It wasn't long ago that molecular phylogenetic studies of animals relied almost exclusively on a single molecular marker: mitochondrial DNA. Graduating with my PhD in 2004 I was part of the last generation of scientists to get away with this. Thankfully, the biggest obstacle to multilocus studies (i.e., the availability of PCR primers for non-model organisms) is becoming a thing of the past with the availability of genomic sequence data. Two recent studies contribute hundreds of new PCR primers for potentially phylogenetically informative regions of reptiles (including the feathered variety).
Townsend et al. (2008; Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: An example from squamate reptiles. Molecular Phylogenetics and Evolution [subscription required] 47:129-142.) use bioinformatic analysis of Fugu, Homo, and Gallus genomes to develop primers for amplification of long, continuous exonic sequences in squamate reptiles (although they also discuss the potential broader taxonomic utility of their markers). The provide >80 loci, but only offer preliminary sequence data to ascertain phylogenetic informativeness for 25 of these. The results were encouraging, the new loci seemed to support previously established relationships; many exhibited considerably greater variation than the well-used RAG1 that seems to perform particularly well among the suite of "stock" loci that have been used rather intensely over the past few years. Their utility is further borne out by Wiens et al.'s new analysis of snake relationships in the latest issue of Systematic Biology (subscription required). As an aside, I couldn't help but notice that Townsend et al. use Invitrogen's VectorNTI software for primer development. This software is supposedly available for free to academic uses, but I've had a hell of time getting a license. I tried writing and calling a few months ago, but had difficulty getting an authorized license to work and have never gotten around to using the program. Anybody else have this problems (or a solution?).
Backström et al. (2008; Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome [subscription required]. Molecular Ecology 17:964-980.) identify and sequence an even larger, and more diverse, set of loci by comparing the complete genome sequence of the chicken to ESTs and trace files from the zebra finch genome. Because they're more interested in asking questions at the population level, they test the utility of their markers for detecting intraspecific/phylogeographic variation and note their discovery of over 800 SNPs across several unrelated individuals of collared flycatchers. Unlike the Townsend study, indels are included in Backström et al.'s samples. They were also able to space their markers throughout the genome. Scott Edwards does a nice job of putting this advance in perspective.
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