Genetic signatures of historical bottlenecks in sympatric lake trout (Salvelinus namaycush) morphotypes in Lake Superior
Authors: Guinand B., Page K.S., Burnham-Curtis M.K. and Scribner K.T.
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Table S1: Observed pairwise values for each morphotype (a-c). Shaded areas represent comparisons among contemporary populations within each morph. For the lean and siscowet morphs, genetic differentiation and associated p-values are reported among pooled historical and/or pooled contemporary samples. When genetic differentiation was found significant, statistical power (SP) estimated using PowSim (Ryman N, Palm S., 2006, Powsim: a computer program for assessing statistical power when testing for genetic differentiation. Mol Ecol Notes 6: 600-602. DOI: 10.1111/j.1365-294X.2006.01378.x) is reported in brackets. SP was systematically <0.70 when genetic differentiation was not found significant; it was then not reported. Samples are labelled as in Fig. 1 (see main text). Significant tests are indicated by an asterisk (*). The Benjamini-Yekutieli false discovery rate procedure has been applied to correct for multiple test (Narum S.R., 2006, Beyond Bonferroni: less conservative analyses for conservation genetics. Conserv. Genet. 7: 783-787. DOI 10.1007/s10592-005-9056-y).
Table S2: Average and single locus estimates of standardized allelic richness observed for each lake trout’s morph. Allelic richness was standardized using the method by Petit et al. (1998, Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12: 844–855.) based on a rarefaction procedure. It was standardized to the smallest sample observed sample from each morph (see Table 1). Italics indicate loci with larger standardized allelic richness in contemporary samples than in samples from the period of collapse. Last column reports the average percentages of decrease in standardized allelic richness for each morph as measured between the time periods indicated. Percentages are reported in Fig. 2 (see main text).
Supplementary Material : Table S1
a - LeanLCHA48 / LIR59 / LGI59 / LIR / LGI / LSR
LWP48 / 0.0013 / 0.0035 / 0.0264 / 0.0278 / 0.0704* (0.81) / 0.0428* (0.74)
LCHA48 / 0.0000 / 0.0160 / 0.0208 / 0.0476* (0.67) / 0.0424* (0.63)
LIR59 / 0.0000 / 0.0000 / 0.0059 / 0.0112
LGI59 / 0.0007 / 0.0000 / 0.0126
LIR / 0.0111 / 0.0101
LGI / 0.0228* (0.99)
historical / 0.006 / P= 0.212
contemporary / 0.015 / P< 0.001 (0.99)
b - Siscowet
SIR59 / SIR / SSR / SC / SGI
SWP48 / 0.0000 / 0.0496* (0.70) / 0.0245 / 0.0563* (0.86) / 0.0500* (0.79)
SIR59 / 0.0062 / 0.0000 / 0.0421 / 0.0197
SIR / 0.0014 / 0.0105 / 0.0000
SSR / 0.0088 / 0.0000
SC / 0.0001
contemporary / 0.004 / P= 0.084
c - Humper
HIR / HC
HIR59 / 0.0187 / 0.0000
HIR / 0.0027
Supplementary Material : Table S2
Time period / LociOgo1a / Onem10 / Scom19 / Sfo1 / Ssa85 / average / % decrease
Lean
Pre-collapse / 2.053 / 1.529 / 4.565 / 1.767 / 2.818 / 2.546
Collapse / 1.637 / 0.899 / 3.837 / 1.159 / 2.316 / 1.969
Contemporary / 1.521 / 0.894 / 3.385 / 0.824 / 2.314 / 1.788 / 1948-1959: -22.66%
since 1959: -9.19%
Siscowet
Pre-collapse / 1.458 / 1.258 / 1.987 / 1.367 / 1.566 / 1.527
Collapse / 1.730 / 0.500 / 1.417 / 1.472 / 0.917 / 1.207
Contemporary / 1.244 / 0.714 / 1.616 / 0.933 / 1.304 / 1.162 / 1948-1959: -20.95%
since 1959: -3.73%
Humper / Collapse / 1.500 / 0.999 / 4.029 / 1.397 / 1.499 / 1.885
Contemporary / 1.474 / 1.085 / 3.534 / 0.535 / 2.102 / 1.745 / since 1959: -7.43%
Note: The estimated standardised allelic richness might be <1 as one allele is systematically subtracted at each locus in the procedure developed by Petit et al. (1998). See this reference for details relative to such a standardisation.