Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave vs. surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark-pigmented "reed" and light-pigmented "stonewort" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a quantitative trait locus (QTL) mapping study using a laboratory bred F₂ and F₄ cave × surface intercross. We identified genomic regions associated with body pigmentation, antennae length and body size. Furthermore, we compared genome-wide differentiation between natural populations and found several genes potentially associated with these habitats. The assessment of the cave QTL regions in the light–dark comparison of lake populations suggests that the regions associated with cave adaptation are also involved with genomic differentiation in the lake ecotypes. These demonstrate how troglomorphic adaptations can be used as a model for related ecotype formation.

中文翻译：

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表型分化的 Asellus Aquaticus 洞穴、地表溪流和湖泊生态型的基因组学

非常适合研究生态型形成的生物具有广泛的分布范围，它们在空间和时间上反复适应多种截然不同的栖息地。在这里，我们在甲壳动物模型Asellus Aquaticus 中研究此类生态型，这是一种常见的等足类动物，在溪流、洞穴和湖泊等多样化的淡水栖息地中发现。以前关注洞穴与地表生态型的研究将色素脱失、眼睛丧失和触角延长归因于几个南欧洞穴系统。同样，对瑞典多个湖泊的调查已经确定存在深色“芦苇”和浅色“石苔”生态型，它们可以在同一个湖中找到。在这项研究中，我们对A的第一份基因组草图进行了测序。水生动物，然后使用它来绘制地表溪流、洞穴和两个湖泊生态型中的读数和调用变体。此外，基因组草图与 RADseq 方法相结合，使用实验室培育的 F ₂和 F ₄进行数量性状基因座 (QTL) 作图研究洞穴×地表交叉。我们确定了与身体色素沉着、触角长度和身体大小相关的基因组区域。此外，我们比较了自然种群之间的全基因组差异，并发现了几个可能与这些栖息地相关的基因。在湖泊种群的明暗比较中对洞穴 QTL 区域的评估表明，与洞穴适应相关的区域也与湖泊生态型的基因组分化有关。这些证明了穴居适应如何用作相关生态型形成的模型。