Department of Biology, Montclair State University.
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York.
Genome Biol Evol. 2020 Aug 1;12(8):1392-1406. doi: 10.1093/gbe/evaa144.
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.
性状缺失代表了一个有趣的进化问题，特别是当它发生在独立的谱系中时。在光照不足的环境中，鱼类通常会进化出“洞穴型”特征，包括色素和眼睛的减少或缺失。在这里，我们研究了一种失明和无色的非洲慈鲷 Lamprologus lethops 中性状缺失的基因组基础，并探讨了可能导致这些缺失的进化力量（选择和漂变）。这种物种是唯一已知的盲慈鲷，仅分布于刚果河下游。现有证据表明，它栖息在深而低光的栖息地。通过基因组测序，我们发现与眼睛形成和色素沉着相关的基因，以及与洞穴型特征相关的其他性状相关的基因，在物种形成后迅速积累了失活突变。受影响的基因中有许多也与墨西哥洞穴鱼（Astyanax mexicanus）和其他物种的洞穴型表型有关。对整个基因组杂合性模式的分析表明，L. lethops 在大约 100 万年前经历了一次显著的种群瓶颈，此后有效种群规模一直保持在较低水平。对具有失活突变的一组基因进行分支长度测试，几乎没有证据表明存在定向选择；然而，总体上较低的杂合性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，严重瓶颈导致的遗传漂变加速，再加上对生理上昂贵性状缺失的定向选择，可能导致该物种的失活突变迅速固定。
