Fish in the Bay – March 2019, UC Davis Trawls – Fish & bug New Year?

March fish report:  Atmospheric rivers and freshwater flushing continue to influence critters in the Bay.  I am coming to the conclusion that fish and bug New Year in Lower South San Francisco Bay begins a few months after our perihelion-centered calendar.  You be the judge.

Station map.
The start of another trawling day.  L-to-R:  Pat Crane, Levi Lewis, Me, Jim Hobbs.

Bay-side Station trawling results.

Upstream of Railroad Bridge.

Fresh!  The waters were unbelievably fresh! (at least by modern standards).  Freshness at or below 1.0 ppt is indicated in blue font in tables above.  My spotty monthly trawl records indicate that it was WAY FRESHER this year than in early 2018.  This year’s freshness AT LEAST rivals the 2017 February Freshwater Flush. 

Cold!  It was still pretty cold.  Longfin Smelt spawn at around 12 degrees C so we continued to be within the Longfin spawning envelope at several stations.  (Last year, temperatures were 14 to 16 degrees C across the board by this time.)  It is looking very good for Longfins here!

Numerous midgenados over Coyote Creek marshes.

Bugnados / Midgenados!  (Jim Hobbs took this photo the following week, on Sunday, March 17th.)  This is what I called midge “Bugnados,” but Jim Hobbs likes to call “Midgenados.”  Either term is fine.  Midgenado is more precise. 

More rain = more midgenados.  Midgenados are more common and intense after wet weather.  Rainstorms cause Bug storms!

Midgenados are whirling cyclones of mating adult midges.  Hatched as mosquito-like larvae in the marsh, they metamorphosize into non-biting mosquito-like adults (some midge species bite, these don’t). Imagine all the tiny fish, bugs, and birds that feed off these things!  Most midges get eaten before they take flight.  We only see the rare survivors – the tip of the Bug-berg so to speak.  They represent smoke from the marsh’s carbon-cycling furnace in a symbolic sort of way.


1. Fish Status

Threadfin Shad & American Shad

Threadfin Shad and American Shad.  The bluish fish at top is a jumbo-sized threadfin shad.  5-inch length is big for an adult Threadfin.  This one is huge!

  • We see lots of young American Shad but only a few mid-sized adults. Youngsters don’t seem to migrate out to sea like they do on the East Coast.  Why does this beautiful fish have an altered life-cycle here?
  • I am increasingly seeing non-native shad as extremely useful as upper-tier carbon-cyclers (my non-scientific term) in local creeks and rivers now that many native species are gone.

LONGFIN SMELT SPAWNING!!!  A full-bodied adult female is shown at top.  She was dropping eggs as we examined her!!!  The male beneath looks hollow-bellied and has a long anal fan for fanning his milt over the eggs. 

It could be random chance that these two were collected together. But face it, what are the odds of catching a sexually ready male and female in the same net?!?!?  I think this was a pair!  Alv1 is a Longfin spawning place!  

Male Longfin

LONGFIN MALE from photo further above.  This male looks exactly like a milting male I photographed last month at Ucoy1!  See how the ventral and anal fins are splayed out in sort of a squishy fused surface.  And, he’s kind of slimy on the bottom.  I think he may be in milting mode. 

Editor’s Note:  A few years ago, Richard Santos, a life-long Alviso resident, community leader, Korean War veteran, and Director of Santa Clara Valley Water District (,  told some of us his memory, as a kid in the 1940s, that there were smelt in the slough near the town of Alviso.  The story always stuck with me.  I do not know if the smelt Richard remembers were Topsmelt or Longfin smelt, but I have long hoped we would find some kind of smelt here.SUCCESS – Longfins are back!

Longfin Smelt caught at station Coy4

Longfins staging downstream.  13 Longfins were caught downstream from Alviso Slough at station Coy4:  6 adult females, one adult male, and six too young to be sexed by eye.

  • It appears that males advance upstream to spawning locations first, possibly staking out a territory or nesting spot.  When ready, females then run upstream to drop eggs near the most attractive male candidates.
  • If this Longfin mating scenario is correct, then finding groups of Longfins segregated by sex (predominantly females downstream, males at upstream locations) would indicate of spawning preparation.
  • Ponder this:  Why do some creatures, like Longfins and Crangon shrimp, adapt a strategy of swimming upstream to drop eggs then scoot back to salty water as quick as they can?  They are hatched in fresh water.  They adapt to salt water as they grow.  Evidently, they do not like freshwater as adults; maybe can’t even tolerate it.  What’s up with that? 
Larval Longfins and other larval fish collected at Ucoy stations on 10 March.

Jim Hobbs took the above photo of Clarke-Bumpus net contents the following day, 10 March.  Amongst the various larval fish at UCoy stations, many were clearly Longfin Smelt.

Levi Lewis and a California Halibut.  

California Halibut.  Levi Lewis is showing off our first Halibut of the year.  This is a monster for Lower South Bay: 430mm (17 inches) standard length.  This one was still below the 22-inch total length limit, but this is the biggest we’ve seen here. 

I presume that halibut will continue to be rare catches for us.  You can see in the Fish Matrix Table below that young Halibut were common in dry years but have become quite rare since winters became wet again. 

California Tonguefish.

California Tonguefish.  Tonguefish is the other dry-year-loving flat fish.  These also became very rare after wet winters. The three caught this March are the smallest I have seen: little baby tonguefish. 

Top:  Speckled Sanddab, Striped Bass, & two Yellowfin Gobies.  Bottom, pregnant Yellowfin Goby.

Typical winter-time catch farther out in the Bay.  Above photo shows of the fish from station LSB1:  Striped Bass, Speckled Sanddab and two Yellowfin Gobies.  Lower photo shows a pregnant Yellowfin Goby.

  • Some Yellowfin Gobies appear to be in spawning mode.  All look long and skinny.  Many have pregnancy pot-bellies.  They also tend to look a little ragged.  Yellowfins prefer warmer weather.
  • Yellowfin Gobies are noxious invaders that take up space, steal resources, or eat the young of other types of fish we would rather see.  But, I doubt we can affect the outcome of this fish war; not with what little we know today.
Fish X-rays:  Northern Anchovy & White Croaker.

Northern Anchovy and White Croaker. These were the only representatives of each species in March.  Both fish appear to have recently grown into their adult form following metamorphosis. 

White Croaker is also special for being one of only 7 caught in all UC Davis / Hobbs Lab trawls since 2010.  Comparable trawls here from late-1981 through 1986 caught 69 of them.  Why did they leave?  Is Lower South Bay better or worse for their absence?

WARNING!  DISTURBING IMAGE BELOW!  Some people may find images of English Sole being eaten alive by parasites unsettling.  If you consider yourself one of those people, please skip to the next photo.

English Sole showing parasite damage.

English Sole infested with parasites.  I have said it before, English Sole have a lot of parasites (see Fish in the Bay, Parasite Paradise edition).  This poor little guy is eaten alive by at least two kinds of worms, maybe three or four!  Why English Sole?  Why now?  

  • I don’t think English Sole parasites are exacerbated by pollution or other human-induced stressors.  However, we will never know if no one ever examines this issue.  And, I don’t think I have the time. 
  • Let’s move on for now.

Shokihaze Gobies.  We saw lots of Shokihaze and Shimofuri babies in January.  These little guys have been growing up ever since.  They are just as invasive but maybe a little less noxious than Yellowfin Gobies.  But they are very cute, and that counts for something.

Arrow Goby?  This is either an Arrow or a Cheekspot Goby recorded as an Arrow.  Both Arrow and Cheekspot Gobies are native.  Both grow to about 2.5 inches.  I am not sure that the dark black patch on the operculum is unique to the Cheekspot.  We do not attempt to distinguish the two in the field because it is simply too hard to do under given workload and time constraints. 

There are still few, if any, good photos of these tiny gobies. I will fix that!

Arrow goby info: 

Cheekspot Goby info:

Fish & Bug Matrix.  Above is the updated table of raw fish counts from UC Davis/Hobbs Lab trawls 2015 to present.  I added more fish species plus shrimp and Corbula clams in the right columns.

  • With over four years of robust data, we can now see some fairly strong correlations between dry years (2015-2016) and wet years (2017-present).  Some fish like it dry, others like it fresh.  Use this table to draw your own conclusions.
  • We are a shrimp farm!  We raise far more shrimp than fish here.  Nonetheless, I did not expect the shrimp explosion that we saw in 2018.  Both Crangon and Exopalaemon populations increased several fold in response to abundant rain.  So far, Palaemon shrimp don’t seem to be as strongly affected by climate changes. But, see how the Crangon vacate the premises almost every February or March? 
  • Did something in 2016 disrupt the Crangon cycle?  See? — Now you are thinking like a shrimp farmer!

2. Shrimp Farm

Crangon franciscorum shrimp with eggs.

Crangon franciscorum.  (aka. Bay Shrimp or Grass Shrimp) The photo shows two Crangon females, all egged up with nowhere to go. (A Shokihaze Goby and part of a Palaemon shrimp are also visible.)  A few Crangon caught in the middle of LSB were berried (bearing eggs) even though it is now very late in the Crangon brooding season.  Crangon numbers have dropped from over 10,000 in January, to 1200 in February, and now only 27 in March.  It is now past time for adult females to retreat back to salty water.

I assume these females got caught short: they want to swim upstream to hatch out their larvae, but the lower Bay and creeks are now too fresh.  These girls might be out of luck.

Several Palaemon from LSB.  A female at top left has eggs.  The yellowish mass behind the heads of some shrimp may be growing egg masses.

Palaemon macrodactylus.  Most of the Palaemon looked uncharacteristically clear-bodied in March.  I suspect it has to do with the low salinity.

Palaemon shrimp tolerate a wider range of salinity but not necessarily strong freshwater flushing.  Vazquez et al. (2016) found that adult P. macrodactylus tolerates salinities from 34 ppt down to 2 ppt.  However, reproductive success and larval survival is increasingly impaired below 5 ppt. 

Palaemon macrodactylus, berried female, two views.

Palaemon macrodactylus movie here shows how at least two pair of chelate legs aid in feeding and grooming: 


Tomato Palaemon?  In past years, some Palaemon got redder and display larger chelated legs up front.  (I called them “Tomato Palaemon.)  Traces of redness can be seen this year, but the trend is not as evident, at least not yet.  Maybe low salinity explains why most of these look uncharacteristically translucent?   

Classic Tomato Palaemon with eggs.

Palaemon – a Red-dragon Queen!   This female with eggs looks more like the classic winter-time “Tomato Palaemon.”  We caught her at station Coy2 where salinity was 1.4 ppt.  So, she should be in serious trouble.  She can survive this low salinity for a few days to a week, but her eggs and young will likely suffer.

  • I do not know if all adult Palaemon turn red and grow large chelated arms.  This could be a feature of older females.  Maybe, like lobsters, large mature females battle for prized brood release spots. 
  • It occurs to me that larger redder ones might migrate farther out in the Bay, like Crangon.  This could explain why I don’t see so many big-armed, tomato-red Palaemon in summer.  
Palaemon with eggs, but not red.

Palaemon female – not red.  This female was also caught at station Coy2. She has eggs, but no redness at all.  Is she younger?  Could she be a different species of Palaemon?  If she and the Red-dragon Queen were to fight, which would win?

I wonder if all our Palaemon are macrodactylus versus another species.  There are now four non-native Palaemon species in the Bay and Delta, two of which I have not yet seen:

  • Palaemon carinicauda, introduced to the Delta and San Joaquin River.
  • Palaemon kadiakenisis, aka. Mississippi Grass Shrimp.
  • Palaemon macrodactylus, shown in photos above, and
  • Palaemon modestus, aka. Exopalaemon modestus shown and discussed farther below. 

It is always possible that some new shrimp invader may show up at any time.

Palaemon macrodactylus

More clear-bodied Palaemon.  Three of the four shown above are berried females.  The little one at top left is smaller and clearer.  Is that little one a male?  Or, is it a younger year class?  I hope to figure this out.

Two Exopalaemon modestus (aka, Palaemon modestus).

Exopalaemon modestus.  “Exos” (aka. Siberian Prawns) always look clear bodied.  These are much more freshwater tolerant and tend to stay near fresher creek outlets. 

ATTENTION: “A recent revision of the genus Palaemon and its relatives has moved shrimps of the genus Exopalaemon back into the genus Palaemon. See de Grave and Ashelby (2013).” 

  • Palaemon modestus (Exos) are not really prawns!  Both Palaemon macrodactylus and Palaemon modestus are caridean SHRIMP, not prawns!   
  • HOWEVER, We will continue to refer to “Palaemon modestus” as Exopalaemon and “Exos” both out of habit and because years of data sheets list them that way. 

Exopalaemon Population Explosion.  Exopalaemon are a new invader here.  First sighting in Lower South Bay was in 2012, albeit they were found at North Bay locations since around year 2000. 

2018 was an Exo blowout.  The Exo population surged, reaching “Peak Exo” in September.  Fortunately, Exo-decline after September brought numbers back down a bit.  But, we may be looking at a much higher Exo baseline population from here on out.  Is that a good thing?  Or, a bad thing? 

3. Other Bugs & a couple of ducks.

Mollusk Watch.  We often see Corbula clams and Eastern Mud Snails because they live on the surface of the slough bottoms.  The other types shown here are less commonly caught. 

  1. Editor’s Comment:  If you are very interested in the history of SF Bay invertebrate invasions, I highly recommend you skim through J.T, Carlton (1977) “Introduced Invertebrates of San Francisco Bay:” 
  2. Another Good benthic critter history and overview here: Nichols et al. (1988) “Ecology of the Soft-bottom Benthos of San Francisco Bay …”  (Some discussion about pollution has been overtaken by decades of improvements to wastewater treatment and pollution prevention since the 1980s, but we are never completely out of the woods.) 

Ribbed Mussel (or Ribbed Horsemussel): Also see: 

Corbicula fluminea (or Asian Clam)

California Horn Snail (Cerithideopsis californica) CALIFORNIA NATIVE. I have long searched for a definite native benthic species – finally found one! These live higher in marsh or mudflats.  They eat diatoms and possibly cyanobacteria too.

Macoma balthica / Macoma petalum (or Atlantic petalum).  Adult Macoma live deep in the mud, so we almost never see a live adult from Otter trawls.  But, we seem to be seeing baby Macoma more frequently over the past year or two.  We THINK this clam could be native or a native hybrid.  But, the Cal-NEMO data base, and many other sources tell us that we really don’t know its origin very well.  It is probably NOT native. 

Corbula Amurensis (or Potamocorbula, or Amur River Clam, or Oberbite Clam) This is the life-sucking demon of Suisun Bay and the lower Delta.  We have them here too, but local conditions and maybe a lot of diving ducks seem to keep them in check.  also see: 

Eastern mud snail (Ilanassa obsoleta): 

  • Eastern Mud Snails out-compete native California Horn Snails.  Horn Snails persist in high salinity or other areas not favorable to Eastern Mud Snails:  
  • Also note: we collected three or four very colorful and clean looking mud snails (see right-side inset).  Freshwater may have cleaned up these normally pitch black and mucky snails.  Or, these may be another type of snail I don’t recognize.
  • Mud Snails of all types harbor worm-like Trematode parasites.  The Trematodes live as larvae in the snails, then parasitize birds and fish that eat the snail.  Some species of trematode parasites also cause “Swimmers Itch” in humans. – DON’T EAT RAW MUD SNAILS!
Surf Scoters to the rescue!

Surf Scoters (Clam & Snail Control) SF Bay is a winter-feeding ground for scoters.  They continued to be abundant far out in the main part of LSB as of early March.  These are some of the voracious clam, worm, and benthic bug eating ducks that, keep our Corbula clams and Eastern Mud Snails in check. 

The left-side photo was posted by Zuo Qiao Qiao on the “Bay Area Birding and Wildlife” Facebook page.  I added it here because it captured a scoter grabbing a clam.  Even with photographic evidence, I continue to wonder how scoters break and digest a clam shell like that. 

Scaup: another type of diving duck.

Lesser Scaup (aka. Bluebills, or Blueys to hunters because of their blue-gray bills).  I think these are Lesser Scaup, but I am not good at distinguishing Lesser from Greater Scaup.  Either way, drakes have black heads.  Hens have a white patch behind the bill.

This group was paddling around Alviso Boat Dock as we pulled up in the morning.  These are more soldiers in the Great Duck Army that protects everything else in the Bay from becoming clam and snail food.  Sadly, they too will be flying north again very soon.       

Dungeness Crab

Dungeness Crab.  This is another rare one for us.  Each year we see a few Dungeness Crabs in LSB.  This is the first I have photographed. 

  • Dungeness Crabs are clam eaters that could be consuming Corbula if we had more of them here.  See Jan Thompson’s “Corbula Conceptual Model” (2010), among other sources,
  • I believe this is a male due to the narrow abdominal flap.  In female crabs, the abdominal flap is broader and rounder in shape.
  • Also, I am sorry to say, he lost a claw while I was handling him (gently, I thought).  The claw should grow back at next molt.  I will be more careful in the future.
Orange-striped Green Anemone.

Orange-striped Green Anemone.  (Diadumene lineata – I think).  We spotted these little anemones at LSB2 in January and March.  I am pretty sure these are invasive Orange-striped Green Anemone or something closely related.  The guide book says they can’t tolerate low salinity below 12 ppt.  If true, freshwater flushing keeps them away from Lower South Bay.   This anemone has also invaded Hawaii:

Tunicates (aka. Sea Grapes) planted on an old piece of oyster shell.

Tunicates and Ctenophores; two things we are not seeing so much this season. (Ctenophores not  shown: We did not see any!)

In past years, large numbers of filter-feeding tunicates and ctenophores (comb jellies) arrived around December or January.  Both seem to bloom like crazy under cold enough conditions.  They always disappeared by summer. 

This year and the previous one, tunicates have tapered off a little and Ctenophores have practically disappeared.  I am assuming extreme freshness is clobbering them.  (Having said that, these particular tunicates, though few, look robust.  Maybe their bloom is just starting now?

Red Algae Watch.  Red Gracilara and Cryptopleura are getting thin but have not disappeared.  The collage above compares red algae collected in January versus March trawls.  Red algae of at least three types have become more abundant each year around November, since 2016.  But these “red non-plants” ( ) decline or disappear in winter.  The winter decline is probably due to less sunlight, cold temperatures, and a lot of fresh water.

I think these red algae species are thought to be universally good in an eco-system like this.  A red algae expert is encouraged to correct me if I am wrong.  As near as I can tell from internet search, they might be native.

4. Herring Alert.

Inland Silverside (top) & Pacific Herring (bottom two).  We caught this trio in Pond A21.  The two baby Herring are more interesting.  Around every March we hope to see results of a good Herring spawn each year.

Bad News: As of the March weekend, it was not looking too good: only 33 Pacific Herring so far in 2019 – see Fish & Bug Matrix far above. 

Juvenile and larval Pacific Herring later in March.

Good News:  Larval Trawls this past weekend, 23-24 March, collected a lot of larval and juvenile Herring.  Hopefully, these will also show up in April Otter Trawls next month.

We got the rain.  Now, pray for Herring!

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