New discoveries in otolith research

Learn about some of the most promising areas in otolith research.

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• Methods
• Tools and references

Methods

New methods in otolith research.

New ageing method for lobster, crab and shrimp

Crustaceans don't have otoliths, but the discovery of growth bands in their eyestalks and gastroliths borrowed heavily from previous otolith research.

Stock mixture analysis combining otolith and genetic markers

The 2010 paper by Smith and Campana reports the first statistical method for stock mixture analysis. This allows a Bayesian framework of the simultaneous consideration of characteristics, including:

• genetic
• otolith
• meristic

Access free downloads, including:

• R package (includes a sample dataset)
• Mix.Fish for Unix
• installation instructions

Statistical program for age validation based on edge analysis

In 2009, Okamura and Semba published a paper detailing a statistical program for validating annual growth band formation based on edge analysis. This looked at whether or not the growing edge of the otolith or vertebra shows an opaque or translucent zone across the year. It was the first statistical analysis developed for analyzing edge-type data, which had usually been analyzed in an ad hoc and non-rigorous manner.

Quality control in production ageing

In an informal survey of fisheries laboratories around the world, we determined that a minimum of 800,000 otoliths are aged annually. Most of these were done in mass production by stock assessment laboratories. Some laboratories used quality control protocols and have validated reference collections, while some didn't.

Recent reviews summarized the best practices of age validation and quality control and criticized the oft-used marginal increment method of age validation.

Age validation of long-lived fish using fallout and radiocarbon from nuclear testing

The best way to validate the ages of long-lived fish is with fallout and radiocarbon from nuclear testing. It has none of the assumptions that plague other approaches.

Elemental fingerprints as natural tags

The early assumption that the elemental and isotopic composition of the otolith might serve as the ideal non-genetic stock marker has faded.

Instead, we've found that the elemental fingerprint works just like a natural tag of a group of fish, with complete stability over short periods of time. This allows us to reliably track the movements of those fish no matter where they go and who they mix with. It's like a large-scale tagging experiment, but without the time and expense of having to tag them in the first place.

We predict this will give better discrimination in many stock mixing situations, even over microsatellite DNA.

Stock mixture analyses based on maximum likelihood estimation

The stock mixture analysis based on maximum likelihood estimation approach is best for classifying fish into groups with elemental fingerprints. This is an area where geneticists are advanced ahead of us as they've been using maximum likelihood estimation-based stock mixture analyses for years.

Discriminant function analysis to classify unknown fish into 2 or more reference groups is common in the otolith field. However, discriminant analysis can give grossly misleading results when you don't know the answer ahead of time (the priors).

Probe-based reconstruction of temperature history using oxygen isotopes

Lots of people have used oxygen isotopes in whole otoliths to determine the mean water temperature in which the fish lived. Some have used micromilling techniques to focus on seasonal or annual temperature histories. The new generation of computer-controlled microsamplers allow even more detailed sampling.

Laser or ion probe-based techniques are the next logical step, allowing (in principle) temperature histories that are:

• monthly
• weekly
• daily

Mass-marking using calcium-binding compounds or temperature

A number of labs and hatcheries are now routinely mass-marking millions of young fish before release into the wild. Some have already used recapture results to test ecological theory, but the possibilities are virtually untapped.

Computer-assisted ageing

Even with the ongoing advances in imaging and artificial intelligence, we're unlikely to see a general purpose, fully automated ageing machine in the near future.

However, the resolution and dynamic range of image analysis systems is improving rapidly, implying that image enhancement will become easier than ever.

We should also see reductions in the numbers of otoliths required for routine ageing. This is due to improvements in quality control and the introduction of maximum likelihood statistical techniques for predicting age based on otolith morphometry.

Tools and references

New otolith atlas for the western Pacific

The book by Chien-Hsiang Lin and Chih-Wei Chang, Otolith Atlas of Taiwan Fishes provides a much-appreciated reference for otolith workers in the western Pacific. It contains photographs and scanning electron microscope images of more than 1000 fish species.

Otolith scanning in 3D

Toni Lombarte and colleagues have announced the development of a 3D scanner for otoliths. The resulting images have very good clarity and can be rotated in 3D when using the appropriate software.

Image and shape analysis software

LASAA at IFREMER in France developed image analysis software for calcified structure. This software allows:

• data extraction
• image enhancement
• otolith shape analysis
• feature measurement
• normal image acquisition capabilities

New paleothermometer

The ideal paleothermometer can be used to reconstruct temperature history without the confounding effects of salinity or water composition. For use with otoliths, stable oxygen isotopes are usually the most reliable option, but only if the isotopic composition of the water is known. An alternative is based on combinations of stable carbon and oxygen isotopes. It doesn't solve for all issues, but it does avoid complications due to water composition.

Web-based otolith identification software

There are a number of otolith atlases around the world which can be used to identify species based on otolith shape and appearance. However, the first instance of web-based automated species identification software was based on otolith shape.

The program uses several mathematical methods of shape analysis, including wavelet analysis. It requires nothing more than uploading a suitably-oriented otolith image on a black background.

Species identifications are currently limited mainly to the Mediterranean, but the image database is being expanded to other areas.

Maximum likelihood software

With the realization that elemental fingerprints can be used very effectively to separate mixtures of fish coming from different sources, there is increasing demand for the maximum-likelihood based software to separate the group mixtures.

Discriminant analysis isn't a good option here, since the 'priors' parameter is unknown. In the elemental and isotopic assays statistical analysis, we've released a working copy of the Integrated Stock Mixture Analysis (ISMA) program (written for the S-Plus environment). You can use it in separating stock mixtures based on elemental fingerprints or other continuous or categorical variables.

New otolith equipment

Several companies around the world have developed new equipment for preparing or interpreting otoliths, such as:

• Benetec's otolith sectioning saw, part of its all-inclusive otolith processing line
• Ratoc System Engineering's semi-automated daily increment measurement system
• South Bay Technology's multilap polishing tool with precise controls over individual otoliths for polishing several otoliths at once

Photographic atlas of fish otoliths

The Photographic Atlas of Fish Otoliths of the Northwest Atlantic Ocean took nearly 20 years to complete. It includes:

• images of lapilli and asteriscii from most families
• an overview essay of factors affecting otolith shape
• light microscopic and scanning electron microscope images of 580 sagittal otolith pairs representing 288 species and 97 families of fish from the northwest Atlantic

High resolution magnetic sector

The magnetic sector is able to distinguish between many isobaric interferences and the target element, thus allowing more accurate assays for certain key elements.