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What is an otolith?

halibut otolith photo

Otoliths, also called ear-bones, are structures made mostly of calcium carbonate that are found in the head of most fish. Otoliths act as sound receptors and also play a role in balance and orientation. As the fish grows, so does the otolith, by deposition of concentric layers of material. Seasonal changes in the fish's growth rate are reflected in the otolith. A year's growth consists of a wider summer zone (reflecting faster growth) and a narrower winter zone (reflecting slower growth). Because halibut spawn in winter, the winter zones are counted to determine the age of the fish in years. These annual growth rings, or "annuli", are very similar in appearance to the growth rings of trees.

Ages are used for estimating growth and mortality rates as well as population age structure. Age data are incorporated into the IPHC's annual stock assessment. In the past, the IPHC also used otolith weight and length to estimate the size of halibut, though this later proved to be inaccurate.

Each year, alternating opaque (summer) and translucent (winter) rings are deposited on the otolith. The oldest age recorded for Pacific halibut is 55 years for a 118 cm male (~36 lbs, net) captured in 1992 in the Bering Sea on IPHC's setline survey. The oldest recorded age for a female is also 55 years. This female was 161 cm long (about 100 lbs, net) and was captured in the Bering Sea in June 2000, also on an IPHC survey. The mean age in years of the commercial catch has been 12-13 for the last several years.

Currently there are four staff members doing production aging of survey, commercial, and tag recovery halibut otolith samples. Sport-caught halibut otoliths from Alaska are also aged. Approximately 30,000 otoliths are read per year.

3D otolith drawing

Notes/guidelines for aging halibut

Aging methods used at the IPHC include the following:

  • Surface Ages: Otolith are read while on a piece of black cloth, immersed in water (to minimize glare from the light source and maximize contrast). The distal surface of the otolith is observed during surface reads; the proximal surface has a deep groove and annuli are obscured.
  • Break & Bake: Break and bake involves scoring the otolith surface through the nucleus with a razor blade, then snapping the otolith in two. We bake one of the halves and keep the other half unbaked so we can still do a surface reading. Baking the sections enhances the contrast between summer and winter zones (winter zones turn dark brown). Previously we heated the otolith sections one at a time over an alcohol flame (Break & burn); however, baking allows us to heat many sections at a time, saving time. We use metal trays for baking; they are divided into 50 indented cells, which keep the otoliths from getting mixed up. The baked sections are then mounted in plasticene and coated with mineral oil or glycerin solution before viewing under a dissecting microscope.

Through 2001, Pacific halibut otoliths were all surface aged at IPHC. The criteria used between 1992 and 2001 included performing break & burn or break & bake age determinations in cases where readers were not confident of the surface age, (e.g., thick/steep edge, opaque or cloudy surface, odd growth pattern, high surface age, etc.). The break & burn/bake method of age determination was validated by a bomb radiocarbon study and since 2002, all longline (survey and commercial) and sport-caught halibut are aged by break & bake technique. Since 2002, only otoliths from the trawl survey collections are surface aged. If the surface age is 5 or greater, the otolith is broken and baked. Trawl-caught otoliths that are obviously older than five are not surface-aged first.

We only collect and read the left or blind side sagittal otolith at IPHC. The right and left otoliths are not mirror images as they are in some species, and right otoliths are harder to read and give less accurate ages. We also do not age crystallized otoliths. Reasons for crystallization are unclear, but crystallization occurs in other fish species as well and one or both of the pair can be affected. The inorganic portion of crystallized otoliths is made up of calcium carbonate, just as in "normal" otoliths, but the crystalline structure is different and growth patterns are difficult to interpret. Total between-reader percent agreement of between 55 and 80% or agreement within one year for 80-95% of the readings is usual for halibut otoliths.

Otoliths contain other useful information besides age. They can be used to identify fish species in stomach contents of other fish or mammals, and have been used as biological "recorders" of environmental changes using growth patterns or trace elements within the structure of the otolith.


Pacific halibut is fished by setline (long strings of line with attached hooks) on the continental shelf from northern California to the Bering Sea. The fishery currently operates eight months each year, from mid-March through mid-November. Chalky halibut has been recognized for decades, although until recently the problem was limited to summer fisheries in the southern fishing areas off Washington and Oregon. Until 1995, landings in most areas have occurred during short fisheries in the early and late summer, and most product was frozen. Since 1995, fisheries occur throughout the open period, and a majority of the product is sold fresh. This, combined with an increased awareness of chalkiness by the marketplace, has created the current situation, where as much as two million pounds of the 60-million pound catch is graded as chalky and thus unmarketable as a premium product, constituting a multi-million dollar loss to the industry.
IPHC research, both in the 1960s and in the late 1990s, have shown chalkiness to be directly associated with a buildup of lactic acid and resulting lowered pH in post-mortem flesh. The condition is specifically associated with a denaturation of muscle proteins resulting in an increased drip loss and a sometimes startling loss of translucence in the flesh. In extreme cases, the flesh gapes, and has little use as a food product. Our research has associated chalkiness with two areas of the coast during late summer and early fall, and male halibut tend to be chalkier than females. It is likely that the areas with the highest rate of chalkiness are associated with high bottom temperatures (12-14 degrees C), which are near the upper thermal limit for the species distribution. Most recently, we have facilitated the use of pH meters in 1-2 day post-mortem fish to determine flesh pH, which is predictive of the developing chalky condition.
The condition is reversible in live fish. Flesh which would otherwise likely be chalky does not develop the condition post-mortem if the fish are allowed a 1-2 day resting period after capture, and before killing.
A number of documents regarding chalky fish have been produced by the IPHC, primarily by Stephen Kaimmer.

This condition, which has been variously described as mushy or jelly-like, has become more frequently reported by recreational halibut fishers in certain parts of Southcentral Alaska, especially in 2011 and 2012. This is not a new phenomenon, with observations being noted as early as 1989. Recent analyses of flesh samples by the State of Alaska's Fish Pathology Lab noted that fish with the condition have large areas of body tissue which are flaccid or jelly-like. The fillets may ooze water and are mushy when cooked. While the cause of the condition is unknown, it is thought to be the result of nutritional deficiencies.

The IPHC is interested in learning about the geographical and seasonal occurrence of the mushy condition in Pacific halibut. To accomplish this, we'd like fishers to submit information on the following:

  1. Date/location/depth of capture (e.g., bay, strait, direction and distance off a certain headland, etc.)
  2. Size and sex (if known) of fish
  3. Stomach contents - did you notice what types of food were in the stomach?
  4. Activity - sport, commercial, or subsistence fishing
  5. How many of the halibut you (or your vessel, if more appropriate) caught that day had the mushy halibut syndrome? How many did not?
  6. Disposition of the mushy halibut - did you keep the fish for your use, or discard the fish, either at sea or on shore?
  7. How many non-mushy halibut did you catch and how many did you release during the day you caught the mushy halibut?

Please submit the above information by This email address is being protected from spambots. You need JavaScript enabled to view it. to the IPHC staff. We would also like to receive any pictures you may have taken. Please attach these to the submission e-mail.

We plan to share information on the occurrence of mushy halibut with other agencies, but all personal information will be kept confidential.

Additional information can be found at http://www.adfg.alaska.gov/static/species/disease/pdfs/fishdiseases/mushy_halibut_syndrome.pdf

Thanks for your assistance!

There's a reward offered for every IPHC tag returned!

Contact us at This email address is being protected from spambots. You need JavaScript enabled to view it.

Wire tag

Traditional wire tags

  • Threaded through the operculum (cheek area) on the dark side of the body.
  • The usual reward is $10 cash or an IPHC tag hat for each tag returned.
  • Some wire tags are worth $100 or $200 and these have the reward printed on the tag.


Spaghetti tags

  • Plastic spaghetti tags were used in the voluntary sport charter-boat tagging program from the 1990s. Tags were attached to either a plastic or stainless steel dart and inserted either in the back of the fish (plastic darts) or the cheek on the dark side (stainless steel dart). Recoveries of this tag type are not very common since releases occurred quite some time ago.


Pop-up archival transmitting tags

  • Attached near the dorsal by a metal dart and leader.
  • Rewards: $500 for tag body*, $50 for the leader and metal dart tag only, $10 or tag hat for leader only.
    *Note that these tags may be found attached to a halibut, free floating, or washed ashore.

PAT tag

PAT tag leader


Electronic archival tags

  • Attached near the dorsal via a plastic "cradle" and wires.
  • $500 reward for the return of the tag body.

Archival tag


"Dummy" archival tags

  • Fish has both a pink wire tag in the cheek and either an internal or external dummy archival tag.
  • Internal "gut" tags have the tag body inside the abdominal cavity with the stalk protruding outside the fish. (below, top)
  • Externally mounted tags are attached near the dorsal. (below, bottom)
  • $100 reward for the return of the archival tag body.
  • $100 reward for the return of the pink wired tag (reward printed on tag).

Internal archival tag

External archival tag


So you've caught a tagged halibut...

and you've decided to collect the data yourself. There are a few of things we'd like you to do:

A. Remove the tag from the fish.

Removal method depends on the type of tag.
  • Traditional wire cheek tag can be removed by untwisting the wire and pulling it through the hole or cutting the cheek tissue. Please do not cut the tag (or yourself).
  • Plastic spaghetti tags with metal or plastic-tipped dart tags must be cut out of the fish so that the dart is completely removed from the flesh. The metal-tipped tags were placed in the cheek while the plastic-tipped ones were inserted behind the fin rays above the head.
  • Pop-up archival transmitting (PAT) tags are attached to a black plastic leader which in turn is attached to a titanium-metal dart which anchors the tag assembly to the fish. Even after the tag body has released and popped up, the leader remains attached to the fish. The metal dart should be cut completely out of the fish and returned with the plastic leader.
  • External electronic archival tags and external archival "dummy" tags are attached by wires that run completely through the body of the fish through the dorsal musculature. The wires should by cut out of the fish and collected along with the tag body, cradle (archival tags) and backing plate on the fish's white side.
  • Internally-implanted electronic archival and "dummy" archival tags do not possess an attaching mechanism; the only thing to remove is the tag itself which will be inside the body cavity.

Don't lose the tag--it's the proof you'll need to get your reward.

B. Measure the fork length of the fish

Measure the length of the fish (preferably in centimeters) from the tip of its mouth (chin) to the fork of its tail. The proper measurement is a flat, horizontal distance rather than a measurement which follows the contour of the fish. Please make certain the fish is on a flat surface and that the mouth is closed.

Measuring the fork length

The best way to make a measurement is to:

  1. Place the fish's chin against a stable vertical surface, such as a wall
  2. Put a marker at the fork of the tail
  3. Remove the fish
  4. Measure the distance from where the fish touched the vertical surface to the marker.

C. Cut out the otolith*

The otoliths, or earbones, are used to determine the age of the fish. There are 3 pairs of otoliths in each fish, though only 1 pair is easily visible. Of this visible pair, we want the one from the white side.

  1. If the fish is round (gills and guts intact) the first thing to do is remove the gills. Make note of where the top part of the gills connects to the backbone: this is where you'll find the otoliths.
  2. Lay the fish white side up and lift open the operculum, or gill cover. Run your finger along the backbone near where the gills used to be. You should feel a bulge. This is the otic capsule.
  3. Using a moderately sharp knife, make a shallow cut and take the top off the capsule. If done right, you should see a cavity with the otolith suspended within.
  4. Place the otolith in a protective container so that it is not crushed.

[Diagram 83K]

* Please don't attempt this if you're not good with knives. Minors (who are old enough to play with knives) should still have adult supervision. The Commission takes no responsibility for any possible injuries resulting from this procedure.

D. Submit the information

In addition to the otolith and fork length, we would like:

  1. Tag number: if the number appears illegible, don't throw the tag away. We can still read it in the lab.
  2. Recovery date: when the fish was caught
  3. Location: preferably latitude/longitude coordinates, though distance and bearing from a landmark would be acceptable (e.g.. 3 miles SW of Cape Barto)
  4. Depth: the depth at which you were fishing, in fathoms (1 fathom = 6 ft)
  5. Sex: male or female, if known
  6. Gear type: longline, troll, trawl, pot, or sport
  7. Landing port: where the fish was brought in
  8. Vessel name and number: if commercially caught
  9. Name and complete mailing address
  10. Reward type: baseball cap or $10.00

If more than one tag is recovered, please keep the information from each fish separate.

Return this information to:

Attn: Joan Forsberg
2320 W. Commodore Way, Suite 300

Seattle WA 98199-1287

Industry Features

Commercial Fishery

Commercial Feature

Commercial halibut fishery updates from Alaska, British Columbia, and the U.S. West Coast.

Sport Fishery

Sport Feature

Sport fishing information from Alaska, British Columbia, and the U.S. West Coast.

Advisory Bodies

Advisory Bodies Feature

The IPHC maintains an auxilary website for its Advisory Bodies at iphc.info.