Email updates

Keep up to date with the latest news and content from BMC Research Notes and BioMed Central.

Open Access Technical Note

Towards the simplification of MHC typing protocols: targeting classical MHC class II genes in a passerine, the pied flycatcher Ficedula hypoleuca

David Canal1*, Miguel Alcaide2, Jarl A Anmarkrud3 and Jaime Potti1

Author Affiliations

1 Estación Biológica de Doñana - CSIC, Department of Evolutionary Ecology, Av. Américo Vespucio s/n, 41092 Seville, Spain

2 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA

3 National Centre for Biosystematics, Natural History Museum, University of Oslo. P.O. Box 1172 Blindern, NO-0318 Oslo, Norway

For all author emails, please log on.

BMC Research Notes 2010, 3:236  doi:10.1186/1756-0500-3-236

Published: 5 September 2010



Major Histocompatibility Complex (MHC) has drawn the attention of evolutionary biologists due to its importance in crucial biological processes, such as sexual selection and immune response in jawed vertebrates. However, the characterization of classical MHC genes subjected to the effects of natural selection still remains elusive in many vertebrate groups. Here, we have tested the suitability of flanking intron sequences to guide the selective exploration of classical MHC genes driving the co-evolutionary dynamics between pathogens and their passerine (Aves, Order Passeriformes) hosts.


Intronic sequences flanking the usually polymorphic exon 2 were isolated from different species using primers sitting on conserved coding regions of MHC class II genes (β chain). Taking the pied flycatcher Ficedula hypoleuca as an example, we demonstrate that careful primer design can evade non-classical MHC gene and pseudogene amplification. At least four polymorphic and expressed loci were co-replicated using a single pair of primers in five non-related individuals (N = 28 alleles). The cross-amplification and preliminary inspection of similar MHC fragments in eight unrelated songbird taxa suggests that similar approaches can also be applied to other species.


Intron sequences flanking the usually polymorphic exon 2 may assist the specific investigation of classical MHC class II B genes in species characterized by extensive gene duplication and pseudogenization. Importantly, the evasion of non-classical MHC genes with a more specific function and non-functional pseudogenes may accelerate data collection and diminish lab costs. Comprehensive knowledge of gene structure, polymorphism and expression profiles may be useful not only for the selective examination of evolutionarily relevant genes but also to restrict chimera formation by minimizing the number of co-amplifying loci.