Methods: molecular procedures and phylogeny estimation
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The protein-coding genes (cyt-b, COI and EF-1α) were all aligned by eye, but we used secondary
structure (Gillespie et al. 2005) to align the 28S rDNA region. We excluded regions of
ambiguous alignment. We partitioned the data matrix into four genes and chose models for each
partition separately using the Akaike Information Criterion (AICc) and Bayesian Information
Criterion (BIC) in jModelTest (Posada 2008). Phylogenetic relationships were estimated using
Baysian approaches in Mr Bayes 3.1 (Ronquist & Huelsenbeck 2003) and BEAST v1.6.1
(Drummond & Rambaut 2007) using the Universitiy of Oslo’s Bioportal (Kumar et al., 2009).
We followed a similar strategy to Segar et al. (2012) (e.g. we used the same priors and clock
model) but ran the Mr Bayes analysis for 10,000,000 generations and heated the cold chain to
0.10.
The outgroup Anaphes nitens (Mymaridae) was pruned before community analyses. Mymaridae
is either the sister to all other Chalcidoidea, or at least a basal clade within the superfamily
(Lopez-Vaamonde et al., 2009). We obtained an ultrametric tree in BEAST (80,000,000
generations, sampling every 4,000 generations) and constrained trees to match our Mr Bayes
consensus tree. We used an HKY model for cyt-b to ensure adequately high Effective Sample
Size (ESS) scores. Convergence was assessed in Tracer v1.5 (Drummond & Rambaut 2007). The
frequency plots of all parameter traces showed bell-shaped curves and ESS scores>>200,
indicating convergence. The average standard deviation of the split frequencies for the Mr Bayes
analysis was 0.003 and the proportion of successful state exchanges between the chains ranged
from 10 to 60% for all chains.
References
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