  The amount of sequence data available today highly facilitates the access to
genes from many gene families. Universal primers amplifying the desired genes
over a range of species are readily obtained by aligning conserved gene
regions, and laborious gene isolation procedures can often be replaced by
quicker PCR-based approaches. However, in case of multigene families, PCR-based
approaches bear the risk of incomplete isolation of family members. This
problem is most prominent in gene families with highly variable and thus
unpredictable number of gene copies among species, such as in the major
histocompatibility complex (MHC). In the present study we (i) report new
primers for the isolation of the MHC class IIB (MHCIIB) gene family in birds,
and (ii) share our experience with isolating MHCIIB genes from an unprecedented
number of avian species from all over the avian phylogeny. We report important
and usually underappreciated problems encountered during PCR-based multigene
family isolation, and provide a collection of measures that may help to
significantly improve the chance of successfully isolating complete multigene
families using PCR-based approaches.

Populations and Evolution;Genomics