As an initial source of molecular characters, individual loci from both the mitochondrial and the nuclear genome are being amplified using PCR and directly sequenced. Targeted loci include many of the workhorses of molecular systematics, including mitochondrial CO1, ND2, 12S, 16S, and the control region, and nuclear 28S, Histone 3, introns from the S7 ribosomal protein, and loci such as myh6 and SH3PX3 with newly available primers.
Sequencing a finite number of mainly protein-coding genes is inadequate for some of the questions under investigation, particularly involving large series of individuals from a single species or from closely related species from different localities along the course of the lower Congo rapids. This is because there is often insufficient variation, particularly within the nuclear genome, to provide signal. Even with variable mitochondrial sequences, when used in isolation, complicating factors such as introgression will go unnoticed.
Consequently, other sources of molecular variation are also being utilized. These include highly variable, non-coding regions, such as microsatellites (short repeated units of 1-4 bases), and SNPs (Single nucleotide polymorphisms: variable sites scattered throughout the genome). SNP libraries will be assembled for several lineages of lower Congo fishes, unlocking molecular variation at the population-species interface, and making possible a fine-scale examination of the relationship between organismal diversification and the peculiar hydrology of the lower Congo.