Fish in the Bay – February/March 2022 Supplemental Report: Gobies, Shrimp, etc.

SF Bay fishes are very active in winter through spring.  Charismatic pelagic fishes like Longfin Smelt, Anchovies, Herring, Topsmelt, and Shad got a lot of attention last month.  Time and space did not permit discussion of all the important issues. …

Gobies, Shrimp, and a few other critters didn’t make it into the February blog, hence this supplemental report that combines some observations from February and early March.


The Goby Chart, 2014 to present.

For several years we recognized April as “Baby Fish Month.”  In April, hundreds to thousands of baby fishes typically show up.  They are tiny: roughly 10 to 20 mm in length.  Most are too small to identify to exact species, but we can see the basic goby shapes. For that reason, the babies are recorded in datasheets as “unidentified gobies.”

The vast majority of “Unidentified Gobies” are probably Yellowfins because there is a sharp spike in Yellowfin Goby counts around the same time of year.  However, other species are likely represented in April baby counts. 

Pregnant fishes in February and March are another line of evidence pointing to the identity of baby fishes in April. 


1. Pregnant fishes of February & March: Yellowfin Gobies.

Yellowfin Gobies.  The Yellowfin count was bit low in February and March: 86 and 90 respectively.  That is fairly typical for late winter.  Like all the other gobies, the Yellowfin population surges by summer until late fall and then appears to dip in winter.    

Cold temperatures trigger adult Yellowfins to swim downstream for the spawn.  Males prepare sheltered mating burrows as females swell with eggs.


Strictly speaking, to call these females “pregnant,” is a technical misuse of the word.  They are full of eggs, but the eggs are not fertile yet.  Each female seeks a suitable male and nest to deposit her eggs.  The male fertilizes and tends the eggs until hatch.  


Literature says that female gobies and sculpins glue their eggs to the roofs of the mating caves.  I believe the above photos are showing a slightly extended ovipositor. 


Literature also says that the Yellowfin Goby spawning season extends from winter through mid-summer.  However, here in LSB, we have only noticed ‘pregnant’ or ‘spent’ Yellowfins in the mid-to-late winter months leading up to April.      


2. Pregnant fishes: Arrow & Cheekspot Gobies.

Arrow Goby with eggs at Alv2 on March 6th

Arrow Gobies and Cheekspot Gobies also brood up with eggs in the months prior to Baby Fish Month.  They may make up another substantial portion of the baby fishes we see in April, albeit, we usually don’t catch as many of these small gobies compared to the larger Yellowfins, Shokihazes, and Shimo/Chameleons.  (We caught only 21 Arrow/Cheekspots in February and 86 in March.)


In March, many Arrow Gobies were ridiculously full of eggs.  At least 21 out of 24 Arrows at station Coy3 were so stuffed they looked like tadpoles.


Arrow Goby hatchery farm at Coy2 in March!


Same pregnant Arrow Gobies in the Photarium, Coy2, 6 March 2022.


A few Cheekspots were also pregnant at upstream stations.  However, none of the roughly 40 Cheekspots caught at deep Bay stations LSB1 and LSB2 showed any signs of eggs. 

Low salinity may trigger spawning in Cheekspot and Arrow Gobies.  For example, we counted a number of pregnant Cheekspots in Guadalupe Slough, immediately downstream from the Sunnyvale wastewater treatment plant in August and September 2021.  We have also observed pregnant Arrows at upstream Coyote stations in late fall months in both 2020 and 2021.  This is in contrast with Yellowfins and many of the pelagic fishes that only seem to spawn during or after the seasonal drop in temperature.


An increase in food availability (or quality) brought about by freshwater flushing might be the trigger that tells Arrows and Cheekspots the right time to spawn.   More observations are needed.


3. Pregnant fishes: Staghorn Sculpins.

Staghorn Sculpin.  We only spotted a few dozen pregnant female sculpins from December thru February.  The total catch was 8 in February which usually is a low month for Sculpin.  The count jumped to 37 in March. 

The March count included a few babies that confirmed that at least some Sculpin had spawned. That is not bad for March, but we were hoping for another blockbuster spawning year.  For comparison, we caught 2,401 Staghorns in March 2021.  

We still hope for an April Sculpin explosion, but the signs are looking kind of weak right now.   


4. Shimofuri & Chameleon Gobies (not pregnant) – an identification guide.

A mix of Shimos and Chameleons at LSB1 when salinity was 24 ppt on Feb 5th.

The Shimofuri/Chameleon Goby population explosion continues!  In February we counted 409 Shimo/Chameleons. In March we caught another 427!   The vast majority of these are Shimofuris. After July 2021, the Shimofuri for the first time surpassed the Yellowfin as our most numerous goby. 

Shimos are also our most recent goby invader.  They were first identified in SF Bay around year 2000 and arrived in Lower South Bay around a decade later.  Love them or hate them, the Shimo/Chameleons are now our #1 goby.

Know your new gobies!

  • Chameleon Gobies prefer to live in near marine salinity, at or above 22 ppt.
  • Shimofuri Gobies live in low salinity brackish waters farther upstream near creek and river mouths.

However, we occasionally find both Shimos and Chameleons that break the salinity rules.  Case in point: in the photo above, salinity was 24 ppt and Shimos and Chameleons appeared to be living happily together.  The Shimos were a little faded and milky-looking in this high salinity, but otherwise no worse for wear.    


How to distinguish Shimofuri from Chameleon Gobies:  The main key is the anal fin.

Lesson #1a: The anal fin of the Chameleon Goby is painted red, white, and black.   In addition, Chameleons have a white margin (edge) on both anal and second dorsal fins.  


The Chameleon Goby anal fin is painted like the flags of Yemen or Egypt.  (The flags of Syria, Iraq, and a few other countries are also red, white, and black, so this rule is very easy to remember!) 


Lesson #1b: Both the anal fin and the second dorsal of the Shimofuri Goby are painted black and orange like the flag of the Cincinnati Bengals.  (Also: San Francisco Giants or Baltimore Orioles for baseball fans.)  

Please note: The Shimo fins shown in these examples are a bit more pale than usual.  This was due to the high salinity at the time.


Shimo/Chameleon side-by-side comparison.


Another Shimo/Chameleon side-by-side comparison.


Shimofuri Goby showing spots under the jaw and over the throat.  

Lesson #2: Shimofuri Gobies have many tiny spots under the jaw.  Both Shimos and Chameleons have face spots on their ‘cheeks.’  The spots do not extend under the jaw and over the throat in Chameleons.


Lesson #3:  Do not rely on body color for identification.  Both Shimofuri and Chameleon Gobies can change body color from light tan to dark brown at will.  The color change can occur in less than 3 to 5 minutes in adult fish.  We have witnessed this color change many times.

  • Light tan with dark longitudinal stripes. We call this color scheme ‘watermelon’ because it is reminiscent of the stripes on a watermelon.  Juveniles of both species always wear the watermelon scheme. 
  • Dark brown with faint broad horizontal bands. When these gobies turn dark the pattern resembles ‘snakeskin’  Males of both species turn very dark to almost black when they defend burrows and guard their eggs.  (It appears that both males and females can darken to ‘snakeskin’ when they want to.)


Watermelon vs. Snakeskin Body Color: The left Shimo is showing ‘watermelon’ stripes.  The Shimo on the right has a slightly darker, almost ‘snakeskin’ body color.   


Lesson #4:  Epaulet (‘shoulder ornament’) color at the base pectoral fins vary from bright orange or yellow to no color in both species.  Bright and conspicuous epaulets are likely a sign of mating readiness.  Consequently, Chameleon Gobies tend to show bright epaulets most often when in near marine-level salinity.  Shimofuris show bright epaulets in lower brackish-level salinities.  In either case, context is key.

(It has also been proposed that Chameleons may possess some sort of distinguishing bump or structure at the base of the pectoral fins.  In both February and March, we performed several Shimo/Chameleon side-by-side examinations and failed to find this feature.  The structure might not be detectable under field conditions.)     


5. Critters that make tiny holes – Sphaeromatid Isopods

Sphaeromatid Isopods.  We found these Sphaeromatid Isopods in loose mud chunks at both Alv3 and Pond A19 stations in February. This was the first time we noticed them “in-situ” – huddled in their own mud burrow homes.  Strong rainwater flushing back in December might have dislodged these chunks.

Another Sphaeromatid ‘pillbug’ at Alv2 on March 6th.

Sphaeromatids.  The Sphaeromatid species we found this time are most likely Sphaeroma quoianum.  These natives of Australia and New Zealand were first identified in SF Bay in 1898. 


More Sphaeromatids in Pond A19 on 5 Feb.

Gnorimosphaeromatids. (Not shown here) Sometimes we find smaller brownish-looking pillbugs with a light tan stripe that may be native Gnorimosphaeroma oregonese, aka, “The Oregon Pillbug.” One of these presumed natives was photographed and blog-posted in January – see item #6: 


6. Critters that make bigger holes – Bat Rays.

Bat Ray holes on the mud bank at Art3 on February 6th.

Bat Rays.  We have not caught a Bat Ray since December.  Like the sharks, Bat Rays avoid Lower South Bay as the waters freshen from winter rains.  But, we still see many traces of their feeding activity on mud banks at low tide.


More Bat Ray holes near station Alv1 in Alviso Slough.

At both the mouth of Artesian Slough and in Alviso Slough, the banks are still pockmarked with Bat Ray craters.  Any critter that burrows in this mud is fair game to a young Bat Ray.

I imagine that Bat Rays feast on Pillbugs, Arrow Gobies, and young Simofuris in addition to all the other fish and bugs that live in these mudflats.


7. Shrimp Wars.

Berried Crangon at Coy4 on 5 Feb.

The Crangon shrimp situation continues to be grim. The numbers for February and March were 191 and 352 respectively.  By themselves, those counts are not so bad.  The Crangon catch usually dips in late winter. 

However, We should have seen hundreds to thousands of berried females from December through February.  Instead, we counted less than 100. 


More Berried Crangon at Coy3 in February.

To add to the Crangon troubles, late and unusually heavy rains in November and December may have impeded female brooders.  Kathy Hieb, Senior Marine Biologist at CDFW, reminded me that adult and berried Crangon do not tolerate salinity much less than 20 ppt. This is a bit ironic since the mission of each mama Crangon is to deliver her hatchlings as far upstream as possible so they can recruit in substantially fresher water. This may be a Crangon weakness that allows Palaemon shrimp to compete here. 

Crangon recruitment is strongly correlated with robust rainwater flushing.  But, we may have gotten too much beneficial rain early this season, and not enough of it in the later parts of last year and this year the Crangon perspective.   As of March, we saw some tiny Crangon recruits, but the numbers are still small and the competition from Palaemon shrimp looks intense at this point.


8. Harbor Seals.

The Calaveras Point Harbor Seals get redder as pupping season approaches.

Many of the seals develop rusty red coats from dissolved iron in the water here. 


Harbor Seals in South San Francisco Bay – 5 Feb 2022

This is the best time of year to catch them at max redness.   


A Harbor Seal watched us as we cruised down Alviso Slough on March 6th.


Some of the seals looked plump and possibly pregnant as we passed by Calaveras Point in March.


Lounging seals on March 6th.  We should see some pups in April.


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