BROWN BAG SEMINAR: It’s Vital: Delta Smelt Reproduction and Resilience

The Interagency Ecological Program (IEP) is a consortium of State and federal agencies that has been conducting cooperative ecological investigations since the 1970s. The IEP relies upon multidisciplinary teams of agency, academic, nongovernmental organizations, and other scientists to conduct collaborative and scientifically sound monitoring, research, modeling, and synthesis efforts for various aspects of the aquatic ecosystem.

In 2018, the Delta Science Program hosted a series of brown bag seminars that highlighted how research and monitoring performed by the IEP is relevant to decisions being made in the Delta.

Lauren Damon has been part of the Interagency Ecological Program since 2008.  She is currently an environmental scientist for the Department of Fish and Wildlife where she co-leads three long-term monitoring surveys in the San Francisco Estuary.  She has spent much of her career studying Delta smelt.  In this seminar, she discusses Delta smelt monitoring and studies on their fecundity that was recently conducted.


The Delta smelt are in the family Osmeridae; the word ‘osme’ is Greek for pungent smell, Lauren Damon began.  “So if you’ve ever held a Delta smelt, either in culture or in the wild, you know that they smell like cucumber, so their family name is very fitting for them.”

They are not large fish; as adults, they reach about two to three inches.  They are found in pelagic habitat which means open water and not near the shores or the bottom.  They are an annual species so they complete their entire life cycle from hatching to spawning in one year.  They feed on small invertebrates, typically zooplankton but also sometimes mysid shrimp.  Delta smelt are endemic to the San Francisco estuary; they are only found in the Bay Delta.  Delta smelt evolved many, many years ago from a landlocked population of surf smelts.

Because they are so intimately entwined with the system because they evolved here and they are highly adaptive to live here, they are a really good at being an indicator of the status and health,” she said.  “Delta smelt are very adaptable to the estuary and the dynamic-ness of the estuary, but when the estuary isn’t functioning very well, the Delta smelt aren’t functioning very well, so we use them as an indicator of the status and health of the estuary.”

Above is a timeline showing the life-cycle of the Delta smelt.  Adults are present in the estuary in the winter and early spring; and then they hatch out and larvae are present later in the spring, and the juveniles and subadults rear over summer and later into the fall.

Delta smelt are opportunistic strategists which mean their life history strategy is to have a short generation times and to produce a lot of offspring.  The graph on the slide is the conceptual model of their survival rate from a 2005 paper, which shows that they produce a lot of eggs, and then there’s high mortality of the earlier life stages leaving a substantial  smaller number of adults at maturity.

Delta smelt populations have experienced some pretty severe declines over the last few decades and so they are listed both in California and federally as threatened; they were petitioned to be uplisted as endangered federally but that was warrant and precluded in 2010, and so they are listed as endangered in California and threatened federally.  Their critical habitat is essentially the California Bay-Delta.

Water is moved around California mainly through the state and federal water projects in the Delta, when the Delta smelt were listed, those water projects needed to get permitted under the Endangered Species Act.  The US FWS consulted with the Bureau and with the Depart of Water Resources to permit their water export facilities that are located in the south Delta; the USFWS developed a biological opinion with ‘Reasonable and Prudent Alternatives’ to minimize those export facilities’ impact to Delta smelt.  Those RPAs called out some specific monitoring surveys and data reporting near real-time to managers so that water managers could adaptively manage Delta smelt and the impacts of the water operations.


The water project facilities in the Delta were designed and constructed in the 1950s and the 60s and as a result, the Department of Fish and Wildlife and the Department of Water Resources agreed that there needed to be some studies in the Bay Delta region to understand how these water projects were going to impact the ecology of the Delta.

This was the early formation of the Interagency Ecological Program, which was the agreement between those two agencies,” said Ms. Damon.  “It’s now nine agencies, but their mission statement is basically the same: to use science to understand how the ecosystem is affected by the water projects and then how we can manage that better.”

Summer Tow-net Survey

The first survey brought online was the Summer Tow-net Survey which started in 1959 and operates from June to August.  The Summer Tow-net Survey samples 32 historic stations ranging from eastern San Pablo Bay to Rio Vista on the Sacramento River and to Stockton on the San Joaquin River. In 2011, 8 supplemental stations were added in the Cache Slough area and the Sacramento Deep Water Ship Channel.

The net is mounted on skis, and the mesh size is such that it targets young fish found in the estuary.  It was originally intended for striped bass because that was what the Department of Fish and Wildlife was most concerned with in the 1950s and 60s, but it proved to be good at catching a variety of fish species throughout the summer that are present.

The survey samples the entire water column using an oblique tow; the net is let out to a specific depth, depending upon how deep the water is, and then over the course of about 10 minutes, it is towed in an oblique direction towards the surface so that it can sample the entire water column.

The map shows the locations of the survey stations in the Delta.  The black dots are the stations that have been around since the survey’s inception; the colored dots are the ones that have been added on later to increase the survey’s spatial coverage.

Fall Midwater Trawl

The Fall Midwater Trawl came online in 1967; the survey samples 122 stations each month from September to December and a subset of these data is used to calculate an annual abundance index. Sampling takes approximately 9 days per month to complete.

The survey operates during the fall with what is more like a traditional trawling net that is held open by doors; the mesh size is quite a bit larger than the tow-net mesh because this survey is targeting a larger size life-stage.   Like the Summer Tow-Net survey, the Fall Midwater Trawl was intended originally for striped bass, but it definitely samples a whole suite of species.  It is also towed obliquely.  The Fall Midwater Trawl is called out in the biological opinion as well as the recovery plan for native fishes, so as things hopefully start to recover, this will be the survey that we use to track their recovery, Ms. Damon said.

The map (lower, left) shows the survey stations for the Fall Midwater Trawl.  These 122 stations range from San Pablo Bay upstream to Stockton on the San Joaquin River, Hood on the Sacramento River, and the Sacramento Deep Water Ship Channel. In recent years, stations in the north Delta and south Delta have been added to increase coverage, particularly for Delta smelt but other species as well.

The Summer Tow-net Survey and the Fall Midwater Trawl are the longest running surveys.  Abundance indices are calculated from both of these surveys.  An abundance index gives an idea of the relative abundance of fish, but Ms. Damon noted that it’s not an absolute abundance, it’s just to compare among years status among years.  Both of these indices were used in the petitioning of Delta smelt when they were first listed in the 1990s.

Particularly in the Summer Tow-net Survey, the one on the bottom, you can see pretty clear the declines that have been experienced, and so these abundance indices are really good for monitoring trends like this over time,” she said.

20mm Survey

When the Delta smelt were listed, there was a need for additional information about larval distribution and abundance, particularly in the south Delta where they were vulnerable to entrainment.  The 20mm survey was started in 1995 during the springtime to target larval and juvenile Delta smelt around 20 mm in length, because that was when the projects need to start enumerating them for take purposes.  Managers wanted to have a heads up about when larval and juvenile fish would be present in the south Delta to minimize their risk of entrainment there as they are not very good swimmers.

The fish collected on this survey are very small, ranging from between 3mm to 45 mm, so the entire sample is brought back into the laboratory for processing.  At the lab, staff look at the samples, separate the fish out of the debris, and a larval fish ID expert identifies the larval fish under a microscope.

The 2004 Biological Opinion requires the 20mm survey results to be provided to managers within 72 hours on the distribution and relative abundance of Delta Smelt throughout the Delta and the upper estuary so that they can adaptively manage pumping operations for them.  The website has an interactive map that allows the public to select a species and view the results from each of the survey stations.  If the circle is white, that means that particular species was not present; the green means there was catch there, and the size of the circle shows the catch per unit effort (CPUE).

Spring Kodiak Trawl

The Spring Kodiak Trawl began in 2002; it was initially the spring midwater trawl that evolved into the Spring Kodiak Trawl to improve detections of Delta smelt.  The survey samples for adult Delta smelt; it is used to predict when spawning will be occurring so they can therefore predict when larval fish will be present in the system.  All of the adult Delta smelt captured in the spring Kodiak trawl survey are examined for their gonad (or reproductive) development.

On the slide below, the top picture is an adult male Delta smelt considered near ripe as his gonads are still relatively small.  The female adult Delta smelt is also considered near ripe as her gonads are small and the eggs and milk are starting to develop.

On the picture above on the right, this is a ripe female in spawning condition; her eggs are very large and full yolked and her ovaries take up pretty much her entire abdomen.  Ms. Damon pointed out the large, discolored eggs in the clutch, explaining that these are left over from a prior spawn, so she’s already spawned at least once.

There is an interactive map on the spring Kodiak trawl webpage that shows where the fish were caught and the numbers of males and females caught at each site; it is possible to drill down into the data and look at what stage of development they were in.


The genesis for the Delta smelt fecundity study came from the Spring Kodiak Trawl where they saw an opportunity to put together a comprehensive study about Delta smelt reproduction. Some of the goals of the study were to define the length-fecundity relationship and to make observations about the time of year they are spawning – is that spawning bound by temperature or size.

The UC Davis fish conservation and culture lab collects wild Delta smelt that they then spawn and rear in captivity; this has provided an opportunity to observe spawning behaviors in captivity.   The researchers wanted to see if wild Delta smelt behaved similarly as their lab-cultured counterparts.  In captivity, Delta smelt are capable of producing a number of multiple clutches per year under controlled conditions and it’s very common for Delta smelt at the fish conservation and culture lab to live longer than two years.  So the researchers wanted to see if Delta smelt were doing the same thing in the wild.

On the slide above, the annual timeline for Delta smelt is at the top; the spawning period from February to May is detailed in the larger graphic on the slide.  When they spawn can be variable, but they can spawn anytime during February through May.  The spawning window is typically bound by temperature.

At the beginning of the spawning season, assuming the female is ready to spawn, a clutch can be released at the onset of spawning.  Then a period of time goes by while the female redevelops her gonads and another clutch of eggs is developed; this is called the spawning interval.  So depending on the length of the spawning window, multiple clutches of eggs can be developed and released.  The spawning interval in culture is around 40 to 50 days; those fish are held at constant conditions, but that is their best estimate of the spawning interval.

The number of clutches a female can release in the spawning window is called the spawning frequency.

For the fecundity study, they took all the near-ripe females caught during the Spring Kodiak Trawl and examined their egg clutches.  They divided them into three phases:  the first was the developing eggs (shown as A in the picture); those eggs are smaller and translucent and don’t have yolks developing yet.  The second category were ripe or near-ripe; these were defined by the eggs being much larger and having a yolk-body that fused together (shown as B in the picture).  The third category were post-spawn eggs which are not pictured on the slide, but those are much larger, darker colored, and mottled looking.

For the fecundity study, they counted all the eggs in the clutches of the near-ripe females as those are the ones that are the viable eggs that contribute to the fecundity.  They conducted the study from 2012 to 2016; they were able to look at 129 fish; the mean fecundity was around 2000 eggs per female.

They then plotted the fecundity as a function of fork length (lower, left) and found that there was no significance in the length-fecundity relationship among years.  “One of our main findings was that this relationship was consistent among years, but what did change is the abundance,” said Ms. Damon.  “We’ve systematically sub-sampled the near-ripe females caught on the spring Kodiak trawls, and in 2012, there were 67 available to us and by 2015, there was only 8 available for us to use.”

So the researchers then grouped them by year and determined that the length-fecundity relationship is a vital rate for Delta smelt.  “In culture, the length-fecundity is essentially the same; the fish can get a lot larger in culture so they have that 80-100mm range filled in quite a bit more, but essentially this relationship is consistent for Delta smelt, so even though there is some variation, we can predict fecundity based on their fork length,” she said.

Another part of this study was to try and describe the spawning window bounds, so the researchers plotted the females that were in spawning condition – those female adult Delta smelt that were ripe or ready to spawn and those fish that had already spawned.

Once we plotted the frequency of those, and found that spawning typically occurs between 9 and 18 degrees, that’s when we observed spawning to be happening,” she said.  “We also found that there was no smelt smaller than 55mm in spawning condition, so we said that that was the minimum size required for spawning.”

Another part of the study was to determine if female adult Delta smelt continue to grow throughout the spawning season.  On the graph on the lower left, the green box plots are pre-spawning females – the ones that were not in spawning condition or those have not spawned yet, and the researchers observed that they do still grow throughout the spawning season.

The motto is that it takes a year to make a smelt, and I would take that a step further and say that it takes a year to make a smelt fecund because they need that growth throughout the whole year,” said Ms. Damon, presenting the graph on the upper right that was generated by Jim Hobbs who plotted the age of smelt to length.  “You’ll see that the larval and juvenile periods are really time for this rapid growth, based on these early life stages growing so they can get as big as possible so they are fecund as adults.  When they become sub-adults in the fall, energetically they shift, switching to more gonad development so growth slows during that time period.  It’s really the larval and juvenile stage that’s really important for ensuring they are of adequate size during the spawning season.”

The researchers also wanted to see if two-year old Delta smelt were contributing at all to the fecundity of the Delta smelt population.  Two-year olds and even 3-years olds are common in culture, but they didn’t know if they were common in the wild.  She presented a graph showing all the lengths of all the individuals caught during the Spring Kodiak Trawl from 2002 to 2015, noting that the red triangles are what were thought to be two-year olds.

Not a whole lot of 2 year olds present in the population in the wild,” she said.  “We don’t know if they were historically more abundant or not, but because two-year olds are disproportionately more fecund than one-year olds, but it might be a benefit to have additional two-year olds available for spawning purposes because they contribute significantly more eggs than one-year olds.

They developed a conceptual model to help them sort out the factors that contribute to the annual fecundity.  “We care about clutch fecundity, but really what we want to know is how many eggs can each smelt produce in a year which is the annual fecundity,” Ms. Damon said.  “Annual fecundity is dependent on the clutch fecundity or how many eggs they produce in a given clutch, and the spawning frequency or how many clutches they can produce.  Essentially that is dependent on their size which is dependent on how much food and resources they have available to them for their whole life, and then the water temperature really dictates when spawning starts and ends and how long the spawning interval is, and that determines how many times they can spawn.  So if you want to boost up the annual fecundity of the Delta smelt, you want to make sure she’s large so her clutch fecundity is high and she has many opportunities to spawn, so the spawning frequency is high.”


Ms. Damon then discussed what this means for Delta smelt resilience and management.

When thinking about resiliency in terms of reproduction, it’s their capacity to produce eggs or how many eggs they produce in a year, or their annual fecundity that’s possible, because theoretically, the more offspring they can produce, the more resilient they will be later on, Ms. Damon said.

They developed a conceptual model for Delta smelt that shows what the reproductive potential could be; she pointed out that this is just a theoretical model so the numbers aren’t real.  They then plotted theoretical previous year class abundance, applied a mortality or survivor curve to that.  The X axis is the month; it starts in April and goes for two years.

You have this abundance, you apply a survivorship curve, and then it leaves you with the number of adults available for spawning which you’ll see is really low in the figure,” she said.  “For every clutch they can produce, their reproductive potential increases quite a bit; then you apply the survivorship curve.  What you could do with this is if you carried out another couple of years, you could use it as a tool to predict how many offspring you need to either increase your population, decrease your population, or maintain your population.  So you can really know how many eggs you need to produce every year to get the certain number of adults that you want.  The good thing about this tool is that you need any more additional monitoring than what we already have available to us.  It doesn’t require any additional monitoring, just some analytics.”

In order to model the reproductive potential, annual fecundity is the surrogate for reproductive potential, which is determined by clutch fecundity and the spawning frequency.  Clutch fecundity is based on female size, and the spawning frequency is based on the spawning interval and the spawning window.  They have the data for female size from the Spring Kodiak Trawl; the spawning interval is 40 to 50 days as estimated from culture, so really what they need to know in order to determine annual fecundity is the spawning window.

The spawning window can be estimated in two ways.  One is to look at the water temperature data that is available on CDEC, but Ms. Damon noted that it is highly variable, so applying the assumptions and determining when the water exceeds 9 degrees can be a little bit of a challenge, but it’s possible.

The other way to estimate the spawning window is to use survey detections so for this study, they considered the onset of spawning when they first saw fish in spawning condition during the Spring Kodiak Trawl and the end of the spawning window then they last caught newly hatched larvae in the 20mm survey.

One of the caveats to this, especially when abundance is low, is just because you don’t catch them doesn’t mean they aren’t there,” she said.  “Keep in mind that these are just estimates and probably they can be improved upon at some point, but this is what we have available so far.

The Spring Kodiak Trawl is only a monthly survey, so she acknowledged the resolution isn’t great.  In order to bound the spawning window for 2012, they looked at data from the Spring Kodiak Trawl, and in that year, they first collected female Delta smelt in spawning condition in February, so it was about the middle of February was when spawning started, she said.  The figure on the right on the slide is a length frequency diagram taken from the 20mm webpage.  The x axis is length, the y axis is frequency, and each one of those individual graphs is a week-long survey.  The highlighted box are fish that are 5, 6, and 7 mm is what were considered newly hatched larvae.  She noted that it was in the middle around the survey 6 is the last time newly hatched larvae were present, so back-calculating a couple of weeks for incubation time, that would put the end of spawning occurring somewhere around the beginning of May.  So for 2012, using this method, they bound the spawning window between about the middle of February to the middle of May.

The researchers then used the same parameters to determine the spawning window for all the years.  On the graph, the years are on the x axis and the green bars are the length of the spawning window, and the black bars represent the spawning events.  The table shows the number of spawning events that were calculated based on the spawning window.  Ms. Damon pointed out that it’s highly variable and every year is different; some years, there may only be one spawning event whereas in other years, they could easily have three spawning events.

I will caveat this and say that not all the females are ready to go on the first day, so this would be a best case scenario,” she said.  “Some of them probably need a little bit more time.  They aren’t going to start on the very first day that the spawning window opens and so not all females are going to be able to get three, but best case scenario is that they could get 3 or more in some years.”

Using this information, they next developed an egg production index that’s a surrogate for reproductive potential.  To calculating the number of eggs that are possible per year, they used the clutch fecundity based on length of the females that were caught in February of the Spring Kodiak Trawl, added all those up, multiplied it by the spawning frequency for that year, which then gave them an egg production index.

The slide on the upper right shows the results.  For 2012 to 2017, the chart shows the relative abundance of eggs capable of being produced per year, which is the Delta smelt’s reproductive potential each year.  She noted that there was quite a change from 2013-2016 and indicating that egg production declined quite a bit.

So what is this good for?  Ms. Damon said they thought maybe it could be used to predict a larval index, so if you know how many eggs you could potentially collect, you could then predict larval abundances using this information.

She presented a slide showing the 20mm index plotted with the egg production index, pointing out that it highly correlates with the trends.  “So basically what this is telling us is that using spring Kodiak trawl data, you can predict what the larval production will be the following year.”


To summarize, if we wanted to increase the annual fecundity of a female, we would want to increase her size, we would want to make sure that she is able to grow throughout her entire life cycle, especially during the spawning season, and that there’s opportunity for multiple clutches,” she said.  “If you’re talking about the population and you want to increase the annual fecundity and the reproductive potential of the population, that’s really going to require some increased egg production for all of the individuals in the population, which means a longer spawning season overall so that all the individuals can benefit from increased clutches.”

You want to make sure that the females are large and can have adequate growth throughout their life-cycle.  So growth and survival are important all year.  This really means that cooler temperatures for survival, especially during the summertime when temperatures typically exceed their tolerances, and of course food availability for growth because we need the fish to be able to grow as large as possible so that their fecundity is as much as possible.”

For management implications, Ms. Damon said that if we want to help Delta smelt be as fecund as possible and improve their reproductive potential, we should provide them more food, which would involve frequent floodplain inundation to exchange the nutrients, restore habitat so there is a productive environment for food to grow, and suppress clams because if invasive species are eating the food, it’s not being used for Delta smelt.

In recent years, she noted that temperatures have been warming up in the earlier in the spring which cuts the spawning window short.  A modeling paper in 2017 by Julia Broome et al linked water temperature with flow, so improving flow throughout the estuary will help keep springtime temperatures low by decreasing the residence time and cool water releases from the reservoirs will keep the estuary cooler to provide spawning opportunities for smelt in the spring, Ms. Damon said.

For future work, they might consider refining the information to study the spawning interval in the wild, as the best estimate of the spawning interval is from culture, so trying to do some studies to see how it works in the wild and how it might vary, based on size and temperature.  They are refining the egg production model so it can be used as a predictor tool.  She concluded by giving an invitation to everyone to start getting creative about how food and temperature conditions can be improved in the estuary.


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