Lección 2 Estructuración Base del Sistema

We additionally tested for historical gene flow by analyzing patterns of intra- genic LD, using information that remains untapped by the multilocus goodness-of-fit test that is often the only assessment of the suitability of the isolation model (via co- alescent simulations). Table 2.6 presents empirical data and simulation results using the LD test statistic x, which ought to exhibit more positive values under a scenario of (historical) gene flow. Five out of six mean observed x values are significantly ele- vated, with stronger signals seen in the most inclusive sample contrast (TAR&CAN

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Table 2.5: WH parameter estimates and isolation model fitting

Pop 1 Pop 2 θ1 θ2 θA τ T Pχ2 Pwwh (S. peruvianum) (S. chilense) TAR TAC 121.6 68.9 101.8 22.8 0.187 0.742 0.878 65.0-298.3 40.7-116.8 58.4-150.3 15.1-30.6 0.08-0.31 TAR MOQ 127.5 87.8 96.8 24.9 0.195 0.521 0.903 70.8.-275.5 51.8-153.4 55.1-145.9 17.0-32.8 0.09-0.32 TAR QUI 129.2 71.1 95.4 25.8 0.200 0.911 0.775 71.4-296.4 44.9-116.8 52.5-144.6 18.1-33.8 0.08-0.32 NAZ TAC 150.9 90.2 73.6 23.5 0.156 0.364 0.563 82.9-257.8 54.5-128.6 45.6-116.4 17.6-30.4 0.09-0.27 NAZ MOQ 144.9 113.8 72.7 25.8 0.178 0.483 0.774 81.3-237.4 65.2-173.0 43.4-120.5 19.0-33.5 0.11-0.32 NAZ QUI 108.7 66.5 95.7 19.9 0.184 0.094 0.293 56.9-220.1 37.6-107.5 56.7-144.5 12.9-26.7 0.09-0.30 CAN TAC 222.9 72.9 87.1 24.6 0.110 0.933 0.649 110.2-591.4 45.5-106.3 51.3-136.1 18.1-31.6 0.04-0.21 CAN MOQ 198.7 89.5 88.6 26.6 0.134 0.898 0.722 108.3-413.4 55.8-135.4 52.5-137.2 19.6-33.9 0.06-0.24 CAN QUI 186.4 65.3 99.2 23.2 0.124 0.395 0.439 94.9-508.0 40.1-100.3 57.4-149.0 16.4-30.1 0.04-0.22 TAR TAC&MOQ 115.4 91.3 102.5 26.6 0.231 0.521 0.853 68.7-218.3 62.0-135.4 60.8-151.5 19.7-34.1 0.12-0.36 CAN TAC&MOQ 191.7 97.5 86.4 28.1 0.147 0.882 0.732 111.9-313.5 68.6-125.7 55.7-132.3 22.4-35.2 0.09-0.26 TAR&CAN TAC&MOQ 203.7 85.8 99.2 27.9 0.137 0.755 0.789 130.6-316.1 60.8-108.5 61.7-150.6 22.5-35.4 0.09-0.22

For each of the 12 interspecific comparisons, the data (cf. Table 2.4) were fitted to the WH isolation model. θ1, population mutation parameter for population 1 (= 4Neµ, estimated over all sites);θ2, population mutation parameter for population 2;θA, population mutation parameter for the ancestral species;τ, scaled time parameter (=2µt). T (= τ/θ) is the estimated time of species divergence in units of 2N1 generations, where N1 is the effective size of population 1. Below the

primary parameter estimates, 95% confidence intervals are shown, determined by 10,000 coalescent simulations. The P-values for both the wwh (Wang et al. 1997) and χ2 _{test statistics are the}

proportions of simulated values ≥ the observed values. The bottom three comparisons contrast pooled samples; within-species pooling was conditioned on (still) observing fixed differences in the multilocus data and low population differentiation (see text)

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vs. TAC&MOQ) and the allopatric contrast CAN vs. TAC&MOQ. Interestingly, locus CT066 exhibits significantly high x values for all samples, and locus CT166 shows significant or nearly significant x values for many of the contrasts; there is a tendency for this signal to be stronger in S. peruvianum. Finally, there are two marginally significantx values for locus CT179 in S. chilense, whereas there is no LD signal of gene flow at any other locus (Table 2.6).

It should be noted that the three pooled-sample contrasts examined in Table 2.6 do not represent independent datasets; the LD test partly rests on a relational framework, in that shared polymorphisms can only be identified in reference to a second sample (population, species, etc.), while exclusive polymorphisms are unique to particular populations or more inclusive samples. In addition to the three pooled- sample comparisons, we also subjected the individual population contrasts to the LD test of (historical) introgression. Figure 2.1 plots the P-values for individual loci in both species, expressed as medians of the individual population contrasts. Consistent with the results for the pooled-sample comparisons, median P-values for loci CT066 and CT166 are between 0.030 and 0.124, reflecting (often) significant or marginally significant values of the LD test statisticx in many single-population contrasts. These results suggest bidirectional interspecific gene flow following initial species divergence, whereas there is no compelling evidence for such a scenario at the other loci (Figure 2.1; but see Discussion).

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Table 2.6: Linkage disequilibrium test of historical gene flow

Sample A (peru) CT066 CT093 CT166 CT179 CT198 CT251 CT268 Observed Simulated

Sample B (chil) meanx meansx

A: TAR&CANvs. 0.751 0.203 0.396 0.179 0.272 0.152 0.123 0.297 0.125 0.016 0.263 0.068 0.340 0.160 0.283 0.402 0.022 B: TAC&MOQ 0.673 0.239 0.244 0.470 0.151 -0.055 0.000 0.246 0.072 0.023 0.167 0.122 0.068 0.248 0.858 0.682 0.034 A: TARvs. 0.650 0.268 0.428 0.224 0.071 0.025 0.090 0.251 0.086 0.031 0.182 0.092 0.263 0.417 0.605 0.351 0.049 B: TAC&MOQ 0.662 -0.110 0.339 0.192 0.089 -0.056 0.109 0.175 0.086 0.028 0.806 0.127 0.291 0.367 0.868 0.308 0.142 A: CANvs. 0.863 0.000 0.619 0.136 0.370 0.100 0.019 0.301 0.108 0.014 0.665 0.030 0.351 0.124 0.399 0.714 0.027 B: TAC&MOQ 0.615 0.299 0.482 0.470 0.192 -0.070 -0.075 0.273 0.081 0.032 0.151 0.049 0.053 0.246 0.871 0.864 0.029

For each of the three pooled-sample contrasts (S. peruvianum vs. S. chilense), the observed LD test statistic x is given in the first line (for each locus and each of six samples), with the proportion of successful coalescent simulations ≥the observed values ofx (P-values) immediately below;P-values <0.07 are highlighted in boldface. The last two columns summarize the observed meanx (withP-values below) and the simulated meanx (assuming no interspecific gene flow) over all loci (see text).

3 Results 66 0 10 20 30 40 50 60 70 80 90 0.00 0.01 0.02 0.03 0.04 0.05 recombination P -v a lu e ( % ) peru chil

Figure 2.1: Scatter plot of average locus-specific rates of recombination and median P- values for single-population contrasts (LD test of historical gene flow). Recombination is expressed asγ per site, and the locus-specific values are the means obtained for theS. peru- vianum populations (i.e., both species are plotted with theS. peruvianum recombination estimates). The P-values are locus-specific medians obtained from up to nine interspecific population contrasts. The arrow highlights a ‘hidden’P-value of 0.033 for locus CT066 in

S. peruvianum. Note that this lower left area of the plot contains the data for loci CT066 and CT166 (cf. Table 2.6).

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4

Discussion

The principal limitation of our previous study of speciation scenarios in wild tomatoes was the availability of only single populations per species, leading to un- certainty about the generality of our initial findings (St¨adler et al., 2005). Here we have shown that consistent demographic estimates under the WH isolation model (Wakeley and Hey, 1997; Wang et al., 1997) are obtained when ‘typical’ populations of bothS. peruvianum andS. chilense are chosen to portray their respective genealog- ical histories, where ‘typical’ refers to samples exhibiting broadly comparable levels and partitioning of nucleotide polymorphism across multiple loci. For example, our originalS. chilense sample (Antofagasta) can now be interpreted as reflecting a local or regional bottleneck (based on unusually low levels of polymorphism and strong haplotype structure) that is certainly not characteristic of the species-wide demo- graphic history following speciation. Consequently, relying on such samples would result in misleading WH parameter estimates, as was anticipated in our previous study (St¨adler et al., 2005). Whereas population-size contraction inS. chilense com- pared to the ancestral species was inferred in that study, our current demographic estimates based on three other populations concur that historical effective popula- tion size has remained fairly constant, while there are consistent signatures of larger effective population size in S. peruvianum (Tables 2.2 - 2.5).