van Oosterhout C, Joyce D A, Cummings S M
School of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK.
Heredity (Edinb). 2006 Aug;97(2):111-8. doi: 10.1038/sj.hdy.6800843. Epub 2006 May 31.
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 >100 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/dS>14 in some pairwise comparisons. Consequently, a curvilinear relationship was observed between the dN/dS ratio and the level of sequence divergence.
这是第一项对野生孔雀鱼和观赏孔雀鱼（孔雀鱼）主要组织相容性复合体（MHC）的基因组序列变异进行量化的研究。我们对56条野生特立尼达孔雀鱼和14条观赏品系孔雀鱼的MHC II类B（DAB）外显子2的196 - 219 bp进行了测序。两个自然种群中的每一个都具有较高的等位基因丰富度（15 - 16个等位基因），而从观赏孔雀鱼中仅扩增出三个或更少的DAB等位基因。野生鱼和观赏鱼之间等位基因丰富度的差异不能完全用近亲繁殖导致的等位基因固定来解释，也不能用未扩增序列（即无效等位基因）的存在来解释。相反，我们认为由于基因转换，相同的等位基因在MHC DAB重复位点上固定。或者，观赏品系中的基因座数量在圈养的100多代中已经收缩，这一假设与MHC进化的手风琴模型一致。我们还通过对假定的肽结合区域（PBR）的序列变异进行成对比较来分析替换模式。在PBR密码子中，非同义替换率（dN）仅略高于同义替换率（dS）。高度分化的序列没有显示出多样化选择的证据，可能是因为自它们分化以来同义替换已经积累。同样，相似等位基因的替换模式也没有显示出多样化选择的证据，可能是因为有利的非同义替换尚未积累。中等分化的序列显示出最高的非同义替换相对率，在一些成对比较中dN/dS>14。因此，观察到dN/dS比率与序列分化水平之间呈曲线关系。
