Fish in the Bay – January 2020: Part 1, Pregnant Sculpin, Saltwater Oddballs, and a Shad Experiment.

Trawl map.

Full Moon and perihelion.   The Moon set at sunrise as we launched on Saturday.  The combination of full moon plus Earth passing closest to the Sun this time of year makes for extreme high tides around midday (and extreme lows near midnight).


Bay-side station trawling results – Rare high-salinity oddballs are highlighted in red.


Upstream of Railroad Bridge.

Fish count:  401 fish were caught over both days.  This is fairly typical for January.  We have seen higher and lower fish counts over the past several Januarys.

The weekend shrimp count was high:  1,596 shrimp (Crangon + Palaemon + Exos).  This would have been a January record but for the Great Crangon Brooding Event last year.  In comparison, the January 2019 shrimp total was 11,289.  I was hoping we would see a similar massive number of brooding Crangon by now.  But, it was not to be.

Crangon are again brooding, but not as many as last year.  If Crangon are indeed protandrous hermaphrodites (born male then become female after about one year), then last year’s brood would still be male and not yet be reproductive.  We did catch many larger berried female Crangon which were presumably born in previous years.  I will discuss further in another blog post.

Turbidity.  Top and bottom turbidity readings (Nephelometric Turbidity Units – NTU) were added in the water quality measurements at top of the tables.  NTUs are relevant to the “Shad Experiment” explained further below. 


Pat Crain and Levi Lewis prepare the trawling rig on Saturday.


Some barnacles stuck to a shell at Alv1.

We nearly always find pieces of living and dead barnacles upstream in both Alviso and Coyote Creek sloughs.  It is a little counterintuitive: salinity is lowest at these locations but with a great deal of variance.  These marine critters tolerate regular pulses of freshwater that should totally discourage them. … Life finds a way, I guess.


1. Sculpin and Gobies.

First catch in Alviso Slough:  Brown American Shad, Staghorn Sculpin, and a Starry Flounder.


Staghorn Sculpin.  This time of year, Staghorns get big, fat, and pregnant.  I believe this one was showing a pregnant full belly.

I have noticed similar white spots over the eyes and face on some Sculpin in previous years.  I do not know if the spots have any significance, like maybe a spawning signal to other Sculpin?  … Seen from above, those white spots could provide a powerful beacon to a hungry heron or egret!


Pregnant Prickly Sculpin.  This was the latest of several pregnant Pricklys caught at upstream stations in recent months.  Extended winter and spring rains in 2019 facilitated repeated spawning.  Now, for the first time, we are catching pregnant Pricklys in our sloughs.

Keep in mind:  We caught NO PRICKLYS in 2015 and only 3 in 2016 – the dry years.  Pregnant Pricklys are very good news. 


Two Shimofuri Gobies (left) and eight Shokihaze Gobies (right) from Station Alv2.

Shokehaze and Shimofuri Goby invasions continue.  We caught both old and young of both Goby types.  I believe this may be the rising crest of a Shoki/Shimo Tsunami that has been sweeping across SF Bay the last few decades.  Their populations here may now be displacing the non-native Yellowfin Goby.


Shimofuri Goby in the Photarium – two views.

Nine Shimofuri Gobies were caught in January compared to 41 Shokihazes.  ~ 1:4 is roughly our typical ratio.


Two Shokihaze Gobies in the hand.


Shokihaze Goby in the Photarium – two views.

I wonder about the purpose of fleshy “whiskers” on the Shokihaze.  There must be some advantage to having them.  The other gobies do not have “beards.”


Pregnant Yellowfin Goby from Artesian Slough on Sunday, January 12th.

Yellowfin Gobies are hardy survivors.  They may yet overcome this ongoing Shoki/Shimo invasion.


2. More Signs of Continued High Salinity.


Aquamarine Blue and Brown Shad side-by-side comparison at Alv3.

Blue Shad continue to be seen upstream in the Alviso Marsh Complex.  These guys turn green and brown within minutes as salinity drops – see Shad Experiment further below.

  • Also note: When I refer to “Blue Shad,” the color is actually “Aquamarine,” Pantone 14-4313 (, or perhaps “Peacock Blue,” Pantone 19-4728.
  • Blue Anchovy dorsal colors are closer to “Royal Blue,” Pantone 19-3955. The importance of this distinction will become apparent later.


Black-tailed Crangon (C. nigricauda).  I continue to question whether we really understand the boundary between C. franciscorum and C. nigricauda.  But, there is no question that we saw a lot of Black-tails (C. nigricauda) in January.


More Black-tailed Crangon!  Presence of C. nigricauda tells us that salinity is high and water temperatures are low.  We usually seem to see them this time of year until freshwater flushing drives them out.  So it seems.


Heptacarpus shrimp from station LSB2.

Heptacarpus Shrimp!  Six were caught in January.  We saw several of these a year ago, in December 2018.  They are common further north in the Bay, but extremely rare visitors in Lower South Bay.  Now here they are again.

As last year, some of these little shrimp are red, others have black stripes.  Presumably they are “Stimpson Coastal Shrimp” (Heptacarpus stimpsoni) or closely related species.


Heptacarpus shrimp in the Photarium.


Bonehead Sculpin.  This is another coastal oddball we have not seen since December 2018.  Like the Heptacarpus shrimp and Black-tailed Crangon, this one drifted in with higher salinity.


Decorator Crabs in Pond A21.  This was even more unexpected.  Decorator Crabs are rare in the deep parts of Lower South Bay.  It is unprecedented to see them all the way down in the Alviso Marsh Complex.

(BTW: They are called “Decorator” Crabs because of their habit of planting anemones, sponges, seaweed, and other materials on their backs for camouflage and protection.  They grow fairly large near the coast.)


Pacific Sardine.  This is the first time a Sardine has been caught in Lower South Bay.  However, they are occasionally caught a little further north in Midwater Trawls in South Bay.

Sardine populations along the West Coast crashed over the last decade.  This is unfortunate. Sardines are essential food for most of the marine mammals we like to see:

NOAA Fisheries reports that Pacific Sardine stocks are currently low, and commercial fishing of them is prohibited:


3. Shad Experiment.

Colorful Shad have been driving me crazy for months now.  As discussed in November and December, their dorsal colors seem to nearly always match ambient salinity.  This made me presume that their colors rapidly change in response to salinity.

American Shad and Threadfin Shad are very common and popular sport and forage fish across North America.  These color changes should be common knowledge.  Yet, I could not find any detailed documentation about this very visible Shad color phenomenon.


Summary of the four trials of the Shad Experiment.

On Sunday, January 12th, I conducted a Shad Experiment as we cruised from stations A19-4 through Coy1. 

Method:  24 American Shad were exposed to alternating salinities.

Equipment:  I used two buckets: one filled with freshwater, the other full of saltwater.  Shad were exposed to varying salinities in a white 6”x16” measuring tray.  A Nikon CoolPix A900 camera documented color changes and time duration.


Shad Experiment, Trial 3 start conditions: Aquamarine Blue Shad at 20 ppt (Ok, one was brownish!)

I am summarizing the results of trial #3 here.  Space does not allow the full series of photo-documentation for all trials in this blog post.

I Facebook posted results of the other trials a few weeks ago:

I also posted a short film of an American Shad undergoing the color change during Trial #4:


Shad Experiment, Trial 3 after freshwater treatment:  Aquamarine Blue Shad turned Brown!

In each of four trials, I found that it generally took about 3 minutes (plus or minus a minute) to turn shad from aquamarine blue to fully brown and vice-versa.


Shad Experiment, Trial 3, saltwater re-added:  Brown Shad turned Aquamarine Blue again!  Victory!!!

Turbidity.  Over the course of all four trials, ambient turbidity ranged from 32 to 183 NTU.  There was no correlation between Shad color and turbidity, e.g. aquamarine blue Shad were caught at station A19-4, and brown Shad were caught at UCoy1 where turbidity was roughly equal.


And, there you have it!  It takes about 3 minutes for an American Shad to make a full-color transition when exposed to appropriate salinity changes.  Threadfin Shad appear to go through the exact same transition, but too few Threadfins were available during the trials to establish a significant correlation.

The bigger question in my mind now:  How in the world do Shad easily tolerate salinity changes that would quickly kill most marine or freshwater organisms?  What a fish!


Dr. Lewis flashes a bemused smile.  Pat Crain drives on.

I would like to acknowledge and thank Pat Crain and Dr. Levi Lewis who respectively drove the boat and pulled the nets.  They also communicated significant verbal fish color lore as I conducted my experiment. I also thank Dr. Hobbs for his oversight & regulatory review.


To be continued.

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