YKL REA Aquatics

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 elements

Coarse 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 km
2

Photo: USFWS

Disconnected lakes

Methods:
waterbodies

not
connected to
flowlines

in the
National Hydrography
Dataset


Results:

Count = 103,600 lakes

Area = 9,400 km
2

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

5,436

Present 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

5,902

Present or Rearing

8,640

Sheefish

Photo: USFWS

Methods: Clipped
from
the
Anadromous

Waters Catalog event
feature class


Results:

AWC Life Stage

Designation

Length

(
km)

Spawning Habitat

117

Present

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 DEM

1.
Add in additional HUCs on boundary of study area that
flow into the study area

2.
Fill pits

3.
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 Habitat

Elevation

Permafrost

Gradient

Slope over area ratio

Stream order

Watershed area

Average watershed annual
precipitation

Average watershe
d annual
temperature

Average

watershed elevation

Average watershed slope over area
ratio

Average watershed slope

Percent permafrost cover in
watershed

Percent 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


Absent

0.97

(263)

Asterospicularia laurae

Shelf: Inner, Mid


Shelf: Outer


Absent

0.78

(64)

Location: Back, Flank


Location: Front


Depth < 3m


Depth
≥

3m

(De'Ath and Fabricious 2000)

Absent

0.56

(9)

Present

0.81

(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 R

ct1<
-
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 validation

1

0.271

0.327

0.248

0.264

2

0.273

0.27

0.262

0.226

3

0.265

0.264

0.24

0.245

4

0.271

0.358

0.238

0.233

5

0.271

0.264

0.251

0.252

6

0.283

0.352

0.257

0.239

7

0.292

0.321

0.249

0.258

8

0.214

0.302

0.246

0.226

9

0.244

0.252

0.265

0.214

10

0.297

0.296

0.267

0.245

summary

0.2681

0.3006

0.2523

0.2402

Model Performance

Photo: USFWS

Confusion Matrix

0

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

0

watershed
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 km
2

1,665

k
m
2

Invasive
Macrophytes

Climate

Change

Precipitation

Permafrost

Fire

Human Uses

Mining

Change Agents

Drivers

CE

General Effect

Infrastructure

Harvest

Contaminants

Temperature

Permafrost thaw

Reduction in age at maturity and shift in
spawning season

Habitat loss, changes in migration routes, increased
sedimentation

Reduction in juvenile fitness;
bioaccumulation in adults

Direct population decline

Expanded ice
-
free season

Temporary increases in nutrient inputs; increase
sedimentatitation

Reduction in habitat

Increased toxicity

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Increased contaminant sources

Change in
deposition rates

Changes in hydrology

Fish species

Habitat

Increase in ground flow;
increase in sedimentation

Invasive
Macrophytes

Climate

Change

Precipitation

Permafrost

Fire

Human Uses

Mining

Infrastructure

Harvest

Contaminants

Temperature

Permafrost thaw

Reduction in age at maturity and shift in
spawning season

Reduction in juvenile fitness;
bioaccumulation in adults

Expanded ice
-
free season

Temporary increases in nutrient inputs

Elodea
spp

could reduce quality of foraging habitat

Increased toxicity

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Increased contaminant sources

Change in
deposition rates

Increased winter
precipitation may increase
overwintering habitat

Dolly
Varden

Salvelinus

malma

Habitat

Increase groundwater flow

i
mproves overwinter
habitat

Direct destruction of habitat, hindrance of migration routes,
increased downstream turbidity and sedimentation

Change Agents

Drivers

CE

General Effect

CE
-
Specific Effect

Direct population decline

Invasive
Macrophytes

Climate

Change

Precipitation

Permafrost

Fire

Human Uses

Mining

Infrastructure

Harvest

Contaminants

Temperature

Permafrost thaw

Reduction in age at maturity and shift in
spawning season

Bioaccumulation of
mercury in adults

Expanded ice
-
free season

Temporary increases in nutrient inputs

Elodea

ssp

could reduce quality of spawning habitat

In creased toxicity

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Increased contaminant sources

Change in
deposition rates

Northern Pike

Esox

lucius

Habitat

Increase depth of active
layer will increase
lake
drainage area

Subsistence harvest pressures on
overwintering populations

Direct destruction of habitat, hindrance of migration routes,
increased downstream turbidity and sedimentation

Change Agents

Drivers

CE

General Effect

CE
-
Specific Effect

Increased winter
precipitation may increase
overwintering habitat

Invasive
Macrophytes

Climate

Change

Precipitation

Permafrost

Fire

Human Uses

Mining

Infrastructure

Harvest

Contaminants

Temperature

Permafrost thaw

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

Reduction in juvenile fitness;
bioaccumulation in adults

Expanded ice
-
free season

Reduction in juvenile feeding habitat

In creased toxicity

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Increased contaminant sources

Change in
deposition rates

High winter flow may affect
spawning habitat

Sheefish

Stenodus

leucichthys

Habitat

Direct population decline and removal
of mature, healthy individuals

Direct destruction of habitat, hindrance of migration routes,
increased downstream turbidity and sedimentation

Change Agents

Drivers

CE

General Effect

CE
-
Specific Effect

Sedimentation of gravel
-
substrate in streams will reduce quality of spawning habitat

Sedimentation of gravel
-
substrate
will
reduce
quality of
spawning
habitat

Invasive
Macrophytes

Climate

Change

Precipitation

Fire

Human Uses

Mining

Infrastructure

Harvest

Temperature

Permafrost thaw

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

Habitat loss, changes in migration routes, increased
sedimentation

Expanded ice
-
free season

Reduction in spawning and rearing habitat

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Chinook Salmon

Oncorhynchus

tshawytscha

Habitat

Direct population decline and removal of
mature, healthy individuals

Change Agents

Drivers

CE

General Effect

CE
-
Specific Effect

Contaminants

Increased toxicity

Increased contaminant sources

Change in
deposition rates

Increase in winter habitat
for juveniles

Permafrost

Reduction in juvenile fitness

Increase stream flow overwinter
reduce egg survival

Sedimentation of gravel
-
substrate will reduce quality of spawning
habitat;
Temporary increases in nutrient
inputs could increase juvenile foraging


Invasive
Macrophytes

Climate

Change

Precipitation

Permafrost

Fire

Human Uses

Mining

Infrastructure

Harvest

Temperature

Permafrost thaw

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

Habitat loss, changes in migration routes,

increased sedimentation

Expanded ice
-
free season

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Chum Salmon

Oncorhynchus

keta

Habitat

Increased stream discharge
could increase
sedimentation and scour
eggs

Direct population decline and removal of
mature, healthy individuals

Change Agents

Drivers

CE

General Effect

CE
-
Specific Effect

Increase stream flow
overwintr

reduce quality of
spawning habitat and egg survival

Reduction in spawning habitat

Sedimentation of gravel
-
substrate in streams will reduce quality of spawning habitat

Invasive
Macrophytes

Connected
Lakes

Change

Agents

Drivers

CE

Permafrost

Human Uses

Mining

Infrastructure

Decrease in lake area; lake
drainage;
increase in methane emissions

Outcompete native aquatic and emergent vegetation

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Lake drying
in summer decreasing connectivity; expanded
ice
-
free season
allow for early
wildlife use (birds and fish);
changes in thermal regimes

Fire

Temporary increases in
nutrient inputs ;
postfire

landslides and debris
flows

Permafrost
thaw

Climate

Change

Precipitation

Temperature

Direct destruction of
lake habitat

Lake area increase through increased precipitation; increased winter

habitat
for aquatic species

Invasive
Macrophytes

Disconnected
Lakes

Change

Agents

Drivers

CE

Permafrost

Human Uses

Mining

Infrastructure

Outcompete native aquatic and emergent vegetation; faster growing vegetation
overtaking lake area

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Direct destruction of
lake habitat

Fire

Temporary increases in nutrient
inputs;
postfire

landslides and debris
flows


Lake area increase through increased
precipitation;
increased winter
habitat for aquatic species

Permafrost thaw

Lake drying in summer decreasing
lake area;
expanded ice
-
free season allow for early wildlife use (birds and fish);
changes in thermal regimes

Climate

Change

Precipitation

Temperature

Decrease in lake area; lake drainage;
increase in methane emissions

Invasive
Macrophytes

Streams

Change

Agents

Drivers

CE

Permafrost

Human Uses

Mining

Infrastructure

Permafrost thaw

Altered
hydrologies
; increased channel disturbance from
flooding; increased discharge and sediment transport; increase in
winter precipitation will increase wildlife overwinter habitat

Outcompete native aquatic and emergent vegetation

Increased potential for establishment of invasive macrophytes and changing fire dynamics

Warming
could
increase extent
of available
habitats; l
ethal
temperature limits for fish and other aquatic organisms
;
change in thermal regimes

Direct destruction of stream habitat, change in conductivity, reduced
flow



Fire

Temporary increases in nutrient inputs;
post fire
landslides and debris flows; increased
channel
disturbance;
altered riparian vegetation and stream shade,
temperature change
regimes

Climate

Change

Precipitation

Temperature

Increased sedimentation rates

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
Shaftel

rsshaftel@uaa.alaska.edu
, 907
-
786
-
4965

Photo: USFWS