DOI: 10.5061/dryad.nd2mb
title: Data from: On the accuracy of paleodiversity reconstructions: a case study in Antarctic Neogene radiolarians

description: The deep-sea Cenozoic planktonic microfossil record has the unique
 characteristics of continuously well-preserved populations of most
 species, with virtually unlimited sample size, and therefore constitutes,
 in principle, a major resource for macroevolutionary research. Antarctic
 Neogene radiolarians in particular, are diverse, abundant and consistently
 well-preserved and evolved rapidly. This fauna is, in theory, a
 near-perfect testing ground for paleodiversity reconstructions. In this
 study we determined the diversity history of these faunas from a new
 quantitative, taxonomically complete data set from Neogene and Quaternary
 sections at several Antarctic sites. The pattern retrieved by our
 whole-fauna data set shows a significant, largely extinctionless
 ecological change in faunal composition and decrease in the evenness of
 species' abundances during the late Miocene, followed 3 Myr later, at
 around 5 Ma, by a significant drop in diversity. We tentatively associate
 this ecological event with a synchronous, regional change in the
 composition of the primary producers, but as yet cannot identify any
 environmental changes associated with the later extinction. Further, our
 whole-fauna diversity history was compared to diversity computed from much
 less complete, biostratigraphically oriented studies of species'
 occurrences, compiled in the Neptune database and reconstructed by using
 subsampling methodologies. Comparison of our whole-fauna and
 subsampling-reconstructed diversity patterns shows that the first-order
 trends are the same in both, suggesting that, to some degree, such
 literature compilations can be used to explore diversity history of
 plankton. However, our results also highlight substantial errors and
 distortions in the reconstructed diversity which make it poorly suited to
 more-detailed studies (e.g., for comparison of diversity history with
 paleoenvironmental history). We conclude that detailed studies of plankton
 diversity, and particularly those attempting to understand the relation
 between diversity and paleoceanographic change, should be based on
 taxonomically comprehensive, quantitative data.
description: Supplementary Table
 1Summary of collected
 samples. N is the number of specimens collected, S the number of species
 found, a and b the number of singletons and doubletons (respectively)
 amongst those species, ACE is Chao and Lee (1992)'s Abundance-based
 Coverage Estimator and u is Good (1953)'s coverage estimator. Depth
 are given in mbsf (meters below sea-floor) and age estimates are taken
 from the Neptune Database embedded age model (Lazarus et al. 1995), which
 is scaled on Berggren et al. 1995.Supplementary Table
 2Antarctic Neogene
 radiolarian data retrieved from the Neptune dataset on the 11th of
 January, 2011.Supplementary Figure
 3Whole-fauna dataset
 diversity vs untrimmed Neptune dataset subsampled diversity. A and B:
 Respectively, in-sample species richness and range-through diversity in
 our whole-fauna dataset. C: Diversity computed from the untrimmed Neptune
 dataset with five different type of subsampling: UW (black line), OW
 (dashed black line), CR (light grey line), O2W (dashed light grey line)
 and SQS (bold dark grey line). Magnetostratigraphy from Berggren et al.
 (1995).Supplementary Figure
 4Extinction and
 origination rates for our whole-fauna dataset (A and D, respectively), the
 UW (B and E) and the SQS (C and F) subsampled untrimmed Neptune
 dataset.Supplementary Figure
 5Shannon H' index
 for studied samples. A. In the first 2,000 specimens. B. In the total
 sample.Supplementary Figure
 6Effect of range-trimming
 on diversity. Black line is without any trimming, dark grey line with a
 light trimming (3% at the top, 1% at the bottom), grey line with a
 moderate trimming (5 and 3%) and light grey line with a very strong
 trimming (12 and 8%).Supplementary Figure
 7Comparison betweeen
 diversity trends using 0.5My bins and 1My bins (bold: with 1My bins, thin:
 with 0.5My bins). A. Range-through diversity in whole-fauna data. B.
 Range-through diversity in subsampled Neptune dataset (black: UW; grey:
 SQS). The quotas for 1My-bins subsampling are 20 collections for UW and
 0.70 for SQS.Supplementary Figure
 8Completeness metrics. A.
 Several species accumulation curves from samples of various ages. B.
 Species-accumulation curve on a typical sample (sample 120-751A-6H-6,
 98/102cm, Late Miocene). Bold black curve is the species accumulation
 curve; light grey curve and dashed light grey line are, respectively, the
 de Caprariis et al. (1976, 1981) curve-fitting and its
 asymptote.Supplementary Code
 9R
 script: Subsampling Neptune.Supplementary Appendix
 10Check of claimed errors
 in Neptune by Lloyd et al (2011).Supplementary Table
 11Checked
 errors.