During March-April 2011, chilli seeds (Capsicum annuum) were used for 2 experimental germination tests conducted at the Plant Growth Facilities at the University of Western Australia. In the first experiment (i.e. Basil neighbour experiment), 3600 chilli seeds were randomly apportioned among 3 treatments, each replicated 4 times and kept randomly interspersed throughout a 5.30 m2 Controlled Environment Room (CER) fitted with high-intensity discharge lamps (standard metal halide supplemented with halogen; 650 μmol of photons s-1 m-2 photosynthetic active radiation). The experimental units consisted of a group of 12 petri dishes, each one containing 25 seeds, which were sandwiched between layers of 2 mm thick felt to retain moisture and ensure darkness. Petri dishes were arranged at c.8 cm from each other and placed in a circle around an adult O. basilicum plant positioned in the centre of the experimental unit (see Figure 1 and detailed description in [17]). Specifically, the O. basilicum plant was either left open to allow both light and chemical communication to take place [OPEN treatment] or sealed in a central cylindrical box covered in black plastic to block all light wavelengths and airborne chemical signals (i.e. no volatile or water-soluble chemicals from any adult plants could affect seed germination) [MASKED treatment]. The CONTROL treatment consisted of seeds arranged around the central cylindrical box, which was left empty but covered in black plastic to account for any effects of the colour of this shield itself.

All seeds and adult plants within a replicate unit were then housed within 2 different sized square boxes (44×44×50 cm & 32×32×45 cm respectively), one inside the other, with the air in between the two boxes removed using a pump to create a vacuum and thus avoid interference between adjacent experimental units at any time. The whole experimental unit was custom-made in colourless cast acrylic material (Moden Glas), which transmitted 92% of visible light, but was opaque to ultraviolet and infrared wavelengths (Figure 1; as per [17]). Each day, all experimental units were randomly re-interspersed throughout the growth room to avoid any potential artefacts due to their position in the room. Similarly each day, individual petri dishes within each unit were randomly re-arranged in the circular configuration around the central box to avoid any potential confounding effects of their position within the experimental unit. Using an U12-011 - HOBO® Temperature/RH Data Logger, we recorded the temperature within the experimental units over 24 h for 25 consecutive days to ensure that any difference in seed germination measured between treatments was not due to differences in the temperature inside the boxes caused by the presence or absence of adult plants (No difference between temperature profiles across treatments over time; Repeated-measure ANOVA, F 46, 115 = 1.11, P = 0.32). Seeds were kept at 18°C during the day, 13°C over night and under a 12 h light: 12 h dark cycle. Seeds were inspected and watered every 24 hrs. To avoid any potential atmospheric exchange of volatiles that could have interfered with our measurements, each experimental unit was transferred one at a time to a separate room where the 2 external square boxes were opened; all petri dishes were then removed and inspected, while the rest of the unit (including the base and the central cylindrical box) was taken outdoors and opened. This procedure was conducted to aerate the adult plants sealed in the box, but was done for all units (i.e. with or without plant in the central cylindrical box). Germination rates in each treatment were monitored and recorded every other day for 12 days, after which the number of germinating seeds reached an asymptote.

The same experimental design described above was then repeated by substituting the basil plants with adult chilli plants (i.e. Chilli neighbour experiment). This experiment was conducted as a control benchmark to enable us to distinguish the possible positive effect of growing next to an adult conspecific from the effect of a potentially beneficial heterospecific.

All statistical analyses were carried out in R using binomial generalised linear mixed effects models (GLMMs) with the base package and the lme4 package [25, 26]. Binomial generalized linear models were used as they are the most valid means of dealing with binomial data, such as germination data, and the mixed effects versions of the models were employed as they are the most valid and powerful means of dealing with a design such as ours, which had nesting (Petri dishes within containers) and repeated measures over time [27]. A separate but similar analysis was conducted for each of the two experiments, based on standard step-wise model simplification [27]. First, a full model was fitted to the data. This contained fixed effects for treatment, time and their interaction, constant random effect for experimental container and Petri dish nested within experimental container, and continuous random time effects for experimental container and Petri dish nested within experimental container. This full model was then sequentially simplified, step-by-step, in the standard way [27]. At each step, a simplified model with one term dropped from the previous best model was compared to the previous best model using both Akaike’s Information Criterion (AIC) and a likelihood ratio chi-squared test. AIC values were computed for each of the candidate models and the model with the lowest AIC value was selected as the best model of the observed data in the standard way [28]. The likelihood ratio chi-squared test produced a p-value indicating whether the simpler model was significantly worse than the previous model; this provided a second test to support the AIC comparison and also provided p-values for significance of model terms. The random effects accounted for the possibility that seeds were affected by some conditions particular to their dish and/or container, and were thus not truly independent replicates. They also accounted for temporal correlation produced by measuring the same unit over time. The significance of dish and container random effects was tested first; if significant then we included them in subsequent models to fully account for any possible pseudoreplication. If these tests indicated an overall difference between treatments, we then tested for differences between the three treatments. This was done by pooling the two most similar treatments, and testing whether this simplified model was better than the model with all treatments differentiated. Pooling was continued until all remaining differences were significant. For more specifics on the analysis, see Additional file 1: Table S1 and S2.