2003. The Journal of Arachnology 31:44–54

AN ANALYSIS OF THE SECONDARY STRUCTURE OF THE

MITOCHONDRIAL LARGE SUBUNIT rRNA GENE (16S) IN

SPIDERS AND ITS IMPLICATIONS FOR PHYLOGENETIC RECONSTRUCTION

Stacey D. Smith1: Department of Biology, Virginia Polytechnic Institute and State

University, Blacksburg, Virginia 24061 USA

Jason E. Bond: East Carolina University, Department of Biology, Howell Science

Complex, Greenville, North Carolina 27858 USA

ABSTRACT. 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.

Keywords: Secondary structure, 16S rRNA gene, Aptostichus, phylogenetic utility