2 Supplementary Methods
4 Processing of sediment samples
210 Pb- dating – Sediment samples from South Center Lake were 210 Pb-dated at the St.
6 Croix River Watershed Station using standard procedures (Engstrom & Schottler 2003), with
8 modifications of the methods of Appleby (2001) and Eakins & Morrison (1978). According to the constant rate of supply model using
210
Pb activity (Appleby 2001) and
137
Cs signals, mass accumulation rates varied between 0.0054 and 0.0597 g cm
-2
yr
-1
(Table S1).
10
Loss-on-ignition (LOI)
–
The methods of Dean (1974) were used to determine sediment
12 composition of organic, inorganic, and calcium carbonate fractions via loss-on-ignition (LOI)
16 techniques (Fig. 1 and Table S1) to provide critical parameters (i.e. water content, estimates of
14 re-mineralization) that supported the sediment dating methodologies described above.
Quantification of phosphorus content
– Sediment layers of 4 cm were sampled (~2 g) in
18 triplicate at the top, middle, and bottom. Samples were thoroughly homogenized and dried at
60°C for 7 days. After measurements of initial dry weight, samples were ashed at 550°C for 2 hours and digested using sulphuric acid (American Public Health Association 1992). This
20 extract was analyzed for ortho-P using the ascorbic acid spectrophotometric method. Although this assay does not estimate total P in the sediment, acid-extracted ortho-P is strongly correlated
22 with total P and mirrors diatom-inferred P concentrations in the water column, reflecting long-
24 term changes in P loading (Engstrom et al.
2009) (Table S1).
1

26 Extracting ephippia from sediments – Individual sediment samples were sifted through a nested series of sediment sieves (30 cm diameter) of 710 µM, 425 µM, and 300 µM mesh size,
28 and gently washed to separate Daphnia ephippia from other subfossil remains. Daphnia pulicaria ephippia were separated from those of other species (Colbourne et al.
1997).
30 Individual ephippia were placed in a small quantity of sterile growth medium. Eggs were carefully extruded from the ephippial casing by applying gentle pressure to its tapered ends using
32 fine-tipped watch-makers forceps. Individual eggs were then carefully pipetted into either cell culture plates (for hatching), or 0.5 ml sterile microcentrifuge tubes, for direct DNA extraction.
34 Clean/sterile pipettes and fresh, sterile growth medium were changed out between samples to eliminate the possibility of cross-sample contamination.
36 We initially sampled ephippia from every other sediment layer throughout the entire core, but increased the temporal resolution by analyzing intermediate layers that fell into the
38 population genetic structure transition zone (Fig. 1). Unfortunately, DNA from eggs in the 36-40 cm layer, representing ~1898 to 1914 AD, did not amplify due to poor natural preservation of the
40 ephippia. In addition, sample sizes decreased in the deepest layers, because of obvious preservation issues for these >1000 year-old eggs. Due to higher sedimentation rates during
42 periods of higher lake productivity, as well as compression of deeper sediments, a 4 cm sediment slice in the upper layers represents 10 years, increasing to ~100 years in the oldest layers (Table
44 S1).
46 Analysis of molecular data
2

48 Microsatellite mapping
– We mapped microsatellite loci to the
Daphnia pulex genome
(Table 1) using known scaffold positions on D. pulex chromosomes (Colbourne et al.
2011).
50 The exact positions of four loci could not be determined because the scaffold on which they are located has not been mapped to the D. pulex genome (Dp173, Dp283, Dp377, Dp461).
52
Genetic differentiation
– Null allele frequencies for each locus were estimated using
54 FreeNA (Chapuis & Estoup 2007) (Table S2). A null-allele-corrected pairwise calculation of F
ST was carried out using the ENA correction (F
ENA,ST
) to estimate genetic differentiation between
56 sediment layers (Table S3), with 1,000 iterations. A Principal Coordinate Analysis (PCoA)
58 using F
ENA,ST
was performed and plotted with GenAlEx (Peakall & Smouse 2006) (Fig. S5).
Allelic richness and private allelic richness – Allelic richness and private allelic richness
60 were standardized using the rarefaction method of the software ADZE (Szpiech et al.
2008).
Sample size between temporal subpopulations was standardized to a sample size g =4, based on
62 the lowest available sample size for a given locus (Table S2). Differences between allelic richness and allelic private richness between the periods of pre- and post-European settlement
64 were tested with a Mann-Whitney U test. Significance was tested with an exact test
66 implemented in the software PAST (Hammer et al.
2001).
Hardy-Weinberg Equilibrium
– Departures from Hardy-Weinberg Equilibrium for each
68 temporal subpopulation were evaluated by calculating F
IS
, the inbreeding coefficient, as estimated from an AMOVA, with 999 iterations implemented in GenoDive (Meirmans &
70 Tienderen 2004)
3

72 Bottleneck – A search for a recent population genetic bottleneck was conducted by calculating the M-ratio, which compares the number of alleles to their range in allele size ( M )
74 (Garza & Williamson 2001). They suggest that as a result of a bottleneck the number of alleles will decrease more quickly than the allele size range, and that allele recovery is correlated with
76 post-population size, thus allowing for identification of bottlenecks long after the bottleneck occurred. This property makes it especially well-suited for the time scale of our study. A
78 population at equilibrium will result in M > 0.68, and should approach 1, if using seven or more loci, as recommended by the authors.
80
82
Phenotypic assays
Radiolabelling the algae – Scenedesmus acutus algae were grown in continuous flow
84 chemostats under LP or HP conditions. After collection, and centrifugation (at 3500 rpm for 30
86 min), precipitated algal cells were re-suspended in 200 mL of COMBO (without N and P
(Kilham et al.
1998)) at a concentration of 1mg C L
-1
. The resuspension was spiked with
33
P (as
88 orthophosphate) at 5.55 MBq L -1 (following He & Wang (2007). Algal suspensions were incubated in a shaker at 20°C, 16:8 light: dark cycle for 72 h. Specific activity of 33
P in the algae was estimated by filtering 5ml of the suspension through a GF/F filter (Whatman International
90 Ltd, Maidstone, England). After addition of scintillation cocktail (2 mL; Ultima Gold, Perkin
Elmer Inc., MA), specific activity was counted in a Beckman Coulter LS 600SC liquid
92 scintillation counter.
4

Supplementary Tables
Table S1. Sediment history with associated environmental variables and historic growth of the human population. Depth represents the top interval of the sediment layers obtained from the core. Percentages of organic material (%Organic), calcium carbonate (%CaCO
3
), and inorganic material (%Inorg.) were obtained from the Loss-on-Ignition (LOI) analysis performed at LacCore, University of Minnesota, and represent the proportions of these components at that particular interval of sediment, respectively. Ortho-phosphorus (ortho-P) for the given sediment interval (4 cm increments) was measured as described above.
Sediment accumulation rate and its standard deviation (Sediment Accum., Error of Sed. Accum.) for a given sediment interval, sediment age and its standard deviation (Age: Bass of Int., Error of Age), and corresponding sediment date (Date A.D.) were obtained from the results of 210 Pb dating performed by the St.
Croix Watershed Station in Minnesota (Note: below a depth of 46 cm, date is inferred based upon the sedimentation rate at the 46 cm interval making this a conservative estimate). The year of the census (Census Year), population of Chisago County, MN for the given decade (Census Pop.), and corresponding population growth (%Pop) were obtained from the United States Census Bureau, U.S. Decennial Census (U.S. Dept of Commerce 2013) for Chisago County,
MN: 1860 – 2010 (Note: Census data approximately match the interval they are listed under). Estimated population size (Est. Pop.) was extrapolated from the census data for a given sediment interval.
Depth % %
Organic CaCO
3
%
Inorg. ortho-P Error of ortho-P
Sediment
Accum.
Error of
Sed. Accum.
Age: Base of Int.
Error of Age
Date A.D. Census
Year
Census
Pop.
% Pop.
Growth
Est. Pop. cm +/-s.d. g/cm 2 *yr +/-s.d. yr +/-s.d mgP g sediment -1
2.480
4
5
6
7
0
1
2
3
34.07 5.00 60.94
36.24 5.96 57.8
37.64 7.60 54.76
ND ND ND
37.94 8.05 54.00
38.68 8.32 53.00
36.61 6.88 56.51
37.58 8.85 53.56
8
9
36.02 8.58 55.40
33.79 7.85 58.36
10 34.67 8.34 57.00
11 32.47 8.72 58.81
12 31.62 9.06 59.32
13 31.24 9.07 59.69
14 30.90 9.20 59.90
15 31.67 9.00 59.32
16 28.72 7.91 63.37
17 31.88 7.25 60.87
18 31.50 7.55 60.95
19 31.45 7.92 60.63
20 32.87 8.81 58.32
3.573
3.767
3.810
5.008
2.971
0.031 0.0383 0.00191
0.040 0.0436 0.00214
0.042 0.0368 0.00166
0.085 0.0436 0.00218
0.097 0.0433 0.00240
0.100 0.0405 0.00196
0.29
3.83
9.91
17.17
25.32
33.85
1.48 2011.2
1.54 2007.7
1.72 2001.6
1.55 1994.4
1.58 1986.2
1.70 1977.7
2010 53887 31.1
2000 41101 34.7
1990 30521 18.7
1980 25717 47.0
55557
50546
43140
35181
28698
22937
5

Depth % %
Organic CaCO
3
%
Inorg. cm
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
34.55
38.57
39.86
28.56
29.64
28.00
29.13
27.40
26.92
27.63
29.18
26.93
26.07
27.22
27.33
29.48
26.56
25.18
24.30
24.02
24.02
25.35
26.72
26.16
24.43
23.91
23.62
23.73
24.06
24.01
24.16
24.35
8.63
9.25
8.76
8.38
8.40
9.32
9.04
8.54
8.37
7.64
7.50
7.83
7.13
6.44
6.21
5.66
5.46
5.89
5.63
4.94
5.29
5.56
6.27
6.21
5.72
5.24
5.31
5.52
5.07
4.95
5.13
4.63
56.81
52.18
51.38
63.06
61.96
62.68
61.83
64.06
64.71
64.73
63.32
65.24
66.80
66.34
66.46
64.87
67.99
68.93
70.06
71.04
70.69
69.10
67.01
67.63
69.85
70.85
71.07
70.75
70.87
71.03
70.71
71.03 ortho-P Error of ortho-P mgP g sediment -1
Sediment
Accum.
Error of
Sed. Accum.
+/-s.d. g/cm 2 *yr +/-s.d.
Age: Base of Int. yr
Error of Age
+/-s.d
Date A.D. Census
Year
3.810
4.400
3.908
1.490
1.103
1.231
0.974
1.090
0.046
0.083
0.035
0.290
0.056
0.035
0.070
0.024
Census
Pop.
% Pop.
Growth
Est. Pop.
0.0343 0.00198
0.0282 0.00199
0.0206 0.00190
0.0289 0.00315
0.0259 0.00335
78.33
87.82
97.27
44.38
58.30
2.01 1967.1
2.41 1953.2
2.80 1933.2
2.99 1923.6
3.81 1914.3
1970 17492 30.4
1960 13419 5.9
1950 12669 -3.5
1940 13124 -0.5
1930 13189 -8.7
1920 14445 6.7
0.0287 0.00514 106.73 4.82 1904.8
0.0597 0.001892 113.04 5.39 1898.5
1910 13537 2.2
1900 13248 27.9
13388
12815
0.0299 0.00785 121.07 6.68 1890.5 1890 10369 29.8 10503
0.0121 0.00315 133.19 9.56 1878.3 1880
1870
7982
4358
83.2
150.0
7367
0.0064 0.00275 155.78 19.01 1855.7
0.0054 0.00510 184.18 45.42 1827.3
0.0063 0.01305 207.29 92.14 1804.2
1778.2
1752.2
1725.8
1699.3
1673.0
1646.4
1860 1743
0
13169
14131
13927
16315
12908
6

Depth % cm
%
Organic CaCO
3
%
Inorg.
53 24.22 4.94 70.84
54 24.10 5.25 70.65
55 24.08 4.88 71.05
56 23.96 5.22 70.82
57 23.79 4.91 71.30
58 24.17 5.08 70.75
59 22.70 4.95 72.35
60 23.68 4.73 71.59
61 23.4 4.97 71.63
62 23.88 5.21 70.91
63 23.94 5.09 70.97
64 23.46 5.48 71.06
65 24.00 5.18 70.82
66 24.57 5.46 69.97
67 24.22 5.07 70.70
68 23.14 5.34 71.52
69 23.18 5.69 71.13
70 25.53 5.48 70.99
71 23.70 5.74 70.56
72 23.75 5.45 70.80
73 23.86 5.59 70.53
74 23.82 5.23 70.95
75 23.96 5.40 70.63
76 23.65 5.28 71.07
77 23.58 5.32 71.10
78 23.25 5.21 71.54
79 22.16 5.03 72.81
80 22.45 5.01 72.54
81 23.22 5.32 71.47
82 23.74 5.06 71.20
83 24.03 5.52 70.45
84 23.80 5.31 70.90
85
86
87
24.02
24.14
24.43
5.31
5.12
5.38
70.67
70.74
70.19 orthoP Error of Sediment Error of ortho-P Accum. Sed. Accum.
+/-s.d. g/cm 2 *yr +/-s.d.
Age: Base of Int. yr mgP g sediment -1
Error of Age
+/-s.d
Date A.D. Census
Year
0.989 0.081
1616.7
1591.4
1563.9
1535.8
1.009 0.107
1507.2
1478.8
1448.1
1418.3
1.056 0.050
1388.9
1359.7
1330.6
1301.4
3.017 0.067
1272.2
1243.4
1212.8
1181.7
2.174 0.058
1150.7
1120.8
1090.5
1061.2
1.311 0.089
1031.9
1001.9
972.4
941.8
1.000 0.101
911.3
880.2
848.5
816.2
0.982 0.091
784.4
754.5
724.8
694.6
665.3
634.5
604.7
Census
Pop.
% Pop. Est. Pop.
Growth
7

Depth % cm
%
Organic CaCO
3
%
Inorg.
88
89
90
91
92
93
94
95
96
24.05
23.91
24.39
24.06
24.14
24.10
23.90
23.98
23.96
5.30
5.40
5.37
5.46
5.60
5.50
5.65
5.67
5.56
70.65
70.69
70.24
70.48
70.25
70.41
70.44
70.36
70.47 orthoP Error of Sediment Error of ortho-P Accum. Sed. Accum.
+/-s.d. g/cm 2 *yr +/-s.d.
Age: Base of Int. yr mgP g sediment -1
1.095 0.048
Error of Age
+/-s.d
Date A.D. Census
Year
572.8
541.5
511.0
479.5
1.071 0.036 446.8
415.1
382.3
348.7
315.1
Census
Pop.
% Pop. Est. Pop.
Growth
8

Table S2. Sample size and population genetic parameters measured in 15 temporal subpopulations of the Daphnia pulicaria South Center Lake population. Due to the small number of eggs in the upper layers, we included additional data for individuals collected from the plankton (lake water) in 2010, or that were hatched from those layers. This was justified based on small genetic differentiation between eggs and adults in the layers where sample size was high enough for comparison (within the 12-16 cm and 20-24 cm layers, F
ST
=0.063 and 0.008, respectively). Dating refers to the top cm of each sediment layer. N a
= number of alleles (GenAlEx), A
R
= allelic richness, A
P
= private allelic richness (rarefaction method ADZE, for g=4)), null allele frequency (Dempster et al.
1977), observed
( H o
) and expected ( H e
) heterozygosity (GenAlEx), inbreeding coefficient, F
IS
(GenoDive), and evidence of a population bottleneck based on the value M , from a
M-ratio test. depth
(cm) year
(AD) adults
(n) eggs
(n)
N a
A
R
A
P null allele frequency
H o
H e
F
IS
(p-value) M
Lake water
4-8
12-16
20-24
24-28
28-32
32-36
40-44
44-48
52-56
60-64
68-72
76-80
84-88
2011
2007
1994
1977
1967
1953
1933
1898
1855
1646
1418
1182
942
695
25
22
12
33
-
-
-
-
-
2
2
-
-
-
-
3*
24
49
24
12
19
29
29
26
32
18
17
10
2.18 1.58 0.036
2.88 1.76 0.091
2.82 1.67 0.039
3.18 1.75 0.026
2.35 1.55 0.005
2.41 1.67 0.041
2.41 1.57 0.009
2.53 1.63 0.018
2.47 1.62 0.019
2.41 1.62 0.021
2.65
2.18
2.29
2.18
1.67
1.62
1.64
1.64
0.027
0.008
0.028
0.005
92-94 447 - 6 1.71 1.49 0.016
*includes 1 egg from the 8-12 cm layer (estimated date 2001 AD)
0.015
0.018
0.043
0.039
0.017
0.015
0.046
0.050
0.020
0.012
0.024
0.025
0.024
0.025
0.057
0.341 0.285
0.339 0.354
0.272 0.324
0.320 0.364
0.256 0.270
0.345 0.321
0.245 0.277
0.251 0.301
0.288 0.299
0.300
0.298
0.276
0.278
0.293
0.218
0.301
0.320
0.299
0.298
0.307
0.299
-0.177 (0.002)
0.062 (0.067)
0.173 (0.001)
0.129 (0.001)
0.077 (0.064)
-0.029 (0.333)
0.143 (0.007)
0.185 (0.001)
0.057 (0.106)
0.019 (0.366)
0.083 (0.023)
0.107 (0.033)
0.099 (0.054)
0.099 (0.118)
0.161 (0.121)
1.28
1.16
1.24
1.05
1.13
1.13
1.20
1.20
1.10
1.16
1.26
1.24
1.27
1.11
1.28
9

Table S3. Pair-wise estimation of F
ST
(Weir 1996) with (above the diagonal) and without (below the diagonal) the ENA correction described in Chapuis and
Estoup (2007). Global F
ST
across all loci and populations with ENA F
ST
= 0.068130, and without ENA F
ST
= 0.068042. lake 4-8 12-16 20-24 24-28 28-32 32-36 40-44 44-48 52-56 60-64 68-72 72-76 84-88 92-94 lake
4-8 0.040
0.039 0.052
0.052
0.053
0.030
0.103
0.090
0.154
0.107
0.101
0.080
0.150
0.123
0.175
0.133
0.155
0.115
0.159
0.114
0.113
0.086
0.143
0.102
0.179
0.124
0.367
0.278
12-16 0.049 0.046
20-24 0.051 0.025 0.027
0.026 0.055 0.098 0.052 0.089 0.143 0.121 0.116 0.076 0.106 0.135 0.287
0.032 0.054 0.032 0.056 0.080 0.062 0.064 0.036 0.063 0.073 0.185
24-28 0.118 0.090 0.052 0.029
28-32 0.153 0.107 0.094 0.054 0.094
0.086 -0.004 0.042 0.074 0.046 0.068 0.013 0.057 0.096 0.229
0.056 0.094 0.079 0.086 0.079 0.067 0.057 0.083 0.190
32-36 0.106 0.080 0.043 0.029 -0.013 0.065
40-44 0.158 0.126 0.095 0.066 0.042 0.098 0.027
0.032 0.052 0.025 0.043 0.002 0.032 0.067 0.209
0.030 0.012 0.023 0.006 0.014 0.030 0.119
44-48 0.180 0.134 0.136 0.079 0.072 0.081 0.051 0.021
52-56 0.166 0.120 0.118 0.063 0.046 0.091 0.026 0.003 -0.002
0.001 -0.002 0.019 0.008 -0.003 0.085
0.001 -0.001 0.004 0.004 0.093
60-64 0.166 0.118 0.113 0.068 0.069 0.081 0.047 0.017 -0.004 -0.001
68-72 0.115 0.084 0.065 0.031 0.011 0.067 -0.007 0.000 0.018 -0.003 0.009
0.009 0.006 -0.008 0.092
-0.001 0.023 0.137
72-76 0.143 0.100 0.094 0.059 0.051 0.054 0.025 0.003 0.005 0.001 0.004 -0.007
84-88 0.180 0.129 0.130 0.075 0.093 0.083 0.071 0.021 -0.007 0.000 -0.009 0.020 0.008
0.011 0.113
0.048
92-94 0.376 0.283 0.292 0.198 0.235 0.194 0.220 0.129 0.096 0.101 0.102 0.145 0.119 0.041
10

Table S4. Detailed results for MatSAM analysis for microsatellite loci with at least one allele that is significantly associated with one of the environmental parameters tested. Allele-specific test results (p>0.001, Bonferroni correction for multiple comparisons) are indicated as significant (1) or non-significant (0).
Wald test (n=394 indiv) Cumulated results for Wald and G-test (n=246 indiv.)
Dp38
Dp43
Dp446
Dp369
Dp433
Dp401
Dp377
Dp461
234
323
329
331
339
271
396
398
186
190
324
326
274
280
181
185
187
3
4
4
4
4
8
8
1
2
2
2
2 unknown unknown unknown unknown unknown
1
1
1
1
1
1
1
1
1
1
0
1
0
1
1
1
1
1
0
0
1
0
1
1
0
1
0
0
1
0
1
1
1
0
0
0
0
1
0
1
0
0
1
0
1
1
0
0
0
1
0
0
0
0
1
0
0
0
0
1
0
0
0
0
0
0
0
0
1
1
0
0
0
0
0
0
1
0
0
1
0
1
1
1
0
0
0
0
1
0
0
0
1
1
0
0
0
0
0
1
1
0
1
0
0
1
0
0
0
0
1
0
0
0
0
0
1
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
1
0
11

Table S5: Depth, age, and ortho-P content of the four sediment layers from which the 9 Daphnia pulicaria genotypes were resurrected. PUE was estimated under low P (LP) conditions, while RE and GR were measured under both LP and high phosphorus (HP) conditions. Numbers represent mean ± 1SD of 5 replicates (PUE), 3 replicates (RE), and 10 replicates (GR) per genotype per P treatment.
Depth Approximate age of Sediment PhosphorusRetention Efficiency (RE) Growth rate (GR) mm day -1
(cm)/Genotype genotypes ortho-P use% efficiency
4-8/1 2008-2002 AD
(mgP gm sediment -1 )
3.48±0.15
4-8/2
4-8/3
20-24/1
20-24/2
20-24/3
52-56/1
60-64/1
60-64/2
2008-2002 AD
2008-2002 AD
1977-1967 AD
1977-1967 AD
1977-1967 AD
1646-1536 AD
1418-1301 AD
1418-1301 AD
“
“
2.75±0.13
“
“
1.13±0.41
0.97±0.08
“
(PUE)
14.89±3.22
15.35±6.45
10.04±0.34
21.06±4.01
21.04±4.93
22.51±2.68
32.27±0.44
18.02±1.93
24.28±2.19
HP LP HP LP
39.28±1.39 48.54±7.96 0.049±0.005
39.70±0.66 54.87±4.80 0.054±0.003
41.85±1.89 60.88±3.26 0.048±0.013
61.64±3.85 68.22±9.95 0.056±0.006
54.51±1.85 75.86±0.69 0.078±0.003
52.65±9.24 74.53±0.59 0.056±0.003
80.24±0.41 74.10±2.64 0.042±0.004
77.96±2.19 82.78±2.23 0.042±0.008
82.44±1.32 82.22±1.67 0.044±0.011
0.022±0.002
0.024±0.006
0.029±0.002
0.025±0.008
0.034±0.007
0.026±0.003
0.059±0.008
0.044±0.005
0.040±0.008
12

Table S6 . Parameter estimates of fixed effects for Linear Mixed Effect models of Phosphorus
Use Efficiency (PUE), Retention Efficiency (RE) and Growth Rate (GR). Genotype Age (GA) is treated as an ordered factor and its linear (GA.L), quadratic (GA.Q) and cubic (GA.C) effects tested by using orthogonal polynomial contrasts.
Estimate
RE
(Intercept) 4.501e-10
P after 10min -8.230e-01
P-treat
GA.L
2.173e-11
9.970e-11
GA.Q
GA.C
GR
(Intercept)
P-treat
GA.Q
-2.052e-11
GA.L: P-treat -4.080e-11
GA.Q: P-treat 6.011e-12
GA.C: P-treat 3.852e-11
-2.086e-11
0.053333
-0.014189
-0.012072
GA.C 0.021515
GA.L: P-treat 0.030660
GA.Q: P-treat 0.002252
PUE
GA.C: P-treat -0.038396
(Intercept)
GA.L
GA.Q
GA.C
-0.57370
0.22305
-0.25844
-0.10838
Std.Error
1.748e-10
5.686e-01
4.037e-12
5.366e-12
6.119e-12
6.468e-12
7.282e-12
8.180e-12
8.778e-12
0.001378
0.001220
0.002757
0.002899
0.002203
0.002440
0.002656
0.02382
0.04302
0.04764
0.05186 t value
2.575
-1.447
5.383
18.580
-3.408
-3.172
-5.603
0.735
4.388
38.69
-11.63
-4.38
7.42
13.92
0.92
-14.46
-24.083
5.185
-5.425
-2.090
13

Supplementary Figures
Fig. S1. Total farmed acreage of farmed land in Chisago County, Minnesota (left y-axes)
(Source: USDA (2013)), and ortho-P measured in the sediment of South Center Lake.
14

Fig. S2. Human population size in Chisago County, MN (Source: United States Census
Bureau, U.S. Decennial Census (U.S. Dept of Commerce 2013) and acreage of total crop production in Minnesota, based on acres harvested of corn, wheat, and soybeans (Source:
USDA (2013)), and acreage of P -based fertilizer use (both right Y-axis) in Minnesota
(Source: USDA Economic Research Service (2013)).
15

Fig. S3. Temporal population genetic structure of the Daphnia pulicaria population of South
Center Lake for K =2, K =3, and K =4 under the admixture model (A). K =2 was estimated to be the most likely value for K (Evanno et al.
2005), as determined by (B) the second order rate of change of the likelihood function with respect to K
(∆
K ), and (C) the likelihood distribution of K ( L(K) ). Sediment depths as in Fig. 1.
16

Figure S4. Allelic frequencies of 15 polymorphic microsatellite loci. Each bar represents allelic frequencies in the temporal subpopulation of the respective sediment layer. Red or orange alleles in the top category (loci with association to environment) showed a significant link to one of the environmental factors (Table S4). The lower 10 loci (loci without association to environment) did not show a significant relationship to the environmental factors measured.
17

Fig. S5. Principal Correspondence Analysis (PCoA) of F
ENA,ST
(null-allele-corrected F
ST
using the ENA correction, see details in
Methods)
18

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20