COMPARATIVE POPULATION GENETIC
STRUCTURE AND DIVERSITY OF YELLOW
PERCH AND WALLEYE: BROAD- AND FINESCALE PATTERNS ACROSS NORTH AMERICA
By Carol Stepien1
with Eva Kramer1, Allyn Spear2, Brian Shepherd2,
Amanda Haponski1 & Oswaldo Sepulveda-Villet1,3
Great Lakes Genetics/Genomics Laboratory
Lake Erie Center & Dept. Env. Sci.
University of Toledo
2USDA ARS Milwaukee, 3U Wisconsin Milwaukee
Walleye Sander vitreus & Yellow Perch Perca flavescens
Fisheries Ecology
• Ecologically & economically
important
–
–
–
–
•
Some of the most popular in the GL
GL fisheries valued at >US $7.1 billion
Greatest abundances in Lake Erie
Growing aquaculture importance
Population stocks have varied in size
– Stochastic annual recruitment
– Food availability, year class strength
– Habitat loss, degradation, exploitation,
invasive species
– Stochastic annual recruitment
•
Fishery stocks are population subunits
that freely interbreed, share a common
gene pool, and are genetically
distinguishable from others
(Hallerman et al. 2003)
Population Genetics Source Info (Stepien et al. 2015)
Population Genetic Approaches
•
•
mtDNA DNA control region sequences
nuclear DNA microsatellite loci
1. Extract & purify DNA
2. PCR amplify target gene(s)
3. DNA sequence or assay allele
lengths
4. Analyze and compare patterns
• Sequence Data for Phylogenetic Relationships:
Maximum-likelihood, Bayesian Mr. Bayes &
BEAST), Haplotype networks
• Microsatellite & Sequence Data for Population
Genetics: AMOVA, Pairwise FST tests,
Bayesian Structure, Barrier Analysis,
GeneClass Assignment, Neighbor-Joining Trees,
Colony to determine possible siblings
Yellow Perch and Walleye
MtDNA Control Region Haplotype Frequencies
Yellow
Perch
N=664
NH=26
HD=0.31
Walleye
N=711
NH=28
HD=0.77
Stepien et al. 2015, 2009, Mol Ecol
Sepulveda-Villet & Stepien 2012, Mol Ecol Haponski & Stepien, 2014,
BMC Evol Biol
MtDNA Control Region
Haplotype Networks
Yellow
Perch
N=664
NH=26
HD=0.31
Walleye
N=711
NH=28
HD=0.77
MtDNA Genetic
Diversity and
Divergence
HD = Haplotypic diversity,
FST = mean genetic divergence
(Weir & Cockerham 1984)
* = significant
(data from Stepien et al. 2015,
2009 Molecular Ecology,
Haponski & Stepien 2014,
Sepulveda-Villet & Stepien
2012 Molecular Ecology)
Yellow Perch
N=664
Walleye
N=711
Water Body
HD
FST
HD
FST
L. Winnipeg
0.00
0.42*
0.65
0.19*
Upper Miss. R.
0.53
0.28*
0.26
0.32*
L. Superior
0.00
0.21*
0.65
0.20*
L. Michigan
0.34
0.18*
0.23
0.29*
L. Huron
0.40
0.19*
0.45
0.22*
L. St. Clair
0.00
0.19*
0.73
0.17*
L. Erie (western)
0.27
0.25*
0.78
0.16*
L. Erie (eastern)
0.07
0.26*
0.82
0.18*
L. Ontario
0.13
0.20*
0.54
0.36*
Northeast
0.48
0.27*
0.48
0.24*
Southeast
0.63
0.47*
0.62
0.37*
Gulf Coast
0.15
0.79*
0.40
0.44*
Mean
0.31
0.29*
0.77
0.26*
Nuclear Genetic
Diversity and
Divergence
HO = Observed heterozygosity
FST = mean genetic divergence
* = significant
(data from Haponski & Stepien 2014,
Stepien et al. 2015,
2009 Molecular Ecology,
Sepulveda-Villet & Stepien 2012
Molecular Ecology)
Yellow Perch
(15 μsat loci)
N=892
Walleye
(9 μsat loci)
N=1125
HO
FST
HO
FST
(μsat)
(μsat)
(μsat)
(μsat)
L. Winnipeg
0.53
0.20*
0.63
0.14*
Upper Miss. R.
0.52
0.27*
0.62
0.15*
L. Superior
0.64
0.18*
0.72
0.06*
L. Michigan
0.54
0.15*
0.73
0.07*
L. Huron
0.61
0.13*
0.73
0.07*
L. St. Clair
0.59
0.19*
0.72
0.07*
L. Erie (western)
0.55
0.17*
0.70
0.07*
L. Erie (eastern)
0.54
0.17*
0.74
0.06*
L. Ontario
0.55
0.16*
0.68
0.07*
Northeast
0.50
0.18*
0.52
0.15*
Southeast
0.60
0.22*
0.68
0.05*
Gulf Coastal
0.39
0.28*
0.56
0.10*
Mean
0.53
0.19*
0.67
0.09*
Water Body
Yellow Perch and Walleye Bayesian
STRUCTURE Analysis from usat Data
•
Yellow
Perch
15 loci
K=17
N=892
Walleye
9 loci
K=9
N=1125
Genetic Barriers Shared Between the Species
(from Barrier v2.2; Manni et al. 2004)
Mantel Tests: Broadscale Genetic Isolation by
Geographic Distance
Yellow Perch
15 loci
N=892
R2=0.39
P<.001
Walleye
9 loci
N=1125
R2=0.23
P<.005
Mantel Tests: No Finescale Genetic Isolation by
Geographic Distance across Lake Erie
Yellow Perch
15 loci
N=892
R2=0.02
P=0.30 NS
Walleye
9 loci
N=1125
R2=0.02
P=.80 NS
Temporal Genetic Consistency for Annual Spawning
Runs of Walleye (Maumee River) using FST
(Stepien et al. 2012 TAFS)
Sampling
year
1995
1998
2003
1998
0.001
2003
0.001
0.002
2007
0.001
0.002
0.001
2008
0.002
0.004
0.001
2007
0.001
FST=genetic divergence among spawning samples (Weir & Cockerham 1984)
• Walleye spawning in the Maumee River showed temporal genetic consistency
• Consistent patterns also found for the Sandusky River and Van Buren Bay groups
Temporal Genetic Differences (FST) for
Lake Erie Yellow Perch
(Sullivan & Stepien 2013 in revision, Conservation Genetics vs. Sepulveda-Villet & Stepien 2011, CJFAS )
Spawning Sample Site
Original
year
2009
A) Anchor Bay MI,
L. St. Clair
2005
0.138*
B) Monroe MI, L. Erie
2004
0.026*
C) Erieau ON, L. Erie
2003
0.037*
D) Fairport OH, L. Erie
2003
0.114*
E) Perry OH, L. Erie
2003
0.041*
F) Erie OH, L. Erie
2001
0.135*
G) Dunkirk NY, L. Erie
2001
0.064*
H) Rochester NY,
L. Ontario
2002
0.055*
MU 4
Anchor Bay
Erieau
Dunkirk
MU 3
Monroe
Erie
MU 2
MU 1
Perry
Fairport
FST = genetic divergence among sites
(Weir and Cockerham 1984)
* = Significant
The genetic composition of yellow perch spawning groups varied year to year
Temporal Genetic Divergence (FST) of
Yellow Perch at Dunkirk NY
(Sullivan & Stepien, 2015, TAFS)
Sampling Date
A
B
C
D
E
A) 5/16/1985
-----
B) 5/15/2001
0.037*
C) 5/13/2004
0.056* 0.055*
D) 5/13/2008
0.125* 0.138* 0.141*
E) 5/13/2009
0.041* 0.072* 0.088* 0.105*
F) 5/13/2010
0.011* 0.041* 0.057* 0.113* 0.014*
-----------------
Spawning Dunkirk NY Yellow Perch showed
high year to year variation
FST = genetic divergence among spawning
samples (Weir & Cockerham 1984)
* = Significant
MU 4
MU3
MU 2
MU 1
Dunkirk
Conclusions
• Genetic diversity is higher in Walleye
than Yellow Perch
• Both species show considerable genetic
structure
• Similar broad-scale spatial patterns
• Congruent glacial refugia & colonization
histories
• Fine-scale population divergence is
greater in Yellow Perch than Walleye
– Likely related to life-history patterns such
as natal site fidelity & kin recognition
• Walleye spawning sites are more
genetically consistent from year to year
than Yellow Perch
Grants:
USEPA
NOAA Ohio Sea Grant
NSF GK-12
Samples-Thank you:
Ohio DNR
Ohio EPA
Michigan DNR
Minnesota DNR
New York DEC
Ontario MNR
PFBC
USGS
USFWS
Kleinschmidt USA
Ohio State University
Indiana State University
Acknowledgments