Is the Sacramento Splittail an Endangered Species?

by Peter Moyle, Dylan Stompe, and John Durand

The Sacramento splittail is a lovely, silvery-white fish that lives primarily in Suisun Marsh, the north Delta and other parts of the San Francisco Estuary (SFE; Moyle et al. 2004). The name comes from its unusual tail, in which the upper lobe is larger than the lower lobe. It is a distinctive endemic species that for decades has fascinated those of us who work in Suisun Marsh.  Splittail are consistently among the most abundant fishes in our samples, despite being uncommon or absent elsewhere. Historically, splittail were distributed from Tulare Lake in the southern Central Valley to roughly the present site of Redding in the north.

 Splittail have a number of attributes that make them special:

  1. Although a member of the minnow family (Cyprinidae), splittail can reach over 40 cm (16 in) in length and live 7-9 years.
  2. They thrive in brackish water (up to 29 ppt salinity), with a preference for low to moderate salinities. Most other minnow species are confined to fresh water.
  3. They are a hardy species with a tolerance for warm temperatures (up to 33 degrees C) and low dissolved oxygen levels (<2 ppt).
  4. They are obligate floodplain spawners. Adults migrate to places such as the Yolo Bypass and Cosumnes River floodplains to spawn during winter flood events. Juveniles leave the floodplain as the water drops and then move downstream to rearing areas such as Suisun Marsh.
  5. Females produce large numbers of eggs, so even a few successful spawners in a low-flow year can maintain populations.
  6. They feed on the bottom. About half their gut contents is detrital organic matter and the other half is invertebrates. Before the invasion of the overbite clam, the main invertebrate prey was opossum shrimp (Neomysis). After the invasion, they added the clams as major part of their diet.
  7. There are apparently two populations, one in the Delta and Suisun Marsh and a much smaller one in the estuaries of Petaluma and Napa rivers (Baerwald et al. 2006).
  8. The Clear Lake splittail, a distinct species derived from the Sacramento splittail, became extinct in the 1960s or 70s.
  9. They support a small fishery both as a food fish and as bait favored by striped bass anglers.

From the information above, you can deduce that splittail should be well adapted to the difficult and often changing conditions in the upper SFE. However, in 1999 splittail were listed by the US Fish and Wildlife Service as a threatened species.  They were taken off the threatened species list in 2003. So, what is going on with splittail populations?

Splittail became confined to the SFE, rather than occupying the entire Central Valley, only in fairly recent times, concurrent with the launch of multiple fisheries studies in the estuary that were designed to track populations of Chinook salmon, striped bass, and Delta smelt.  These programs provide a good basis for evaluating overall population trends. The best data on trends comes from the UC Davis Suisun Marsh monthly sampling program (otter trawls), which started in 1980 and which has kept track of abundance of young-of-year (YOY) fish, yearlings, and adults (Figure 1).

Splittail numbers (trawl catches) were high at the beginning of the Suisun study and then declined, despite three good spawning years (1980, ‘82, and ‘86). Numbers then became extremely low through 1994, coinciding with the drought of 1987-92.   As a result, the species was petitioned for listing under the Endangered Species Act in 1992. Recruitment increased slightly in 1995, followed by another poor spawning year in 1996. Overall numbers stayed fairly low through 1999, after which all age classes experienced a generally upward trend to the present. The dramatic increase in abundance after 1999 led to delisting in 2003. The delisting was supported by more research on life history, environmental tolerances, and population dynamics (Moyle et al. 2004).  A life history model also showed that population trends were strongly driven by wet years in which large numbers of juveniles were produced by adults spawning on the floodplains. However, even in drought years enough spawning can take place to maintain a small population. Increased resilience of splittail to drought may be the result of improved access to floodplain habitat since the 1990s, when the Cosumnes River Preserve and the Yolo Bypass were developed for wildlife. Presumably, this meant that even during dry years, short high-flow events provided splittail with opportunities for successful spawning.

Figure 1. Trends in yearly splittail catches in the UC Davis otter trawl sampling program, 1980-2018. Annual numbers are based on catches from monthly sampling at 17-21 stations. Note that fluctuations in catch are largely driven by recruitment of young-of-year (blue) to the population, although population persistence is largely driven by the abundance of adult splittail (grey).

The next question becomes, do other fish surveys in the estuary reflect what is going on in Suisun Marsh in terms of population trends? The California Department of Fish and Wildlife (CDFW) Fall Midwater Trawl Survey shows continued decline (Figure 2), but it is a pelagic (open water) survey that does a poor job of capturing bottom-oriented species like splittail. The Bay Study Otter and Midwater Trawl surveys (not shown) have catches similar to the CDFW Fall Midwater Trawl, with small catches of splittail. The U.S. Fish and Wildlife Service (USFWS) Beach Seine Survey (Figure 2,3), in contrast, shows trends similar to the Suisun Marsh Study, reflecting that it samples inshore areas where young splittail occur as they leave floodplains. .

The salvage data from the south Delta water export pumps (State Water Project, Federal Central Valley Project) show large numbers of young splittail during years when numbers are also high in the Suisun Marsh Study (Figure 2). The pumping plants appear to take large numbers of splittail only during wet years, when juveniles are moving downstream en masse to rearing areas.  Splittail numbers peak in the USFWS Beach Seine Survey in the same years, reflecting their bias towards collecting young moving downstream from spawning areas.

It is worth noting the response of splittail to drought in the surveys that catch them in the greatest numbers (Figure 2). Early in the Suisun Marsh Study, splittail catches showed dramatic declines, apparently because reproduction was minimal during extended drought. In wet years following droughts, there was typically a surge in recruitment of young fish. The drought response was muted in later surveys apparently because enough older fish were in the population to sustain the population until better spawning conditions returned. This was well demonstrated by the splittail response to the 2012-16 drought, during which numbers rose to record levels.

Figure 2. Standardized catches of splittail in five fish surveys. Note the extremely low catches of the fall midwater trawl survey compared to other surveys (y-axis scaling). Periods of drought are represented by shaded areas and dashed vertical red line represents the invasion of the SFE by the Asian clam. Details of standardization and each trawl survey can be found in Stompe et al. (in review, 2020).


There are several lessons that can be drawn from this story.  First, the splittail is a resilient species that can thrive in a limited part of upper SFE (the North Delta Habitat Arc, Moyle et al. 2016) that includes the Yolo Bypass and Cosumnes River floodplain for spawning, the Sacramento River for dispersing the young, and Suisun Marsh as a nursery area. The splittail is not in danger of immediate extinction although its status needs to be carefully monitored, especially during long periods of drought, given its limited distribution. In the short run (10-20 years) it can be regarded as a management success because favorable flows and restored floodplains appear to have worked. It is also possible that splittail have benefitted from operation of the Salinity Control Gates on Montezuma Slough that has kept Suisun Marsh salinities at favorable levels throughout the summer months, even in dry years. However, more studies are needed to nail down exactly what factors are limiting their abundance and to find ways to expand their range.

A second lesson is that for each species some surveys are better than others for determining trends for splittail and other species (e.g. Suisun Marsh Otter Trawl vs. Fall Midwater Trawl).

A third lesson is that research pays.  A number of diverse studies on splittail were conducted after it was listed, contributing to its being delisted. However, further study of splittail is still needed to prevent decline in a rapidly changing estuary. There are other species in the region that could also benefit from study before they get listed, to find out if listing is necessary.

The Sacramento splittail has demonstrated resilience that keeps it from being regarded once again as threatened or endangered, despite its limited range. Recent changes in federal water policy that allow more fresh water to be exported from the Delta may cause additional stress to splittail populations, resulting in a need to return it to the long list of threatened and endangered fishes in California.

Further Reading

Baerwald, M., V. Bien, F. Feyrer, and B. May. 2006. Microsatellite analysis reveals two genetically distinct splittail (Pogonichthys macrolepidotus) populations in the San Francisco Estuary. Conservation Genetics. DOI: 10.1007/s10592-006-9157-2.

Moyle, P.B., R. D. Baxter, T. Sommer, T. C. Foin, and S. A. Matern. 2004. Biology and population dynamics of Sacramento splittail (Pogonichthys macrolepidotus) in the San Francisco Estuary: a review. San Francisco Estuary and Watershed Science [online serial] 2(2):1-47.

Moyle, P., J. Durand, A. Manfree. 2016. The North Delta habitat arc: an ecosystem strategy for saving fish. UCD Center for Watershed Sciences, California WaterBlog. November 6. 2016.

Moyle, P.B., R. M. Quiñones, J.V.E. Katz, and J. Weaver. 2015.  Fish Species of Special Concern in California.  3rd edition.  Sacramento: California Department of Fish and Wildlife.

Stompe, D. K., P.B. Moyle, A. Kruger, and J.R. Durand (in review). Integrating use of fish surveys in the San Francisco Estuary.  San Francisco Estuary and Watershed Science.

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