Coulmance Floriane, Akkaynak Derya, Le Poul Yann, Höppner Marc P, McMillan W Owen, Puebla Oscar
Leibniz Center for Tropical Marine Research, Bremen, Germany.
Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany.
Mol Ecol. 2024 Feb;33(4):e17047. doi: 10.1111/mec.17047. Epub 2023 Jun 20.
Coral reefs rank among the most diverse species assemblages on Earth. A particularly striking aspect of coral reef communities is the variety of colour patterns displayed by reef fishes. Colour pattern is known to play a central role in the ecology and evolution of reef fishes through, for example, signalling or camouflage. Nevertheless, colour pattern is a complex trait in reef fishes-actually a collection of traits-that is difficult to analyse in a quantitative and standardized way. This is the challenge that we address in this study using the hamlets (Hypoplectrus spp., Serranidae) as a model system. Our approach involves a custom underwater camera system to take orientation- and size-standardized photographs in situ, colour correction, alignment of the fish images with a combination of landmarks and Bézier curves, and principal component analysis on the colour value of each pixel of each aligned fish. This approach identifies the major colour pattern elements that contribute to phenotypic variation in the group. Furthermore, we complement the image analysis with whole-genome sequencing to run a multivariate genome-wide association study for colour pattern variation. This second layer of analysis reveals sharp association peaks along the hamlet genome for each colour pattern element and allows to characterize the phenotypic effect of the single nucleotide polymorphisms that are most strongly associated with colour pattern variation at each association peak. Our results suggest that the diversity of colour patterns displayed by the hamlets is generated by a modular genomic and phenotypic architecture.
珊瑚礁是地球上物种最为多样的群落之一。珊瑚礁群落一个特别显著的方面是礁鱼所呈现出的各种颜色图案。众所周知，颜色图案在礁鱼的生态和进化过程中发挥着核心作用，例如通过信号传递或伪装。然而，颜色图案是礁鱼的一个复杂性状——实际上是一系列性状——难以以定量和标准化的方式进行分析。这就是我们在本研究中以哈姆雷特鱼（Hypoplectrus spp.，鮨科）作为模型系统所要解决的挑战。我们的方法包括一个定制的水下相机系统，用于在原位拍摄方向和大小标准化的照片、颜色校正、将鱼的图像与地标和贝塞尔曲线相结合进行对齐，以及对每个对齐鱼的每个像素的颜色值进行主成分分析。这种方法识别出了导致该群体表型变异的主要颜色图案元素。此外，我们通过全基因组测序对图像分析进行补充，以针对颜色图案变异进行多变量全基因组关联研究。这第二层分析揭示了哈姆雷特鱼基因组中每个颜色图案元素的明显关联峰，并能够表征在每个关联峰处与颜色图案变异最强烈相关的单核苷酸多态性的表型效应。我们的结果表明，哈姆雷特鱼所展示的颜色图案多样性是由模块化的基因组和表型结构产生的。
