Table from Portik et al.'s Conservation Genetics paper reporting new primer pairs for amplification of nuclear loci (left side) and a phylogeny generated using some of these loci from Stanley et al.s' 2011 MPE paper on cordylids (right panel).
A new study by Portik et al. used the anole genome to develop more than 100 new primer pairs for the amplification of nuclear-encoded DNA from squamates, some of which have already proven useful for inferring relationships within and among species. Portik et al.’s carefully thought out strategy for marker development – which focused on rapidly evolving protein-coding loci – ensures that their loci will be particularly useful for phylogenetic analyses. First, Portik et al. focused on intronless protein-coding genes, with the goal of limiting length variation and simplifying alignment. Second, recognizing low variability relative to non-coding regions as a potential limitation of protein-coding loci, Portik et al. focused exclusively on developing markers from loci that are more variable than the first third of RAG-1 (one of the most useful and widely-used of the nuclear genes used previous phylogenetic studies of squamates). This strategy yielded 104 genes and led to development of primers for 170 gene fragments ranging from 407-2,492 bp. Portik et al. conducted limited PCR testing on 70 of these loci and found varying degrees of success across five squamate families, including Scincidae, Varanidae, Agamidae, Cordylidae, and Gekkonidae. More importantly, some of the loci have already proven useful for phylogenetic studies of skinks (Portik et al. 2010 , Portik et al. 2011), cordylids (Stanley et al. 2011) and iguanids (anole genome paper, which is currently in press at Nature).
While high throughput sequencing technology will eventually render PCR primers and Sanger sequencing nothing more than curiosities from a previous generation, this time is at least a few years away. In the meantime, Portik et al. have given the herpetological community some very useful new tools to play with.
