Reliable phylogenetic reconstruction, as a framework for evolutionary inference, may be difficult to achieve in some groups of organisms. Particularly for lineages that experienced rapid diversification, lack of sufficient information may lead to inconsistent and unstable results and a low degree of resolution. Coincidentally, such rapidly diversifying taxa are often among the biologically most interesting groups. Aphids provide such an example. Due to rapid adaptive diversification, they feature variability in many interesting biological traits, but consequently they are also a challenging group in which to resolve phylogeny. Particularly within the family Aphididae, many interesting evolutionary questions remain unanswered due to phylogenetic uncertainties. In this study, we show that molecular data derived from the symbiotic bacteria of the genus Buchnera can provide a more powerful tool than the aphid-derived sequences. We analyze 255 Buchnera gene sequences from 70 host aphid species and compare the resulting trees to the phylogenies previously retrieved from aphid sequences, only. We find that the host and symbiont data do not conflict for any major phylogenetic conclusions. Also, we demonstrate that the symbiont-derived phylogenies support some previously questionable relationships and provide new insights into aphid phylogeny and evolution.

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