The question regarding possible psuedogenes from the blood-meal analysis is prudent since duplication of mitochondrial regions in reptiles have been shown to occur (Fujita et al. 2007). If this is the case for the current study, the assumption would be that the particular tick specimen that we analyzed fed on K. polyzonus and that the lizard contigs 2, 3 and 4 would be 16S psuedogenes of this species.
However, several points would argue against this possibility.
1. Most detectable mitochondrial duplications are very recent events and either mutates to a state where the 16S genes will not be detectable any more or changes are limited to an extent that the ancestry of these genes can still be traced, i.e. their closest ancestors are still the original 16S genes from the same species. The sequences obtained from contig 1, 2, 3 and 4 all retrieve different best hits of the cordylid family using BLASTN and phylogenetic analysis do not cluster them into a monophyletic clade. If contig 2, 3 and 4 where pseudogenes, their mutations would seem to have converged to resemble the 16S genes from other cordylid species. This would seem to be unlikely.
2. The authors of the original study on Cordylid systematics (Stanley et al. 2011) sampled many Cordylid species and did not find any evidence of pseudogenes in their sample set and specifically not for K. polyzonus (personal communication). Another extensive study on K. polyzonus biogeography that used 16S data (Engelbrecht et al. 2011) also did not detect any pseudogenes (personal communication). This does not exclude the presence of psuedogenes, but do provide more evidence that pseudogenes are not necessarily prevalent in the Cordylid family.
3. Whether gene duplication can occur in the erythrocytes after ingestion and prolonged storage in the tick gut could be a possibility, but we consider this to be unlikely, since cell division of erythrocytes do not occur.
4. One of the ticks that fed successfully in the previous study was recently analysed six months after feeding and we still found intact nucleated erythrocytes to be prevalent in the gut. This provides evidence that the blood meal can be stored in an intact form for prolonged periods, a feature that Nuttalliella namaqua shares with argasid ticks. We have already showed that nymphal and adult stages feed rapidly, similar to argasid ticks and know that argasids can feed relatively soon after a previous meal (3-4 weeks). Prolonged storage of the blood meal coupled with multiple feedings over a short period of time would therefore provide us with the possibility of detecting multiple hosts.
5. We have subsequently sampled five other tick specimens and performed gut meal analysis on them as described in the previous study. In these cases all ticks had nucleated erythrocytes in their guts and DNA analysis indicated that each tick possessed DNA from a single lizard species, each specimen having fed on a unique lizard. In none of these we found any indication of multiple gene copies. This would argue that these ticks only had a single blood meal recently and suggest that the previous detection of multiple gene copies could have been valid.

In conclusion, no evidence for the presence of pseudogenes in Cordylid lizards exists at the current moment. Consideration of the biology of N. namaqua also provides us with reasonable grounds to infer that multiple feeding and storage of mixed blood meals may occur under field conditions. We would therefore contend that multiple feedings are a viable alternate hypothesis for the presence of pseudogenes in the lizard DNA found in the tick gut meal extracts.

References
Engelbrecht HM, Mouton PLeFN, Daniels SR (2011) Are melanistic populations of the Karoo girdled lizard, Karusasaurus polyzonus, relics or ecotypes? A molecular investigation. African Zool 46: 146-155.
Fujita MK, Boore JL, Moritz C (2007) Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae). Mol Biol Evol: 24, 2775-2786.
Stanley EL, Bauer AM, Jackman TR, Branch WR, Mouton PLeFN (2011) Between a rock and a hard polytomy: Rapid radiation in the rupicolous girdled lizards (Squamata: Cordylidae). Mol Phylogenet Evol 58: 53–70.