John Carlos GarzaEric C. AndersonTommy Williams
Brian SpenceKerrie Pipal
Libby Gilbert-Horvath
John Carlos GarzaEric C. AndersonTommy Williams
Brian SpenceKerrie Pipal
Libby Gilbert-Horvath
Spatial and temporal variation in structure and abundance of coho
salmon in California
Status of coho salmon in California, USA
• Population declines, local extinctions
• Management units: Evolutionarily Significant Units (ESUs)
– Southern Oregon/Northern California Coast Coho Salmon ESU (SONCC) –Threatened
– Central California Coast Coho Salmon ESU (CCC) – Endangered
• All populations have protected status
• Life history– Anadromous, reproduce in natal streams,
semelparous
– 3-year life cycle; 3 brood years, little temporal gene flow
SONCC
CCC
Oregon
California
Gilbert-Horvath et al. (in press), 18 microsatellite loci
Background: phylogeography of coho salmon in California
• 30 sites surveyed for young-of-year in 2003
• Significant hierarchical genetic structure– Greatest divergence at
broadest geographic scale
• Klamath River basin distinct from other northern populations
Central California ESUNorthern California ESUKlamath River basin
Gilbert-Horvath et al. (in press), 18 microsatellite loci
Background: phylogeography of coho salmon in California
Bayesian Clustering Analysis-Individual Genotypes
Gilbert-Horvath et al. (in press), 18 microsatellite loci
Background: phylogeography of coho salmon in California
Klamath South Coast (Ten Mile, Noyo, Lagunitas, Scott, etc)
North Coast (Mad, Eel, Mattole, etc)
Factorial Correspondence Analysis-Individual Genotypes
Study design: temporal monitoring• Survey populations at two time points
– Time series data at a regional scale– Examine allele frequency change over time
• Timepoint 1: baseline sampling in rivers throughout California in 2003 (n=1,976)
• Timepoint 2: revisited same sites in 2015 (n=2,223)– Expanded to include Oregon sites
• Four generations between surveys– Sampled two cohorts of the same brood cycle
Sampling locations• Sampled juveniles in
natal streams• Spatially stratified
electrofishing protocol• 46 sites yielded coho
salmon in 2015• n=75 maximum per site California
2003 survey2015 survey
A. McHuron
43o N
37o N
Oregon
Analytical objectives• Analysis of family structure• Examine patterns of population
structure at multiple spatial scales• Assess temporal stability of genetic
composition of populations • Estimate effective population size (Ne)
Genotype data: 95 SNP locin=4,199 individuals
A. McHuron
Results• Sibship reconstruction: full
siblings detected in almost all populations
• Mean sibship size by site -> • Mean sibship size by year
• 2003 = 2.2• 2015 = 3.3
• Family structure may obscure or distort population structure– Omit full sibs from population
analyses (revised n=2,460)
20032015
=
Results from Colony v2.0.6.1 (Wang 2008, Jones and Wang 2010)
0
20
40
60
80
100
0 20 40 60 80 100
Num
ber o
f spa
wer
s pe
r pop
ulat
ion,
201
5
Number of spawners per population, 2003
Temporal trends in reproduction• 32 paired temporal
population samples
• Estimated number of spawning adults that produced each sample of juveniles
• Net decrease in number of spawners between 2003 and 2015
Results from Colony v2.0.6.1
C. Nicol
Paired population sample
Effective population size• Method in development: estimating Ne using the temporal method,
accounting for family structure using Colony output• Upper bound of Ne difficult to estimate due to small sample sizes
Population
central California northern California Klamath River (northern)
0
50
100
150
200
250
300
350
400
WAG RED KT
D
CAS NVJ
KSH
TNL
LIT
NO
Y
ALB
KCC
LOL
SCC
KSS
BSA
BIG
LDG
LAG
PUD
RPR
FWC
EHT
KMG
KTS
LTU
Ne
(Max
imum
Lik
elih
ood
Estim
ate) MLE lower bound of Ne
Lower Confidence Interval
Upper Confidence Interval
Temporal trends in reproduction, by population: estimated number of spawning adults in 2003 and 2015
0
10
20
30
40
50
60
70
Cou
nt
Population samples (north to south)
Winter 2003
Winter 2015
0
0.1
0.2
0.3
0.4
0.5
0.6
-0.05 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4
Rel
ativ
e pr
opor
tion
of p
airw
ise
com
paris
ons
FST
Between ESUs (n=781 comparisons)
Basins within SONCC (n=354)
Basins within CCC (n=322)
Tributaries within basin (n=77)
Population between years (n=30)
Relative divergence between populations: distributions of pairwise
FST estimates
100
ROAb
WILb
WILa
75
82
TNCb
TNRb
50
TNLa
TNLb NOYb
74
PUDb
PUDa
COTaLOLb
LOLa LDGa
97
REDb REDa
WLKbLAGa
61
LAGbLDGb
ALBb
LITbLITa
91
GCSb
GCNb
NVJbNVFb
ALBaNVJa
BIGaBIGb
BSAaBSAb
99 SCCa
SCCbCASb
CASaNOYa
WAGaWAGb
85
MTTa
MTTbMDSa
MDSb86
FWCb
FWCa
99
EHTb
EHTa
52
82
LTUa
LTUb
MPLbRPRbMPLa
RPRa
96
CHEbCHJb
KMGa
KBVaROVb
ROKbKSHaKSCa
KSCb
KSSaKSSb
53
58
KTSb 85
KTDb
KTDa
KTSa
ROTb
KSHb
KCCa
ROIb
KCCb
KMGb
Phylogeographic structure
• High-level topology concordant with geography and management units
• Tributaries within basins cluster together, except in largest basins (Klamath & Rogue rivers)
• Temporally coherent genetic composition in majority of paired temporal samples
Southern Oregon/Northern
Calif. ESU
Central Calif. ESU
N
Full siblings omitted
100
ROAb
WILb
WILa
75
82
TNCb
TNRb
50
TNLa
TNLb NOYb
74
PUDb
PUDa
COTaLOLb
LOLa LDGa
97
REDb REDa
WLKbLAGa
61
LAGbLDGb
ALBb
LITbLITa
91
GCSb
GCNb
NVJbNVFb
ALBaNVJa
BIGaBIGb
BSAaBSAb
99 SCCa
SCCbCASb
CASaNOYa
WAGaWAGb
85
MTTa
MTTbMDSa
MDSb86
FWCb
FWCa
99
EHTb
EHTa
52
82
LTUa
LTUb
MPLbRPRbMPLa
RPRa
96
CHEbCHJb
KMGa
KBVaROVb
ROKbKSHaKSCa
KSCb
KSSaKSSb
53
58
KTSb 85
KTDb
KTDa
KTSa
ROTb
KSHb
KCCa
ROIb
KCCb
KMGb
Phylogeographic structure
• High-level topology concordant with geography and management units
• Tributaries within basins cluster together, except in largest basins (Klamath & Rogue rivers)
• Temporally coherent genetic composition in majority of paired temporal samples
NTributary samples
100
ROAb
WILb
WILa
75
82
TNCb
TNRb
50
TNLa
TNLb NOYb
74
PUDb
PUDa
COTaLOLb
LOLa LDGa
97
REDb REDa
WLKbLAGa
61
LAGbLDGb
ALBb
LITbLITa
91
GCSb
GCNb
NVJbNVFb
ALBaNVJa
BIGaBIGb
BSAaBSAb
99 SCCa
SCCbCASb
CASaNOYa
WAGaWAGb
85
MTTa
MTTbMDSa
MDSb86
FWCb
FWCa
99
EHTb
EHTa
52
82
LTUa
LTUb
MPLbRPRbMPLa
RPRa
96
CHEbCHJb
KMGa
KBVaROVb
ROKbKSHaKSCa
KSCb
KSSaKSSb
53
58
KTSb 85
KTDb
KTDa
KTSa
ROTb
KSHb
KCCa
ROIb
KCCb
KMGb
Paired temporal population samples
Phylogeographic structure
• High-level topology concordant with geography and management units
• Tributaries within basins cluster together, except in largest basins (Klamath & Rogue rivers)
• Temporally coherent genetic composition in majority of paired temporal samples
N
Fractional ancestryW
ILa
WIL
bKC
CaKC
CbKM
GaKM
GbKS
CaKS
CbKS
HaKS
HbKS
SaKS
Sb
KTSa
KTSb
KTDa
KTDb
RPRa
RPRb
MPL
aM
PLb
LTUa
LTUb
MDS
aM
DSb
FWCa
FWCb
EHTa
EHTb
MTT
aM
TTb
WAG
aW
AGb
TNLa
TNLb
PUDa
PUDb
NOYa
NOYb
CASa
CASb
BIGa
BIGb
LITa
LITb
ALBa
ALBb
BSAa
BSAb
NVJa
NVJb
LAGa
LAGb
LOLa
LOLb
LDGa
LDGb
REDa
REDb
SCCa
SCCb
K = 2
K = 3
K = 4
K = 5
3/5
K = 6
1/5
1/5
5/5
4/5
1/5
5/5
5/5
Structure v2.3.4 on paired temporal populations, full siblings omitted
Genetic analysis of Mattole River cohosalmon young-of-year
• Baker Creek tributary, Mattole River, California
• YOY (young-of-year) were sampled – August 2013 (Brood year 12/13)– August 2014 (Brood year 13/14)
• Genetic analyses – 90 SNP loci– Colony v2 to resolve familial relationships– Population assignment test using nearby
reference populations– Ancestry analysis
Ancestry analysis (Structure v2.3.4)CO
Ta
EHTa
EHTb
FWCa
FWCb
MDS
a
MDS
b
MTR
MTT
a
MTT
b
MTT
Ba
MTT
Bb
MTT
C
PUDa
PUDb
TNLa
TNLb
K = 2 (5/5)
K = 3 (3/5)
K = 3 (2/5)
K = 4 (3/5)K = 4 (2/5)
K = 5 (4/5)
K = 5 (1/5)
K = 6 (2/5)
K = 6 (1/5)
K = 6 (1/5)
K = 6 (1/5)
Cot
tane
va
Eel RiverFreshwater Ck Mad R
Mattole R Ten Mile RPudding Ck
MTTBa: BY12MTTBb: BY13
Conclusions• Statewide decrease in number of spawning adults that
produced the sampled juveniles– Impact of 5-year drought on habitat
• Regional-scale geographic structure remains concordant with management unit boundary
• Significant spatial population structure – Particularly between ESUs, and among populations of
northern ESU • Little divergence between tributaries of the same basin• Minimal temporal structure: within-population genetic
composition relatively consistent over time• Ancestry and affiliation of small populations influenced
by migrants from nearby basins
Implications for conservation• Connectivity of populations• Extinction risk in susceptible small populations
– Benefit of straying from productive populations• Periodic re-evaluation of strategies
– Identify populations or areas of concern– Where are recovery efforts having a positive impact?
A. McHuron
AcknowledgementsAcknowledgements• NOAA Fisheries Service, Southwest Fisheries Science
Center, Fisheries Ecology Division– Molecular Ecology Team: Ellen Campbell, Anthony Clemento, Cassie
Columbus, Laney Correa – Landscape Ecology Team: Heidi Fish, Alex McHuron, Casey
Sheridan, Emily Tucker
• California Department of Fish & Wildlife
Funding Sources
National Marine Fisheries Service
Fisheries Restoration Grant from the California Department of Fish & Wildlife M. Bond
Photo Copyright (C) 2002-2015 Kenneth & Gabrielle Adelman, California Coastal Records Project, www.Californiacoastline.org
Thank you!