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, that remains largely unanswered. The scale-eating cichlid fish Perissodus microlepis is a remarkable example of extreme ecological specialization achieved by morphological and behavioral laterality. Its asymmetric mouth is accompanied by a pronounced lateralized foraging behavior, 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.

自然种群中左右不对称性多态性的产生与维持机制，是一个长期悬而未决且极具吸引力的科学问题。食鳞慈鲷小鳞朴丽鱼（Perissodus microlepis）是通过形态与行为偏侧性实现极端生态特化的经典范例。其不对称口部伴随显著的偏侧觅食行为：左弯形态型偏好取食猎物右侧鳞片，右弯形态型则反之。这一显著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）惊人程度的教科书级案例。然而，该物种这种惊人偏侧性的遗传基础仍未被阐明。本研究通过对野生捕获个体的高通量DNA测序（high-throughput DNA sequencing）数据进行分析，对该问题展开了探究。研究人员借助双酶切限制性位点相关DNA测序（double digest restriction-site associated DNA sequencing, ddRADseq）与混合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）标记阵列。通过ddRADseq共获得超过155,000个SNP位点，PoolSeq则获得390万个SNP位点。在剔除由地理结构导致的虚假关联后，研究人员在左、右形态型间鉴定出1个（ddRADseq数据集）以及38或378个（PoolSeq数据集）存在分化的基因组窗口。这一结果帮助我们锁定了可能携带该性状相关基因的候选基因组区域。由此可见，该有趣性状的遗传基础可能受多个基因位点共同调控。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，并最终阐明维持这一典型偏侧性现象的进化过程。