interlaboratory standardization of coast-wide chinook salmon genetic data for international harvest...
TRANSCRIPT
Interlaboratory Standardization of Coast-wide Chinook Salmon Genetic Data for International Harvest Management
Year 2 Progress Report
Paul Moran
Conservation Biology Division
Northwest Fisheries Science Center
Portland, Oregon30 November 2005
Anton Antonovich, Alaska Department of Fish and GameBill Ardren, US Fish and Wildlife Service, AbernathyMelissa Baird, Northwest Fisheries Science Center
Michael Banks, Oregon State University Terry Beacham, Canadian Department of Fisheries and Oceans
Reneé Bellinger, Oregon State University Scott Blankenship, Southwest Fisheries Science Center Craig Busak, Washington Department of Fish and Wildlife
Matt Campbell, Idaho Department of Fish and GameCheryl Dean, Southwest Fisheries Science Center
Nick Decovich, Alaska Department of Fish and GameCarlos Garza, Southwest Fisheries Science Center
Chuck Guthrie, Alaska Fisheries Science Center, Auk BayEric Kretschmer, US Fish and Wildlife Service, AnchorageDavid Kuligowski, Northwest Fisheries Science Center
Tricia Lundrigan, University of Washington Paul Moran, Northwest Fisheries Science Center
Shawn Narum, Columbia River Intertribal Fish Commission Devon Perce, Southwest Fisheries Science Center
Madison Powell, University of Idaho Lisa Seeb, Alaska Department of Fish and Game
Jim Shaklee, Washington Department of Fish and WildlifeChristian Smith, Alaska Department of Fish and Game
Ora Stefanowski, US Fish and Wildlife Service Jeff Stephenson, Columbia River Intertribal Fish Commission
Janine Supernault, Canadian Department of Fisheries and OceansDavid Teel, Northwest Fisheries Science Center
Bill Templin, Alaska Department of Fish and GameDon VanDoornik, Northwest Fisheries Science Center
Ken Warheit, Washington Department of Fish and WildlifeJohn Wenburg, US Fish and Wildlife Service
Richard Wilmot, Alaska Fisheries Science Center Ruth Withler, Canadian Department of Fisheries and OceansSewall Young, Washington Department of Fish and Wildlife
GAPSCollaborators2005
Chinook microsatellite standardization objectives
• Develop a standardized coast-wide DNA baseline that will resolve lineages and stocks within the region for which the CTC is responsible
• Facilitate future expansion of the DNA baseline and addition of novel genetic markers through exchange of DNA samples
• Develop a data base application to support the dissemination and growth of the baseline
0
1
2
3
4
5
6
Microsatellite marker (N = 62)
Num
ber
of
lab
orat
orie
s
L
85.32
500
1000
1500
K
89.57
100.0075.00
4.25 bp
500100015002000
L K
89.07 93.21
75.00 100.00
4.14 bp
70 75 80 85 90 95 100
Fragment size (bp)
Rel
ati v
ef lu
o re s
cen t
unit s
Few loci in common
Precise but inaccurate sizing
Challenges to microsatellite standardization
2-Year GAPS study design
• Year 1: Standardization– Select a common set of markers– Standardize allele designations– Select baseline populations for year 2
• Year 2: Baseline development– Verification via blind samples– Sample exchange– Data collection and storage– Power analysis
“Marker (=locus) sets” and “Sample sets”
Markers*• 62 sponsored loci
• 25 candidate loci
• 13 finalists for baseline construction
Samples• 500-sample survey set
(10 individuals from each of 47 populations, range-wide)
• 96-sample reference set (8 individuals from each of 12 regions)
• 96-sample blind tests (diverse mixture samples)
• 15,000-sample baseline set(144 individuals from each of 105
populations )
*Current focus on microsatellites, future interest in SNPs
Blind test of standardizationA) Initial submission
Locus Lab 1 Lab 2 Lab 3 Lab 4 Lab 5 Lab 6 Lab 7 Lab 8 Lab 9 Average
Ogo2 0.987 1.000 1.000 1.000 0.993 0.000 1.000 0.993 1.000 0.886
Ogo4 0.439 1.000 1.000 0.995 1.000 0.000 0.995 0.994 0.990 0.824
Oki100 0.978 1.000 1.000 1.000 1.000 1.000 1.000 0.970 1.000 0.994
OMM1080 1.000 1.000 0.995 1.000 1.000 0.000 1.000 0.994 1.000 0.995
Ots201b 0.984 1.000 1.000 1.000 1.000 0.993 0.995 0.985 1.000 0.990
Ots208b 0.994 1.000 1.000 1.000 1.000 1.000 0.995 0.970 0.995 0.996
Ots211 1.000 1.000 0.994 1.000 0.993 0.955 0.994 0.985 0.994 0.884
Ots212 0.989 1.000 1.000 1.000 1.000 0.989 0.995 0.994 1.000 0.886
Ots213 0.987 1.000 0.982 1.000 0.985 0.000 1.000 1.000 1.000 0.999
Ots3M 1.000 1.000 0.988 0.994 1.000 0.000 1.000 1.000 0.995 0.980
Ots9 1.000 1.000 1.000 1.000 1.000 0.823 1.000 1.000 1.000 0.991
OtsG474 0.995 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 0.999
Ssa408 0.987 0.929 1.000 1.000 1.000 1.000 1.000 1.000 1.000 0.991
Average 0.949 0.995 0.997 0.999 0.998 0.597 0.998 0.991 0.998 0.955
Partially corrected concordanceB) Partially corrected
Locus Lab 1 Lab 2 Lab 3 Lab 4 Lab 5 Lab 6 Lab 7 Lab 8 Lab 9 Average
Ogo2 0.987 1.000 1.000 1.000 0.993 0.988 1.000 0.993 1.000 0.996
Ogo4 0.994 1.000 1.000 0.995 1.000 0.968 0.995 0.994 0.990 0.993
Oki100 0.978 1.000 1.000 1.000 1.000 1.000 1.000 0.970 1.000 0.994
OMM1080 1.000 1.000 0.995 1.000 1.000 0.938 1.000 0.994 1.000 0.995
Ots201b 0.984 1.000 1.000 1.000 1.000 0.993 0.995 0.985 1.000 0.990
Ots208b 0.994 1.000 1.000 1.000 1.000 1.000 0.995 0.970 0.995 0.996
Ots211 1.000 1.000 0.994 1.000 0.993 0.955 0.994 0.985 0.994 0.994
Ots212 0.989 1.000 1.000 1.000 1.000 0.989 0.995 0.994 1.000 0.992
Ots213 0.987 1.000 0.982 1.000 0.985 0.994 1.000 1.000 1.000 0.999
Ots3M 1.000 1.000 0.988 0.994 1.000 0.949 1.000 1.000 0.995 0.980
Ots9 1.000 1.000 1.000 1.000 1.000 0.979 1.000 1.000 1.000 0.991
OtsG474 0.995 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 0.999
Ssa408 0.987 0.929 1.000 1.000 1.000 1.000 1.000 1.000 1.000 0.991
Average 0.992 0.995 0.997 0.999 0.998 0.981 0.998 0.991 0.998 0.994
Example blind test errors from one of the laboratories
No. Source of Error
6 Faint or large allele dropout - DNA quality
4 Conversion typo
4 Sample order?
1 Artifact?
Current Chinook Coast-wide baseline
• ~16,000 individuals• 110 populations (>230 samples)• 37 regions, Gulf of AK to Central Valley CA• Preliminary analyses complete
– Descriptive pop gen– Power analysis
Standardized GAPS loci 0
10
20
30
40
50
60
70
80
Ots9
Ots3M
.
OtsG474
Ogo4Ogo2
Ots21
2
Ssa40
8
Ots21
1
Oki100
Ots21
3
Ots20
1
Ots20
8
Omm
1080
Locus
# al
lele
s
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
OtsG474
Ots9
Ots3M.
Ogo2
Ogo4
Ots212
Ssa408
Ots201
Ots211
Ots213
Oki100
Ots208
Omm
1080
Locus
He
tero
zyg
os
ity
0
0.05
0.1
0.15
0.2
0.25
Oki100
Omm
1080
Ots208
Ots211
Ots213
Ssa408
Ots201
Ots212
Ots9Ogo
2Ogo
4
Ots3M.
OtsG474
Locus
FS
T
•Alleles per locus: 37.6 (7 – 71)
•Heterozygosity: 0.85 (0.52 – 0.95)
•FST: 0.071 (0.03 – 0.22)
CTC Coast-wide microsatellite baseline 2005
Microsoft PowerPoint Presentation
California CVU Columbia sp
Alaska/BC Transboundary
Central BC Coast
Deschutes fall
E Vancouver Is
Klamath Basin
California Coast
L Columbia fa
L Columbia sp
L Skeena
L Thompson
Columbia tule Mid Fraser
Mid Oregon CoastNass
N California, S Oregon Coast
N Gulf Coast; Alsek
N Puget Sound
N Thompson
NSE Alaska; King SalmonNSE Alaska; Chilkat
Rogue
Snake R fa
S Puget Sound
S Mainland
SSE AlaskaSSE Alaska; Stikine
U Columbia su/fa
U Fraser
U SkeenaWashington Coast
Washington Coast
W Vancouver IsWillamette
N Gulf Coast; Situk
Snake sp/su
L Fraser
Simulated 100% “mixture” analysis
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
Simulated mixed fishery sample
0
0.05
0.1
0.15
0.2
0.25
0.3
Cen
tral
Val
ley
fall
Cen
tral
Val
ley
sprin
g
Cen
tral
Val
ley
win
ter
Cal
iforn
ia C
oast
Kla
mat
h R
Bas
in
Nor
th C
A,
Sou
th O
rego
n co
ast
Rog
ue R
iver
Mid
Ore
gon
Coa
st
Nor
th O
rego
n C
oast
Low
er C
olum
bia
sprin
g
Low
er C
olum
bia
fall
Will
amet
te R
iver
Mid
Col
umbi
a tu
le f
all
Mid
and
Upp
er C
olum
bia
sprin
g
Des
chut
es f
all
Upp
er C
olum
bia
sum
mer
fal
l
Sna
ke R
fal
l
Sna
ke R
spr
ing/
sum
mer
Was
hing
ton
Coa
st
Sou
th P
uget
Sou
nd
Nor
th P
uget
Sou
nd
Low
er F
rase
r
Low
er T
hom
pson
Riv
er
Nor
th T
hom
pson
Riv
er
Mid
Fra
ser
Riv
er
Upp
er F
rase
r R
iver
Eas
t V
anco
uver
Isl
and
Wes
t V
anco
uver
Isl
and
Sou
th B
C M
ainl
and
Cen
tral
BC
Coa
st
Low
er S
keen
a R
iver
Upp
er S
keen
a R
iver
Nas
s R
iver
Upp
er S
tikin
e R
iver
Tak
u R
iver
Sou
ther
n S
outh
east
Ala
ska
SE
Ala
ska,
Stik
ine
Riv
er
Kin
g S
alm
on R
iver
Chi
lkat
Riv
er
Als
ek R
iver
Situ
k R
iver
California CVColumbia sp
Alaska/BC Transboundary
Central BC Coast
Deschutes fa
E Vancouver Is
Klamath Basin
California Coast
L Columbia fa
L Columbia sp
L Skeena
L Thompson
Columbia tule Mid Fraser
Mid Oregon CoastNass
N California, S Oregon Coast
N Gulf Coast; Alsek
N Puget Sound
N Thompson
NSE Alaska; King SalmonNSE Alaska; Chilkat
Rogue
Snake R fa
S Puget Sound
S Mainland
SSE AlaskaSSE Alaska; Stikine
U Columbia su/fa
U Fraser
U SkeenaWashington Coast
Washington Coast
W Vancouver IsWillamette
N Gulf Coast; Situk
CTC Coast-wide microsatellite baseline 2005
Snake sp/su
Results summary
• Concordant genotyping among laboratories• High heterozygosity (~500 alleles)• No obvious HW departures or linkage
disequilibrium• High concordance with previous genetic studies• Powerful mixture analyses, both proportional
estimates and individual assignment
Ahead…
• Expand baseline• Comprehensive power analysis• Safe and secure repository for data• QC and certification of new labs