Evolutionary Biology Group, Department of Biological Sciences, University of Hull, Hull, United Kingdom.
Mol Biol Evol. 2012 Jun;29(6):1631-44. doi: 10.1093/molbev/mss012. Epub 2012 Jan 18.
The immune genes of the major histocompatibility complex (MHC) are characterized by extraordinarily high levels of nucleotide and haplotype diversity. This variation is maintained by pathogen-mediated balancing selection that is operating on the peptide-binding region (PBR). Several recent studies have found, however, that some populations possess large clusters of alleles that are translated into virtually identical proteins. Here, we address the question of how this nucleotide polymorphism is maintained with little or no functional variation for selection to operate on. We investigate circa 750-850 bp of MHC class II DAB genes in four wild populations of the guppy Poecilia reticulata. By sequencing an extended region, we uncovered 40.9% more sequences (alleles), which would have been missed if we had amplified the exon 2 alone. We found evidence of several gene conversion events that may have homogenized sequence variation. This reduces the visible copy number variation (CNV) and can result in a systematic underestimation of the CNV in studies of the MHC and perhaps other multigene families. We then focus on a single cluster, which comprises 27 (of a total of 66) sequences. These sequences are virtually identical and show no signal of selection. We use microsatellites to reconstruct the populations' demography and employ simulations to examine whether so many similar nucleotide sequences can be maintained in the populations. Simulations show that this variation does not behave neutrally. We propose that selection operates outside the PBR, for example, on linked immune genes or on the "sheltered load" that is thought to be associated to the MHC. Future studies on the MHC would benefit from extending the amplicon size to include polymorphisms outside the exon with the PBR. This may capture otherwise cryptic haplotype variation and CNV, and it may help detect other regions in the MHC that are under selection.
主要组织相容性复合体 (MHC) 的免疫基因以核苷酸和单倍型多样性的极高水平为特征。这种变异是由病原体介导的平衡选择维持的，这种选择作用于肽结合区 (PBR)。然而，最近的几项研究发现，一些群体拥有大量的等位基因簇，这些等位基因被翻译成几乎相同的蛋白质。在这里，我们探讨了在选择作用的核苷酸多态性很少或没有功能变异的情况下如何维持这种多态性的问题。我们研究了四个野生孔雀鱼 Poecilia reticulata 群体的 MHC 类 II DAB 基因的大约 750-850 bp。通过对一个扩展区域进行测序，我们发现了 40.9%的更多序列（等位基因），如果我们只扩增外显子 2，这些序列就会被遗漏。我们发现了几个基因转换事件的证据，这些事件可能使序列变异同质化。这减少了可见的拷贝数变异 (CNV)，并可能导致在 MHC 及其他多基因家族的研究中对 CNV 的系统低估。然后，我们将注意力集中在一个单一的簇上，该簇由 27 个（总共 66 个）序列组成。这些序列几乎完全相同，没有选择信号。我们使用微卫星来重建群体的人口统计学，并利用模拟来检验如此多相似的核苷酸序列是否可以在群体中维持。模拟表明，这种变异不是中性的。我们提出，选择作用于 PBR 之外，例如，作用于免疫相关基因或与 MHC 相关的“庇护负荷”。未来对 MHC 的研究将受益于扩大扩增子的大小，以包括 PBR 之外的外显子的多态性。这可能会捕获否则隐藏的单倍型变异和 CNV，并可能有助于检测 MHC 中其他受选择影响的区域。
