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Understanding the Scale and Mechanisms of Connectivity between Splittail Populations and the Implications for Management

Primary Investigator

Melinda Baerwald
Adult splittail captured in gill net.
Credit: Melinda Baerwald


Splittail, Pogonichthys macrolepidotus, is found only in the San Francisco Estuary and is listed as a California Species of Special Concern. There is an urgent need to understand splittail population dynamics in order to better manage and protect this native minnow. It is now known that two splittail populations exist, one spawning primarily in the Central Valley and one spawning in the Napa and Petaluma rivers. These populations may have unique life history or population dynamics and should be managed independently to preserve their unique genetic identities.

Project Purpose

Our research study compared key characteristics and potential long-term viability of the two splittail populations by integrating genetic, physiological, and modeling approaches. The genetic component investigated the potential overlap in range distribution of the two populations during the non-spawning season. This information will enable more focused monitoring and/or habitat conservation if either population is considered threatened or endangered in the future. Genetics also enabled us to estimate effective population size, which is extremely useful for predicting each population’s current and future viability and can be considerably smaller than census population size. The physiological component examined responses of each population to different environmental factors that vary between the spawning grounds (i.e. temperature and salinity) and investigate the potential for these populations to adapt to local conditions. Both juvenile and adult life stages were used to determine conditions that can be tolerated and conditions that are preferred in order to gain insight into each population’s environmental preferences and potential selective factors that may influence splittail population structure and long-term viability.

Objectives of the Study

Results from the genetic and physiological studies were used to develop a comprehensive splittail model to determine the degree of connectivity between the two splittail populations and assess extinction risk for each population. Our interdisciplinary approach ultimately enables a more comprehensive understanding of each population’s geographic distribution, genetic integrity, growth potential, response to environmental conditions, and potential extinction risk.


Gill net set in Honker Bay to study Splittail populations.


Transporting juvenile splittail caught in the Petaluma River back to UC Davis.



VI Alpha tag (Northwest Marine Technologies) implanted in adult splittail. These tags can identify individuals and will be used for the physiology studies.




What We Learned

Effective Population Size: We found that the Central Valley population has an effective population size that is considerably (~3x) larger than the San Pablo (Petaluma/Napa) population. This finding suggests that more focused monitoring and/or habitat conservation should occur for the San Pablo Bay population since its population size is considerably reduced in comparison to the Central Valley population.


Distribution Patterns: When examining age-0 splittail distribution patterns, we found that the two populations are predominantly spatially segregated when water flow rates are average or below average, but substantial geographic overlap may occur during years of high flow rates.  Similarly, adults exhibit increased spatial overlap between the populations during spawning seasons with high flow rates. Intermittent spatial intermixing, however, has not weakened the observed genetic distinctions between the two populations during the past decade. The mechanisms enabling continued population differentiation despite flow-dependent spatial overlap are currently unknown.


Physiological preferences and tolerances: Wild-caught splittail of both juvenile and adult life stages were used for preference and tolerance challenges in order to gain insight into each population’s environmental preferences and potential selective factors that may influence splittail population structure and long-term viability. We showed that splittail populations varied little in upper thermal tolerance limits (critical thermal maxima ranging from 33.7-34.6°C), but did vary in preferred temperatures. In general, juvenile San Pablo and Central Valley fish preferred 19-21°C, as did San Pablo adults. Central Valley adults selected cooler temperatures of 14-19°C. Salinity tolerance and associated osmoregulatory capacities also differed among splittail populations and lifestages. In hatchery-born and wild caught juvenile San Pablo splittail, we found upper salinity tolerances to be 16 ‰, which was higher than the upper salinity tolerance of 14 ‰ for wild caught juvenile Central Valley splittail. This, in conjunction with differential magnitudes of osmoregulatory disturbances between Central Valley and San Pablo splittail in response to salinity, supported our hypothesis of inter-population variation. In wild-caught adults, we found both populations to tolerate salinities of up to 11 ‰, with 100% survival for 336 hr. Cellular and tissue osmoregulatory disturbances, assessed by measuring plasma osmolality and ions, skeletal and ventricular muscle moisture and Na+-K+-ATPase during a 24 to 336 hr 11 ‰ salinity treatment, showed evidence for impaired osmoregulatory capabilities in adult Central Valley relative to San Pablo splittail. Osmoregulatory disturbances under this salinity treatment corroborated findings for juvenile splittail and further supported our hypothesis of variation in salinity tolerance between Central Valley and San Pablo splittail. Overall, the improved salinity tolerance of San Pablo juvenile and adult splittail is consistent with its higher salinity habitat. Population differences in salinity tolerance and temperature preference support the recommendation of population specific management that acknowleges differential habitat preferences and preserves resiliency to salinity demonstrated in San Pablo fish. 


Modeling: Results from the genetic and physiological studies were used to inform a more comprehensive splittail model, which saught to determine the degree of connectivity between the two splittail populations and assess extinction risk for each population. The modeling effort has resulted in two models, which demonstrate that the two populations are capable of surviving independently. The Central Valley population is essentially invulnerable to extinction. While the San Pablo population is stable, its extinction risk is higher because it is considerably smaller and exists in a very limited environment. However, considerable flow of Central Valley individuals into the San Pablo population results in the distinctive San Pablo genetic composition being swamped by the Central Valley. Since it is in conflict with existing data, considerable reproductive linkage between the two populations is not a realistic alternative.

Project Information

Funding Amount: 
PSP Year: 

Start and End Dates

07/01/2011 to 03/31/2015

Grant Documents

Executive Summary

Scope of Work

Final Project Report

Coequal goals

The Delta Stewardship Council was created in legislation to achieve the state mandated coequal goals for the Delta. "'Coequal goals' means the two goals of providing a more reliable water supply for California and protecting, restoring, and enhancing the Delta ecosystem. The coequal goals shall be achieved in a manner that protects and enhances the unique cultural, recreational, natural resource, and agricultural values of the Delta as an evolving place." (CA Water Code §85054)