Fish in the Bay – July 2019, UC Davis Trawls – Brown-back Anchovies and Bat Rays

It was another mixed-up weekend in July owing to extreme summer tides and some rough afternoon weather that preempted trawling station LSB2 on Sunday.

The other mixed-up event is the recent departure of Dr. Hobbs from UC Davis to an Associate Research Scientist position with Calif Dept of Wildlife in Stockton.

Good news:  I am so happy that Jim finally found financial and professional stability in this career move away from the perils of soft money contracts to support his under-appreciated efforts to save the world.

Bad news:  The long-term future of Jim’s important survey work could be jeopardized in his absence.  The monthly trawls in Lower South Bay since 2010 have been held together by Jim’s strenuous dedication and personal sacrifice.  There is no institutional driver to maintain this continuous biological record in the most urbanized corner of San Francisco Bay.  A steady succession of scientists of Jim’s caliber must continually step in to fill the leadership role in securing contracts to sustain this project.

Human life is short.  Everyone must earn a living at some point.  Who is going to keep counting these fish and bugs? (Other than, perhaps, the Emperor of Japan?  – see section 6, “Know your Gobies and Sculpins,” far below.)

Hopefully, UC Davis, the various funding agencies, and future generations of fish scientists will continue to recognize LSB trawl data as a project worth sustaining.


Trawl map.


Bay-side station trawling results.


Upstream of Railroad Bridge.


A slightly fresh summer season:  Salinity continues to be a little low for this time of year owing to the late-spring rains.  The PPT range is still in the single digits at most stations upstream of the Bay.  The late-season freshness has boosted the catch of Prickly Sculpin well into summer.

The freshness seems to be doing good things for Crangon shrimp as well.


1. Marsh Growth and “Blue Carbon.”

Mud chunks falling off the levee. As in previous months, some of these chunks were very fresh, indicating active erosion on the west bank, just downstream of Alviso.  This natural process may eventually wear down the old salt pond levee between the Pond A8 Complex and Alviso Slough.  New marsh should fill in the adjacent pond on the other side of the levee.  From that point on, the marsh will rise with sea level.

The active colony of Alkali Bulrush and similar marsh plants continue to add new dirt to this low un-engineered levee top via a process of carbon sequestrated growth, death, and decay.  In other words, these fresh mud chunks may be comprised largely of atmospheric carbon pulled into plant tissue in prior years. Blue Carbon!  (

This is a big question in my mind:  How much of this local marsh sediment accumulation is “allochithonous” versus “autochthonous?” Sorry for the big words.  You need them for a quick google search of papers on the topic.  With respect to sediment:

  1. Allochithonous: formed in the region where found. … as oppose to …
  2. Autochthonous: composed largely of organic debris moved far from the place where the base organisms lived

The Alviso Marsh Complex receives a lot of sediment via Guadalupe River, Coyote Creek, and other local creeks, and often even more from Northern California via the Delta.  But, local marsh plants contribute quite a lot of carbon themselves.  There appears to be a lot more marsh growth here than can be explained by “autochithonous” sediment accumulation alone!

For now, I am trying to figure out a way to track this progress, … one mud chunk at a time.


Dr. Hobbs with chunks of Bryozoan.

Bryozoan chunks. Dr. Hobbs pulled up these unusually large Bryozoan colonies at Station Alv1.  Tiny Bryozoan animals and their bushy colonies (in the deep Bay we seen encrusting types) are analogous to coral.  Bryozoans may be a potent filter-feeding force in these sloughs.   Like coral, their skeletons are comprised of calcium carbonate, so they are yet another random potential source of Blue Carbon!

For new readers, Bryozoans are explained here:



East bank of Alviso Slough.

Spur and Groove formation.  As mentioned before:  Dr. Lewis told me this grooved bank (Alviso Slough east bank) is analogous to a “Spur and Groove” (SAG) formation in coral reefs. (

This Rogers et al. (2013) paper explores wave-driven hydrodynamics that shape spurs and grooves in coral reef formation.

A 1998 book “Issues in Environmental Geology: A British Perspective” mentions spur and groove” with respect to an estuarine marsh edge in Wales:  “… one of two distinct marsh edge morphologies: [1] a clifflet (≤ m high) [where wave energy is low, but still close to the main tidal channel], or [2] a ramp of erosional mounds … with spur and grove topography running at approximately right angles to the marsh edge [along coastal stretches exposed to greater wave energy].”   (See p.350 –

So, YES, it is appropriate to refer to this particular salt marsh topography as “Spur and Groove!”. 


2. Shrimp Watch.

Palaemon shrimp: red versus tan.

Palaemon shrimp.  Good news!  Non-native Palaemon and Exopalaemon shrimp populations are not exploding even as native Crangon proliferate.  (Albeit, Exopalaemon have expanded dramatically since introduction here around 2012.  But, they are still minor players in the shrimp war here.)

Red Palaemon.  I continue to puzzle over why we always find a few red Palaemons amongst the tan ones.  Until this year, I figured that red Palaemon must be more sexually mature (they tend to be large), or perhaps the red ones are acclimated to saltier water or diet.  But, in this example, a small red pregnant Palaemon was caught in fresher water.  Then, immediately downstream, much bigger tan Palaemons were found downstream, some pregnant, some not.   (BTW: Both Palaemon above show 10 serrations on the rostrum, ±1, so they should be the same species. … Is redness a random mutation?)

(BTW: I seem to be seeing more Sphaeromatidae isopods this year, as shown above, probably owing to the abundant rains.   But, we don’t actually keep a count of these little pill bugs.)


Baby Crangon from Coy3.

Crangon! The really good news is that native Crangon shrimp (C. franciscorum) are back up again.  6087 baby Crangon were caught in this July’s trawls (notwithstanding having no trawl in LSB2) compared to 2405 Crangon in July 2018.

What you don’t see in the raw numbers is that all of our July Crangon were young-of-year.  These are the progeny of the Great Crangon Brooding Event from roughly Dec 2018-March 2019.


Shrimp graph from Hobbs’ raw data.

Shrimp trends.  I graphed 4.5 years of Hobbs’ shrimp data above to show the raw numbers caught of native Crangon versus non-native Palaemon and Exos.

In the dry years 2015 and 2016, Palaemon almost always outnumbered native Crangon. Then huge rains and flooding hit us in February 2017.  From February through April 2017, only one (1) Crangon was caught in Hobbs’ trawls!  At that time, it made me think that rains and freshwater were bad for Crangon.

But such was not the case!  Consistent with abundant Crangon literature, and not apparent to me at the time, the rains helped Crangon recruitment.  Crangon rebounded.  2000 were caught in October 2017.  Then the population bounced back big; peaking to almost 18,000 in August 2018 despite good, but not great, rains that year.

Crangon – 3rd population bounce?  I hesitate to go out on a limb to predict that we should see huge Crangon catches the next few months.  The past winter’s brooding was huge, the spring rain was right, and we just caught 6087 Crangon babies in July.  Let’s pray for the biggest Crangon bounce ever!


3. Snail Watch?

Eastern Mud Snails massed at Alv3.

Eastern Mud Snails continue to congregate on the west bank at station Alv3.  They are commonly caught at all downstream stations, but this station is their favorite place, by far.

This is at the terminus of the Guadalupe River.  The downstream end of creeks and rivers are where sediment and nutrient laden debris tend to drop out of suspension, hence Alv3 and UCoy2 tend to be snail, corbula clam, and/or Exopalaemon shrimp hot spots.


4. Anchovies! Have Brown-backs returned?

We saw lots of golden greenish Anchovies on Sunday.  However, the color has faded away to the point that I want to call many of them “Brown-backs.”  I think these may be second-generation descended from ocean-going Green-backs.  Or maybe these individuals did come in from the ocean, but have been living in the Bay or marshes for a long time now.


These look like Brown-backs, but there is just enough green in them to throw me off.

The Anchovy Story – from anecdotal photo evidence:

2016 was a huge Anchovy year according to Hobbs’ trawl data:  8089 caught in 2016 versus little more than 3,000 in any other recent year.  2016 was also the last year we saw large numbers of uniformly Brown-backed Anchovies in the marshes.

2017-2018. Anchovies got clobbered by the Freshwater Flush of February 2017 (like Crangon).  The local Anchovy populations did not bounce back the following summer as salinity rose (unlike Crangon).  Even worse, our native brown-backs practically disappeared.  We were eventually invaded by ocean-going (my guess) green-backs and blue-backs.  The following year, there was a cohort of Golden Green-backs at several Lower Coyote Creek stations in the summer months of 2018, but no true brown-backs.

In May and June 2019, I saw many golden Anchovies with traces of green, but basically golden-backed.  And now this: Clear to pinkish brown-backs with just the smallest trace of green or gold.   My personal suspicion is that some portion of ocean-going Green-backs became year-round-residents here.  Water here is fresher, warmer, and much more turbid than ocean water.  Those factors alone influence Anchovy growth rate and color development.  An added likely factor is predation which probably culls the most colorful Anchovies out of the local gene pool.

And Voila, two years later our native Brown-back population appears to be reestablishing from ocean-going Green-back stock.  Admittedly, 2019 Anchovies do not appear short and stocky, like true brown backs.  Maybe we just need another year or two?



Green-backs continue to invade our Alviso Marsh brown-back territory and probably always will unless or until the Brown-back population reestablishes.

Recall that Hubbs (1925) reported that the Anchovy Green-back / Brown-back boundary was near Sausalito!  That suggests that we still have a huge Brown-back deficit.


Pile of Anchovies covered in Bat Ray slime from Pond A21.

Brown-backs!?!?!?   To a casual observer, these appear to be brown-backs.  But in each individual, close examination revealed a trace signature of green-back lineage.


Brown-backed Anchovies showing varying flashes of green or gold.


Blue-backs in Pond A21. By random chance, I noticed the two faded blue-backs shown above.  There could have been others that I did not have a chance to capture before they were counted and tossed back to the pond.  And, as with green-to-gold-brown-backs, there is a spectrum ranging from very blue (top fish) and greenish-blue (lower fish).  I suspect that blues and greens interbreed at some rate.  And, both blues and greens fade as they acclimate to Alviso Marsh’s warmth and freshness.  But, as near as I can tell, blues never transition to gold or brown.  Only greens do that.


A Rigorous Anchovy Photo Survey from one station.  It’s still not enough!

A rigorous study of this Anchovy Color Mystery will require photographing every fish under standard lighting conditions, possibly at different light angles.  Also, they must be photographed live.  (Color fades within 10 minutes after death.  Yes, I have crudely timed this!)

My methods are crude, but cost is low for now.


5. California Halibut.

California Halibut in fresh brackish water!  Until now there has been a strong correlation between warm salty water and California Halibut in LSB.  Warm dry years were good for Halibut.  Recent wet years pushed Halibut out of LSB.

But this July weekend, we caught 13 young Halibut.  Several of those were picked up at stations in single digit salinity.  Halibut do not normally inhabit waters so fresh!


6. Know your Gobies and Sculpins.

Shokihaze Goby and Prickly Sculpin.

Continuing the Photarium photography experiment.  The Shokihaze Goby (top left) and Prickly Sculpin (bottom right) are shown in hand, and in Photarium below.

Prickly Sculpin in the Photarium.

In water, the Prickly Sculpin camouflage pattern is much more distinct.  It almost looks like a different fish.

This one will soon be beating it back upriver to do the mating dance.  Large numbers of Pricklys tell us that last winter’s rains were very good.  As mentioned in the previous post, it looks like Pricklys went through multiple rounds of spawning due to extended rains this year.


Shokihaze Goby, aka, Bearded Goby. (Non-native. Year first caught in SF Bay: 1997).

Much of what we know about Shokihaze Gobies in the Bay-Delta comes from Steve Slater’s work.  (You may recall, Steve accompanied us on the Hobbs trawls last May.)

Slightly unrelated note:  Steve also confirmed that the recently abdicated Emperor of Japan, Akihito, is one of the principal goby experts in the world. Akihito’s father, Emperor Hirohito, built his own marine laboratory at the Imperial Palace in Tokyo.  (However, Hirohito himself focused on hydrozoans.)

A few years ago, Akihito was consulted by CDFW to identify our two other non-native gobies: Chameleon Gobies (mainly in South Bay – first found in SF Bay around 1978) and Shimofuri Gobies (North Bay and Delta – first found in 1985) for the 2010 “Tracy Fish Facility Studies, California, Volume 44 – Special Publication.  – See pp. 274-274.

Japanese Emperors were born into limitless wealth and power.  Yet, they spent much of their lives studying fish and bugs.  How cool is that?


Longjaw Mudsucker – out of water view.

Longjaw Mudsuckers continue to be one of our favorite native fish.  They are considered a “gobid,” even though we may not refer to them as a goby.


Same mudsucker in the Photarium.

Arrow Gobies in the hand.

Arrow Gobies! The big mouths on these fish should indicate these are Arrows (Clevelandi ios), not Cheekspots (Ilypnus gilberti).  It is always very hard to distinguish the two by simple eyeball examination.

As I had learned in previous months:

  • Arrow Gobies have bigger mouths (the corner of the maxilla extends under and behind the eye) and tend to live on shallow mudflats.
  • Cheekspots display a shorter, stubbier snout (and short maxilla) and tend to inhabit the deep estuary channels and Bay.
  • Either goby can show a dark blue or black “cheek spot” on the operculum and the corner of the mandible is hard to see under field conditions – which makes life difficult for fish biologists.


Arrow Gobies in the Photarium.

The 29 Arrow/Cheekspot Gobies in July were caught mostly in the ponds and sloughs.  I did not photograph the two caught at LSB1, so I cannot determine which species those were.


Another Arrow Goby in the Photarium.

All of the Arrow/Cheekspots I photographed a few months ago were Cheekspots.  This may indicate a seasonal trend:  Cool weather favors Cheekspots, warm weather favors Arrows.


Arrow Gobies and Cheekspot Gobies are tiny: less than 2 inches.  


7. Interesting vegetation.


Dodder: aka, Beggarweed, Devil’s Guts, Strangleweed, Witch’s Hair, Wizard’s Net, etc.

Dodder (alternate spelling: Dotter) the Plant from Hell.  Dodder is very conspicuous this summer.  We assume abundant rains may have accelerated this year’s growth.

Dodder is the orange parasitic plant, similar to mistletoe in trees.  The plant is entirely comprised of a tangle of orange “angle hair” or “witch’s hair” aside from some tiny white flowers.  (I couldn’t get close enough to get a good flower shot – maybe next time.)


Dodder in Pond A21.

Dodder feeds mainly on pickleweed in the marsh, but that may be because Pickleweed happens to be a particularly tender and juicy victim for this type of Dodder.  Baby Dodder plants seek the juiciest victims by smell.  If a young Dodder fails to sniff out a good host within a couple of days of sprouting, it likely dies.


Red Algae Watch – 14 July 2019.  BTW: all of these are edible.

Red algae is back!  We found Red Gracilaria (long stringy stuff) and Cryptopleura (broader leaved weed) along with green Ulva (aka, sea lettuce) at most stations.  They all die back when it gets cold and fresh around January, but seem to be bouncing back in ever greater profusion each year – to my untrained eye.

Red Algae with tunicates.

Tunicates on the seaweed.  Until now, we have always found tunicates farther out in the deep Bay, AKA: stations LSB1 and LSB2, very rarely farther upstream, and mainly in cool winter seasons.  I thought temperature and/or salinity was generally keeping tunicates away from Alviso Marsh.

But now this:  Some sprigs of Red Gracilaria and Cryptopleura had tunicates attached to them in very warm and fairly fresh water!  Only a total of 25 were counted, but it is interesting to find tunicates at an unexpected time and place.

(BTW:  The non-native Atlantic Oyster Drills (one shown above) are common nowadays, but NOT a good sign.  As their name suggests, they drill into oysters and clams and eat them.)


8. Bat Rays!

Ale Zaydahr-Kulka with baby Bat Ray from Coy4.

Bat Rays tend to arrive with the warm weather.  This is the Bat Ray pupping season, so we caught pups and one adult.


Jim Hobbs with adult Bat Ray from Pond A21.


Bat Ray collage: 33 baby Bat Rays from LSB1

The big Bat Ray catch was at LSB1 in the deep Bay.  33 baby Bat Rays were caught in one trawl!  Jim counted them very carefully on a rocking boat.


9. Boat Rescue and Bad Luck.

Lower South San Francisco Bay: Safety First!

Warning!  Lower South San Francisco Bay is deceptively shallow!  The murky brown waters hide an unseen danger (to boaters).  The deep main channel is narrow and surrounded by thousands of acres of shallow mudflats.  Mudflats are easily seen at low tide, but disappear as tide rises.  If you stray off the main channel, you may get marooned!

The guys above cut too close to the channel edge off Lower Coyote Creek south shore (still visibly far out in the Bay).  The boat’s motor sucked up mud and shut down.  Prevailing winds steadily pushed their boat further into the mud.  So, Dr. Hobbs and crew gave them a tow back to Alviso Launch.

It is a basic law of the sea: if you see someone in distress, you must help.  And, this was a potentially dangerous situation; maybe not life-threatening, but certainly a threat to health and equipment.

Unfortunately, the 45-minute rescue delay forced a reordering to the rest of the day’s trawls.  We had to trawl Pond A21 before the tide fell.  As a result, deep Bay trawls at LSB1 and LSB2 had to be shifted to last.  And, as expected this time of year, afternoon winds kicked up against outgoing tide making it too rough to trawl the last station – LSB2.

Imagine all the Baby Bat Rays and blue-backed Anchovies we may have missed!



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