Likelihood scores, harmonic means and Bayes factors approximated under Tracer for each partitioning strategy of the MrBayes 3.1.2 analyses for the gene trees.

<p>The Bayes factors are given for each possible comparison of strategies in the three last columns of the table. The analyses with the partitioning strategies ‘12v3’ are the best analyses for both genes (COI and EF1-α). The analysis with the partitioning strategy ‘BySix’ is the best analysis for the combined dataset, and is chosen for the dating analyses as a tree prior.</p

non-outlier-loci

The columns of the table correspond to the non-outlier loci presented in Campagne et al. 2016 (Heredity). Rows, correspond to individuals (described in the file sample-info.txt)

Model-based analysis of diversification rates in Apameini moths.

<p>Varying-rate model considers all possible bipartitions of tree and finds bipartition giving the highest likelihood when net diversification rates are optimized separately to each partition. Decreasing-rate model assumes that previously recovered (with varying-rate model) shift point node have retained the ancestral diversification rate present at the root node.</p>a<p>ΔAIC is the difference in AIC scores between each model and the overall best-fit model (here, varying-rate model with ε = 0).</p>b<p>The data reject the constant-rate model in favour of the varying-rate model under ε = 0 and 0.95 (<i>p</i><0.001). Rate-decrease model does not show a simple nested relationship with varying-rate model, but AIC strongly favours the varying-rate model.</p>c<p>Maximum-likelihood estimate of the net diversification rate r in lineages Myr⁻¹ (r, r1 and r2 are the net diversification rate of the subtree partition containing the nine Apameina genera where diversification rates shifted).</p>*<p>Maximum likelihood estimate of the extinction rates ε in lineages Myr⁻¹.</p

Phylogenetic relationships of the tribe Apameini within the superfamily Noctuoidea under Bayesian inference.

<p>Posterior probabilities (PP) are indicated above the nodes (* indicates a value up to 0.95). When no values are indicated, it means that the PP was <0.95, except for some basal nodes for which the support is annotated. Groups of interest are highlighted by vertical bands of different colours referring to the colour of the clades. The Apameini, Sesamiina and Apameina (excluding the three genera <i>Staurophora</i>, <i>Calamia</i> and <i>Litholomia</i>) nodes are respectively labelled N1, N2 and N3. Names of the species for which a habitus is displayed are specified under the pictures (Pictures: EFA Toussaint & BP Le Ru).</p

Mean ages and 95% HPD heights for the major nodes of the chronogram (Figure 2).

<p>SMC =  Clade comprising the following genera : <i>Staurophora</i>, <i>Macronoctua</i>, <i>Calamia</i>.</p

Likelihood scores, harmonic means and Bayes factors approximated under Tracer for each partitioning strategy of the MrBayes 3.1.2 analyses for the combined dataset.

<p>The Bayes factors are given for each possible comparison of strategies in the four last columns of the table. The analysis with the partitioning strategy ‘BySix’ is the best analysis for the combined dataset, and is chosen for the dating analyses as a tree prior.</p

Historical biogeography of the tribe Apameini reconstructed using the DEC model based on the median-BEAST chronogram.

<p>A coloured square indicating the most likely ancestral area is displayed at each node of the topology. Colours of the squares correspond to the colour of the areas presented in the map at the bottom left corner of the chronogram. Asterisks above the nodes indicate a strong support for the recovered areas (>2 log-likelihood units against the second better score). A 5 Myr-timescale is placed at the bottom of the chronogram and goes from the mid-Oligocene to the Holocene. The vertical bars next to the genera names delimit the two subtribes (Apameina in orange and Sesamiina in green). The biogeographical scenario for the tribe is presented in two maps at the bottom of the figure. Dotted-lines above the maps specify the related epoch (Left map: Oligocene and right map: Miocene). The origin of the group is highlighted by a yellow and red symbol, and the major dispersal events are shown with arrows.</p

Likelihood scores, and Bayes factors approximated under Tracer for the different sets of calibration used in Beast 1.6.2.

<p>The analysis with the Yule model of speciation with no geological constraint and no corrections for age uncertainties is the best analysis, and is chosen for the main figures in the text.</p

Maximum credibility tree with median ages (Myr) from the Bayesian uncorrelated uniform analysis under BEAST for the superfamily Noctuoidea.

<p>A 5 Myr-timescale is placed at the bottom of the chronogram and spans the Cretaceous to the Holocene. Brown hourglasses at the corresponding nodes indicate the calibration points used to ultrametrize the topology. For the fossil calibration, a picture of the moth in question retrieved from Douglas SD & Stockey RA (1996) is presented in the bottom left-corner. Horizontal blue bands represent the 95% HPD heights (in Myr) for the major nodes of the chronogram. Vertical bands and pastilles at the nodes of different colours referring to the colour of the clades highlight groups of interest. For the groups of major interest, the name is given in a box of the clade colour. Abbreviations for the clade names are: Ere.  =  Erebidae, Eut.  =  Euteliidae, Hel.  =  <i>Helicoverpa</i>, and Nol.  =  Nolidae. Genera of the Sesamiina and Apameina subtribes show respectively green and orange branches. Names of the species for which a habitus is displayed are specified under the picture (Pictures: EFA Toussaint & BP Le Ru).</p

sample information

'Field.ID' corresponds to the field numbers/IDs in which a larvae was sampled; 'Type.of.field', describes whether the field sampled was Bt maize (i.e., Bt) or a non-Bt crop (maize or sorghum, i.e., nBt)