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3.2.4 Fish Community Diversity


Goal: B. Protect and enhance native aquatic and terrestrial species, especially sensitive and at-risk species and natural communities

Objective: 3. Protect and enhance native fish populations

WAF Attribute: Biotic condition

What is it?

The abundance of individual fish and the diversity of fish species present can tell a lot about the conditions in waterways and watersheds. Two metrics of fish community condition were used, based on indicators used by the South East Queensland Ecosystem Health Monitoring Program (Australia). These metrics are:

  • Percentage of native species expected (PONSE). This is a measure of observed number of fish species (species richness) compared to expected number of species based on expert knowledge and observations in other regions of the river. The primary source for expected species was the Sierra Nevada Ecosystem Project (SNEP), with adjustments based on survey effectiveness (see below under “Data manipulation”).
  • Proportion native species (PNS). This is the percentage of native species of total fish caught or observed (not species number). This metric assesses what proportion of the community is composed of native species. Native/exotic identity was determined using information from the SNEP report.

In addition to these fish community composition measures, local Chinook salmon population assessment was used for the Lower Feather and Lower Yuba regions. Population is scaled from 0 to 100 by comparing recent six-year geometric mean of abundance to DFG targets for population restoration (Table 1).

Why is it Important?

Fish are a common and familiar component of freshwater environments, and fish communities reflect a range of natural and human-induced disturbances through changes in abundance and species composition. Ecological assessments based on fish community structure have the advantage over more traditional physical and chemical indices (e.g. conductivity, turbidity, nutrients) in that fish provide an integrated measure of stream condition due to the mobility, relatively long-life, and high trophic level of the animals involved (SEQ EHMP methods). Low native species presence can be an indicator of high disturbance levels, which disrupt natural community balance and exclude stress-intolerant species and/or non-generalists. Presence of exotic species is also a good indicator of poor ecological health (Meador et al. 2003). Many invasive species are highly competitive generalists, and can exclude local species. In addition, exotics may be able to establish due to altered habitat processes (i.e. higher water temperatures, changes in mean water level) or through direct human introduction (i.e. stocking, discard of aquarium fish).

Native salmonid species are of great ecological, economic, and cultural importance to local communities. They also serve as strong indicators of habitat quality and integrity in river systems, particularly with regard to water temperature, sediment load, and barriers to passage. The Central Valley spring-run Chinook salmon in particular is listed as a threatened species under the ESA, giving them a high priority for restoration. The main threats to the remaining populations are loss and degradation of habitat. In particular, rising water temperature combined with loss of upstream spawning and rearing habitats blocked by dams has diminished available juvenile summer habitat greatly. Within the Feather River Watershed, only two populations persist. One, in the Feather River itself, is completely dependent on the Feather River FIsh Hatchery to maintain itself. The other, in the Yuba River, is of unknown status.

What is the target or desired condition?

Ideally, native fish communities will be fully intact and contain no invasive or introduced species. A PONSE and PNS of 100 indicate that every expected species was found in the area, and no exotic species were caught.

For Chinook populations, the target condition is taken from DFG’s Central Valley targets (DFG 1988). Because the targets are given for the Sacramento Basin as a whole, the five-year geometric mean proportion of total population for the subwatersheds was used to determine a specific restoration target for the Feather and Yuba populations. The target for population for each of the Feather and Yuba was based on the proportion of the total observed returning salmon to the Sacramento River that returned to each of these rivers.

Table 1. Target Chinook populations for Feather and Yuba Rivers

Sacramento Feather River Yuba River
Chinook Run Target
Proportion of Returning Sacramento River Salmon Target Population Proportion of Returning Sacramento River Salmon Target Population
Fall 450,000 0.237 106,659 0.044 19,726
Spring 23,300 0.206 4,796    

What can influence or stress condition?

Primary stressors for native fish communities are habitat degradation, high fine-sediment load, increasing maximum water temperatures, and introduced species. Salmonids are negatively impacted by increased maximum water temperatures, sediment loads, habitat loss, barriers to passage, and predation by black bass and striped bass on their young.

What did we find out/How are we doing?

Overall scores for all subwatersheds based on fish community composition and abundance of salmon in the lower watershed are given in Table 2.

Fish Community Composition

Survey information was limited, with only a few surveys and years per subwatershed. Most surveys were performed during only a few months per year, so annual aggregation and trend analysis was most appropriate. Although not all surveys were conducted identically, with combinations of electrofishing, snorkeling, and passive monitoring, results could be compared once converted into PONSE and PNS values. No data were available in the Lower Bear subwatershed. Score calculation was straight-forward, with 100 indicating all expected native species detected and no exotic species caught (with 0 indicating the reverse). Current status for each subwatershed was calculated by averaging across all sites for their most recent years. The PONSE and PNS are given in Tables 3 and 4, respectively. The majority of native species caught were Chinook salmon (in the Lower Feather and Lower Yuba) and Rainbow trout (in all subwatersheds).

Table 2. Report Card scores for fish community condition for subwatersheds

Goal Measurable Objective Subwatershed Score
B. Protect and enhance native aquatic and terrestrial species, especially sensitive and at-risk species and natural communities 2) Protect and enhance native fish communities. NFF 47
MFF 63
LF 55
NY 47
MY 51
SY 38
DC 23
LY 48
UB 51
LB n/a


Figure 1. Fish community condition scores and community sampling sites across subwatersheds. Salmon monitoring occurs on the Lower Feather and Yuba rivers and sites are not shown.


Table 3. Percent of native species expected (PONSE) values for subwatersheds. 95% C.I. refers to 95% confidence intervals.

Region Name PONSE Minimum Maximum N 95% C.I.
DC Deer Creek 0.182 0.000 0.600 11 +/-0.11
EBNFF East Branch North Fork Feather 0.444 0.000 0.667 9 +/-0.12
LB Lower Bear NA NA NA 0 NA
LF Lower Feather 0.542 0.000 1.000 6 +/-0.31
LY Lower Yuba 0.600 0.200 0.800 3 +/-0.39
MFF Middle Fork Feather 0.417 0.167 0.667 2 +/-0.49
MY Middle Yuba 0.267 0.167 0.333 5 +/-0.08
NFF North Fork Feather 0.500 0.500 0.500 2 NA
NY North Yuba 0.208 0.000 0.500 4 +/-0.21
SY South Yuba 0.175 0.000 0.500 38 +/-0.05
UB Upper Bear 0.250 0.000 0.500 12 +/-0.09

Table 4. Proportion native species (PNS) values for subwatersheds. 95% C.I. refers to 95% confidence intervals.

Region Name PNS Minimum Maximum N 95% C.I.
DC Deer Creek 0.281 0.000 0.818 11 +/-0.16
EBNFF East Branch North Fork Feather 0.826 0.000 1.000 9 +/-0.21
LB Lower Bear NA NA NA 0 NA
LF Lower Feather 0.999 0.998 1.000 6 +/-0.00
LY Lower Yuba 0.758 0.273 1.000 3 +/-0.48
MFF Middle Fork Feather 0.847 0.694 1.000 2 +/-0.30
MY Middle Yuba 0.758 0.214 1.000 5 +/-0.29
NFF North Fork Feather 0.437 0.144 0.731 2 +/-0.58
NY North Yuba 0.730 0.000 0.999 4 +/-0.48
SY South Yuba 0.580 0.000 1.000 38 +/-0.13
UB Upper Bear 0.765 0.000 1.000 12 +/-0.21

A Regional-Kendall trends analysis (see Section 4.3) was performed on PONSE data from each subwatershed, as well as the overall region. Results are shown in Tables 5 and 6; no significant trends were found.

Table 5. Regional-Kendall trend analysis of PONSE values for subwatersheds. “Tau-b” is a Regional-Kendall test statistic.

Region Tau-b Significant? p Slope Magnitude
DC -0.375 No 0.480 0.000
EBNFF 0.143 No 0.706 0.000
LB Insufficient data    
LF 0.282 No 0.126 0.000
LY 0.000 No 0.712 0.000
MFF Insufficient data    
MY -0.250 No 0.617 0.000
NFF Insufficient data    
NY 0.000 No 0.564 0.000
SY 0.000 No 0.773 0.000
UB 0.125 No 0.724 0.000

Table 6. Regional-Kendall trend analysis of PNS values for subwatersheds. “Tau-b” is a Regional-Kendall test statistic.

Region Tau-b Significant? p Slope Magnitude
DC -0.625 No 0.157 -0.175
EBNFF -0.429 No 0.450 -0.014
LB Insufficient data    
LF 0.054 No 0.810 0.000
LY 0.000 No 0.712 0.000
MFF Insufficient data    
MY 0.000 No 0.617 0.000
NFF Insufficient data    
NY 0.333 No 0.564 0.000
SY 0.000 No 0.773 0.000
UB 0.125 No 0.724 0.011

Chinook Salmon Population

Chinook populations were analyzed in the Lower Feather and Lower Yuba subwatersheds. Although salmon spawn in the Lower Bear River, no regular monitoring of spawning is conducted there. Annual population sizes for the fall- and spring-run Chinook in both rivers are shown in Figures 2a and b. Current condition was calculated as described above, and the scores are given in Table 7. Note that the Feather River fall-run is composed of about 20% hatchery fish, whereas the spring-run is entirely maintained by hatchery fish. Confidence in these scores is slightly lower, because the data for the most recent years (2006-2009) are considered preliminary. However, these numbers are usually only adjusted slightly so all conclusions should be valid.

Trends were calculated using a Mann-Kendall analysis, and results are given in Table 8. Overall conditions are shown in Table 1, with salmonid scores averaged with the Lower Feather and Lower Yuba fish community scores. Note that the only positive trend was for the spring-run of Lower Feather Chinook. This is despite very low numbers in 2008-2009. The spring-run is an endangered population. Both Feather River populations had a spike in abundance around 2001-2003, and have diminished since. It is unclear whether this is natural variation or due to anthropogenic factors.

Figure 2. Chinook fall-run (2A) and spring-run (2B) populations



Table 7. Current state assessment for Chinook populations compared to targets for the populations. 95% C.I. refers to 95% confidence intervals.

Population 5-yr Geometric Mean 5-yr




95% C.I. %


Target Score
Lower Upper
FR Fall 30,949 11,021 89,464 13,701 69,911 31.3% 106,659 29.02
FR Spring 1,735 989 2,674 1,258 2,392 100% 4,796 36.17
YR Fall 5,724 2,604 17,630 2,944 11,129 0% 19,726 29.02

Table 8. Trend analysis for Chinook populations over last 40 years. “Tau-b” is a Mann-Kendall test statistic.

Population Tau-b Significant? p Slope Magnitude
FR Fall 0.137 No 0.1425 381.6
FR Spring 0.480 Yes <0.0001 82.6
YR Fall 0.171 No 0.0641 132.4

Table 9. Overall scores and trends for subwatersheds. This score is a combination of scores from the fish community metrics and salmon population estimates. “n.s” means that the trend was not significant. “n/a” means that data were not available.

Region Overall Score Trend
DC 23.16 n.s.
EBNFF 63.50 n.s.
LB NA n/a
LF 54.81 n.s./pos.
LY 48.45 n.s.
MFF 63.18 n.s.
MY 51.21 n.s.
NFF 46.87 n.s.
NY 46.92 n.s.
SY 37.76 n.s.
UB 50.73 n.s.

Temporal and spatial resolution

There is an uneven distribution of fish monitoring sites across the watershed and a tendency for these sites to be associated with FERC relicensing processes and thus rivers with regulated flows and large dams and reservoirs. The highly-regulated South Yuba had a disproportionately large number of sites relative to other subwatersheds. Because of the association of fish community monitoring with FERC re-licensing, most data have been collected recently. Returning salmon have been well monitored in this watershed for many years, though the methods for assessing population health have changed over the years. Currently there is extensive monitoring of returning adults in the lower watershed, but not as extensive monitoring of juvenile rearing, growth, and return to the ocean.

How sure are we about our findings (Things to keep in mind)

For both fish community and salmon population assessments assumptions were made about targets (species richness and abundance). Modifications of these targets because of habitat variation (fish community metrics) and new estimates of target populations (salmon) would change the corresponding condition scores.

There were sufficient data to be confident about the fish community findings and the spawning salmon abundances to be confident in the trends measured. Longer term monitoring will be needed to estimate trends in fish communities with greater confidence.

Technical Information

Data sources:

DWR fish community survey data on the Feather River (1997-2005, 6 locations)

FRCRM 2001, 2003 electrofishing data (multiple creeks)

NID, FERC survey data on the Yuba and Bear River (2008-2009)

Friends of Deer Creek fish community survey data (2007-2008)

Vaki Riverwatcher 2008-2010

DFG Annual Reports Chinook Salmon Spawner Stocks in California’s Central Valley (1953-2009)

Data transformation and analysis:

Unidentified species:

Unidentified species were not relevant to PONSE calculation, and were only included in PNS if the native/exotic status was well-defined (i.e. “unidentified sculpin” or “unidentified bass,” given that only native sculpins and exotic bass are found in the species lists).


Survey data for each site were combined annually, so that each site had only a single data point for each year. Fish abundances from individual surveys were added together to form one “total survey.” Subwatershed trends were then determined via a Regional-Kendall analysis across all sites within the subwatershed. Current state was determined by averaging PONSE and PNS scores for the most recent year at each site within the subwatershed. Most datasets included only a few samples per year in a few months, so monthly analysis was impossible.

Expected native species:

Expected native species were determined through a combination of factors. First, a list of species native to the Sacramento River Basin was taken from the SNEP report (SNEP, 1996). Then the subwatersheds were divided into low and high elevation sites, and the native fish were divided accordingly depending on habitat preferences. Elevation decisions were made by estimating whether each subwatershed was primarily lowland/foothills or in the mountainous region of the watershed. Finally, the lists were reduced to only fish that had been caught in at least one of the relevant subwatersheds. This limited the number of expected species to only those known to be found by the electro-fishing surveys employed. Expected species for the Lower Feather were slightly expanded, because the surveys conducted there were more thorough than in other regions. Final expected species lists are given in Table 10.

Table 10. Expected species for different subwatersheds

Low elevation
LF Rainbow trout(RBT), Sacramento sucker (SSK), Sacramento pikeminnow (SPM), Speckled dace (SPD), Hardhead (HHD), Pacific lamprey (PLP), River lamprey (RLP), Tule perch (TUP)
LB No surveys conducted.
High elevation
NFF RBT, SSK, SPM, SPD, Riffle sculpin (RIS), California roach (RCH)
MY RBT, SSK, SPM, SPD, RCH, Lahontan redside (LRS)

Salmon abundance

The abundances for the most recent years (2006-2009) are considered preliminary. Confidence in current state is accordingly slightly lower.


SE Queensland EHMP methods

Meador, M. R., L. R. Brown, and T. Short. 2003. “Relations between introduced fish and environmental conditions at large geographic scales.” Ecological Indicators 3:81-92.

Sierra Nevada Ecosystem Project Final Report to Congress. 1996. “Status of the Sierra Nevada”.

California Dept. of Fish and Game: Chinook escapement estimate from March 9, 2010

CALFED Vision for Chinook Salmon, February 3, 1997