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Eckert et al.: Local adaptation at fine spatial scales

Running Header: Eckert et al.: Local adaptation at fine spatial scales

SUPPLEMENTAL FILE (File S2: Supplemental Tables and Figures)

Local adaptation at fine spatial scales: an example from sugar pine (Pinus lambertiana, Pinaceae)

Andrew J. Eckert, Patricia E. Maloney, Detlev R. Vogler, Camille E. Jensen, Annette Delfino Mix, and David B. Neale

Last updated: 02/21/2015

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Eckert et al.: Local adaptation at fine spatial scales

Table S1.Sampling locations, sample sizes, and environmental data by plot

Popa / Plot / Lat / Long / nPb / nGb / AWC50 / AWC25 / WC 15 BAR / SAND / SOLAR RAD / MINTEMP / MAXTEMP / ANN PPT / GDD MAY / GDD AUG / ELEV
bl / bl1 / 38.97554 / -120.09912 / 5 / 9 / 4.5 / 3.28 / 3.8 / 83.2 / 88.09 / -6.71 / 23.00 / 1070 / 10 / 278 / 2061
bl / bl2 / 38.97345 / -120.09864 / 5 / 6 / 4.5 / 3.28 / 3.8 / 83.2 / 88.68 / -6.71 / 23.00 / 1218 / 10 / 278 / 2087
bl / bl3 / 38.97413 / -120.09793 / 4 / 9 / 4.62 / 2.99 / 5.6 / 85.0 / 80.61 / -6.71 / 23.00 / 1218 / 10 / 278 / 2074
carn / carn1 / 39.23659 / -120.07723 / 5 / 8 / 7.54 / 5.38 / 4.8 / 67.4 / 75.23 / -7.10 / 24.30 / 849 / 13 / 244 / 2001
carn / carn2 / 39.23576 / -120.07667 / 6 / 9 / 7.54 / 5.38 / 4.8 / 67.4 / 83.56 / -7.10 / 24.30 / 849 / 13 / 244 / 1983
carn / carn3 / 39.23498 / -120.07710 / 4 / 7 / 7.54 / 5.38 / 4.8 / 67.4 / 83.87 / -7.10 / 24.70 / 724 / 22 / 253 / 1988
cb / cb1 / 39.24374 / -119.99953 / 0 / 8 / 4.5 / 3.28 / 3.8 / 83.2 / 86.34 / -7.20 / 24.10 / 605 / 14 / 257 / 1918
cb / cb2 / 39.24369 / -119.99799 / 0 / 8 / 4.5 / 3.28 / 3.8 / 83.2 / 76.81 / -7.20 / 24.10 / 605 / 14 / 257 / 2020
cb / cb3 / 39.24249 / -119.99961 / 0 / 7 / 4.5 / 3.28 / 3.8 / 83.2 / 77.98 / -7.20 / 24.10 / 605 / 14 / 257 / 2009
glen / glen1 / 39.08483 / -119.91031 / 3 / 9 / 5.42 / 4.34 / 3.2 / 41.5 / 61.79 / -7.01 / 24.10 / 716 / 8 / 311 / 2111
glen / glen2 / 39.08451 / -119.91240 / 6 / 9 / 5.42 / 4.34 / 3.2 / 41.5 / 60.86 / -6.40 / 24.20 / 565 / 8 / 319 / 2124
glen / glen3 / 39.08321 / -119.91258 / 9 / 10 / 5.42 / 4.34 / 3.2 / 41.5 / 78.52 / -6.40 / 24.20 / 565 / 8 / 319 / 2149
gran / gran1 / 39.15671 / -120.15614 / 5 / 9 / 7.54 / 5.38 / 4.8 / 67.4 / 84.56 / -7.10 / 23.70 / 848 / 15 / 203 / 2012
gran / gran2 / 39.15726 / -120.15758 / 3 / 8 / 7.43 / 5.16 / 7.6 / 67.7 / 80.61 / -7.10 / 23.70 / 848 / 15 / 203 / 2026
gran / gran3 / 39.15695 / -120.15690 / 4 / 8 / 7.54 / 5.38 / 4.8 / 67.4 / 89.46 / -7.10 / 23.70 / 848 / 15 / 203 / 2041
hvn / hvn1 / 38.95196 / -119.93456 / 5 / 9 / 4.5 / 3.28 / 3.8 / 83.2 / 80.20 / -6.91 / 23.80 / 815 / 14 / 302 / 1985
hvn / hvn2 / 38.95111 / -119.93384 / 6 / 9 / 4.5 / 3.28 / 3.8 / 83.2 / 79.76 / -6.91 / 23.80 / 815 / 14 / 302 / 2003
hvn / hvn3 / 38.95002 / -119.93491 / 4 / 9 / 4.5 / 3.28 / 3.8 / 83.2 / 74.63 / -7.40 / 22.50 / 815 / 0 / 251 / 1982
my / my1 / 38.84631 / -120.01100 / 0 / 7 / 4.5 / 3.28 / 3.8 / 83.2 / 64.61 / -6.91 / 23.59 / 938 / 17 / 330 / 2019
my / my2 / 38.84646 / -120.01032 / 0 / 9 / 4.66 / 3.01 / 5.6 / 85.0 / 62.72 / -6.91 / 23.59 / 938 / 17 / 330 / 2033
my / my3 / 38.84596 / -120.00987 / 0 / 7 / 4.5 / 3.28 / 3.8 / 83.2 / 67.18 / -6.91 / 23.59 / 938 / 17 / 330 / 1988
pit / pit1 / 38.89721 / -120.00628 / 3 / 11 / 3.74 / 2.78 / 2.6 / 92.5 / 61.79 / -6.91 / 24.80 / 658 / 33 / 345 / 2012
pit / pit2 / 38.89696 / -120.00528 / 3 / 8 / 3.74 / 2.78 / 2.6 / 92.5 / 60.86 / -6.91 / 24.80 / 658 / 33 / 345 / 2019
pit / pit3 / 38.89638 / -120.00467 / 7 / 9 / 3.74 / 2.78 / 2.6 / 92.5 / 78.52 / -6.91 / 24.80 / 658 / 33 / 345 / 2050
spsp / spsp1 / 39.04570 / -120.15046 / 2 / 4 / 4.98 / 3.35 / 6.2 / 64.7 / 86.88 / -6.40 / 23.00 / 868 / 15 / 281 / 2078
spsp / spsp2 / 39.04697 / -120.14969 / 2 / 5 / 5.06 / 3.35 / 6.2 / 64.7 / 89.08 / -6.40 / 23.00 / 868 / 15 / 281 / 2068
spsp / spsp3 / 39.04766 / -120.14632 / 2 / 5 / 5.06 / 3.35 / 6.2 / 64.7 / 84.75 / -6.40 / 23.00 / 868 / 15 / 281 / 2025
tc / tc1 / 39.22768 / -119.92539 / 5 / 7 / 4.5 / 3.28 / 3.8 / 83.2 / 58.11 / -7.70 / 23.19 / 780 / 1 / 287 / 2050
tc / tc2 / 39.20785 / -119.92751 / 4 / 8 / 4.5 / 3.28 / 3.8 / 83.2 / 71.03 / -7.80 / 23.40 / 797 / 0 / 288 / 1942
tc / tc3 / 39.20929 / -119.92707 / 6 / 10 / 4.5 / 3.28 / 3.8 / 83.2 / 75.19 / -7.80 / 23.40 / 797 / 0 / 288 / 1921

aPopulations are those defined in Maloney et al. (2011): bl, Bliss State Park; carn, Carnelian Bay; cb, Crystal Bay; glen, Glenbrook; gran, Granlibakken; hvn, Heavenly; my, Meyers; pit, Sand Pit; spsp, Sugar Pine State Park; tc, Tunnel Creek.

bSample sizes (n) for phenotypic trait data (P, number of maternal trees) and genotypic data (G).

Supplemental Materials

Eckert et al.: Local adaptation at fine spatial scales

Table S2.Loadings on the top four principal components (PCs) for each of the 11 climate and soil variables associated with 30 plots sampled from 10 populations located around Lake Tahoe.

Climate variablea / PC1 / PC2 / PC3 / PC4
Eigenvalue / 3.632 / 2.379 / 2.094 / 1.364
PVEb / 33.02 / 21.63 / 19.04 / 12.40
awc50 / 0.454 / 0.227 / -0.176 / 0.057
awc25 / 0.420 / 0.306 / -0.191 / -0.046
wc 15 bar / 0.379 / -0.170 / 0.142 / 0.214
sand / -0.285 / -0.380 / -0.216 / 0.387
solar rad / 0.324 / -0.153 / 0.078 / 0.396
mintemp / 0.045 / 0.216 / 0.592 / 0.247
maxtemp / -0.158 / 0.518 / -0.264 / 0.235
ann ppt / 0.152 / -0.425 / 0.274 / 0.158
gdd may / -0.186 / 0.290 / 0.032 / 0.676
gdd aug / -0.446 / 0.106 / 0.248 / -0.071
elev / 0.047 / 0.260 / 0.549 / -0.197

aClimate averages for each location and plot based on PRISM data for 30-year averages (Daly et al. 1994 and FHTET): awc50, available water capacity in top 0-50 cm depth; awc25, available water capacity in top 0-25 cm depth; wc 15 bar, soil water capacity at 15 bars; sand (%), percentage sand content (sand:silt:clay); solar rad, percentage maximum solar radiation input for 40 latitude (Buffo et al. 1972); mintemp (°C), minimum annual temperature (January); maxtemp (°C), maximum annual temperature (July); ann ppt, total annual precipitation in mm; gdd aug, growing-degree days in May above 5°C; gdd aug, growing-degree days in August above 5°C. elev, elevation a.s.l. (m).

bPVE, percent variance explained.

Table S3.Summary of Type-III Wald F-tests with Kenward-Roger (1997) degrees of freedom for fixed effects in linear mixed models used to estimate maternal tree phenotypic trait values.

Collection Year / Block
Trait / F / df1 / df2 / P / F / df1 / df2 / P
HT / 0.0130 / 1 / 22.7 / 0.9106 / 0.0129 / 1 / 3265.60 / 6.20e-05
BF / 2.3759 / 1 / 15.2 / 0.1438 / 3.9965 / 1 / 3282.60 / 0.04568
RS / 4.8719 / 1 / 30.04 / 0.0351 / 18.433 / 1 / 909.83 / 1.95e-05
d13C / 0.1892 / 1 / 16.46 / 0.6692 / 2.6923 / 1 / 404.32 / 0.1016
d15N / 0.7581 / 1 / 10.09 / 0.4042 / 90.3289 / 1 / 409.36 / <2e-16

Table S4.Pearson’s correlation coefficient (r) and corresponding P-values (below the diagonal) from an asymptotic t-test as employed in the cor.test function in R for maternal tree phenotypic trait values

Trait / HT / BF / RS / d13C / d15N
HT / --- / -0.280 / -0.048 / 0.116 / -0.214
BF / 0.0036 / --- / -0.229 / 0.057 / 0.077
RS / 0.6265 / 0.0181 / --- / 0.144 / 0.080
d13C / 0.2379 / 0.5599 / 0.1396 / --- / -0.091
d15n / 0.0275 / 0.4347 / 0.4142 / 0.3531 / ---

Figure S1. The distribution of various statistics related to genetic diversity by plot. Plots are grouped into populations on the left. Whiskers on the boxplots extend to the data extremes, with limits of the box extending to 1.5 times the interquartile range. (A) The distribution of the minor allele frequency across plots. Minor alleles were defined using all trees, so that the minor allele is not necessarily the SNP allele with the lowest frequency in each plot. (B) The distribution of observed heterozygosity across plots. (C) The distribution of expected heterozygosity across plots.

Figure S2. The distribution of the hierarchical fixation index for plots relative to the total (Fplot,total). Whiskers in the boxplot extend to the data extremes, and the edges of the box are defined as 1.5 times the interquartile range. Red points give the top 12 observed values of Fplot,total, which are all greater than three times the median in their magnitude. The inlaid box lists the SNP names for each of these outliers and ordered from largest (Fplot,total = 0.194) to smallest (Fplot,total = 0.094). The three bolded values (0_9577_01-266, and 2_1865_02-592) are also outliers for correlations to environment and/or phenotypes.

Figure S3. The distribution of the squared allelic correlation (r2) between all 112,575 unique pairs of 475 SNPs. Note that the x-axis is on a log10 scale.

References

Buffo J, Fritschen LJ, Murphy JL(1972) Direct solar radiation on various slopesfrom 0 to 60 degrees north latitude. USDA Forest Service Research Paper PNW-142.Portland, Oregon, USA.

Daly C, Neilson R, Phillips D(1994) A statistical-topographic model for mappingclimatological precipitation over mountainous terrain. Journal of Applied Meteorology 33:140–158.

Kenward MG, Roger, JH (1997) small sample inference for fixed effects from restricted maximum likelihood.Biometrics 53:983–997.

Maloney PE, Vogler DR, Eckert AJ, Jensen CE, Neale DB(2011) Populationbiology of sugar pine (Pinus lambertiana Dougl.) with reference to historicaldisturbances in the Lake Tahoe Basin: Implications for restoration. Forest Ecology and Management262:770–779.

Supplemental Materials