Genomic Analysis of the Only Blind Cichlid Reveals Extensive Inactivation in Eye and Pigment Formation Genes.
Genomic Analysis of the Only Blind Cichlid Reveals Extensive Inactivation in Eye and Pigment Formation Genes.
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DOI：
10.1093/gbe/evaa144
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发表时间：
2020-08-01
影响因子：
3.3
通讯作者：
Alter SE
中科院分区：
文献类型：
--
作者：
Aardema ML;Stiassny MLJ;Alter SE
性状丧失是一个有趣的进化问题，特别是当它发生在独立的谱系中时。在光线不足的环境中，鱼类通常会进化出“troglomorphic”特征，包括色素和眼睛的减少或丧失。在这里，我们调查的基因组基础的性状损失的盲目和脱色的非洲慈鲷，Lamprologus lethops，并探讨进化的力量（选择和漂移），可能有助于这些损失。这一物种是唯一已知的盲丽鱼，是刚果河下游的特有物种。现有的证据表明，它栖息在深，低光照的栖息地。利用基因组测序，我们发现，与眼睛形成和色素沉着，以及其他性状与troglomorphism相关的基因，积累失活突变后迅速形成。L. lethops中受影响的许多基因也与墨西哥洞穴鱼（Astyanax mexicanus）和其他物种的troglomorphic表型有关。基因组杂合性模式分析表明，L. lethops经历了一个显着的人口瓶颈约1 Ma，之后有效的人口规模仍然很低。对失活突变基因子集的分支长度测试显示定向选择的证据很少;然而，低的总体杂合性可能会降低检测此类信号的统计能力。总的来说，全基因组模式表明，从一个严重的瓶颈加速遗传漂变，也许有助于定向选择的生理上昂贵的性状的损失，导致失活突变迅速固定在这个物种。
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.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
14.9
作者：
Abascal F;Zardoya R;Telford MJ
通讯作者：
Telford MJ
影响因子：
3.4
作者：
Alter SE;Brown B;Stiassny ML
通讯作者：
Stiassny ML
影响因子：
9.8
作者：
Cavallari N;Frigato E;Vallone D;Fröhlich N;Lopez-Olmeda JF;Foà A;Berti R;Sánchez-Vázquez FJ;Bertolucci C;Foulkes NS
通讯作者：
Foulkes NS
影响因子：
9.8
作者：
Bandah-Rozenfeld, Dikla;Collin, Rob W. J.;den Hollander, Anneke I.
通讯作者：
den Hollander, Anneke I.