An Analysis of the Secondary Structure of the Mitochondrial Large Subunit rRNA Gene (16S) in Spiders and Its Implications for Phylogenetic Reconstruction

We investigated the pattern of molecular variation with respect to secondary structure in the 16S ribosomal RNA gene and its phylogenetic implications for arachnids with a focus on spiders. Based on a model by Gutell et al. (1996), secondary structures were proposed for the 39 half of 16S in the mygalomorph spider Aptostichus atomarius. Models were also constructed for a hypervariable length of the 16S in three other arachnids, which revealed a trend of stem and loop reduction in more advanced arachnids. Using a simple statistical approach to compare functional regions, we found that internal and external loops are more variable than stems or connection regions. Down-weighting or excluding regions which code for the more variable loops improved tree topologies by restoring the monophyly of the genus Aptostichus, a group supported by combined 16S, COI, and morphological data in other analyses. This study demonstrated the utility of considering secondary structure for DNA sequence alignment and phylogenetic reconstruction in spiders.