within marine organisms has applications in stock assessment, taxonomics, and ecomorphological studies, with shape variation markedly influenced by both genetics and the surrounding environment. Geometric morphometrics (GM) is an alternative approach to the “traditional” method of collecting linear measurements and applying multivariate statistical methods to these data. Landmark- and outline-based GM methods are suggested to have several advantages over the “traditional” method. Due to the increasing popularity of GM methods in the modern literature, this chapter first compares different morphometric techniques, and then reviews the methods applied to recording structures, with a focus on GM outline-based analyses. It is clear that outline methods have become a popular method of analysis for structures such as otoliths, particularly for the purpose of distinguishing between population components. However, for other structures such as beaks this technique is only in its early stages of application and is more difficult to apply but shows great promise for future studies. The advantages of using a holistic approach, incorporating several techniques including outline analysis for stock identification purposes is discussed.

Using otoliths for fish stock discrimination: status and challenges

Otoliths are calcified structures and the information contained within their chemistry or shape can be used to infer life history events, migration patterns, and stock structure of a fish population. Understanding how otolith chemistry is affected by temperature, salinity, interactive effects of abiotic factors, ontogeny, physiology, etc. is essential for the reconstruction of the environment that affected the fish. Otolith shape is also affected by environmental conditions in addition to the genotype. The applications of otolith chemistry and shape for stock discrimination have increased in recent years because of the advancements in analytical methods and the related software. The stock identification methods sometimes provide variable results but if we use complementary approach the information generated could be more reliable which can be used to prepare effective management and conservation strategies. It appears warranted to generate more information on the factors influencing otolith chemistry and shape especially when two or more factors exert synergetic influence. Therefore, the objectives of this review paper were to provide comprehensive information on various factors influencing the otolith chemistry and shape, and the utility of otolith chemistry and shape for fish stock discrimination with an emphasis towards the research areas needing additional studies.

Perfect representation of a convex 2D contour with only one Fourier component

Shape analysis of a closed 2D contour is an important topic within biological shape analysis, where Fourier methods to reproduce the shape with a limited number of parameters have been and still are of vital importance. An example is within marine management research on fish, where shape analysis of otolith (earstone) contours is performed for species identification as well as for stock discrimination purposes. In both cases, it is expected that the fewer parameters that are needed in a method to reproduce the contour sufficiently good, the better. This contribution outlines how a convex contour of any shape can be represented to any wanted accuracy by only one Fourier component. The key idea is to allow a flexible choice of a predetermined number of x-values along an x-axis that goes through the two most distant points of the contour. The y-variable along the perpendicular y-axis is then monotonically transformed to a z-variable so that the minium and maximum z-values on the contour have the same distance from the x-axis. The x-values of the contour points are now chosen so that the corresponding z-values on the contour follows a perfect sinusoid if the x-values were equidistant. The method is illustrated by application to lasso contours of Norwegian Coastal Cod (NCC) and North East Arctic Cod (NEAC) otolith images, where the average new x-positions for the individual otolith contours were applied to all otoliths. The results show that a considerably better fit to the original individual otolith contours were obtained by applying the invers FFT to the new y-values than by the frequently applied 2D EFDs (Elliptical Fourier Descriptors) approach, for the same number, m < 11, of frequency components. A promising classification result was also obtained by the linear Fisher discrimination method and cross validation applied to the individual x-values for the NCC and NEAC otoliths, with 82% score for NCC and 80% score for NEAC with sample sizes 367 and 240, respectively.

Otolith shape as a classification tool for Chinook salmon (Oncorhynchus tshawytscha) discrimination in native and introduced systems

Chinook salmon (Oncorhynchus tshawytscha) are widely distributed across the globe, with native stocks in the North Pacific Ocean and self-sustained populations in both the Northern and Southern hemispheres. In their native range, Chinook salmon face many conservation and management challenges, including depleted stocks, loss of genetic diversity, and hatchery influences, whereas naturalized range expansion poses a threat to novel ecosystems. Therefore, ways to improve stock discrimination would be a useful tool for fishery managers. Here, we evaluated otolith shape variation in Chinook salmon as a potential tool for stock discrimination using wavelet coefficients and Fourier harmonics in three case studies at multiple spatial scales. We adopted a simple Classification Tree model that used otolith shape variation to separate Chinook salmon groups. We found best performance of the model occurring between hemispheres, followed by Oregon basins, within-watershed Elk River, Oregon, and lastly among South American basins. Otolith shape analysis is a promising tool for stock discrimination if used in conjunction with other methods to better understand plasticity of anadromous species that use pan-environmental systems.