Fish in the Bay – January 2020: The Longfin Chronicles, Part 3.

Longfin trawl results from January 2nd & 3rd.

Operation “Save Our Smelt” 2020/21, week three.  By this point, over 100 adult Longfin Smelt breeders had been safely delivered to the UC Davis Fish Conservation & Culture Lab (FCCL).  Weather was still cold, and Longfins were still abundant at all locations in Pond A21 and along the main stem of Lower Coyote Creek. 

A few notes about the 2/3 January trawls (see map above):

  • 138 Longfin Smelt were caught on Saturday and 287 on Sunday. Only roughly 40 of the biggest were kept.  The rest were released.
  • The UC Davis team did not trawl inside Pond A21. Low tides in early morning made the Pond too shallow for otter trawls.  Plus, there were more than enough Longfins in the main channel. 
  • Micah attempted one trawl in the deeper bay (trawl #16 on the 3rd). No Longfins were caught there.  Other trawls in the deep Bay also confirmed that there are few, if any, Longfins beyond the mouth of Coyote Creek.  Winter cold temperatures trigger Longfins to push upstream into the spawning marshes.  That is where we catch them now.


Zero-Dark-Thirty (again) at the Alviso docks.

As usual, we launched early to collect, and return with, breeding-age longfin adults by around noon.  But, we were not alone.  A steady stream of weekend anglers and duck hunters launched with us.


Another Hunt for Longfins.

Scenes from the Longfin hunt: Micah Bisson & Alex Scott trawling & prepping the collection tank.

Collection of Longfin Broodstock is the sole purpose of these additional December-thru-January trawls. 

Longfin Smelt are fragile fish.  Nets, tubs, and tanks must be rigged and managed to minimize stress.  We must catch healthy adults alive and unharmed.  The larger fish that are collected are held up to five hours in the portable collection tank for transport back to Alviso then pick up for delivery to the FCCL lab in Byron.  Upon arrival at the lab, they are tagged, a fin-clip is taken for genetic identification, and the smelt are introduced to their new home. 

We hope at the end of that stressful process that these fish will still be inclined to continue spawning in laboratory tanks.  So far, it’s working.  But, there are always at least a few losses.  We must always strive to reduce the losses. 


Alec examines Longfins in his dip net.

Every Longfin is precious now.  50 years ago, when Longfins were still common, people would beach seine and eat these tasty fish.  Now we assume that each spawning season could be the last.

Younger fish less than 80 mm standard length are gently returned to the marsh.  Smaller fish produce fewer eggs, so they are less desirable for lab rearing.  With luck, the young ones will survive and grow.  We can pick them up next year if they make it. 


Alec and Micah prepping tubs and tanks for another trawl.

Longfin Smelt like it cold. 14 degrees C (~ 57 degrees F) is the rule-of-thumb maximum comfort temperature for Longfins.  They can tolerate higher temps, but stress-level increases and survival rate decreases in warmer water. 

Temperature is Rule Number One!  Longfins are programmed to spawn when temperature drops.  Shad, English Sole, Crangon shrimp, and many other estuarine critters similarly time their spawning migrations to the change in seasons.  This makes December and January some of our busiest fish months.


All the other fishes. 

While Micah & Alex focus all their attention on careful management of Longfins.  I examine all the other fish and bugs: 


1. Northern Anchovies

A few big adult Blue-backs continue to be seen amongst each small horde of juvenile Anchovies.

Northern Anchovies. We continue to catch sea-going Blue-backed adults in addition to many, many post-larval, juvenile, and young adults.  These must represent at least two, somewhat distinct, Anchovy populations.


Blue-backs versus Green/Brown-backs.  Amongst juvenile and young adult Anchovies, we see both blues and greens of varying hues.  What proportion of these colors are attributable to genetics versus environment?   


Individual Anchovies slowly change color in response to salinity.  Like Shad, they “blue-up” in higher salinity and “brown-down” as water gets fresher.  However, some juvenile Anchovies seem to be either “hatched green,” or “hatched blue;” that is to say, the initial color at the crown of the head just after metamorphosis is either distinctly green or distinctly blue. 

Two populations??  From literature, we know that Anchovies around the world spawn both at sea (around 20 to 40 kilometers off the coast) and in estuarine marshes. 

  • Sea-going Northern Anchovies spawn in late winter through spring.
  • But, our local, in Bay, Anchovies spawn from summer until winter.
  • Biologist Carl Hubbs, in 1925, observed such stark differences in morphology (length and number of vertebrae) that he nominated the San Francisco Bay resident population as a separate species or sub-species.


Green Anchovy (top) and Blue Anchovy (bottom).  Trawl #10 on 3 January.  Salinity was 14.7 ppt.

Studies of Northern Anchovies, up and down the coast of California, indicate that sea-going and estuarine Anchovies may intermingle quite freely, but still establish genetically distinct populations from time to time.  I think this is influenced by prevailing weather conditions, like the current ‘La Nina’ that seems to be enhancing in-Bay recruitment right now.

(Levi Lewis sent me some recent Northern Anchovy papers. I skimmed a few, but have not fully absorbed them yet.)


Juvenile Anchovy – just after metamorphosis (I think!)

  • Newly hatched Northern Anchovies metamorphosize to juveniles at around 60 to 75 days. The translucent 35 mm-long juvenile, shown above, has just graduated from larval stage.  Clearly, tiny ones like this are the progeny of Anchovies that spawned in warm marshes by late fall.  (The cold-snap on 6-8 November probably terminated the summer-fall Anchovy spawn.)
  • Big Blue-backs swam into the Bay after the winter cold-snap. I would guess that they do not like warm Bay water, but who knows?
  • Mixed blue and green juveniles and young adults could represent a mingling of sea-going and estaurine Anchovy populations.
  • Genetic or otolith studies could solve this riddle pretty quickly!


The Summer Spawn.  Good News!  Anchovy babies continue to recruit.  Contrary to my dismal expectations, baby Anchovies seem to be thriving this winter.  Unlike many other species in LSB, Anchovies don’t suffer when rain is scarce.  They appear to be increasing in size and numbers every week. 

What can we learn from visual inspection?

  1. The bunch of babies shown above were “hatched green.” Green chromatophores are already visible behind the eyes and at the crowns.
  2. Redness in the gill area of many of these young juveniles could be normal development. On the other hand, as noted last week, one literature source indicated that redness “in the brain and dorso-cranial musculature” of captive herring was caused by B-vitamin deficiency.  See p. 185:
  3. Mysids are excellent food for fingerling fish. These Anchovy babies are still too small to eat mysids, but it is good to see that food will be available as they grow. 
  4. Parasites! A small Cymothoid Isopod parasite crawled out of one of these baby’s gills.  (I call them “devil bugs” because their tails look like devil horns.)  I have more to say about this particular parasite in another post.


More Anchovy babies and another “Sea Louse” (copepod parasite).

Sea Lice!  We continue to find a few sea lice attached to young Anchovies.  These pests live here!


Anchovy and Sea Louse closeup.


2. More lurking predators.

Side-scan sonar detected three more big fish on Saturday.  The first two could have been either Sturgeon or Leopard Shark.  The third was definitely a Sturgeon. 


Striped Bass at Trawl #4 on Saturday.  Many Longfin Smelt and/or Anchovies could fit in that fat belly!


3. Shad colors and silvery Pearl Essence.

Two Threadfin Shad (above) & two American Shad (below).  Trawl 5, at mouth of Mud Slough.

Threadfin & American Shad.  Pelagic fishes have silvery sides.  This reflective “cloak of invisibility” makes them hard to see by predators from aside and below. Both the silver sides and color-changing top are composed of thin layers of guanine crystals. 

Guanine extracts from fish and guano have been used in cosmetics for centuries.  It is likely that you are wearing some of this “pearl essence” on your skin, or in your hair, now:      


The dorsal sides of both American and Threadfin Shad change in response to salinity, but Threadfins have an extra layer of silver that makes this harder to see. 



Brown Shad, Trawl #17 near station Coy2 on 3 January.

Brown Shad.  We picked up a bunch of American and Threadfin Shad from Trawl #17 near Station Coy2 (just downstream of the railroad bridge).  The Shad were brown due to low salinity (8 ppt) just after slack low tide. 

After we refreshed water in the measuring tray, we quickly realized that we had last refilled our bucket at a previous trawl location far downstream in saltier water.  The Shad were turning green!


Green Shad.  The shad miraculously “greened-up” upon addition of saltier water!

Salinity in the bucket was 17.4 ppt – well into the green-Shad range.  I held these fish a few extra minutes to again demonstrate the color-changing power of the Shad!  In this instance, the change took less than 7 minutes.  We released them shortly after they turned green.

Also note:  Low salinity at station Coy2 was a bit of a surprise.  There had been no significant rain.  I am guessing that water releases at Anderson Dam are freshening this stretch of Coyote Creek.   


American Shad & Threadfin Shad in the Photarium.

Chaff – the ultimate defense.  In addition to mirror-sides and color-changing top, Shad, and most other Clupeiforms, like Anchovy, Herring, and Sardine, have an extra level of camouflage defense: Under duress, they slough off shiny scales to produce a cloud of glitter to confuse predators.


4. Shrimp Wars.

A mix of Crangon and Palaemon Shrimp.

Crangon Shrimp numbers are increasing but continue to be low. We are now catching dozens per trawl rather than handfuls.  Nonetheless, by this time of year, we should be seeing thousands of berried females.


Cold temperatures trigger female Crangon to swim upstream to deposit eggs.  Many Crangon show developing egg masses, but berried females are still few and far between.  Why are we seeing so few? 

I hope the Crangon are waiting for the big atmospheric river and low salinity to tell them to deliver their eggy broods, Otherwise, this will be a very bad year for Crangon franciscorum!


Blue-spot Crangon (Crangon nigromaculata).  Perhaps 20 to 30 percent of all Crangon we have been catching are the Blue-spot variety.  Blue-spot Crangon are the coastal/marine species,  Usually, we see very few of them in Lower South Bay.  In this salty year, they are a sizable presence.

Note: Technically, the scientific name of these shrimp is “black-spot” Crangon.  However, the spots are blue.  I call them “blue spots.”


5. Plainfin Midshipman (aka Singing Toadfish)

Plainfin Midshipman.  Every year we catch a few to several of these “glow-in-the-dark” toadfish.  Those we catch are always young and small; this is primarily a coastal species. 

This one, shown above, was bigger than usual.  You can see multiple long chains of tiny dots over his head, along his back and sides, under his jaw and belly, and along his tail.  Every one of those dots (over 700 of them) are light-emitting-photophores!”  The fish lights up to hunt prey, to camouflage itself, and possibly to attract mates.  


Another Plainfin Midshipmen!  The following day, 3 January, we caught a slightly bigger Midshipman at our first trawl before dawn.  You may recall that Plainfin Midshipmen don’t just light up, they also sing!  The “Type 1” males sing for up to 2-hours to find a mate. 

Plainfin Midshipman video from Elkhorn Slough here:


Another busy day at Alviso Docks.

We returned at noon.  Duck hunters were also returning.  Sturgeon anglers were still heading out.


Alviso Yacht Club and diving ducks.

A small mixed flock of GoldenEye, Bufflehead, and Ruddy Ducks loafed in the shadow of the Alviso Yacht Clubhouse.  This is their safe-zone.  They risk getting shot almost anywhere else. 


Alec secures the boat as we wait for FCCL to arrive for Longfin pickup.


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