Fish in the Bay – 11 Nov 2018 UC Davis Trawls – Anchovy Color Hypothesis.

This is a special edition of “Fish in the Bay” to further develop the San Francisco Bay Colorful Anchovy Hypothesis. 

As mentioned several times in the past, San Francisco Bay anchovies come in at least three distinct colors with some additional color variations in between.  I have searched internet literature to find a similar example of anchovy color diversity but have not come up with much.

Our SF Bay anchovies come in both blue AND green – plus more colors.

No one seems to have rigorously investigated dorsal pigmentation in anchovies, one of the world’s most important fish in terms of coastal and estuarine ecology.

  • What genetic factors cause pigmentation on the anchovy dorsal surface?
  • What environmental factors influence anchovy dorsal colors? Can anchovy dorsal color be used as a proxy for environmental monitoring of sea surface temperatures, Dinoflagellate (food) population densities, or other factors?
  • Is anchovy dorsal color permanent in individual adult fish? Or, does the hue change in response to temperature and illumination?


This is a world-class mystery.  And, San Francisco Bay is a world-class laboratory where anchovies literally swim in to show us all the possible electric metal-flake colors that they can express.

The above photo is of fish collected on 11 November 2018 from Pond A21.  It shows some of the diversity of anchovy color: blue, emerald green, green-gold, and clear/brown.  Long-time readers know, and I will again describe further below, that local anchovies did NOT show this range of color at this location in 2016, and maybe prior.  What happened?


Biologist Carl Hubbs is the originator of the San Francisco Bay Anchovy Color Hypothesis.  He first described ocean-going Green-back versus resident Brown/clear/gray-back anchovies in San Francisco Bay back in 1925: (see page 18).  At the time, Hubbs noted that ocean-going green-backed anchovies did not venture very far into the Bay, with most being caught in the vicinity of Sausalito.

BTW: A main conclusion of Hubbs 1925 paper was that Herring, Sardine, and Anchovy populations along the California Coast generally tend to have fewer vertebrae further south and into warmer water.  He also noted that shorter anchovies tend to have bigger heads in proportion to body length.  In other words, at risk of misstating, these fish mature faster in warmer water, hence skeletal growth ceases before all vertebra form.

Hubbs also concluded that stubby little San Francisco Bay clear, gray, or brown-back anchovies were a subspecies worthy of the name Engraulis mordax nanus Girard.  (The name “Girard” after a mid-nineteenth century ichthyologist who had first described this distinct San Francisco Bay subspecies.)


In recent years, Jim Hobbs and his UC Davis researchers have confirmed and extended the Hubbs observations of green and brown anchovies.  Just as importantly, modern Hobbs Lab/UC Davis observations show that ocean-migrating green-backs now venture far south into San Francisco Bay.


In addition, the Hobbs team has added observations of blue-back anchovies with color gradations in between. (Photo taken at Station LSB1 on 20 October 2018.)


Baby anchovies have no color.  Young fish hatched in San Francisco Bay show no color. This is probably true of all young anchovies. Thus, a difference between green-back and brown-back anchovies would seem to be that the later never develop dorsal color. It is still unknown if all anchovies are capable of expressing dorsal color over time under the right conditions, or if there are specific “races” (the Carl Hubbs term) of anchovies that are capable of expressing different colors.

Dr. Levi Lewis often reminds me that many anadromous fish, like salmonids, “silver up” as they age and particularly after they migrate to the ocean.  Do anchovies respond the same way?  Do locally recruited Brown-backs never express dorsal color simply because they have never made the trip out to the deep, cold, salty Pacific?  And, do ocean-going blue and green-backs slowly lose color as they loiter in the Bay?

From crude macro-photo observation, I suspect “silvering up” and “coloring up” are two different phenomena.   I have seen very few examples of silvering up, but it appears to involve a thickening of scales and increasing scale reflectivity.  Coloring up seems to be expressed by pigments in chromatophores (metallic colors created by guanine crystals in Iridophores – described further below) beneath dorsal scales.  In that way, anchovies and other Clupeiformes become more silver flanked via one mechanism as they age, and they may additionally develop bright dorsal counter-shading colors via another process.


UC Davis trawls caught mostly Brown-back anchovies in Lower Coyote Creek in November 2016.  Some brown-backs (also described as clear or gray) appear to be adults with stunted growth.  Is this in fact a separate “race” of anchovies as Hubbs proposed in 1925?   Unlike blue and green-backs, these brown-backs show no pigmentation on the dorsal side.  The back appears translucent.  The brownish tinge seems to come from the fish’s internal color.


2016 was a warm, dry year, and anchovy populations were up.  Anchovies spawn in warmer water and flee when flushing rivers make it too fresh.  Back then, I did not take much notice of anchovy colors because most that I saw were brown!


In January and February 2017, we experienced the “Freshwater Flush.”  Local anchovy populations were decimated – literally cut to almost 1/10th previous numbers.  True brown-back anchovies became far less common.

The photo collage above shows anecdotal evidence in the aftermath of the anchovy disaster.  Every anchovy photographed here showed weak blue or green pigmentation; there were no true brown-backs in the bunch!  Were these ocean migrants who moved in to replace the now dead resident population?  And, had their colors faded?  Or, are these some kind of hybrids?


Weakly colored anchovies are nearly always present.  This is a fish caught in November 2018.  We see many examples of young-ish anchovies (young-of-year or at most second-year fish) that are clear-backed, but they also show traces of green or blue flecks of color.  Will these fish develop more color as they age?  Or, does color not develop in warm, turbid Bay water?


The crown of the head usually shows green color first and strongest.  Also notice the dark spots (some biologists call these “punctilations”) on, or within, the head and dorsal scales.  I initially thought the dark spots might be nascent or dead chromatophores that are not expressing blue or green color.  I am not so sure anymore.  However, true brown-backs appear to have far fewer dark punctilations in addition to having no chromatophores.

Some random fish color background information:

  1. From a Wikipedia article: (

“During vertebrate embryonic development, chromatophores are one of a number of cell types generated in the neural crest, a paired strip of cells arising at the margins of the neural tube. These cells have the ability to migrate long distances, allowing chromatophores to populate many organs of the body, including the skin, eye, ear, and brain. Fish melanophores and iridophores have been found to contain the smooth muscle regulatory proteins [calponin] and caldesmon.[34]

Leaving the neural crest in waves, chromatophores take either a dorsolateral route through the dermis, entering the ectoderm through small holes in the basal lamina, or a ventromedial route between the somites and the neural tube.” 

The article goes on to describe different types of chromatophores in fish and the hues they produce:  … in general, iridophores are considered to generate iridescent or metallic colours, whereas leucophores produce reflective white hues.[12]


  1. Papers cited discuss instances of chromatophores altering fish colors to aid courtship, feeding, or hiding. A Meyer-Rochow, Royuela (2002) abstract briefly describes a mechanism by which smooth muscle proteins and calcium ions may control pigment dispersion in response to exposure to bright light in two species of Antarctic fishes.


  1. I also found this long discussion: “The Physiology and Behavior of Color in Fishes.” It gives some good additional clues that anchovy blues and greens arise from the type of chromatophores called “Iridophores” that make use of plate-like crystals of guanine and other purines in response to (1) neural stimulus (short time delay) and/or (2) hormonal signals (long time delay), or (3) morphological/external factors (very long time delay or even permanent color change).

Development and migration of chromatophores is an energy-intensive process.  So, if fish don’t need, or can’t afford, color for camouflage or mating display, the colors can fade.  Home aquarium hobbyists are often dismayed to find their prized fish graying out due to: lack of sunshine, poor food quality, wrong temperature, lack of potential mates, or other factors.


Close-up of pigmentation (chromatophores) versus punctilation.  This fish, caught in November 2018, shows both blue and green hues.  Many of the pigmentation flecks appear larger and beneath some of the black punctilation spots.   Why are some areas green and others blue?  What brings out this color, aside from age of the fish?


A dark fish with half-developed color.

June 2018 – The fish above was injured during netting or handling.  See how the color changed from blue-green to gold immediately proximate to the injury?  How did trauma cause a sudden change in color expression?  How does healthy cellular metabolism sustain beautiful blue and green colors?   (Notice that the gold color is not the same as Brown/clear-backed anchovies.  The traumatized area has pigmented gold flecks as opposed to absence of pigmentation.


Anchovy freezing experiment.  At this point, I had to investigate whether anchovy colors persist after death and freezing.  Anchovy dorsal color would be a great tool in the lab if colors persisted.  But alas this was not to be.

I photographed, bagged, and froze, a number of anchovies in October.  You can see some results above.  All color disappears from blue-backs and green-backs after freezing.  Anchovies with intense color look a little darker than brown-backs after freezing, but no color.  Where does the color go?

We all know that many types of fish lose or change color soon after death.  Somewhere, buried in each affected cell is a molecular machine that sustains and modifies color during life.  Proteins are built (evidently as guanine crystals in Iridophores) and reflect in blue, green, or gold hues.  When the animal dies, the color quickly fades away.

If we could understand what factors influence this bio-machinery that makes the color, we might be able to use our anchovies as roving indicators of sea and Bay water conditions.


Bigger puzzle than just anchovies!  We also netted some American Shad in November.  The photo is showing two anchovies (Brown-back at top right, Green-back in the middle) with two American shad – one green, one golden.

I noticed in spring 2018 that American shad closer to the Bay tend to be greener.  The same type of fish farther up in Alviso Slough or Coyote Creek tend to be more golden.

Like anchovies, American Shad roam from freshwater to salty seawater. Unlike anchovies, the shad spawn and spend more time in fresh water.  Why are some green, and some golden?  Is dorsal color reversible in American Shad?


More American shad from November trawling:  two anchovies at top, then two shad, then another anchovy at bottom.


American Shad from station LSB2 in March 2018.  These two were caught in colder, saltier water.  Deeper blue-green dorsal color in American Shad appears to correlate with either lower temperature, or higher salinity, or both.


The dorsal color mystery extends to Pacific Herring too!  The two young herring are representative of all I have photographed to date in Lower South Bay, always young and brown/clear-backed, UNTIL NOW.


Pacific herring, November 2018 in Pond A19.  I assume this is a yearling.  It is still small (70 mm).  But, it is older and slightly larger than all the juvenile herring I photographed before.  This one has similar blue-green countershading.

Notice that the blue-green color is not uniform within each scale.  The color is expressed as tiny flecks in the skin beneath transparent scales similar to what we see in anchovies and shad.


Pacific herring, May 2018 at LSB station.  The discovery of a mature blue-green backed herring motivated me to re-examine an older photo of a young herring I took in May.  Look carefully! I can now see tiny flecks of blue within or under its dorsal scales.  The process of dorsal color development appears to be the same, or at least very similar, in Anchovies, Shad, and Herring.

Blue-green countershading provides tremendous survival advantages for pelagic fishes.  What genes control this biochemical process?  And more importantly, how does this color expression change in response to environmental factors?

We can’t read our fish like a book until we learn the language!


Anchovies, shad, and herring are all members of the broader Clupeiformes order of fishes.  The color phenomenon should be similar, if not the same amongst all three species.   If we could read Clupeiformes colors, we would have a very useful environmental monitoring tool.  … Or, maybe not!


Good News!  The UC Davis team has been tracking Anchovies and other fish in Lower South Bay for over eight years.  Comparable monthly otter trawl data for 20 stations have been assembled covering several years of seasonal and decadal changes.  Life-cycle patterns of dozens of local and migrating fish, including Northern Anchovies, American Shad, and Pacific Herring are now becoming clear.

Disclaimer: Above table shows raw numbers of fish collected per trawl or set of trawls.  Numbers do not represent Catch Per Unit Effort (CPUE).  In some instances in 2015 multiple trawls at same location were averaged or ignored.  In a few cases, individual trawls were less than the standard 10-minute duration.  This table does not account for those variations in procedure!

Bad news:  I have only begun to document the Anchovy Color Mystery.  Using my unsophisticated approach and lackadaisical pace, it will take me decades to fully unravel this issue – maybe even a century or two.  We will need a little help to solve this Clupeiformes Color Mystery.  Or, leave it to me:  I’ll figure this out eventually.

Too many fish, too little time!

And, Happy Thanksgiving!




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