, Volume 63, Issue 3, pp 167–181

Structure, diversity and evolutionary patterns of expressed MHC class IIB genes in chub (Squalius cephalus), a cyprinid fish species from Europe

Original Paper

DOI: 10.1007/s00251-010-0495-3

Cite this article as:
Seifertová, M. & Šimková, A. Immunogenetics (2011) 63: 167. doi:10.1007/s00251-010-0495-3


The polymorphism of exon 2 of the DAB genes (major histocompatibility complex [MHC] class IIB) was investigated for the first time in the freshwater cyprinid fish species, Squalius cephalus, in the wide range of its distribution in Europe. We identified 111 different MHC class IIB variants in 15 chub populations distributed from Finland to Spain. The sequence analysis showed that many structurally important amino acid sites that were conserved among tetrapods were also conserved in chub. The analysis of recombination indicated that it does not play an important role in producing and maintaining the variation of DAB genes analyzed in the present study. The exon 2 was shown to be subjected to intense positive selection. Phylogenetic analysis and sequence identities suggest the presence of two class IIB loci (DAB1-like and DAB3-like) in chub. Nevertheless, the presence of three DAB3-like sequence variants in several individuals indicates the duplication of the DAB3 gene. A contrasting selection pattern was found in DAB1-like and DAB3-like genes, which suggests the potential functional differences between these genes. Some DAB sequence variants were shared among the populations of different mtDNA lineages. The phylogenetic analyses did not confirm any biogeographical pattern of the genetic structure of MHC IIB in chub, which is in line with balancing selection and trans-species polymorphism in MHC genes. Nevertheless, cluster analysis based on the presence/absence of DAB sequence variants in the populations showed the phylogeophraphical pattern corresponding to the mtDNA lineages, which indicates that neutral selection can partially explain the MHC IIB evolution in chub.


MHC class IIB genesCyprinidaeSelectionRecombinationPolymorphism

Supplementary material

251_2010_495_MOESM1_ESM.pdf (68 kb)
Tab. S1Results of the likelihood ratio tests of positive selection on exon 2 of MHC class IIB in Squalius cephalus. A test statistic was computed as 2(LbLa), where La and Lb are the log-likelihood value for each of the nested models being compared (M0 and M3; M1a and M2a; M7 and M8). PSS positive selected site, n number of sequences in the analysed alignment. (PDF 68.1 kb)
251_2010_495_MOESM2_ESM.pdf (223 kb)
Tab. S2Geographical distribution of Sqce-DAB1 and Sqce-DAB3 sequences found in 15 populations of Squalius cephalus collected from European Rivers. (PDF 223 kb)

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  1. 1.Department of Botany and Zoology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic