Genetic variation and geographic structure of coastal ... · Primordia values of above and below...
32
Genetic variation and Genetic variation and geographic structure of coastal geographic structure of coastal cutthroat trout at the northern cutthroat trout at the northern extent of their range, extent of their range, Prince William Sound, Alaska Prince William Sound, Alaska Kitty E. Griswold Kitty E. Griswold USGS/BRD Conte Anadromous Fisheries Research Center USGS/BRD Conte Anadromous Fisheries Research Center Turners Falls, MA Turners Falls, MA University of Massachusetts, Amherst University of Massachusetts, Amherst Kenneth P. Currens Kenneth P. Currens NWIFC, Olympia WA NWIFC, Olympia WA Gordon H. Reeves Gordon H. Reeves PNW Research Station, Corvallis, OR PNW Research Station, Corvallis, OR
Transcript of Genetic variation and geographic structure of coastal ... · Primordia values of above and below...
Genetic variation and Genetic variation and geographic structure of coastal geographic structure of coastal cutthroat trout at the northern cutthroat trout at the northern
extent of their range, extent of their range, Prince William Sound, AlaskaPrince William Sound, Alaska
Kitty E. GriswoldKitty E. GriswoldUSGS/BRD Conte Anadromous Fisheries Research CenterUSGS/BRD Conte Anadromous Fisheries Research Center
Turners Falls, MATurners Falls, MAUniversity of Massachusetts, AmherstUniversity of Massachusetts, Amherst
Kenneth P. CurrensKenneth P. CurrensNWIFC, Olympia WANWIFC, Olympia WA
Gordon H. ReevesGordon H. ReevesPNW Research Station, Corvallis, ORPNW Research Station, Corvallis, OR
Genetic structure at the local scaleGenetic structure at the local scale
Why use genetic tools?Why use genetic tools?
Patterns tell us Patterns tell us about species about species historyhistory
Relative degree of Relative degree of isolation/gene flowisolation/gene flow
Over space and Over space and time landscapes time landscapes are dynamicare dynamic
Distributional range of Distributional range of coastal cutthroat troutcoastal cutthroat trout
Gulf of Alaska
Northern extent of range Northern extent of range (8,000 ybp)(8,000 ybp)
Gulf of Alaska
Prince William Sound
150 years350 years
Two sites above presumed waterfall barriers
Goals for this talkGoals for this talk
Genetic variation in Prince William Sound, Genetic variation in Prince William Sound, AK with two genetic toolsAK with two genetic tools
Correlation of genetic and geographic Correlation of genetic and geographic distance in coastal cutthroat trout in distance in coastal cutthroat trout in Prince William Sound, AKPrince William Sound, AK
Otolith microchemistry analysisOtolith microchemistry analysis
Types of genetic variation and Types of genetic variation and their applicationstheir applications
Mitochondrial DNAMitochondrial DNA• maternally inherited• doesn’t undergo recombination
AllozymesAllozymes
Microsatellite DNAMicrosatellite DNA• hypervariable • tandem repeats (AGAGAGAG)
Ancestral LineagesAncestral Lineages
KinshipKinship
Data AnalysisData Analysis
Haplotype diversity within Prince William Haplotype diversity within Prince William SoundSound
Genetic variation within sampling locationsGenetic variation within sampling locationsAlleles per locusAlleles per locusHeterozygosityHeterozygosity
Genetic variation among sampling Genetic variation among sampling locationslocations
Genetic distanceGenetic distanceTest models of genetic structureTest models of genetic structure
Isolation by distance (IBD)Isolation by distance (IBD)
Dispersal of organisms has limit which Dispersal of organisms has limit which leads to a geographic patternleads to a geographic pattern
Isolation by distance Isolation by distance genetic differentiation increases with distancegenetic differentiation increases with distance
Migrants/generation (M) geographic Migrants/generation (M) geographic distance (d) distance (d)
Mantel test for significanceMantel test for significanceRegression Regression
Slope of line describes model fitSlope of line describes model fit
One dimensional stepping stone One dimensional stepping stone modelmodel
Slatkin (1993)
One dimensional stepping stone One dimensional stepping stone modelmodel
Slatkin (1993)
Log(distance)
Log(M)
Slope=-1.0
MtDNA MtDNA ResultsResults
ND-1 ND 5-6D-Loop(N=79)
16 RFLP’s
Within sample genetic variation Within sample genetic variation Alleles/LocusAlleles/Locus
0
2
4
6
8
1 0
1 2
Col
umbi
a B
ay
Una
kwik
Inle
t
Gun
boat
Lak
es
Wes
t Arm
Stu
mp
Lake
Gre
en Is
land
She
lter C
r (be
low
)
She
lter C
r (ab
ove)
Mak
aka
Cr
Haw
kins
Cr (
belo
w)
Haw
kins
Cr (
abov
e)
Milt
on L
ake
Cop
per R
iver
Sampling location
Alleles/Locus
Within sample genetic variation Within sample genetic variation average heterozygosityaverage heterozygosity
0 . 0 0
0 . 1 0
0 . 2 0
0 . 3 0
0 . 4 0
0 . 5 0
0 . 6 0
0 . 7 0
0 . 8 0
0 . 9 0
1 . 0 0
Col
umbi
a B
ay
Una
kwik
Inle
t
Gun
boat
Lak
es
Wes
t Arm
Stu
mp
Lake
Gre
en Is
land
She
lter C
r (be
low
)
She
lter C
r (ab
ove)
Mak
aka
Cr
Haw
kins
Cr (
belo
w)
Haw
kins
Cr (
abov
e)
Milt
on L
ake
Cop
per R
iver
Sampling location
He
12
3
4
5
6
78
910
11
12
13
00.
050.
100.
150.
200.
25
CordovaOrca Bay
Models of IBDModels of IBD
PostPost--glacial colonization route glacial colonization route
Shoreline migration route (5Shoreline migration route (5--10 km)10 km)
Shortest distance between sites Shortest distance between sites (open water)(open water)
Results IBD Mantel testsResults IBD Mantel tests
PostPost--glacial colonization route glacial colonization route (p<0.009)(p<0.009)
Shoreline migration route (5Shoreline migration route (5--10 km 10 km open water) (p=0.015)open water) (p=0.015)
Shortest distance between sites Shortest distance between sites (open water) (p>0.05)(open water) (p>0.05)
IBD slopeIBD slope
-0.5
0.0
0.5
1.0
1.5
2.0
2.5
0.0 0.5 1.0 1.5 2.0 2.5 3.0
log(kM)
log(
M)
Shelter Bay (above x below)
Hawkins Cr (above x below)
Columbia Bay x Unakwik Ilet Columbia Bay
x Green Is
Columbia Bay x Gunboat Lk
Slope= -0.836
ConclusionsConclusionsGeographic pattern of genetic variationGeographic pattern of genetic variation
Northwest PWS sites significantly lower numbers of Northwest PWS sites significantly lower numbers of alleles and average heterozygosityalleles and average heterozygosity
Genetic distance appeared to be Genetic distance appeared to be correlated to geographic distancecorrelated to geographic distance
Support for IBDSupport for IBDEast west dispersal following shorelinesEast west dispersal following shorelines
Above barrier sites unresolvedAbove barrier sites unresolved
12
3
4
5
6
78
910
11
12
13
00.
050.
100.
150.
200.
25
CordovaOrca Bay
Otolith MicrochemistryOtolith Microchemistry
Use elevated levels of Sr/Ca ratios in Use elevated levels of Sr/Ca ratios in otoliths to infer entry to seawaterotoliths to infer entry to seawater
Otolith microchemistryOtolith microchemistry
Coastal cutthroat trout, Shelter Bay, AK
0
0.001
0.002
0.003
0.004
primordia edge
1+2+
3+
4+5+
6+
Sr/Caratio
Primordia to edge
Shelter Bay Anadromous cutthroat trout
0
0.001
0.002
0.003
0.004
1 3 5 7 9 11 13 15 17 19
primordia to edge
Sr/C
a ra
tio
3+ trout
Otolith microchemistryOtolith microchemistry
Primordia values of above and Primordia values of above and below barrier coastal cutthroat below barrier coastal cutthroat
trouttrout
Shelter Bay, Alaska Anadromous cutthroat trout
0
0.001
0.002
0.003
0.004
1 3 5 7 9 11 13 15 17 19
primordia to edge
Sr/C
a ra
tio
3+ trout
Shelter Lake, Alaska cutthroat trout
0
0.001
0.002
0.003
0.004
0.005
1 3 5 7 9 11 13 15 17 19
primordia to edgeSr
/Ca
ratio
3+ trout
Primordia samples of above and below populationsnot significantly different (p > 0.05)
Size at ageSize at age
Size at age coastal cutthroat trout
01234567
0 100 200 300 400
length in mm
age
Shelter BayAnadromousShelter Lake
Bottom lineBottom line
Genetic tools useful for describing Genetic tools useful for describing geographic variation in coastal geographic variation in coastal cutthroat troutcutthroat trout
Scale the tool to the questionScale the tool to the question
Genetic tools used in combination Genetic tools used in combination with ecological measures with ecological measures
Sites in northern PWS have reduced genetic diversity
Populations of coastal cutthroat trout in PWS range from being similar to different with IBD patterns
AcknowledgementsAcknowledgements
Oregon State UniversityOregon State UniversityOregon Cooperative Fisheries Research UnitOregon Cooperative Fisheries Research UnitChugach National Forest, CordovaChugach National Forest, CordovaExxon Valdez Trustee CouncilExxon Valdez Trustee CouncilAlaska Department of Fish and GameAlaska Department of Fish and GameIndividuals Janet Hanus, Dave Schmid, Merlyn Individuals Janet Hanus, Dave Schmid, Merlyn Schelske, Dave Saiget, George Covell, Kathryn Schelske, Dave Saiget, George Covell, Kathryn Ronenberg.Ronenberg.Coastal cutthroat trout symposium travel grantCoastal cutthroat trout symposium travel grant
0.2
0.4
0.6
0.8
I
II
III
IV
V
VI
VII
Copper Ri ver
Milton Lake
Hawkins Creek(above barrier)
Hawkins Creek(below barrier)
Makaka Creek
Shelter Bay(above barrier)
Shelter Bay(below barrier)
Green Island
Stump Lake
West Arm,Bay of Isles
Gunboat Lakes
Unakwi kInlet
Columbi a Bay
Bayesian Structure of PopulationsBayesian Structure of Populations
(Pritchard et al. 2000)
