Intraspecific and intragenomic variation as measured from the dual control regions of the Western Cottonmouth, Agkistrodon piscivorus leucostoma mitochondrial genome

Abstract

Snake mitochondrial genomes have the unusual feature of dual control regions. Control regions are intergenic areas that are responsible for DNA replication and transcription initiation. Although they are functional, they do not code for protein, and it is hypothesized that these regions can sustain greater rates of mutation than other parts of the genome. Despite this assumption, there are no published studies that compare control regions from multiple individuals from a population. In this study, I successfully sequenced both control regions from individual cottonmouth snakes (Agkistrodon piscivorus leucostoma) collected from a single, large, interbreeding population living within a 20-mile radius near Caddo Lake, Texas. The dual control regions within this population showed three polymorphisms at paralogous bases within the two control regions. There were also two indels found only in control region 2. These polymorphisms could be grouped into eight haplogroups, suggesting the control regions may sustain a high level of mutation and would be an appropriate marker for future biogeography or population genetic studies. When the two control regions from individuals were compared, several instances were found where a polymorphism in one control region disagreed with the paralogous base in the other control region. These results suggest homologuos recombination may be a slow or random process or that the two regions are beginning the process of divergence.