Secondary structure of the mitochondrial large subunit rRNA (16S) and its implications for the phylogenetic reconstruction of the coleopteran family Lampyridae

John C. Day1 & Raphäel De Cock2

1. Centre for Ecology and Hydrology (CEH) Wallingford, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB U.K.
2. Evolutionary Ecology Group, University of Antwerp, Belgium

ABSTRACT The complex diversity of the bioluminescent beetles belonging to the family Lampyridae has rendered the morphological classification prone to constant critical re-evaluation and revision. Recent molecular studies have attempted to assist in these evolutionary revisions, commonly employing a region of the mitochondrial encoded large subunit (16S) rRNA. We present a 16S secondary structure model for the Lampyridae in order to evaluate the impact on the phylogenetic reconstructions of fireflies and glow-worms. Potential pairings and mutual information were analyzed to identify site interactions present within each genus resulting in consensus secondary structures. Helix 75 was found to be poorly conserved even between closely related genera making homologous alignment problematic and it is recommended that this region should be excluded from future analysis. A comparative examination of stem and loop regions revealed that external and internal loop regions have evolved 1.6 times faster. Down-weighting variable loop regions provided little impact on the tree topology despite these differences in evolutionary rates.

KEYWORDS: 16S rRNA, mitochondrial genome, bioluminescence, phylogenetics, DNA secondary structure
Secondary structure of the mitochondrial large subunit rRNA (16S) and its implications for the phylogenetic reconstruction of the coleopteran family Lampyridae