Trait loss represents an intriguing evolutionary problem, particularly when it occurs across independent lineages. Fishes in light-poor environments often evolve “troglomorphic” traits, including reduction or loss of both pigment and eyes. Here, we investigate the genomic basis of trait loss in a blind and depigmented African cichlid, Lamprologus lethops, and explore evolutionary forces (selection and drift) that may have contributed to these losses. This species, the only known blind cichlid, is endemic to the lower Congo River. Available evidence suggests that it inhabits deep, low-light habitats. Using genome sequencing, we show that genes related to eye formation and pigmentation, as well as other traits associated with troglomorphism, accumulated inactivating mutations rapidly after speciation. A number of the genes affected in L. lethops are also implicated in troglomorphic phenotypes in Mexican cavefish (Astyanax mexicanus) and other species. Analysis of heterozygosity patterns across the genome indicates that L. lethops underwent a significant population bottleneck roughly 1 Ma, after which effective population sizes remained low. Branch-length tests on a subset of genes with inactivating mutations show little evidence of directional selection; however, low overall heterozygosity may reduce statistical power to detect such signals. Overall, genome-wide patterns suggest that accelerated genetic drift from a severe bottleneck, perhaps aided by directional selection for the loss of physiologically expensive traits, caused inactivating mutations to fix rapidly in this species.

中文翻译：

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基因组分析的唯一盲丽鱼科动物揭示了眼睛和色素形成基因的广泛失活。

特质丧失代表着一个有趣的进化问题，尤其是在跨独立世系发生时。在光线较差的环境中，鱼类通常会进化出“三色性”特征，包括色素和眼睛的减少或丧失。在这里，我们研究了在盲目和色素沉着的非洲丽鱼科动物Lamprologus lethops中性状丧失的基因组基础。，并探讨可能造成这些损失的进化力（选择和漂移）。该物种是唯一已知的盲鲷，是刚果河下游的特有物种。现有证据表明，它栖息在较暗的低光照环境中。使用基因组测序，我们显示了与眼睛形成和色素沉着相关的基因，以及与滋养相关的其他特征，在物种形成后迅速积累了失活的突变。在L. lethops中受影响的许多基因也与墨西哥穴居鱼类（Astyanax mexicanus）和其他物种的拟态表型有关。整个基因组的杂合性模式分析表明，L。lethops经历了大约1 Ma的显着人口瓶颈，此后有效人口规模仍然很低。对具有失活突变的基因子集的分支长度测试几乎没有方向选择的证据。但是，较低的总体杂合度可能会降低检测此类信号的统计能力。总体而言，全基因组模式表明，由于严重瓶颈而导致的遗传漂移加速，可能是由于方向选择而丧失了生理上昂贵的性状，导致失活的突变在该物种中迅速修复。