Article Figures & Data
Figures
- Figure 1.
—Map of the study site in Argyll, Scotland showing the sampled forest blocks. Sika were introduced at Carradale. In the text sample sites are referred to by number as follows: 1, South Kintyre (-25 km); 2, Carradale (0 km); 3, Achaglachach (40 km); 4, Knapdale (50 km); 5, Kilmichael (55 km); 6, Birdfield (75 km); 7, North Cowal (100 km); 8, East Cowal (105 km); 9, Glendaruel (110 km); 10, South Cowal (115 km). Values in parentheses are distances from introduction point.
- Figure 2.
—The proportion of sika-like deer, plotted against distance north from the introduction point at Carradale (thick line). The gray areas bounded by dashed lines show the proportion of individuals carrying apparently introgressed alleles at nuclear or mitochondrial loci (sika-like hybrids below thick line; red-like hybrids above thick line).
- Figure 3.
—Estimated relative densities (relative number of deer per square kilometer) of sika (ns) and red (nr) deer, assuming equal rates of increase (rs = rr = 9.2% yr-1) and a carrying capacity of sika β = 1.5 times greater than red (αrr = αrs = 1.5, αss = αsr = 1.5); dispersal rate σ = 3.69 km yr-1. The observed proportions of sika-like individuals in samples (dots) are compared with the estimates [p = ns/(ns + nr); top left curve]; log[L] = -10.49.
- Figure 4.
—Log-likelihood contour plots for introgression into the sika-like population (a) and the red-like population (b), plotted against the current rate of hybridization H*, and past introgression I*. The rate of backcrossing into the sika-like population is assumed to be proportional to the overall proportion of red deer (H = H*q, I = I*q). The most likely values (with 2-unit support limits) are H* = 0.0121 (0.0033–0.0279) and I* = 0.00123 (0.00044–0.00193); log(L) = -168.50. For the red-like population sika alleles are assumed to have a frequency of u0 = 0.0049 in the ancestral red population. The most likely values (with 2-unit support limits) are H* = 0.0051 (0.0009–0.0149) and I* = 0.0004 (0–0.0027); log(L) = -152.71. Contours are spaced at 1 unit of log likelihood, and so the 2-unit support limits are at the second contour.
- Figure 5.
—Plots of red introgression into sika (a) and sika introgression into red (b). Points show the observed frequency of red or sika alleles within the opposite taxa, compared with the predicted frequency of introgressed alleles (upper smooth curve). The lower dashed lines show the contribution to this prediction from alleles that have been present for more than four generations and are at linkage equilibrium (i.e., from ancestral polymorphism and past introgression).
Tables
- TABLE 1
Microsatellite locus primer sequences, PCR conditions, and locus reference
Locus MgCl2 (mm) DMSOa (%) Annealing temperature Reference BM6438 2.0 5 52–54 Bishop et al. (1994) RM095 2.0 5 52–54 Bishop et al. (l994) RME025 2.0 5 48–50 Grosse et al. (1995) OarFCB048 2.0 10 52–54 Buchanan et al. (1994) OarFCB193 2.0 10 52–54 Buchanan and Crawford (1993) BOVIRBP 2.0 10 52–54 Moore et al. (1991) MM012 2.0 10 48–50 Mommens et al. (1994) VH054 2.0 5 52–54 Pierson et al. (1994) HH064 2.0 5 52–54 Henry et al. (1993) DRB003 2.0 — 46–54 Paterson and Pemberton (1997) TGLA387 2.0 5 50–52 Georges and Massey (1992) d-loop 2.0 — 50 Cook (1993); Kocher et al. (1989); Nagata et al. (1998) -
↵a Percentage of dimethylsulfoxide by reaction volume.
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- TABLE 2
For each locus, the allele sizes (in base pairs) are listed, followed by their classification as “sika” or “red” alleles and their frequency within sika-like and red-like individuals
Locus (no. alleles) Allele Race Frequency in sika Frequency in red BOVIRBP (9) 144 Sika 0.6061 0 146 Sika 0.0555 0.068 150 Red 0 0.1238 152 Red 0 0.0936 154 Red 0.0173 0.117 156 Red 0.0694 0.2982 160 Red 0 0.1987 162 Red 0 0.0146 166 Red 0 0.0146 Ø Red 0.2517 0.0714 FCB193 (14) 101 Red 0 0.0635 103 Red 0.0152 0.0076 105 Red 0 0.0076 107 Red 0 0.1224 109 Red 0 0.0319 111 Red 0 0.3035 113 Red 0 0.0794 115 Red 0 0.0153 117 Red 0 0.0076 119 Red 0 0.1411 121 Red 0 0.1295 127 Red 0 0.0076 129 Sika 0.9848 0 139 Red 0 0.0077 Ø Red 0 0.0751 RM095 (11) 122 Red 0 0.0379 126 Sika 0.9937 0.0061 128 Red 0 0.0689 130 Red 0 0.0627 132 Red 0.0063 0.2195 134 Red 0 0.2985 136 Red 0 0.106 138 Red 0 0.0031 140 Red 0 0.0613 142 Red 0 0.0861 144 Red 0 0.0153 0 Red 0 0.0345 REM025 (5) 157 Red 0 0.0092 171 Red 0 0.8159 173 Red 0 0.0945 197 Sika 1.000 0 209 Red 0 0.0061 Ø Red 0 0.0742 BM6438 (6) 251 Red 0.0127 0.4932 253 Red 0 0.231 255 Red 0 0.1857 263 Red 0 0.0122 267 Sika 0.3228 0 277 Sika 0.6646 0 Ø Red 0 0.078 VH054 (14) 79 Red 0 0.012 81 Red 0 0.043 83 Red 0 0.0122 85 Red 0 0.0373 87 Red 0 0.3941 89 Red 0 0.0994 91 Red 0 0.147 93 Red 0 0.0123 96 Red 0 0.012 97 Red 0 0.006 102 Red 0 0.028 106 Red 0 0.0661 110 Sika 1.000 0.009 139 Red 0 0.003 Ø Red 0 0.1184 HH064 (11) 107 Red 0.0128 0.0482 117 Red 0 0.003 119 Red 0 0.018 121 Red 0 0.0238 123 Red 0 0.0181 125 Sika 0.9551 0.0178 127 Red 0 0.0239 131 Red 0.0256 0.4132 133 Red 0.0064 0.1634 135 Red 0 0.0579 137 Red 0 0.0059 Ø Red 0 0.2067 TGLA387a (27) 128 Red 0 0.0029 130 Red 0 0.0059 132 Red 0 0.0029 134 Sika 0.9487 0.0147 138 Red 0 0.0059 139 Red 0 0.0029 140 Red 0 0.0608 141 Red 0 0.0207 142 Red 0 0.0576 143 Red 0 0.0059 144 Red 0.0064 0.0724 172 Red 0 0.0059 198 Red 0 0.0029 (–13) + Ω Red 0 0 (–12) + Ω Red 0 0.0059 (–11) + Ω Red 0 0.0029 (–10) + Ω Red 0 0.0059 (–9) + Ω Red 0 0.0088 (–8) + Ω Red 0.0064 0.0177 (–7) + Ω Red 0 0.0148 (–6) + Ω Red 0 0.0209 (–5) + Ω Red 0.0256 0.0178 (–4) + Ω Red 0.0064 0.0179 (–3) + Ω Red 0 0.0089 (–2) + Ω Red 0.0064 0.0118 (–1) + Ω Red 0 0.0059 Ω Red 0 0.0669 Ø Red 0 0.5323 DRB003 (10) 151 Red 0 0.0341 157 Red 0.0128 0.3886 159 Red 0 0.003 161 Red 0 0.0824 163 Red 0.0064 0.0061 167 Red 0.0128 0.0642 171 Red 0 0.0061 181 Red 0 0.003 187 Sika 0.0192 0 189 Sika 0.9487 0.0245 Ø Red 0 0.3881 MM012 (3) 89 Red 0 0.741 91 Red 0 0.256 93 Sika 1 0.003 Ø Red 0 0 FCB048 (4) 143 Red 0.0513 0.9028 145 Red 0 0.0309 155 Sika 0.7949 0.0063 157 Sika 0.1538 0 Ø Red 0 0.0599 The frequencies are maximum-likelihood estimates, assuming the presence of null alleles (Ø); these estimates are made without assuming that missing data are due to null homozygotes (see text).
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↵a At TGLA387, some alleles were very long (>250 bp) and so are scored relative to a reference allele of 250 bp, designated Ω.
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- TABLE 3
Classification of individuals at each site into pure red or sika: heterozygotes at a single locus, introgressed mtDNA, or complex hybrids
Site (sample size) Pure sika Single heterozygote mtDNA hybrid Complex hybrid Pure red Single heterozygote mtDNA hybrid Complex hybrida 1 (n = 2) 0 1 0 0 0 0 0 (0, 0, 1) 1 (n = 40) 26 5 3 (0, 2, 0) 3 0 0 (0, 5, 0) (1, 1, 0) 3 (n = 33) 16 7 0 (0, 5, 0) 5 2 0 (0, 2, 0) (0, 3, 0) 4 (n = 29) 7 5 0 (0, 2, 0) 10 2 1 (0, 0, 1) (0, 3, 0) (0, 3, 2) 5 (n = 9) 2 1 0 0 4 1 0 (0, 0, 1) 6 (n = 40) 0 0 0 0 35 3 1 (0, 1, 1) 7 (n = 48) 0 0 0 0 43 3 0 (0, 0, 1) (0, 2, 0) 8 (n = 12) 0 0 0 0 12 0 0 0 9 (n = 11) 0 0 0 0 10 1 0 0 10 (n = 22) 0 0 0 0 20 1 0 (0, 0, 1) -
↵a Classified by three numbers: whether the mtDNA is introgressed (0/1); the number of loci heterozygous for introgressed alleles; and the number homozygous for introgressed alleles. (The “homozygotes” are most likely heterozygous for null alleles; see text.)
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- TABLE 4
The maximum-likelihood estimate for null allele frequencies (Ø), and frequency of introgessed alleles (u) for each of the loci at which apparent homozygotes for rare alleles was seen
Locus Ø freq (pooled) u freq Observed vs. expected number of each genotype log(L) (1 d.f.) Ø Ø RR + ØR RS SS + ØS Red 0.231 0.0151 9 153 4 1 0.02 TGLA387 8.88 153.13 3.80 1.20 Red 0.398 0.0243 26 133 4 4 0.12 DRB003 26.47 132.51 4.69 3.33 Red 0.195 0.0060 6 159 1 1 0.46 FCB048 6.36 158.64 1.61 0.40 Sika 0.057 0.0331 0 1 4 74 0.66 BOVIRBP 0.26 0.39 4.75 73.6 Sika 0.117 0.0389 1 1 5 72 0.02 HH064 1.08 0.84 5.19 71.90 Alleles are pooled into null (Ø), red (R), and sika (S). Missing data are assumed to be null homozygotes. The last column gives the difference in log likelihood by comparing the numbers of observed and expected numbers in each genotypic class (1 d.f.). For none of the five loci is there a significant deviation from the hypothesis that missing data represent null homozygotes (see also Appendix at http://helios.bto.ed.ac.uk/evolgen/).
- TABLE 5
Analysis of linkage disequilibrium in red- and sika-like individuals for each site at which the phenotype was present
Number of introgressed alleles (observed vs. expected) G-statistic (P value) Randomization test P value 0 1 2 3 4 5 Site (sika) 1 0 1 2.00 — 0.37 0.37 0.1573 2 29 6 1 0.24 0.480 28.83 6.41 0.72 0.6225 3 16 7 0 0 0 1 13.62 0.001 14.56 7.28 1.82 0.30 0.038 0.0038 0.0086 4 7 5 1 1 0 1 6.64 0.078 5.52 5.52 2.76 0.92 0.23 0.046 0.2488 5 2 1 0.38 — 2.15 0.72 0.5386 Site (red) 1 0 1 2.00 — 0.37 0.37 0.1573 2 3 0 0 0 0 1 12.84 0.003 1.15 1.43 0.90 0.37 0.12 0.029 0.0249 3 5 2 1 1 1.80 0.632 4.13 3.22 1.25 0.32 0.6138 4 11 3 0.69 — 11.30 2.42 0.4047 5 4 2 0.76 — 4.30 1.43 0.3845 6 36 3 1 1.68 0.201 35.30 4.41 0.28 0.4327 7 43 4 1 1.26 0.275 42.36 5.29 0.33 0.5331 8 12 — — 12 9 10 1 0.09 — 10.04 0.91 0.7594 10 20 2 0.18 — 20.09 1.83 0.6649 The observed and expected numbers of individuals with 0–5 introgressed alleles. The G-statistic tests against the null hypothesis that introgressed alleles are in linkage equilibrium (approximated by a Poisson distribution). The associated p value is calculated using the asymptotic χ2-distribution. The last column gives the number of times the observed G value was exceeded in 1000 random permutations of the dataset. Significant deviations indicate introgressing alleles are in linkage disequilibrium, suggesting recent hybridization in that site.
