热带淡水湖以其高度的生物多样性而闻名,尤其是东非五大湖以其对丽鱼科鱼的适应性辐射而闻名。虽然对现存物种群的比较系统发育分析揭示了它们多样化的模式和过程,对谱系内的进化轨迹知之甚少,环境驱动因素的影响,或现已灭绝的多样性的范围和性质。来自地质年轻化石记录的时间结构古数据,例如化石计数,尤其是古老的DNA(aDNA)数据,将有助于填补这个巨大的知识空白。高环境温度可能不利于DNA的保存,但完善的方法现在允许数据生成,甚至从保存非常差的样本。这里,我们首次显示来自热带湖泊沉积物的鱼类化石产生内源性aDNA。尽管内源含量普遍较低,样本脱落率高,高通量测序的应用,在某些情况下,序列捕获允许将17%的分析鱼类化石的分类分配和系统发育放置到家庭或部落级别,包括长达2700年或重量小于1毫克的遗骸。当针对升高的温度进行调整时,aDNA降解与样品的热年龄之间的关系类似于针对来自寒冷环境的陆地样品所描述的关系。被调查的查拉湖之间的成功率和aDNA保存不同,基伍和维多利亚,可能是由底水氧合的差异引起的。我们的研究表明,热带湖泊的沉积物记录可以保留数千年时间尺度上鱼类分类群快速多样化的遗传信息。
Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.