Data from: Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation

This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (76-67 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by morphological and molecular data and (iii) indicated temporal variation in diatom assemblages on the inter- and intra-specific level. Diatom assemblages from a short core from Lake Naivasha show a drastic shift over the last 200 years, as littoral species (e.g. Navicula) are replaced by more planktonic ones (e.g. Aulacoseira). Within that same period, we detected periodic changes in the respective frequencies of distinct haplotype groups of Navicula, which coincide with wet and dry periods of Lake Naivasha between 1820 and 1938 AD. Our genetic analyses on historical lake sediments revealed inter- and intra-specific variation in diatoms, which is partially hidden behind single morphotypes. The occurrence of particular genetic lineages is probably correlated to environmental factors.

本研究解析了肯尼亚热带湖泊岩芯沉积物中硅藻的形态与遗传多样性。我们开发了一种靶向硅藻的遗传检测技术，以核酮糖-1,5-二磷酸羧化酶/加氧酶大亚基（rbcL）基因的一段76-67 bp的短区域作为基因条形码。本研究的分析结果涵盖三方面：(i) 验证了将rbcL作为硅藻条形码标记应用于沉积物样本的可行性；(ii) 证实了形态学与分子检测所得结果存在显著相关性；(iii) 揭示了硅藻群落在种间与种内水平上的时间动态变化。取自奈瓦沙湖短岩芯的硅藻群落在近200年间发生了剧烈转变：沿岸物种（如舟形藻属*Navicula*）逐渐被更具浮游习性的物种（如直链藻属*Aulacoseira*）所取代。在同一时期内，我们检测到舟形藻属不同单倍型类群的频率呈现周期性变化，该变化与公元1820年至1938年间奈瓦沙湖的干湿周期高度契合。针对历史湖泊沉积物的遗传分析显示，硅藻存在种间与种内变异，这类变异在单一形态型下往往被部分掩盖；特定遗传谱系的出现大概率与环境因子存在关联。