YKL REA Aquatics

Becky Shaftel, Leah Kenney, and Timm Nawrocki

Aquatics in the REA

Conservation elements Distribution mapping methods and results Conceptual models Management questions

Aquatic conservation elementsCoarse filters• Streams and rivers• Connected lakes• Disconnected lakes

Fine filters• Chinook salmon• Chum salmon• Sheefish• Dolly Varden• Northern pike

Photo: ADF&G

Photo: ADF&G

Streams and rivers

Methods: flowlines from the USGS National Hydrography Dataset

Results: Length = 454,000 km

Connected lakes

Methods: waterbodies connected to flowlines in the National Hydrography Dataset

Results:Count = 31,600 lakes Area = 25,800 km2

Photo: USFWS

Disconnected lakes

Methods: waterbodies not connected to flowlines in the National Hydrography Dataset

Results: Count = 103,600 lakesArea = 9,400 km2

Photo: USFWS

Chinook Salmon

Methods: Clipped from the Anadromous Waters Catalog event feature class

Results:

Photo: USFWS

AWC Life Stage Designation

Length (km)

Spawning Habitat 5,436Present or Rearing 13,522

Chum Salmon

Photo: USFWS

Methods: Clipped from the Anadromous Waters Catalog event feature class

Results:

AWC Life Stage Designation

Length (km)

Spawning Habitat 5,902Present or Rearing 8,640

Sheefish

Photo: USFWS

Methods: Clipped from the Anadromous Waters Catalog event feature class

Results:AWC Life Stage

DesignationLength

(km)Spawning Habitat 117Present 6,036

Fish Distribution Models

Photo: USFWS

Evaluate model performance

Classification tree and random forest

models

ADF&G AFFID species

occurrence data

GIS source data

Predict species habitat across REA

study area

Fish distributions

Create stream network and

landscape predictor variables in GIS

Process AFFID data for use in models

Stream Network Used TauDEM to process DEM1. Add in additional HUCs on boundary of study area that

flow into the study area2. Fill pits3. Calculate flow direction (D8 method)4. Calculate contributing area 5. Create stream network based on curvature method and

drop analysis

Predictor Variables

Photo: USFWS

Predictors of Fish HabitatElevationPermafrostGradientSlope over area ratioStream orderWatershed areaAverage watershed annual precipitationAverage watershed annual temperatureAverage watershed elevationAverage watershed slope over area ratioAverage watershed slopePercent permafrost cover in watershedPercent lake cover in watershed

Process AFFID data- Select all presences by

fish in AFFID- Select absences from

projects in AFFID that listed fish community sampling as an objective

- Resample data in areas of high intensity to match densities in other HUCs

- Shift points along flow direction grid until they reached the stream network

- Extract all predictor variables to each data point for model development

Classification Trees

Photo: USFWS

Classification Tree Analysis Steps:– Identify the groups– Choose the variables– Identify the split that

maximizes the homogeneity of the resulting groups

– Determine a stopping point for the tree

– Prune the tree using cross-validation

Absent0.97(263)

Asterospicularia laurae

Shelf: Inner, Mid Shelf: Outer

Absent0.78(64)

Location: Back, Flank Location: Front

Depth < 3m Depth ≥ 3m

(De'Ath and Fabricious 2000)

Absent0.56(9)

Present0.81(37)

Misclassification rates: Null = 15%, Model = 9%

Random Forests

Creates many classification trees and combines predictions from all of them:- Start with bootstrapped samples of data- Observations not included are called out-of-bag (OOB)- Fit a classification tree to each bootstrap sample, for each

node, use a subset of the predictor variables.- Determine the predicted class for each observation based

on majority vote of OOB predictions- To determine variable importance, compare

misclassification rates for OOB observations using true and randomly permuted data for each predictor

Run models in Rct1<-mvpart(pres.f~.,data=fish.pred1[s1,],xv="1se")rf1<-randomForest(pres.f~.,data=fish.pred1[s1,],ntree=999)

Photo: USFWS

CT training CT validation RF training RF validation1 0.271 0.327 0.248 0.2642 0.273 0.27 0.262 0.2263 0.265 0.264 0.24 0.2454 0.271 0.358 0.238 0.2335 0.271 0.264 0.251 0.2526 0.283 0.352 0.257 0.2397 0.292 0.321 0.249 0.2588 0.214 0.302 0.246 0.2269 0.244 0.252 0.265 0.214

10 0.297 0.296 0.267 0.245summary 0.2681 0.3006 0.2523 0.2402

Model Performance

Photo: USFWS

Confusion Matrix0 1 Error

0 313 96 23.5%1 98 282 25.8%

Dolly Varden

Results:~ 32,000 km of predicted summer habitat (restricted to stream reaches > 1 km in length)

Photo: USFWS

Predictor 1 0watershed elevation 541 m 299 m

watershed slope 22% 10%watershed annual precip. 596 mm 521 mm

watershed annual temp. -1.36 C -1.41 C

Watershed area 71 km2 1,665 km2

Invasive MacrophytesClimate Change

Precipitation

Permafrost

FireHuman Uses

Mining

Change Agents

Drivers

CEGeneral Effect

Infrastructure

Harvest

Contaminants

Temperature

Perm

afro

st

thaw

Reduction in age at maturity and shift in spawning season

Hab

itat l

oss,

chan

ges i

n m

igra

tion

rout

es,

incr

ease

d se

dim

enta

tion

Red

uctio

n in

juve

nile

fitn

ess;

bi

oacc

umul

atio

n in

adu

lts

Dire

ct p

opul

atio

n de

clin

e

Expa

nded

ice

-fre

e se

ason

Tem

pora

ry in

crea

ses i

n nu

trien

t inp

uts;

incr

ease

se

dim

enta

titat

ion

Red

uctio

n in

hab

itat

Increased toxicity

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Incr

ease

d co

ntam

inan

t so

urce

s

Cha

nge

in

depo

sitio

n ra

tes

Cha

nges

in h

ydro

logy

Fish species

Habitat

Increase in ground flow; increase in sedimentation

Invasive MacrophytesClimate Change

Precipitation

Permafrost

FireHuman Uses

Mining

Infrastructure

Harvest

Contaminants

Temperature

Perm

afro

st

thaw

Reduction in age at maturity and shift in spawning season

Red

uctio

n in

juve

nile

fitn

ess;

bi

oacc

umul

atio

n in

adu

lts

Expa

nded

ice

-fre

e se

ason

Tem

pora

ry in

crea

ses i

n nu

trien

t inp

uts

Elod

ea sp

p co

uld

redu

ce q

ualit

y of

fora

ging

hab

itat

Increased toxicity

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Incr

ease

d co

ntam

inan

t so

urce

s

Cha

nge

in

depo

sitio

n ra

tes

Incr

ease

d w

inte

r pr

ecip

itatio

n m

ay

incr

ease

ove

rwin

terin

g ha

bita

t

Dolly VardenSalvelinus malma

Habitat

Increase groundwater flowimproves overwinter habitat

Dire

ct d

estru

ctio

n of

hab

itat,

hind

ranc

e of

mig

ratio

n ro

utes

, inc

reas

ed d

owns

tream

turb

idity

and

sedi

men

tatio

n

Change AgentsDriversCEGeneral EffectCE-Specific Effect

Dire

ct p

opul

atio

n de

clin

e

Invasive MacrophytesClimate Change

Precipitation

Permafrost

FireHuman Uses

Mining

Infrastructure

Harvest

Contaminants

Temperature

Perm

afro

st

thaw

Reduction in age at maturity and shift in spawning season

Bio

accu

mul

atio

n of

m

ercu

ry in

adu

lts

Expa

nded

ice

-fre

e se

ason

Tem

pora

ry in

crea

ses i

n nu

trien

t inp

uts

Elod

ea ss

p co

uld

redu

ce q

ualit

y of

spaw

ning

ha

bita

t

In creased toxicity

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Incr

ease

d co

ntam

inan

t so

urce

s

Cha

nge

in

depo

sitio

n ra

tes

Northern PikeEsox lucius

Habitat

Increase depth of active layer will increase lake drainage area

Subs

iste

nce

harv

est p

ress

ures

on

over

win

terin

g po

pula

tions

Dire

ct d

estru

ctio

n of

hab

itat,

hind

ranc

e of

mig

ratio

n ro

utes

, inc

reas

ed d

owns

tream

turb

idity

and

sedi

men

tatio

n

Change AgentsDriversCEGeneral EffectCE-Specific Effect

Incr

ease

d w

inte

r pr

ecip

itatio

n m

ay i

ncre

ase

over

win

terin

g ha

bita

t

Invasive MacrophytesClimate Change

Precipitation

Permafrost

FireHuman Uses

Mining

Infrastructure

Harvest

Contaminants

Temperature

Perm

afro

st

thaw

Reduction in age at maturity and shift in spawning season to later

Red

uctio

n in

juve

nile

fitn

ess;

bi

oacc

umul

atio

n in

adu

lts

Expa

nded

ice

-fre

e se

ason

Red

uctio

n in

juve

nile

feed

ing

habi

tat

In creased toxicity

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Incr

ease

d co

ntam

inan

t so

urce

s

Cha

nge

in

depo

sitio

n ra

tes

Hig

h w

inte

r flo

w m

ay a

ffec

t sp

awni

ng h

abita

t

SheefishStenodus leucichthys

Habitat

Dire

ct p

opul

atio

n de

clin

e an

d re

mov

al o

f mat

ure,

hea

lthy

indi

vidu

als

Dire

ct d

estru

ctio

n of

hab

itat,

hind

ranc

e of

mig

ratio

n ro

utes

, inc

reas

ed d

owns

tream

turb

idity

and

sedi

men

tatio

n

Change AgentsDriversCEGeneral EffectCE-Specific Effect

Sedi

men

tatio

n of

gra

vel-s

ubst

rate

in st

ream

s will

redu

ce q

ualit

y of

spaw

ning

ha

bita

t

Sedimentation of gravel-substrate will reduce quality of spawning habitat

Invasive MacrophytesClimate Change

Precipitation

FireHuman Uses

Mining

Infrastructure

Harvest

Temperature

Perm

afro

st

thaw

Reduction in age at maturity; earlier spawning season; increased parasite infection

Hab

itat l

oss,

chan

ges i

n m

igra

tion

rout

es,

incr

ease

d se

dim

enta

tionEx

pand

ed i

ce-f

ree

seas

on

Red

uctio

n in

spaw

ning

and

rear

ing

habi

tat

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Chinook SalmonOncorhynchus tshawytscha

Habitat

Dire

ct p

opul

atio

n de

clin

e an

d re

mov

al

of m

atur

e, h

ealth

y in

divi

dual

s

Change AgentsDriversCEGeneral EffectCE-Specific Effect

ContaminantsIncreased toxicity

Incr

ease

d co

ntam

inan

t so

urce

s

Cha

nge

in

depo

sitio

n ra

tes

Increase in winter habitat for juvenilesPermafrost

Red

uctio

n in

juve

nile

fitn

ess

Incr

ease

stre

am fl

ow

over

win

ter r

educ

e eg

g su

rviv

al

Sedi

men

tatio

n of

gra

vel-s

ubst

rate

will

redu

ce q

ualit

y of

spaw

ning

hab

itat;

Tem

pora

ry in

crea

ses i

n nu

trien

t inp

uts c

ould

incr

ease

juve

nile

fora

ging

Invasive MacrophytesClimate Change

Precipitation

Permafrost

FireHuman Uses

Mining

Infrastructure

Harvest

Temperature

Perm

afro

st

thaw

Reduction in age at maturity; earlier spawning season; increased egg incubation time

Hab

itat l

oss,

chan

ges i

n m

igra

tion

rout

es,

incr

ease

d se

dim

enta

tion

Expa

nded

ice

-fre

e se

ason

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Chum SalmonOncorhynchus keta

Habitat

Increased stream discharge could increase sedimentation and scour eggs

Dire

ct p

opul

atio

n de

clin

e an

d re

mov

al

of m

atur

e, h

ealth

y in

divi

dual

s

Change AgentsDriversCEGeneral EffectCE-Specific Effect

Incr

ease

stre

am fl

ow o

verw

intr

redu

ce q

ualit

y of

sp

awni

ng h

abita

t and

egg

surv

ival

Red

uctio

n in

spaw

ning

hab

itat

Sedi

men

tatio

n of

gra

vel-s

ubst

rate

in st

ream

s will

redu

ce q

ualit

y of

spaw

ning

ha

bita

t

Invasive Macrophytes

Connected LakesChange Agents

Drivers

CE

Permafrost

Human Uses

Mining

Infrastructure

Dec

reas

e in

lake

are

a; la

ke d

rain

age;

in

crea

se in

met

hane

em

issi

ons

Out

com

pete

nat

ive

aqua

tic a

nd e

mer

gent

veg

etat

ion

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Lake

dry

ing

in su

mm

er d

ecre

asin

g co

nnec

tivity

; ex

pand

ed ic

e-fr

ee se

ason

allo

w fo

r ear

ly w

ildlif

e us

e (b

irds a

nd fi

sh);

chan

ges i

n th

erm

al re

gim

es

Fire

Tem

pora

ry in

crea

ses i

n nu

trien

t inp

uts ;

pos

tfire

land

slid

es a

nd d

ebris

flow

s

Perm

afro

st

thaw

Climate Change

Precipitation Temperature

Dire

ct d

estru

ctio

n of

lake

hab

itat

Lake

are

a in

crea

se th

roug

h in

crea

sed

prec

ipita

tion;

incr

ease

d w

inte

r ha

bita

t for

aqu

atic

spec

ies

Invasive Macrophytes

Disconnected LakesChange Agents

Drivers

CE

Permafrost

Human Uses

Mining

Infrastructure

Out

com

pete

nat

ive

aqua

tic a

nd e

mer

gent

veg

etat

ion;

fast

er g

row

ing

vege

tatio

n ov

erta

king

lake

are

a

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Dire

ct d

estru

ctio

n of

lake

hab

itat

Fire

Tem

pora

ry in

crea

ses i

n nu

trien

t inp

uts;

pos

tfire

land

slid

es a

nd d

ebris

flo

ws

Lake

are

a in

crea

se th

roug

h in

crea

sed

prec

ipita

tion;

incr

ease

d w

inte

r hab

itat f

or a

quat

ic sp

ecie

s

Perm

afro

st th

aw

Lake

dry

ing

in su

mm

er d

ecre

asin

g la

ke a

rea;

exp

ande

d ic

e-fr

ee se

ason

allo

w fo

r ear

ly w

ildlif

e us

e (b

irds a

nd

fish)

; cha

nges

in th

erm

al re

gim

es

Climate Change

Precipitation Temperature

Dec

reas

e in

lake

are

a; la

ke

drai

nage

; inc

reas

e in

met

hane

em

issi

ons

Invasive Macrophytes

StreamsChange Agents

Drivers

CE

Permafrost

Human Uses

Mining

Infrastructure

Perm

afro

st

thaw

Alte

red

hydr

olog

ies;

incr

ease

d ch

anne

l dis

turb

ance

from

flo

odin

g; in

crea

sed

disc

harg

e an

d se

dim

ent t

rans

port;

incr

ease

in

win

ter p

reci

pita

tion

will

incr

ease

wild

life

over

win

ter h

abita

t

Out

com

pete

nat

ive

aqua

tic a

nd e

mer

gent

veg

etat

ion

Increased potential for establishment of invasive macrophytes and changing fire dynamics

War

min

g co

uld

incr

ease

ext

ent o

f ava

ilabl

e ha

bita

ts;

leth

al te

mpe

ratu

re li

mits

for f

ish

and

othe

r aqu

atic

or

gani

sms ;

cha

nge

in th

erm

al re

gim

es

Dire

ct d

estru

ctio

n of

stre

am h

abita

t, ch

ange

in c

ondu

ctiv

ity,

redu

ced

flow

Fire

Tem

pora

ry in

crea

ses i

n nu

trien

t inp

uts;

pos

t fire

land

slid

es a

nd d

ebris

flow

s;

incr

ease

d ch

anne

l dis

turb

ance

; alte

red

ripar

ian

vege

tatio

n an

d st

ream

shad

e,

tem

pera

ture

cha

nge

regi

mes

Climate Change

Precipitation Temperature

Incr

ease

d se

dim

enta

tion

rate

s

Management Questions

How, where, and when could Essential Fish Habitat (EFH) be affected by predicted changes in

climate?

- Primarily a literature review. SNAP does not currently have models predicting changes in aquatic habitats, such as stream temperature or hydrologic regime

Photo: USFWS

Management Questions

Where and how might mineral resource

development affect fishery habitat?

- From BSWI RMP: field validated information on historic and current mining sites and high, medium, and low mineral potential by sections

- Other options include ARDF and permit data

Photo: USFWS

Review

Please review and provide comments:- Distribution models for fish and habitats- Conceptual models and text descriptions for fish

Not yet final: - Northern pike distribution model- Conceptual models and text descriptions for habitats

Contact: Rebecca Shaftelrsshaftel@uaa.alaska.edu, 907-786-4965 Photo: USFWS