Fish in the Bay – 16-17 June 2018 UC Davis Trawls – Yellowfin Gobies Strike Back!

Hi everyone.  Some photos and thoughts from my ride-along with the UC Davis team on Saturday, June 16th.

I continue to tweak the map of trawling stations above.  Most recently, I muted the trawl station in Pond A6.  The Hobbs crew trawled in Pond A6 occasionally until around 2014 or 2015.  After that point, Pond A6 became too shallow for otter trawling.  (One of the ongoing successes of salt pond restoration is that sedimentation filling up tidal ponds very quickly in Lower South Bay.)

Saturday, 16 June – Bay-side trawls

Sunday, 17 June – upstream and east of Railroad Bridge

Good news: 

1) Total fish counts increased in June. The May Saturday/Sunday counts were 204/382.  The June counts were more than double: 594/826.

2)  Native Crangon shrimp continue to dominate the Bay-side Alviso territory, albeit non-native Palaemon & Exopalaemon shrimp have seized control of the upper Coyote Creek segment.

Bad news:  The increased fish count is mostly attributable to non-native yellowfin gobies.  We appear to have been “flash mobbed” by yellowfins!  

We seem to have had a very late “Baby Fish Month.”  In previous years (2013?-2017), thousands of tiny, unidentifiable “baby fish” were recorded in April or May.  This year, we didn’t see a true “baby fish month,” but this surge in yellowfins seems to indicate it happened in late May or early June.  Additionally, low counts of yellowfin gobies before, and high counts after, seem to confirm that “baby fish month” mainly represents the annual surge of yellowfins.  What a disaster!  Last month, I gleefully anticipated that native staghorns may have crushed this yellowfin monopoly.  I was wrong.  Invasive Yellowfins are back in business!

Yellowfin Gobies!  (a native Arrow Goby is shown in far background.)

Above, Dr. Hobbs, Emily Trites, and Pat Crain prepare for launch from Alviso near noon.

New Moon + Aphelion = daytime Lower Low Tide. Usually trawling days start around 8:00 AM.  But, this June weekend had extreme low tides during daylight hours:  New moon happened on June 13th (bringing spring tides) and we were sliding toward aphelion on July 6th (Earth’s furthest point from the Sun means the moon dominates tides: lower low tide occurs during the day at this time of year.)

As a result, the Hobbs float plan had us launching close to noon, just after lower low tide when many of the sampling stations are untrawlable, and in some cases, unnavigable due to lack of water.

Starry Flounder.  The first trawl in Alviso Slough pulled up only three fish, which is kind of typical.  But, the small sliver of good news is that two of the three were young Starry Flounder, and subsequent trawls indicated that summer-time starrys are again beginning to recruit.  2017 was a good year for starrys with new recruits peaking around August.  In contrast, 2016 and at least a few previous years saw less recruitment of starrys but many more young California Halibut.

Both Starry Flounder and California Halibut spawn in, or near, estuaries.  In both cases, ripe females release thousands to millions of eggs.  If fertilized, developing young drift into viable nursing areas providing food and other conditions needed for rapid growth.  A significant difference is that starrys are optimized for freshwater recruitment.  Starry flounder actually seek the mouths of creeks and rivers for spawning, and that’s where successful rearing occurs – assuming the creeks and rivers experience enough freshwater flushing to support the starry nursery.

Staghorn Sculpin from station Alv2.  A three-spined stickleback and yellowfin goby are also shown at top of photo. 

Staghorn Sculpin.  Despite signs of huge staghorn recruitment in March and subsequent months, numbers are dropping off.  This is another fish that appears to like it fresh – at least when young.  New recruits surge shortly after winter rains and then drop off precipitously as the marshes get warmer and saltier.  Literature indicates that staghorns tolerate an extreme range of salinity as adults, from freshwater to hyper-saline.  But, recruitment of this local population is enhanced by wet weather flushing.  I do not know why they decline so sharply through the summer:  Predation?  Lack of food? Competition with other species?


Shiner Surfperch were netted at Alv3 and nearby stations; 11 total on Saturday.  Total shiners for 2018 is now fifteen.  The 2018 shiner count is already higher than seen all year in either 2016 or 2017.  This is the most common surfperch found on the Pacific coast, from Alaska to Baja.  But, for some reason, once common in Lower South Bay, shiners are now infrequently seen here.  I do not know if that is a good or bad thing.

All the shiners shown above, and caught thus far this year, are very young.  These in the photo above were probably born only a few months before.  Shiners are born live at about the length of the end of your thumb.  Young shiners are more tolerant of freshwater than adults, which may explain why we mainly see young shiners in Lower South Bay.  Shiner Surfperch are essentially born fertile, albeit females do not bear young until a year old.  So, even these tiny guys could be a reproducing population.

Arrow Gobies.  The June weekend was also unusual for all the native Arrow Gobies caught:  27 on Saturday and 25 on Sunday.  Usually, zero to a few are caught in a day of trawling.  This was the highest number seen for at least a few years.  Arrow Gobies are a small goby, rarely growing longer than 2 inches.  I assume they face heavy competition, if not predation, from larger Yellowfin Gobies.  If true, relative scarcity of yellowfins the past few months could explain the higher-than-usual number of Arrow Gobies now.

Crangon.  The biggest catch of Crangon was made once we entered the main stem of Lower Coyote Creek and continued out into the Bay.  The above photo shows the mixed bag of Crangon with yellowish Synidotea (isopods), followed by lesser numbers of Palaemon shrimp from the Coy4 station.

Non-native Palaemon and Exopalaemon shrimp were more numerous in the further upstream Sunday trawls.  I had not been paying close attention to distributions of these different shrimp species until now.  Dry years favor Palaemon shrimp.  But counterintuitively, the 2018 crop of Crangons has seized control of saltier bay-side locations.  Both Jim Hobbs and Pat Crain have mentioned to me that a strong winter freshwater pulse favors Crangon recruitment.  But after that, I suppose it must be a shrimp-eat-shrimp world, with the strongly recruited type of shrimp dominating the other, all else being equal.

Submerged Aquatic Vegetation (SAV).  Also notice the two types of “seaweed” in the photos above.  Fragments of both red and green algae were observed in at least three Lower Coyote and LSB stations.  Lower South Bay, and San Francisco Bay generally, does not have much SAV, so I am always on the lookout for signs of improvement.  Each summer, I spot a few fragments here and there.  So far, I don’t see much change, just evidence that SAV exists for now.


Palaemon shrimp showing off their clear bodies on Saturday.  Very young palaemon, and especially exopalaemon, are translucent to nearly transparent.  Palaemon get darker reddish to brown as they age.

Older Palaemon.  These shrimp turn into redder “tomato Palaemons” as they age. They also grow big boxer-like arms.  I assume this is a mating-related phenomenon.  I do not know if males, females, or both, turn into tomato-palaemons.  But, relative numbers suggest that only the very few and strongest shrimp make it to the tomato stage.  Until now, I thought that “tomato Palaemons” were only seen in wintertime, mainly in January.  These two shown above are not as red as some I have seen in January, but they are clearly into the tomato phase of their life cycle.

Plainfin Midshipmen – a big surprise!  A total of 37 Plainfin Midshipmen were caught on Saturday.  This is unprecedented.  Since 2010, the Hobbs trawls have netted perhaps one or two midshipmen per year, if that.  These were all very young, so they must have hatched nearby.  And, because they were found at three separated locations, they likely came from multiple broods.  Why here?  Why now?  This fish spawns under rocks, of which there are not very many in Lower South Bay.

Plainfin Midshipmen are common on the Pacific Coast and in Suisun Bay.  Yes, this is the famous “Singing Toadfish” that kept Suisun Bay houseboat dwellers awake at night back in the 1980s.  You may remember that Midshipmen have networks of light-producing photophores on their undersides.  They also come in three sexes: Male Type 1, Male Type 2, and Female.

A tray full of baby midshipmen. The young have a lateral striped pattern across their backs.  The lighter colored bars turn uniform brown as the fish ages.  This fish is noted as being very tolerant of low Dissolved Oxygen, albeit that tolerance does not appear to be a factor related to its presence in Lower South Bay.  For various reasons, this is a truly amazing fish.

Pacific Sea Nettle.  This was the only jellyfish seen in June, but it is a beauty!  Check out the rich orange and red colors.  If I had a sea-life aquarium, (and knew how to care for and feed a jellyfish), I would want this one in the tank.  Jim Hobbs’ theory is that high temperatures in the lower Bay keep the jellies away. … And, numbers of both comb jellies and medusa-type jellies continue to drop as summer approaches.   (You can also see three black-tailed crangon shrimp in the photo.)

Blood-spot mysids.  This is more of a field note to myself.  I noticed that mysids at LSB1 station had red spots just behind the head.  I had not seen this before, and I do not know if this is related to something these mysids had just eaten or if this is a different type of mysid.  Either way, mysids are good – everything eats them.  (BTW: I made up the name “Blood-spot mysid.”  As far as I know, the name does not exist in scientific literature.  Do not cite!) 

Northern Anchovies (brown-backs).  The June weekend gave me a chance to further study the colors of Northern Anchovies.  Jim Hobbs has long been a fan of the 1925 Carl Hubbs observations of San Francisco Bay native “brown-back” anchovies versus ocean-going “green-backs.”  Two of the brown-backs caught on Saturday are shown above.  (I also Facebook posted a longer photo-essay of Anchovy observations.)

Brown-backs (AKA: clear or gray-backs) tend to be restricted to Bay and marsh areas far from the ocean.  In recent years, Jim Hobbs has pretty well documented that the brown-back population appears to spawn in the Bay as was suggested by Hubbs in 1925.

Northern Anchovies (green-backs).  Green-backs have long been observed as the main anchovy ocean-going population.   Nonetheless, Jim Hobbs’ surveys since 2010 have consistently seen green-backs well into marsh areas and co-occurring with resident brown-backs.

The two fish shown above are not great representatives of the green-back type, but they were the best I could do this weekend.  The top fish is almost a cross between brown-back and green-back, or perhaps a young green-back.  The bottom fish is true to green-back type, but the color is more golden green than emerald green.


Northern Anchovy (blue-backs???).  What is this?  Blue-back anchovies?!?!?  I have seen and commented about rare blue-back anchovies since late-2016.  Until now, blue-backs seemed to be strange one-off catches.  As we approached LSB stations, I fully expected to see trays full of emerald green green-backs.  Instead, we found dozens of consistently large and peacock blue-backed fish.  Carl Hubbs did not mention blue-backs in 1925.  Is this a new thing?

More blue-backs.  I noticed that many young anchovies with undeveloped color also appeared to be blue-back types under close inspection.  In previous years, when I saw an odd blue-back, I couldn’t be exactly sure I wasn’t seeing a reflection of the blue sky or off my blue shirt.  This year, the anchovies are vivid blue.  This is not an illusion!   Why did anchovies turn bluer in 2018?

Maybe someone who fishes anchovies far out to sea can help illuminate this blue versus green situation?  I speculate that anchovy color may be related to sea surface temperature (??).  Various signs in other fish and jellyfish populations this year reflect a cool Pacific upwelling scenario.  Cool ocean conditions may also promote (or draw further south) blue-back anchovy populations.  Green-backs may represent a more southern, slightly warmer water segment of sea-going anchovies.  IF THIS IS TRUE, Northern Anchovies caught in the Bay could provide a wonderful barometer for tracking ocean conditions off the coast:  Blue = cool ocean; Green = warm ocean.  (Please note: I am not a fish expert!  I do not have professional reputation to protect.  Reckless speculation is what I do!)

Cool Pacific = Anchovies.  Warm Pacific = Sardines.  Coincidentally, Bruce Herbold facebook posted Anchovy information of his own later in June. Bruce provided a web link to an article describing results of a Chavez et al. paper linking ocean conditions that favor either anchovies or sardines.  The diagram above from Chavez et al. (2003) shows how physical conditions favor either Anchovies or Sardines as important prey fish in the Pacific.

My gut reaction is:  1) We need to do this for San Francisco Bay.  2) Anchovies may be the best indicator species of ocean and Bay temperature, salinity, and other conditions.   Maybe anchovies could serve as ocean-going “mood rings!”  It is already documented that brown/clear backs reflect a warm marsh upbringing.  We just need to further flesh out the green versus blue-backed relationship.

Bay Fish Barometer.  With colorful anchovies in mind, I felt inspired to make a notional diagram showing how certain fish species indicate prevailing weather and ocean conditions.  I show four quadrants: 1. Warm Pacific, 2. Cool Pacific, 3. Dry Winter, and 4. Wet Winter.  In actuality, ocean temperature and winter rain conditions are at least semi-independent of each other.  But despite that, each of the two regimes (warm-cool / dry-wet) are strong drivers of local fish populations.

… For instance, Prickly Sculpin shows up in Lower South Bay marshes only after robust creek flushing.  Similarly, but for different reasons, English Sole is a strong indicator of cool ocean upwelling coupled with freshwater flushing.  Sightings of Striped Mullet in the Delta in late-2014, and in Lower South Bay in May 2015, were unambiguously linked to warm Sea Surface Temperatures (SST) of that El Nino-like year.  So, it’s not only about anchovies, but anchovies might be the key.

What if anchovy colors alone, or in combination with other fish populations, could accurately diagnose coastal and estuarine conditions?  And, what better fish than anchovies?  Bruce also directed me to some additional articles from Pew Charitable Trusts that discuss the importance of anchovies as “The Most Important Prey Fish in the Pacific!”

We have much to learn from our Bay anchovies.

Shokihaze Goby.  The shokihaze shown above from Pond A21 was notably big, with a big bulbous head.  Adult Shokihaze and Shimofuri gobies grow into this look.  I do not know if it is a strictly male or female appearance.  But, after you observe a number of them, you begin to appreciate a true monster of the species.  Literature says a ripe adult female has 4,000 to 20,000 eggs. Obviously, very few shokihaze eggs grow to maturity in competitive Lower South Bay.  This species is so familiar to me now that it is hard to believe that this Asian species was first discovered in San Francisco Bay in 1997, a mere 21 years ago!


A Speckled Sanddab is the fish below the small starry flounder.  This was another odd-ball caught in Pond A21 late in the afternoon.  Speckled Sandabs are very common on the coast, but rare in Lower South Bay.  November 2017 appears to be the last time a sanddab was trawled in this area.  Prior to that, 39 were caught way out at LSB stations in January 2017, just before the big February Flush.  The Bay was saltier than usual on Saturday, as you can see in data sheets far above. Sanddabs appear to be another good candidate for the “Dry Winter” quadrant of the Bay Fish Barometer: a coastal fish that makes a home in the Bay, but only after the Bay salts up.

End of the day.  We headed back to Alviso Launch late in the afternoon / early in the evening around 7:00 PM.  As usual, wind and waves were picking up.  Here we are rounding the corner from Lower Coyote Creek into the mouth of Alviso Slough.  We had good luck that it didn’t get as rough as it usually does that late in the day.

Until next time!





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