I am currently investigating whether one species of Artibeus (leaf-nosed bat) is actually two. I started with mtDNA sequences (Cytb and COI) from GenBank and have Bayesian trees for both loci showing two distinct, well-supported clades. The pairwise distances are relatively high, so now I am wondering about the possibility that these sequences are pseudogenes of COI before I test any nuclear loci. The COI data are partial cd's.
What is the best method/software to test for pseudogenes in this situation? Thanks in advance!
Dear Melissa,
Please find attached an interesting paper by Rouchka and Cha (2009) which figures out and discusses various methodologies to detect pseudogenes:
"Current Trends in Pseudogene Detection and Characterization"
I hope it will help you with coming across the best solution!!
Best wishes,
Temim
Dear Temim,
Thanks for the paper-- I will start with some of these techniques.
Best Regards,
Melissa
Hi Melissa: you can try to separate mtDNA from nuclear DNA and then perform PCR only on mtDNA and check if you can identify one or two different mitochondrial haplotypes.
If you are not capable of separating mtDNA from nuclear DNA, you can try to perform PCR with forward primer targeted to cytB or COI and reverse primer on the adjacent mitochondrial genes. The PCR products that you would get would truly be mtDNA, not pseudogenes.
It might be useful to determine any differential mutational patterns present between the two sequences. E.g. various statistical tests for selection. Presumably if you're dealing with a pseudogene there should be no underlying mutational pattern within a species (e.g. synonymous = non synonymous). If this hypothesis is violated then presumably the gene is under purifying/positive selection and not a pseudogene.
This is only one method…there are likely many others.
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