Conservation Genetics

Two decades of genetic consistency ina reproductive population in the face of exploitation: Patterns of adult and larval walleye (Sander vitreus) from Lake Erie’s Maumee River

Amanda E. Haponski1,2, Carol A. Stepien1

1The Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, 6200 Bayshore Road, Toledo, OH 43616, USA

C.A. Stepien (all correspondence)

1The Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, 6200 Bayshore Road, Toledo, OH 43616, USA

e-mail: , phone: 419-530-8362, fax: 419-530-8399

Present Address: A.E. Haponski

2Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109, USA

TableS1Genetic pairwise divergences betweensamples of larval walleye from the Maumee River. FST values (Weir and Cockerham 1984) are below the diagonal and those for exact tests of differentiation (χ2) are above. All comparisons are not significant.

Collection year and site / 2010 L1a / 2010 L2a / 2010 L2b / 2011 L2 / 2011 L3
2010 L1-powerplant intake peak a (N=26) / --- / 26.93 / 24.33 / 46.20 / 31.72
2010 L2-river mouth peak a (N=22) / <0.001 / --- / 35.14 / 43.08 / 32.92
2010 L2-river mouth peak b (N=48) / <0.001 / 0.005 / --- / 34.41 / 21.24
2011 L2-river mouth (N=23) / <0.001 / 0.005 / <0.001 / --- / 14.68
2011 L3-upstream (N=25) / <0.001 / 0.003 / <0.001 / <0.001 / ---

Table S2Summary of genetic variation for Maumee River walleye per microsatellite locus from 12 annual spawning runs (totaling 600 adults) and larval samples (144).

Locus / Source / TA (ºC) / NA / Size range / FIT / FST / FIS / Selection
Svi4 / Borer et al. (1999) / 60 / 11 / 104−124 / 0.002 / 0.004 / -0.002 / neutral
Svi6 / “ / 60 / 22 / 126−186 / 0.023 / 0.000 / 0.023 / neutral
Svi17 / “ / 54 / 11 / 96−118 / 0.006 / 0.000 / 0.006 / neutral
Svi18 / “ / 65 / 6 / 116−126 / 0.108 / 0.000 / 0.109 / neutral
Svi33 / “ / 60 / 15 / 80−108 / 0.001 / 0.002 / -0.001 / neutral
SviL2 / Wirth et al. (1999) / 53 / 11 / 254−287 / 0.015 / 0.000 / 0.015 / neutral
SviL3 / “ / 53 / 24 / 187−273 / -0.009 / 0.000 / -0.008 / neutral
SviL4 / “ / 54 / 21 / 119−161 / 0.084 / 0.001 / 0.083 / neutral
SviL6 / “ / 54 / 18 / 104−140 / 0.029 / 0.001 / 0.028 / neutral
SviL7 / “ / 54 / 30 / 172−238 / 0.023 / 0.003 / 0.020 / neutral
Svi2 / Eldridge et al. (2002) / 60 / 16 / 188−222 / -0.007 / 0.000 / -0.007 / neutral
Svi7 / “ / 60 / 15 / 154−186 / 0.007 / 0.000 / 0.006 / neutral
Svi14 / “ / 54 / 29 / 152−214 / 0.002 / 0.000 / 0.003 / neutral
Svi20 / “ / 50 / 21 / 144−198 / 0.025 / 0.011 / 0.013 / positive
Total / --- / --- / 250 / --- / 0.021 / 0.002 / 0.020 / ---

Table shows annealing temperature (TA), number of alleles (NA), allelic size range (base pairs, bp), genetic deviation across all combined samples (FIT), mean genetic divergence among loci (FST), inbreeding coefficient (FIS,average divergencewithin a spawning group), and identification of loci showing possible evidence of selection with the program Lositan (Beaumont and Nichols 1996; Antao et al. 2008) and BayeScan (Foll and Gaggiotti 2008).

Table S3Pairwise comparisons for 13 nuclear μsat loci between annual spawning run males (above diagonal) and females (below diagonal), with values on diagonal indicating comparisons between the sexes for that year, based on: (a) FST (Weir and Cockerham 1984) and (b) exact tests of differentiation (χ2; Raymond and Rousset 1995). No females were collected in the 1995 sample. *=significant following sequential Bonferroni correction (Rice 1989).NF=female sample size and NM=male sample size.

(a) Fst

1998
(NM=14) / 2005
(NM=36) / 2006
(NM=29) / 2007
(NM=25) / 2008
(NM=25) / 2009
(NM=24) / 2010
(NM=24) / 2011
(NM=27) / 2012
(NM=41) / 2013
(NM=32)
1995 (NF=34) / 0.000 / 0.000 / 0.000 / 0.000 / 0.001 / 0.000 / 0.000 / 0.000 / 0.000 / 0.005
1998 (NF=14) / 0.000 / 0.000 / 0.000 / 0.000 / 0.001 / 0.007 / 0.000 / <0.001 / 0.000 / 0.013
2005 (NF=12) / 0.001 / 0.000 / 0.000 / 0.000 / 0.005 / 0.003 / 0.002 / 0.000 / 0.001 / 0.010
2006 (NF=22) / 0.002 / 0.008 / <0.001 / 0.000 / 0.001 / 0.006 / 0.000 / 0.003 / 0.000 / 0.006
2007 (NF=23) / 0.000 / 0.000 / 0.000 / 0.003 / 0.001 / 0.002 / 0.001 / 0.003 / 0.008 / 0.010
2008 (NF=25) / 0.003 / 0.003 / 0.000 / 0.007 / 0.011* / 0.012 / 0.003 / 0.004 / 0.008 / 0.011
2009 (NF=24) / 0.001 / 0.002 / 0.000 / 0.000 / 0.000 / 0.001 / 0.006 / 0.002 / 0.005 / 0.013
2010 (NF=24) / 0.003 / 0.000 / 0.001 / 0.000 / 0.004 / 0.000 / 0.000 / 0.006 / 0.001 / 0.011
2011 (NF=21) / <0.001 / 0.012 / 0.002 / 0.006 / 0.007 / 0.001 / 0.005 / 0.008 / 0.000 / 0.006
2012 (NF=5) / 0.000 / 0.000 / 0.000 / 0.000 / 0.004 / 0.000 / 0.000 / 0.009 / 0.000 / 0.004
2013 (NF=16) / 0.000 / 0.001 / 0.007 / <0.001 / 0.007 / 0.003 / 0.006 / 0.010 / 0.000 / 0.011

(b) χ2

1998
(NM=14) / 2005
(NM=36) / 2006
(NM=29) / 2007
(NM=25) / 2008
(NM=25) / 2009
(NM=24) / 2010
(NM=24) / 2011
(NM=27) / 2012
(NM=41) / 2013
(NM=32)
1995 (NF=34) / 18.09 / 21.29 / 22.09 / 13.86 / 27.95 / 22.92 / 21.55 / 20.86 / 26.32 / 33.08
1998 (NF=14) / 13.54 / 22.60 / 32.09 / 26.62 / 24.74 / 29.65 / 21.06 / 24.36 / 23.30 / 41.52
2005 (NF=12) / 21.70 / 22.86 / 26.71 / 26.14 / 37.78 / 32.92 / 42.37 / 22.15 / 30.73 / 54.49*
2006 (NF=22) / 30.89 / 27.59 / 36.87 / 15.17 / 38.26 / 39.13 / 29.33 / 35.07 / 23.89 / 43.47
2007 (NF=23) / 27.15 / 21.33 / 28.38 / 32.88 / 22.57 / 37.46 / 30.73 / 25.00 / 35.42 / 38.83
2008 (NF=25) / 34.25 / 45.67 / 37.41 / 51.46 / 57.61* / 55.64* / 35.22 / 33.02 / 45.85 / 65.23*
2009 (NF=24) / 24.57 / 23.51 / 16.44 / 20.90 / 22.86 / 30.70 / 40.24 / 38.41 / 30.72 / 46.59
2010 (NF=24) / 24.12 / 16.66 / 19.33 / 20.84 / 30.79 / 17.27 / 25.20 / 49.31 / 27.81 / 55.77*
2011 (NF=21) / 23.50 / 34.16 / 28.72 / 38.11 / 46.76 / 20.94 / 28.15 / 31.01 / 27.12 / 31.56
2012 (NF=5) / 21.17 / 30.27 / 22.12 / 24.52 / 46.04 / 18.83 / 18.04 / 33.31 / 26.51 / 30.83
2013 (NF=16) / 28.82 / 22.99 / 31.44 / 32.01 / 41.06 / 30.04 / 34.22 / 29.96 / 22.55 / 37.60

Table S4Pairwise comparisons for 13 nuclear μsat loci between birth year cohorts of adult males (above diagonal) and females (below diagonal), with values on diagonal indicating comparisons between the sexes for that year, based on: (a) FST (Weir and Cockerham 1984) and (b) exact tests of differentiation (χ2; Raymond and Rousset 1995). There were no significant differences.NF=female sample size and NM=male sample size.

(a) Fst

1996
(NM=5) / 1998
(NM=6) / 1999
(NM=14) / 2001
(NM=5) / 2003
(NM=60) / 2005
(NM=5) / 2007
(NM=14) / 2008
(NM=23) / 2010
(NM=12)
1996 (NF=20) / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
1998 (NF=9) / 0.000 / 0.000 / 0.006 / 0.000 / 0.000 / 0.000 / 0.002 / 0.000 / 0.001
1999 (NF=20) / 0.000 / 0.000 / 0.007 / 0.008 / <0.001 / 0.000 / 0.009 / 0.004 / 0.008
2001 (NF=9) / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
2003 (NF=35) / 0.001 / 0.000 / 0.006 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.010
2005 (NF=14) / 0.000 / 0.000 / 0.000 / 0.000 / 0.001 / 0.000 / 0.000 / 0.000 / 0.000
2007 (NF=7) / 0.000 / 0.000 / 0.009 / 0.010 / 0.000 / 0.009 / 0.000 / 0.000 / 0.001
2008 (NF=4) / 0.002 / 0.002 / 0.003 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.003
2010 (NF=4) / 0.000 / 0.000 / 0.010 / 0.000 / 0.000 / 0.012 / 0.016 / 0.000 / 0.000

(b) χ2

1996
(NM=5) / 1998
(NM=6) / 1999
(NM=14) / 2001
(NM=5) / 2003
(NM=60) / 2005
(NM=5) / 2007
(NM=14) / 2008
(NM=23) / 2010
(NM=12)
1996 (NF=20) / 20.91 / 21.85 / 22.17 / 12.96 / 16.08 / 16.51 / 8.93 / 19.90 / 11.62
1998 (NF=9) / 15.53 / 26.61 / 33.05 / 20.16 / 21.15 / 22.79 / 26.33 / 23.35 / 28.64
1999 (NF=20) / 19.57 / 20.20 / 36.15 / 24.78 / 22.60 / 27.07 / 23.97 / 34.23 / 29.57
2001 (NF=9) / 17.34 / 16.64 / 29.03 / 11.84 / 18.58 / 23.68 / 20.43 / 23.89 / 23.61
2003 (NF=35) / 22.56 / 14.11 / 44.97 / 11.99 / 12.76 / 30.08 / 14.71 / 17.58 / 50.88
2005 (NF=14) / 15.59 / 21.04 / 28.65 / 21.50 / 26.12 / 19.50 / 20.10 / 29.81 / 34.95
2007 (NF=7) / 20.75 / 18.46 / 31.73 / 25.47 / 17.70 / 31.16 / 16.02 / 21.49 / 24.69
2008 (NF=4) / 21.91 / 30.20 / 36.97 / 26.00 / 25.16 / 20.16 / 22.89 / 35.73 / 29.60
2010 (NF=4) / 27.12 / 26.58 / 48.59 / 16.41 / 33.41 / 35.56 / 29.27 / 17.26 / 22.75

Fig. S1Bar graphs showing allelic frequencies of Maumee Riverwalleye adult spawning run years and birth year cohorts and larvae for locus Svi20 (identified as under possible positive selection) and SviL4 (a selectively neutral locus, used for comparison).Svi20 was identified as showing possible evidence of selection with the programs Lositan (Beaumont and Nichols 1996; Antao et al. 2008) and BayeScan (Foll and Gaggiotti 2008; see Table S2).