DOI: 10.5061/dryad.2fqz612pk
title: Data from: Diversity dynamics of microfossils from the Cretaceous to the Neogene show mixed responses to events

description: Microfossils have a ubiquitous and well-studied fossil record with
 temporally and spatially fluctuating diversity, but how this arises and
 how major events affect speciation and extinction is uncertain. We present
 the first application of PyRate to a micropaleontological global
 occurrence data set, reconstructing diversification rates within a
 Bayesian framework from the Mesozoic to the Recent in four microfossil
 groups: planktic foraminiferans, calcareous nannofossils, radiolarians and
 diatoms. Calcareous and siliceous groups demonstrate opposed, but
 inconsistent, responses in diversification. Siliceous groups increased
 origination from ~104 Ma, maintaining high rates into the Cenozoic.
 Calcareous microfossils diversification rates significantly decline across
 the Cretaceous–Paleogene boundary, while rates in siliceous microfossil
 groups remain stable until the Paleocene–Eocene transition.
 Diversification rates in the Cenozoic are largely stable in calcareous
 groups, whereas the Paleogene is a turbulent time for diatoms.
 Diversification fluctuations are driven by climate change and fluctuations
 in sea surface temperatures, promoting selectivity in both microfossil
 composition and foraminiferal size. Extinctions appear induced by changes
 in anoxia, acidification, and stratification, while speciation tends to be
 associated with upwelling, productivity, and ocean circulation. These
 results show promise for further quantitative analyses in
 micropaleontological diversity studies and effects of major transitions in
 the fossil record. Despite extensive occurrence data, regional
 diversification events were not recovered, neither were some global
 events. These unexpected results show the need to consider multiple
 spatiotemporal levels of diversity and diversification analyses, and
 implies occurrence data sets of different clades may be more appropriate
 to testing some hypotheses than others.
description: Microfossil data used in this study was collected from NSB
 (Neptune Sandbox Berlin). NSB holds information of over one million
 species occurrences of several microfossil groups pulled from scientific
 drilling programs. Four fossil groups were downloaded: planktic
 foraminifera, calcareous nannofossils, diatoms, and radiolarians into
 R using the package ‘NSB Companion’ v.2.1. The data was then processed to
 correct any synonymous species, removing non-valid taxa, and a dating
 uncertainty of ±0.25 my was applied to occurrence sample ages. The data
 was then manipulated into a suitable format table of taxon-occurrence
 range entries so it could be processed by PyRate.
 PyRate implements three different preservation models (the
 default non-homogeneous Poisson process, homogeneous, and time-dependent
 Poisson processes) that vary the allowed heterogeneity of the preservation
 rates through time. All three of these preservation models were run on all
 four fossils groups in separate analyses, while compositional effects on
 preservation rates were assessed by grouping calcareous microfossils
 (foraminiferans and nannofossils) and siliceous microfossils (radiolarians
 and diatoms) into two further analyses. PyRate analyses for each taxonomic
 group were run as array jobs of the ten replicates generated on the Blue
 Pebble cluster at the University of Bristol (Advanced Computing Research
 Centre) using the recommended reversible jump Markov Chain Monte Carlo
 algorithm, generating 10<sup>7</sup> iterations, and sampling
 every 5,000 iterations. Convergence was assessed in Tracer version 1.7,
 using the effective sample size (ESS) to assure the posterior distribution
 is suitably represented. Although not all model runs completed the
 iterations within the 72-hour walltime, all model runs converged (ESS
 &gt; 200) providing representative values for preservation rates and
 species longevity of each species. Model selection for
 each microfossil group used a maximum-likelihood framework to allocate the
 best fitting preservation. The fit of each model was calculated in the
 Akaike Information Criterion (AIC), providing a statistical method of
 assessing the fit of qualitatively different preservation models. The
 sensitivity of the analyses to occurrence dating precision was
 investigated by running four additional PyRate analyses with decreasing
 occurrence ranges (±0.20, ±0.15, ±0.10, ±0.05 my) using default
 preservation model settings (NHPP). 
description: Neptune Sandbox Berlin (NSB) is an open source database of
 microfossil occurrence data including planktic formainifera, calcareous
 nannofossils, radiolarians, and diatoms.  Thousands of
 marine plankton microfossil species are catalogued from hundreds of
 deep-sea ocean drilling sections. The data includes age models for all
 sections and the geochronologic data used to create these age
 models. To access the database you will need to email
 Dr Johan Renaudie, MfN Berlin - johan.renaudie@mfn-berlin.de or Dr David
 Lazarus, MfN Berlin - david.lazarus@mfn-berlin.de to gain a username and
 password. See Renaudie et al. (2020) for more information about the
 creation, maintenance, and features of the database.
 PyRate is readily available to download from Daniele
 Silvestro's GitHub: https://github.com/dsilvestro/PyRate
 Using PyRate we implemented the reversible jump Markov Chain
 Monte Carlo algorithm, generating 10<sup>7</sup> iterations,
 and sampling every 5000 iterations. Convergence was
 assessed in Tracer v1.7 (Rambaut et al. 2018) using the effective sample
 size (ESS) to ensurethat the posterior distribution was suitably
 represented. Tracer is freely available from:
 http://tree.bio.ed.ac.uk/software/tracer/ All analyses
 were completed within Python and R which are both free to access and
 download. All files uploaded to this dataset use Python, R, Microsoft
 Word, Microsoft Excel, any image viewer compatible with .tiff files, and
 any .txt document viewer.