Fish in the Bay – January 2019, UC Davis Trawls – American Shad, Crangon, and Anchovies are up!

Wet winter brings more fish!  Hello everyone.  This is a slightly abbreviated post focusing on the ongoing booming populations of American Shad, Crangon shrimp, and colorful Anchovies.  In terms of just those three species, we had a really good month!

January trawls also picked up a number of other new discoveries and positive trends, – especially for Longfin Smelt – but some of that will have to be transmitted in a second post.

Saturday, 12 January – Bay-side trawls
Sunday, 13 January – upstream and east of Railroad Bridge

High Dissolved Oxygen (DO) across the board.  On Saturday, all stations showed over 100% oxygen saturation from top to bottom of the water column.  The highest value was 17 mg/l (183% saturation) in Pond A21. 

Sunday oxygen was not quite so saturated but still very high:  All stations ranged from 70 to 110% saturation.  The lowest Sunday value was 7 mg/l (72% saturation) at station DMP-1.  Looking back two years in my own records, we have seen a few instances of DO around 10 mg/l during cold January trawling, but until now, no higher.  

Winds were still, and water color in the main stem of Coyote Creek was noticeably green.  Nonetheless, both those conditions are fairly common here in December and January.  Somehow, we hit a supersaturated DO sweet-spot this January weekend.

1. American Shad Population Boom.

American Shad at Station Alv1

These young shad seem to be making their way upstream with the onset of cold temperatures. We can see in the multi-year fish table further below, that this happens here each winter.  This is a little weird for a couple of reasons.

According to Shad literature from the East Coast: American Shad spawn in rivers, the fry grow for a season before transiting to the ocean where they grow for 3 to 4 years to reach sexual maturity.  Warming ocean temperatures induce them to returning to their natal streams. 

  • Our shad are almost all still juveniles, one-to-two years old at most.
  • Bay water temperatures are still cooling, and we don’t know if these juveniles have yet ventured into the ocean.
  • We also don’t know if these shad hatched in Guadalupe River or Coyote Creek watersheds.  I would presume so.  Dr. Hobbs is much less certain.
  • Why are these young shad running to the creeks?  This is not consistent with East Coast shad behavior.
  • BTW: I’ve read a few accounts, like the one linked above, telling us that American Shad eat primarily copepods at sea.  From that, I presumed that they are filter-feeders. But apparently, they switch to mysids, insects, and probably amphipods as they transition to freshwater.  And, Bruce Herbold chided me last month that this fish is primarily a “picker,” not a filter-feeder.
More American Shad at station Alv2

The overall shad population explosion represents a state change in the Alviso Marsh Complex.  UC Davis/Hobbs Lab trawls over four years, from December 2010 through December 2014, caught a total of 314 American Shad.  As you can see in the Fish Table below, we caught more shad in either 2017 or 2018 alone.  We even caught way more American Shad this past month than in the first four years of Hobbs trawls!

Is a non-native shad explosion a good thing?  I have mentioned before, in the interest of full disclosure, I like this fish.  They may be non-native here, but American Shad are adaptable survivors.  Unlike Striped Bass, shad do not pose a predatory threat to every other type of fish in the system.  Like it or not, American Shad are doing well.

Colorful American Shad

American Shad in brown river color (upper photo).  These two were part of the upstream Alv1 catch. 

American Shad in green (lower photo).  The lower two were caught at Station Alv2. 

As usual, the back color of some is greener as we get closer to the Bay.  But, distance between stations Alv1 and Alv2 is 1.5 miles at most.  These little fish should be able to swim that distance in very little time, most of it simply by riding the sloshing tide.  Do they change color that quickly?  If so, how and why?

American Shad from Pond A21

We usually find a mix of green and brown American Shad at the middle stations.  To fully investigate this brown-green shad phenomenon, I would have to carefully photograph each shad caught.  I am not sure I have the time. And, unlike the blue/green/brown Anchovy phenomenon further explored below, I am pretty sure shad and herring back colors do NOT represent separate races (the term used by Hubbs (1925)) or subspecies.

Multi-year Fish Table

Fish Table.  I added more species to my multi-year monthly fish table.  As always, this table is showing raw numbers of fish caught in monthly trawls.  I did not convert these numbers to “Catch Per Unit Effort” (CPUE) which would be the professional thing to do.  Albeit, all but a few trawls during the past four years were 10 minutes in duration.  I leave the CPUE conversion for Dr. Hobbs and his lab, since it is their data, and I am not professional.

  1. Shad and Longfin Smelt numbers continue to increase. 
  2. Pacific Herring did well last year.  We should expect to see more of them by March.
  3. Staghorn Sculpin and English Sole populations increased in 2017.  Starry Flounder are off to a good start this year.  But so far, 2017 was the best year for Starrys.
  4. California Halibut and California Tonguefish are the biggest losers during wet years.  They are both common coastal fish, so not in danger.  But, wet winter flushing apparently keeps them out of Lower South Bay.
  5. OMG!  We just caught more Crangon in January alone than any of the three years prior to 2018!

2. The Great Crangon Brooding Migration of 2018/19.

Jon Kuntz and Pat Crain with a tubful of Crangon from station Coy4. 

The Crangon Explosion continues.  Who wants to count them?

Another tubful of Crangon from station LSB2.
Smaller Crangon and male Crangon from LSB2. 

Crangon caught in the middle of Lower South Bay (Stations LSB1 and LSB2) were predominantly smaller and non-egg bearing.  This is consistent with literature that tells us that pregnant female Crangon migrate upstream in response to cold temperatures. Males and young Crangon tend to remain in deeper Bay or coastal waters. 

Berried Crangon at Station Coy2. 

At upstream stations we continued to catch predominantly females bearing eggs (“berried females”).  This is a textbook example of a December-January Crangon brooding event right here in Lower South Bay! 

If you recall, the number of Crangon caught in December trawls was almost evenly split between Bay-side and Upstream-of-Railroad Bridge stations:  4526 versus 4429 shrimp.  By January, over 95 percent of the 10,419 Crangon were caught at Bay-side stations.  This leads me to believe that the 2017/18 Crangon brooding migration is nearing its end.

Remember that Crangon are amongst the last true natives of San Francisco Bay.  This annual or intermittent brooding migration probably began here sometime after the last Ice Age.  It continues to this day despite loss of habitat, loss of flushing water, and decades of raw sewage discharge that occurred over much of the last century.   

3. Northern Anchovies: Blue, Green, and Anchovy Babies.

In December, I was messaged by Bill Keener, at Golden Gate Cetacean Research (  He pointed me to a November Bay Nature article about Humpback Whales feeding on our anchovies: 

Bill also directed me to research papers indicating that ocean-going Anchovy populations along the California coast declined over the past decade or so. 

Apparently, Northern Anchovies tend to move closer to shore as their ocean populations shrink. This makes me speculate that we see green and blue-backed anchovies far south in the Bay today because falling oceanic populations are now concentrating closer to the coast and into the estuary.  

Anchovy from station Alv2. 

This is yet another worn out looking blue-back anchovy.  We continue to conjecture that blue-back anchovies are migrating into the Bay to spawn.  Unlike American Shad, Anchovy colors fade, but they do not change.  Blue or green anchovies appear to express color a short time after growing to juvenile stage and remain that color for life, as near as we can tell.

(This anchovy has a nasty copepod parasite attached to its side which I will describe in a later post.)

Young Anchovy from station Alv2. 

Young Anchovy from station Alv2.  From its profile, the above young-of-year anchovy (roughly 50mm) looks like a brown-back, but blue iridescence is visible at the crest of the head on closer inspection.

Anchovies from station Coy4

Anchovy color fades in winter, and juvenile Anchovies show little color at all.  Four or five fish in this group from Coy4 could easily be mistaken for brown-backs.  But, all show signs of green or blue color on the heads and backs. 

More Anchovies from Coy4 (also showing a Shiner perch and one Longfin). 

A few of the anchovies shown above show dark dorsal color with traces of blue pigment.  All had at least some flecks of blue or green in the head, if nowhere else, as shown in photos below.

Mature Anchovies, station Coy4.

At least one faded blue-back and faded green-back were in the bunch shown above.

Three young-of-year Anchovies from station Coy4.

The young Anchovy at left is showing a common color pattern: blue just over the eyes and green a little further back.  But, others at the same size and apparent age show all green or all blue at the same location.  It would be interesting if blue-green juveniles represented hybrids or a different variety. I fear genetic testing could be needed to solve this puzzle.

Another young anchovy from Coy4. 

In addition to blue-green flecks on the head, this young one has green material in his gut.  I am guessing that the green gut is from phytoplankton that had recently been consumed.

Young-of-year anchovy showing a deeper blue hue.
Two very young anchovies from LSB1.
  • The upper anchovy shows no trace of color other than an orange-brown reflection off the eye. 
  • The lower anchovy shows a very faint trace of blue on the head. 
  • Both these fish almost certainly hatched in the Bay fairly recently.
Three young blue-back anchovies from LSB2. 
Adult green-backs at Coy2.
Young green-backs at Coy3.

Anchovies in Lower South Bay and the Alviso Marsh Complex display different dorsal colors from an early age.  Amongst very young fish, there seems to be a distribution of more blueness out in Lower South Bay to more greenness up Lower Coyote Creek, with considerable overlap.  We can’t yet entirely rule out effects of diet or salinity in color development.  Temperature seems to affect color intensity in adults, but even color intensity could be more closely related to spawning readiness.

Are there any Anchovy experts who could help unravel this colorful mystery?

4. Some other fish caught in January.

Pacific Herring.

Herring spawning starts about this time of year.  In a month or two we should start seeing young Herring in the nets.

Longfin Smelt.

December 2018 was the record month for Longfins: 151 caught.  Then the record was smashed in January: 365!  This fish, like the Delta Smelt, is disappearing from the San Francisco Bay-Delta system.  For some reason, Longfins are booming here.  Dr. Hobbs continues to search for winter larval Longfins as salinity drops.

Also note: 

  • Most Longfins were caught in Ponds A19 and A21 in December.  But in January, there were no Longfins caught in the ponds even as more Longfins were caught almost everywhere else.
  • There were so many Longfins caught in January that Jim Hobbs had to shorten the typical 10-minute trawl duration at five stations to avoid collecting too many of these endangered fish.
Starry Flounder and English Sole

Starrys and Sole are two other fishes that do well in wet years.

Shiner Perch

We don’t see very many Shiners in Lower South Bay nowadays, but a few continue to show up.  All six caught in January were young-of-year and about the same small size.

Yellowfin Goby

Yellowfin Goby numbers fell in 2018.  But don’t worry, this noxious invasive fish is not going away.

I have much more to cover, but I will save it for a later post. … Until next time.

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