Understanding current and future biodiversity responses to changing climate is pivotal as anthropogenic climate change continues. This understanding is complicated though by the multitude of available metrics to quantify dynamics, and by biased sampling protocols. Here, we investigate the impact of sampling protocol strategies using a data-rich fossil record to calculate effective diversity using Hill numbers for the first time on Paleogene planktonic foraminifera. We sample 22,830 individual tests, in two different size classes, across a seven-million-year time slice of the Middle Eocene featuring a major transient warming event, the Middle Eocene Climatic Optimum (MECO; ~40 million years ago (Ma)), at study sites in the mid-latitude North Atlantic. Using Generalized Additive Models (GAMs), we investigate community responses to climatic fluctuations. After correcting for any effects of fossil fragmentation, we show a peak in generic diversity in the early and mid-stages of the MECO as well as divergent trajectories between the typical size-selected community (> 180 µm) and a broader selection including smaller genera (> 63 µm). Assemblages featuring smaller genera are more resilient to the climatic fluctuations of the MECO than those assemblages that feature only larger genera, maintaining their community structure at the reference Hill numbers for Shannon’s and Simpson’s Index. These results raise fundamental questions about how communities respond to climate excursions. In addition, our results emphasise the need to design studies with the aim of collecting the most inclusive data possible, to allow detection of community changes and determine which species are likely to dominate future environments. 

Full descriptions of the supplementary data are given in the provided .pdf along with snapshots of the data. Supplementary Table 1, 3-8 and 11-12 are also provided in .csv format. All analysis and code is provided in  Supplementary_Material.pdf and uses R.