Molecular evolution of the pDo500 satellite DNA family in Dolichopoda cave crickets (Rhaphidophoridae)

We sequenced 199 genomic or PCR amplified satDNA repeats of the pDo500 family from 12 Dolichopoda species. For the 38 populations under study, 39 pDo500 consensus sequences were deduced. Phylogenetic analyses using Bayesian, Maximum Parsimony, and Maximum Likelihood approaches yielded largely congruent tree topologies. The vast majority of pDo500 sequences grouped according to species designation. Scatter plots and statistical tests revealed a significant correlation between genetic distances for satDNA and mitochondrial DNA. Sliding window analyses showed species specific patterns of variable and conserved regions. The evolutionary rate of the pDo500 satDNA was estimated to be 1.63-1.78% per lineage per million years.The pDo500 satDNA evolves gradually at a rate that is only slightly faster than previously published rates of insect mitochondrial COI sequences. The pDo500 phylogeny was basically congruent with the previously published mtDNA phylogenies. Accordingly, the slowly evolving pDo500 satDNA family is indeed informative as a phylogenetic marker.Only a small fraction of a typical eukaryotic nuclear genome constitutes rDNA or protein-coding genes, whereas a large fraction of all higher eukaryotic genomes consists of repetitive sequences and heterochromatic satellite DNA (satDNA) [1,2]. Recent sequencing of various genomes have confirmed that the remarkable variability in genome size among eukaryotes is to a large extent due to different amounts of repetitive DNA, of which non-coding tandemly repeated DNA is a major part [3-7].Typically, satDNA consists of numerous very similar repeated sequences, tandemly arranged in a head to tail orientation in large clusters up to 100 million bp in length [1]. These clusters are usually located in the heterochromatic parts of the chromosomes, mainly in the regions close to the centromeres and telomeres. Repeat size can vary largely within and between species; from only a few base pairs up to several thousand base pairs [8-1