Blind catfish evolution

About one hundred cave catfishes have been described. Most of them are found in the Americas, in particular in South America but a few species also thrive in Central and North America. No genomic approach to decipher cave associated genomic changes, nor to estimate cave colonization periods have yet been carried out, despite high quality genomes have been assembled for the Mexican blindcat Prietella phreatophila and for the Colombian blind catfish Trichomycterus rosablanca. We filled this gap, by additionally sequencing the genomes of four blind and depigmented catfishes from Peru (three Trichomycterus and one Astroblepus), as well as the genomes of four close surface relatives. We first extracted a large set of light-related genes, such as phototransduction and crystallin genes, and found contrasting decays of these sequences in different cave species, from 1% of pseudogenes in T. rosablanca to 48% in P. phreatophila. Molecular dating using the percentage of pseudogenes indicates that catfishes settled in caves at different periods, ranging from Early Pliocene to Late Pleistocene, supporting the hypothesis that surface catfishes were able to recurrently and rapidly adapt to caves and thrive during a few million years in this environment. On the other hand, genome-wide analysis of protein-coding genes shows a weaker purifying selection on mildly deleterious mutations in cavefishes, a process that is more pronounced in the oldest cave species. Thus, these highly specialized cavefish with restricted distributions may become evolutionary dead-ends after spending a few millions of years in the subterranean environment This repository contains every result files, which can be analysed using the Rscript "Silucave_mainscript_analysis.R"目前已记述约100种穴居鲶鱼（cave catfishes），其中绝大多数分布于美洲，尤以南美洲为主，另有少数物种栖息于中美洲与北美洲。尽管学界已针对墨西哥盲鲶*Prietella phreatophila*与哥伦比亚盲鲶*Trichomycterus rosablanca*组装出高质量基因组，但目前尚无研究通过基因组学研究手段（genomic approach）解析与穴居适应相关的基因组变化，或估算穴居定居的时间节点。 本研究填补了这一空白：我们额外对4种来自秘鲁的盲眼、脱色素鲶鱼（其中3种为*Trichomycterus*属，1种为*Astroblepus*属）及其4种近缘地表种群的基因组进行测序。首先，我们筛选出大量与光感知相关的基因，如光转导（phototransduction）与晶体蛋白（crystallin）基因，并发现不同穴居物种中这些基因序列的退化程度存在显著差异：*T. rosablanca*的假基因（pseudogenes）占比仅1%，而*P. phreatophila*的假基因占比高达48%。 基于假基因占比的分子定年分析显示，鲶鱼进入洞穴环境的时间跨度从上新世早期直至更新世晚期，这支持了"地表鲶鱼可反复快速适应洞穴环境，并在数百万年内于该生境中繁衍"的假说。 另一方面，全基因组水平的蛋白编码基因分析表明，穴居鲶鱼对轻度有害突变的纯化选择（purifying selection）作用有所减弱，且这一过程在最古老的穴居物种中表现得更为显著。因此，这些分布受限的高度特化穴居鲶鱼，在地下环境中度过数百万年后，或最终演化成为演化死胡同。 本仓库包含所有结果文件，可通过R脚本`Silucave_mainscript_analysis.R`进行分析。