Monitoring Fish Populations


Two common methods used to monitor fish populations are:

Physical Monitoring.  Scientists monitor fish population abundance and movement through methods such as pit tagging, snorkel surveys, electrofishing, and sonar monitoring. These approaches can also measure the physical conditions of fish habitat including water quality, water temperature, streamflow, and gravel composition.

Genetic Analysis. Genetic analysis tells scientists a lot of about the life history of a fish. Field biologists take a small fin clip from a fish and analyze the DNA — looking for small differences in nucleotide sequence – by a molecular biological technique called single nucleotidepolymorphism (SNP) analysis. From this genetic test, we can get clues as to the level of exchange of genetic information among populations (degree of inbreeding), native or hatchery lineage, and identify related populations in the same or nearby watersheds.

Genetic isolation can arise from fish passage barriers and along with declining population numbers, and can cause genetic bottlenecks. Populations with a lack of genetic diversity causes population inbreeding making them more susceptible to environmental threats since their adaptive capacity is impaired.

Maximizing biodiversity is an effective ecological risk mitigation strategy that can help inform where conservation efforts should be focused to protect native populations.

Science into Action


Using physical monitoring and genetic analysis to track fish populations will provide us better information for our conservation plans to protect native, wild fish. Below are two projects using genetic analysis. 

Saving the Rainbows. Southern steelhead represent the southern edge of the species’ range and are critically vulnerable to climate change. CalTrout’s project, the Native Rainbow Trout Project, will increase resiliency of native rainbow trout populations in Southern California and facilitate recovery of endangered southern steelhead.

These land-locked populations in Southern California are the remnants of steelhead runs over 100 years earlier.

They were identified by molecular genetic analysis by a study completed in 2014, and are recognized as the last remaining genetics sources of these historical salmonid populations. Learn more.

Fall River Fish Tagging. In 2012 researchers at CWS noticed an unusual thing happening in the Fall River.  Rainbow trout were spawning in September. 

With the combination of genetic data and location where the fish go spawn, we were able to determine that there are two distinctly different populations of trout in the Fall River, one that spawns in Bear Creek and one that spawns near the springs. Learn more.

Saving the Rainbows: Finding Shelter for Rescued Native Trout in Southern California

CalTrout is using spatial and genetic analysis to plan for relocating native trout if they become threatened by wildfire or drought. Southern steelhead represent the southern edge of the species’ range and are critically vulnerable to climate change. CalTrout’s project, the Native Rainbow Trout Project, will increase resiliency of native rainbow trout populations in Southern California and facilitate recovery of endangered southern steelhead.

Learn More