Fish Assemblage Metrics: Key Focal Species Physical Habitat Metrics Based On Life History Stage Associations and

Population Dynamics; Responses of Native and Invasive Species

Populations

Sean Hayes,

Director of Fisheries Ecosystem Research Unit, NMFS

Southwest Fisheries Science Center

Salmon Ocean Ecology Team Leader(enabler?)

???

This one time……….

in Scott Creek…

John clarified…“So we hope ….we can develop metrics based on specific life history associations with physical habitat conditions, and develop a rating system of alternatives based on understanding how these specific life history associations with physical habitat conditions would play into the dynamics of population growth and recovery ”

Freshwater?

Ocean?Can we fix something

here?

2 adults return to spawn

4,000 eggs are laid

800 fry hatch

200 smolts go to sea

10 reach adulthood

To make more fishhere?

How do we DO and MEASURE that?

Metrics

1. Growth 2. Food3. Survivorship in the new habitat

- Water quality, predators….

4. migration behavior/timing/recruitment in/out of the new habitat

5. subsequent measures of marine survival

GOAL- try to change certain perspectives

Benefits of Wetland rearing

• Case studies– Yolo Bypass- Sacramento– Scott Creek

Ted Sommer - DWR

Knaggs Ranch Agricultural Floodplain Pilot Project Results 2011-2012

UCD, DWR, NMFS, Cal TroutUSBR and others..

Pilot Project

5-acres

Average Length and Weight48 mm

1.09 grams

Fish planted 1/31/12

The Knaggs Ranch Pilot Project:Testing Chinook growth on an

experimental agricultural flood plain

5x the weight in 6 weeks

Scott Creek example

Typical spring downstream migrant (smolt?)

After 5-6 months rearing in estuary

100mm

Steelhead in Scott Creek

~20% of “smolts” use it- but comprise 85% of returning adults

Food

• Scott Creek Estuary- benthic crustaceans Corophium and Eogammarus sp

• Yolo Bypass- seed banks of midge cocoons (Hydrobaenus saetheri)- (Benigno and Sommer 2009)

• Mokelumne River- Large Pulse flood events from reservoirs produce zooplankton communities including lipid rich Daphnia (Kern et al in prep)

Migration & Survival of Juvenile Salmonids in

California’s

Central Valley

&

San Francisco

Estuary

R.B. MacFarlaneA.P. KlimleyS.L. LindleyA.J. AmmannP.T. SandstromC.J. MichelE.D. Chapman

Coleman Hatchery

Red Bluff Diversion Dam

Ord Bend

Sacramento

Confluence with Delta Cross Channel

Rio Vista Bridge

Chipp’s IslandBenicia Bridge

Golden Gate Bridge

Butte City Bridge

Colusa Bridge

Thomes Creek Confluence

GCID

X 1000= Survival

Fall Run acoustic tracking 2012spring 2012 Pilot Effort

Tagging goals

• Fall run- CNFH– 140 x 2 early/late Apr

Cumulative Survival across all reaches of Sacramento River for Fall Run Chinook

0

0.2

0.4

0.6

0.8

1

0100200300400500

River km

Cu

mu

lati

ve

Su

rviv

al

Group 1 (April 19)

Group 2 (May 1)

5% !!

Central Valley Predator Issues

Cumulative Survival across all reaches of Sacramento River for Fall Run Chinook

0

0.2

0.4

0.6

0.8

1

0100200300400500

River km

Cu

mu

lati

ve S

urv

ival

Group 1 (April 19)

Group 2 (May 1)

The Predator Issue….. Just how bad is it?

Loboschefsky, E., Benigno, G., Sommer, T., Rose, K., Ginn, T., Massoudieh, A., and Loge, F. 2012. Individual-level and Population-level Historical Prey Demand of San Francisco Estuary Striped Bass Using a Bioenergetics Model. San Francisco Estuary and Watershed Science 10(1).

• Sacramento Bay/Delta populations of striped bass consume….~25,000,000 KG of fish per year

5% survival

…of 12 million fish

(600,000 left….)the single largest Chinook release in CA 10,000,000 fish * 5g= 50,000 kg

50,000kg/25,000,000= ….0.2%of striped bass annual metabolic requirements

The envelope continued

• CA hatcheries release 50million fish (some years)…• Mostly sub-yearling, some yearlings… ave 10g fish?

10g *50,000,000= 500,000kg hatchery salmonids

500,000/25,000,000 kg= 2%

“Striped Bass are not a problem for salmon…. they rarely appear in their diet…”

Striped bass can eat every single juvenile salmon in the Sacramento/San Joaquin basin and they still wont be a significant part of striped bass diet…

Salmon Life cycle

The salmon life cycle

Image courtesy of S. Lindley

Escapement+ Harvest=~105,000 4,000

eggs are laid

800 fry hatch

????

10 reach adulthood

CNFH Fall Run12,000,000 fry

~0.8% ‘return’

95%mortality-~600,000 smolt enter the ocean

Marine survival 15-20%!!!

Scott Creek Predation- how much can a few birds really eat?

1939 kJ/day

11.3 g at 4.16 kJ/g

47 kJ/steelhead

41 steelhead/day

1230 steelhead/month

Lagoon Recruitment

0

2000

4000

6000

8000

10000

12000

14000

16000

18000

Smolt trap Lagoon Recruitment

2007

2008

2009

3 Months x 2 Mergansers = 6000 Juveniles!

Summer Lagoon Population Dynamics

0

500

1000

1500

2000

2500

1-Jul 21-Jul 10-Aug 30-Aug 19-Sep 9-Oct 29-Oct 18-Nov

# o

f fi

sh

in

la

go

on

2007

2008

2009

Point Reyes Bird Observatory

Consumption Excretion

Back-calculating consumption

Recapture

0.84%N= 35,000

Consum

ption

Back-calculating consumption

~ 27%

~ 30-50%of juvenile salmonids consumed by

Western gulls

In the last 100 feet of stream!

Metrics

1. Growth 2. Food3. Survivorship in the new habitat

- Water quality, predators….

4. migration behavior/timing/recruitment in/out of the new habitat

5. Entrainment/Entrapment?6. Subsequent measures of marine survival

Fish die…

get over

it!

Conclusions

• Multiple metrics can be measured• Fairly straight forward

– Lots of know-how in RR basin– Logistics cheaper/easier than Sacramento

• Don’t be afraid of predator issues– trade off of mortality for growth can lead to increased

marine survival

• Given the loss of wetland habitat…– You can probably only improve

Upper river

Lower river

Delta

Estuary

0

20

40

60

80

100

Reach

% C

umul

ative

Sur

viva

l

1 5 10

Late Fall Chinook Cumulative Downstream migration and survival 2007-2009

Only 7% make it to the ocean!

Points to include

• Metrics• Benefits of floodplain/estuarine/wetland

rearing• Examples of predation• Scott creek• Central valley- coleman vs striped bass• Final metric must be marine returns

Experiment to Determine Excretion probability

+ + +

• Rapid Growth

CosumnesRiver

Natural habitat &Rapid Growth

Photos: C. Jeffres

What ?Predators?(Frechette and Osterback)

460 Kcal/day= 50-100 coho parr

River growth vs. floodplain growth

Jeffres et al 2008

Fish released Average Length and Weight 3/12/12 76.2 mm

5.27 grams

Floodplain fatties!

Black lines indicate upper watershed growthBlue lines indicate migration to estuary and growth

J an J ul J an J ul J an J ul J an J ul J an

For

k Le

ngth

(m

m)

0

50

100

150

200

250

Mean

5th %

95th %

YOY 1+ 2+ 3+

Growth patterns from egg to smolt

Oceanupper watershed estuary/lagoon

Size threshold for ocean survival

80% of returningadults use estuary pathway