Supplementary materials for PhD thesis "Temporal genetic diversity in phytoplankton in the Gulf of Naples": Chapter 4 - Pn libraries alignment and Clone Library sequence 050404 & 200704

This dataset comprises the files contained on a CD-ROM which was attached to the thesis when it was submitted in 2006. It was uploaded to ORDO in 2025 for preservation purposes. For more information, please refer to the thesis “Temporal genetic diversity in phytoplankton in the Gulf of Naples" via ORO.Thesis abstractThis thesis dealt with genetic diversity in groups of phytoplankton on a temporal scale. The aim of the study was to investigate diversity and the seasonal distribution of that diversity during the year.Chapter Two examined the diversity and seasonal distribution of ultraplankton <5 μm in surface waters between 2003 and 2004 using 16S class level probes and clone libraries.Chapter Three examined the distribution of ultraplankton using the 16S probes over four depth profiles during 2005. The results showed the presence of Prymnesiophyceae and Cryptophyceae during the whole year and at most depths. The Chrysophyceae showed a marked preference for summer. All three classes showed highest signal just below the surface between 2 and 10 m. The Pelagophyceae were present in February in surface waters, but at 50 to 70 m in May and August. Diversity within these classes was high and other taxonomic classes were detected in the clone libraries. The seasonality within genotypes in the Cryptophyceae was visible and comparisons to known cultures could be made.The diatom genus Pseudo-nitzschia was investigated in Chapter Four using newly developed genus specific primers. Thirteen genotypes were detected during the year, some of which showed seasonal preferences, for example P. multistriata in October, and others that were present most of the year, for example P. galaxiae LSU-clade 2 present from May until October. The three annual blooms of P. galaxiae were investigated in Chapter Five using LSU and ITS. The blooms were shown to be dominated by different ITS genotypes that recur in the same period of the year, every year. The results from P. galaxiae indicated a possible mechanism for speciation whereby populations may become separated in time rather than space.

本数据集包含2006年提交学位论文时随附的光盘（CD-ROM）中的全部文件，于2025年上传至ORDO以进行长期保存。如需获取更多信息，请通过ORO查阅学位论文《那不勒斯湾浮游植物的时间尺度遗传多样性》（Temporal genetic diversity in phytoplankton in the Gulf of Naples）。

学位论文摘要
本论文围绕浮游植物类群的时间尺度遗传多样性展开研究，旨在探究全年范围内的物种多样性及其季节分布规律。

第二章 研究采用16S类群水平探针（16S class level probes）与克隆文库（clone libraries）技术，对2003至2004年表层水体中粒径小于5微米的超微型浮游植物（ultraplankton）的多样性与季节分布特征进行了分析。

第三章 于2005年通过四次深度剖面采样，利用16S类群水平探针分析了超微型浮游植物的垂直分布特征。研究结果显示，定鞭藻纲（Prymnesiophyceae）和隐藻纲（Cryptophyceae）在全年多数深度中均有检出；金藻纲（Chrysophyceae）则显著偏好夏季生境；三类藻纲的信号峰值均出现在表层下方2至10米的水层。远洋藻纲（Pelagophyceae）在2月的表层水体中被检出，而在5月与8月则分布于50至70米的水层。上述类群内部的遗传多样性较高，克隆文库中还检测到其他分类学类群；隐藻纲的基因型季节分布特征显著，且可与已知培养菌株进行比对分析。

第四章 利用新开发的属特异性引物，对伪菱形藻属（Pseudo-nitzschia）展开研究。全年共检出13个基因型，部分基因型表现出明显的季节偏好，例如多纹伪菱形藻（P. multistriata）仅在10月检出；而另有部分基因型全年多数时段均可检出，例如从5月至10月均存在的银河伪菱形藻LSU进化支2（P. galaxiae LSU-clade 2）。

第五章 利用大亚基核糖体RNA（LSU）与内部转录间隔区（ITS）分子标记，对银河伪菱形藻的三次年度水华事件进行了分析。结果显示，每次水华均由特定的ITS基因型主导，且这些基因型会在每年的相同时段重复出现。基于银河伪菱形藻的研究结果，本论文提出了一种潜在的物种形成机制：种群可通过时间隔离而非空间隔离实现分化。