Data from: Timing marine-freshwater transitions in the diatom order Thalassiosirales

With species found throughout both marine and fresh waters, the diatom order Thalassiosirales is one of the most phylogenetically and ecologically diverse lineages of planktonic diatoms. A clear understanding of the timescale of Thalassiosirales evolution would provide novel insights into the rates and patterns of species diversification associated with major habitat shifts, as well as provide valuable context for understanding the age and evolutionary history of the model species, Cyclotella nana (= Thalassiosira pseudonana). The freshwater fossil record for Thalassiosirales is extensive, well characterized, and generally supportive of a Miocene origin for the major freshwater lineages. The marine record is, by comparison, more sparse and in many cases, unverified. The discovery of freshwater thalassiosiroids in Eocene sediments pushed the freshwater fossil record considerably further back in time, highlighting an apparent gap of some 30 million years. An alternative interpretation is that the Miocene and Eocene reports represent competing hypotheses. In the absence of additional independent and decisive fossil data, I explored the relative plausibility of these two scenarios with Bayesian relaxed molecular clock methods under a range of fossil calibration schemes. Although I found no support for the Eocene fossil dates, the two major freshwater colonization events probably occurred much earlier than previously thought—as early as the Paleocene for Cyclotella, followed by an Eocene origin for the cyclostephanoid lineage. Much of the extant freshwater diversity in both lineages traces back to the Miocene, however, giving the impression of a single Miocene origin. Efforts to infer the timescale of Thalassiosirales evolution more accurately would benefit from a systematic reevaluation of the marine fossil record and formal integration of fossil species into existing phylogenetic hypotheses.

辐杆藻目（Thalassiosirales）的物种广泛分布于海洋与淡水水域中，是浮游硅藻中系统发育与生态多样性最为丰富的类群之一。明确该类群演化的时间尺度，不仅可为解析与主要生境转变相关的物种分化速率与模式提供全新视角，还能为理解模式物种小形圆筛藻（Cyclotella nana，等价于假微型海链藻Thalassiosira pseudonana）的起源年代与演化历史提供关键背景。
辐杆藻目的淡水化石记录丰富且特征清晰，整体支持主要淡水类群起源于中新世（Miocene）。相比之下，其海洋化石记录则较为零散，且多数未经证实。在始新世（Eocene）沉积物中发现的淡水辐杆藻类（thalassiosiroids）化石，将淡水化石记录的年代大幅提前，凸显出约3000万年的明显时间空缺。另一种解读则认为，持中新世与始新世起源观点的研究属于相互对立的假说。
在缺乏额外独立且决定性的化石数据的前提下，本研究采用贝叶斯宽松分子钟（Bayesian relaxed molecular clock）方法，在多种化石校准方案下探究了这两种假说的相对合理性。尽管本研究未发现支持始新世化石年代的证据，但两次主要的淡水定殖事件的发生时间可能远早于此前认知：小环藻属（Cyclotella）的定殖最早可追溯至古新世（Paleocene），而环链藻类群（cyclostephanoid）的起源则发生于始新世。不过，两个类群现存的多数淡水多样性类群都可追溯至中新世，这使得人们误以为其仅起源于中新世。
若要更精准地推断辐杆藻目的演化时间尺度，需系统性重新评估其海洋化石记录，并将化石物种正式整合至现有的系统发育假说中。