Evolution of MHC class IIB in the genome of wild and ornamental guppies, Poecilia reticulata

Abstract

This is the first study to quantify genomic sequence variation of the major histocompatibility complex (MHC) in wild and ornamental guppies, Poecilia reticulata. We sequenced 196-219 bp of exon 2 MHC class IIB (DAB) in 56 wild Trinidadian guppies and 14 ornamental strain guppies. Each of two natural populations possessed high allelic richness (15-16 alleles), whereas only three or fewer DAB alleles were amplified from ornamental guppies. The disparity in allelic richness between wild and ornamental fish cannot be fully explained by fixation of alleles by inbreeding, nor by the presence of non-amplified sequences (ie null alleles). Rather, we suggest that the same allele is fixed at duplicated MHC DAB loci owing to gene conversion. Alternatively, the number of loci in the ornamental strains has contracted during 4100 generations in captivity, a hypothesis consistent with the accordion model of MHC evolution. We furthermore analysed the substitution patterns by making pairwise comparisons of sequence variation at the putative peptide binding region (PBR). The rate of non-synonymous substitutions (dN) only marginally exceeded synonymous substitutions (dS) in PBR codons. Highly diverged sequences showed no evidence for diversifying selection, possibly because synonymous substitutions have accumulated since their divergence. Also, the substitution pattern of similar alleles did not show evidence for diversifying selection, plausibly because advantageous non-synonymous substitutions have not yet accumulated. Intermediately diverged sequences showed the highest relative rate of non-synonymous substitutions, with dN/dS414 in some pairwise comparisons. Consequently, a curvilinear relationship was observed between the dN/dS ratio and the level of sequence divergence.

Transmission of a fatal clonal tumor by biting occurs due to depleted MHC diversity in a threatened carnivorous marsupial

“…We estimated that 10% of clones sequenced contained at least 2 bp of cloning error. This figure is more conservative than has previously been reported in the literature (40). Clustal W was used to align sequences, with some manual adjustments (41).…”

Balancing Selection, Random Genetic Drift, and Genetic Variation at the Major Histocompatibility Complex in Two Wild Populations of Guppies (Poecilia Reticulata)

“…We also detected preferential amplification of certain alleles that could downwardly bias the observed number of DAB alleles, a technical complication we ameliorated by screening large numbers of clones from a small number of individual fish and by using different primer combinations. Although it is widely accepted that PCR bias can compromise molecular genetic studies (Kobayashi et al 1999), only recently have stringent screening protocols been adopted, such as those used here, in investigations of multigene families (Lukas and Vigilant 2005;van Oosterhout et al 2006a). The current study highlights the need for careful experimental design, as amplification bias and null alleles could potentially compromise studies of the MHC.…”

“…This PCR error rate implies that the expected proportion of correct sequences of 219 bp is 61.9%, and there are predicted to be approximately 27.6% with one, 7.6% with two, and 2.1% with three artificial PCR base substitutions. To minimize the probability of erroneously identifying artificial sequences as actual DAB alleles, we only recognised ''real'' alleles as those that occurred in two independent PCRs or differed by more than three base pairs from another sequence found within the same individual (see van Oosterhout et al 2006a). …”

“…This analysis indicated that the LA population showed a significant frequency of null alleles in Pr80 (Brookfield 1 estimator r ϭ 0.1573), but all other loci were free of scoring errors and null alleles. For all subsequent analyses, the putative null alleles at this locus were removed using MICRO-CHECKER 2.2.3 (van Oosterhout et al 2004a(van Oosterhout et al , 2006b). We used Fstat 2.9.3.2 (http://www2.…”

Are large wattles related to particular MHC genotypes in the male pheasant?

“…The pheasant MHC (MHCPhco) is highly polymorphic with two unlinked gene clusters, which correspond to those found in the fowl (BLB and YLB genes, for the black grouse, Tetrao tetrix, see Strand et al 2007), both comprising class I and IIB genes (3-4 genes). The exon 2 of the B complex coding for the b1 chain is the most variable part of MHC class IIB genes and it is commonly used for population genetic analyses (Ditchkoff et al 2001;Oliver and Piertney 2006;van Oosterhout et al 2006;Zhang et al 2006). …”