Data from: Towards understanding the genetic basis of mouth asymmetry in the scale-eating cichlid Perissodus microlepis

How polymorphisms consisting in left–right asymmetries are produced and maintained in natural populations is a tantalizing question, which remains largely unanswered. The scale-eating cichlid fish Perissodus microlepis is a remarkable example of extreme ecological specialization achieved by morphological and behavioural laterality. Its asymmetric mouth is accompanied by a pronounced lateralized foraging behaviour, where a left-bending morph preferentially feeds on the scales of the right side of its prey, while the opposite is true for the right morph. This striking asymmetry made this fish a textbook example of the astounding degree of ecological specialization and negative frequency-dependent selection. Yet, the genetic basis underlying this spectacular laterality remains unknown. We addressed this question through analyses of wild-caught fish using high-throughput DNA sequencing data. A novel array of SNP markers was developed by ddRAD sequencing (ddRADseq) and the use of pooled DNA samples (PoolSeq). We obtained more than 155 000 SNPs using ddRADseq and 3 900 000 SNPs with PoolSeq. Among these, we identified one (ddRAD) SNP, and 38 or 378 (PoolSeq) windows that are differentiated between the left and right morphs accounting for spurious associations due to geographic structuring. This allowed us to uncover candidate genomic regions that potentially contain genes for this trait. Then, this interesting trait has a genetic basis that is likely to be influenced by multiple loci. This result contributes to a greater understanding of the genetic bases of left–right asymmetry and, ultimately, the evolutionary processes governing the maintenance of this striking case of laterality.左右不对称性多态性在自然种群中如何产生并维持，是一个长期悬而未决的极具吸引力的科学谜题。食鳞慈鲷（Perissodus microlepis）是通过形态与行为侧化实现极端生态特化的典型范例：其不对称的嘴部伴随显著的偏侧化觅食行为——左弯型个体优先取食猎物右侧的鳞片，右弯型个体则反之。这种鲜明的不对称性使其成为生态特化与负频率依赖选择（negative frequency-dependent selection）程度惊人的经典教科书案例。然而，这种显著侧化现象背后的遗传基础仍未被揭示。本研究通过对野生捕获个体的高通量DNA测序数据分析，对该问题展开探究。研究人员利用双酶切限制性位点相关DNA测序（ddRAD sequencing，简称ddRADseq）结合混合DNA样本测序（PoolSeq）技术，开发了一套全新的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）标记体系。通过ddRADseq共获得超过155,000个SNP位点，PoolSeq则获得390万个SNP位点。在此基础上，我们筛选出了可区分左右形态型的基因组区域：ddRAD测序获得1个差异SNP位点，PoolSeq则获得38或378个差异基因组窗口，该结果校正了由种群地理结构所导致的虚假关联。这使得我们得以挖掘出该性状潜在的候选基因组区域。由此可见，该有趣性状的遗传基础极有可能受多个基因座共同调控。本研究结果有助于我们更深入地理解左右不对称性的遗传基础，并最终阐明维持这种显著侧化现象的进化过程。