Data from: Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using of dense linkage mapping in non-model organisms

The genetic dissection of naturally occurring phenotypes sheds light on many fundamental and longstanding questions in speciation and adaptation and is a central research topic in evolutionary biology. Until recently, forward-genetic approaches were virtually impossible to apply to non-model organisms, but the development of next-generation sequencing techniques eases this difficulty. Here, we use the ddRAD-seq method to map a color trait with a known adaptive function in cichlid fishes, well-known textbook examples for rapid rates of speciation and astonishing phenotypic diversification. A suite of phenotypic key-innovations are related to speciation and adaptation in cichlids, among which body coloration features prominently. The focal trait of the present study, horizontal stripes, evolved in parallel in several cichlid radiations and is associated with piscivorous foraging behavior. We conducted interspecific crosses between Haplochromis sauvagei and H. nyererei, and constructed a linkage map with 867 SNP markers distributed on 22 linkage groups and total size of 1130.63cM. Lateral stripes are inherited as a Mendelian trait and map to a single genomic interval that harbors a paralog of a gene with known function in stripe patterning. Dorsolateral and midlateral stripes were always co-inherited and are thus under the same genetic control. Additionally, we directly quantify the genotyping error rates in RAD markers and offer guidelines for identifying and dealing with errors. Uncritical marker selection was found to severely impact linkage map construction. Fortunately, by applying appropriate quality control steps, a genotyping accuracy of >99.9% can be reached, thus allowing for efficient linkage-mapping of evolutionarily relevant traits.

对自然表型的遗传解析，可为物种形成与适应性演化领域诸多基础性且长期存在的科学问题提供阐释，同时也是进化生物学的核心研究议题。直至近年，正向遗传学方法仍几乎无法应用于非模式生物，但下一代测序（next-generation sequencing）技术的发展打破了这一研究瓶颈。本研究采用ddRAD-seq技术，对慈鲷鱼类中一项具有明确适应性功能的体色性状开展定位研究——慈鲷是教科书中广为人知的物种形成速率快、表型多样性惊人的经典类群。慈鲷的物种形成与适应性演化关联着一系列关键表型创新，其中体色特征尤为突出。本研究的目标性状为横向条纹：该性状在多个慈鲷辐射演化类群中经历了平行演化，并与食鱼性觅食行为密切相关。我们以撒氏朴丽鱼（Haplochromis sauvagei）与尼氏朴丽鱼（H. nyererei）进行种间杂交，构建了一张包含867个单核苷酸多态性（single nucleotide polymorphism, SNP）标记的连锁图谱，该图谱涵盖22个连锁群，总长度达1130.63cM。侧条纹呈孟德尔式遗传，其定位区间仅为单个基因组区域，该区域内存在一个已知参与条纹图案形成的基因的旁系同源基因。背侧条纹与中侧条纹始终共同遗传，因此二者受同一套遗传调控机制控制。此外，我们直接量化了RAD（限制性位点相关DNA，restriction-site associated DNA）标记的基因分型错误率，并为错误的识别与处理提供了标准化操作指南。研究发现，未经审慎筛选的标记选择会严重影响连锁图谱的构建质量。所幸通过实施恰当的质量控制流程，可将基因分型准确率提升至99.9%以上，从而能够高效开展演化相关性状的连锁定位研究。