Cis-by-Trans Regulatory Divergence Causes the Asymmetric Lethal Effects of an Ancestral Hybrid Incompatibility Gene

The Dobzhansky and Muller (D-M) model explains the evolution of hybrid incompatibility (HI) through the interaction between lineage-specific derived alleles at two or more loci. In agreement with the expectation that HI results from functional divergence, many protein-coding genes that contribute to incompatibilities between species show signatures of adaptive evolution, including Lhr, which encodes a heterochromatin protein whose amino acid sequence has diverged extensively between Drosophila melanogaster and D. simulans by natural selection. The lethality of D. melanogaster/D. simulans F1 hybrid sons is rescued by removing D. simulans Lhr, but not D. melanogaster Lhr, suggesting that the lethal effect results from adaptive evolution in the D. simulans lineage. It has been proposed that adaptive protein divergence in Lhr reflects antagonistic coevolution with species-specific heterochromatin sequences and that defects in LHR protein localization cause hybrid lethality. Here we present surprising results that are inconsistent with this coding-sequence-based model. Using Lhr transgenes expressed under native conditions, we find no evidence that LHR localization differs between D. melanogaster and D. simulans, nor do we find evidence that it mislocalizes in their interspecific hybrids. Rather, we demonstrate that Lhr orthologs are differentially expressed in the hybrid background, with the levels of D. simulans Lhr double that of D. melanogaster Lhr. We further show that this asymmetric expression is caused by cis-by-trans regulatory divergence of Lhr. Therefore, the non-equivalent hybrid lethal effects of Lhr orthologs can be explained by asymmetric expression of a molecular function that is shared by both orthologs and thus was presumably inherited from the ancestral allele of Lhr. We present a model whereby hybrid lethality occurs by the interaction between evolutionarily ancestral and derived alleles.

多布然斯基-穆勒（Dobzhansky and Muller, D-M）模型通过两个或多个基因座上的谱系特异性衍生等位基因间的相互作用，阐释了杂交不亲和（hybrid incompatibility, HI）的演化进程。契合于‘杂交不亲和源自功能分化’的预期，诸多参与物种间杂交不亲和的蛋白编码基因均呈现适应性演化的特征，其中包括杂交致死拯救基因（Lethal hybrid rescue, Lhr）——该基因编码一种异染色质蛋白（heterochromatin protein），其氨基酸序列经自然选择作用在黑腹果蝇（Drosophila melanogaster）与拟暗果蝇（Drosophila simulans）间发生了广泛分化。黑腹果蝇与拟暗果蝇的F1杂交雄性子代的致死表型，可通过敲除拟暗果蝇的Lhr得以挽救，但敲除黑腹果蝇的Lhr则无此效果，这表明该致死效应源自拟暗果蝇谱系中的适应性演化。此前有研究提出，Lhr基因的适应性蛋白分化反映了其与物种特异性异染色质序列之间的拮抗协同进化，且LHR蛋白定位异常会导致杂交致死。本研究得到了与该基于编码序列的模型相悖的意外结果。我们使用在天然表达调控条件下的Lhr转基因构件，未发现黑腹果蝇与拟暗果蝇的LHR定位存在差异，也未发现LHR在二者的种间杂交子代中出现定位异常。与之相反，本研究证实Lhr直向同源基因（orthologs）在杂交遗传背景中呈现差异表达：拟暗果蝇Lhr的表达量为黑腹果蝇Lhr的两倍。进一步研究表明，这种不对称表达由Lhr基因的顺式-反式调控分化（cis-by-trans regulatory divergence）所导致。因此，Lhr直向同源基因所呈现的不等效杂交致死效应，可通过二者共有的分子功能的不对称表达得以解释——该分子功能推测均继承自Lhr的祖先等位基因。本研究提出了一个新模型，据此杂交致死由演化上的祖先等位基因与衍生等位基因之间的相互作用所引发。