Harmonized data and R code for "Coherent response of zoo- and phytoplankton assemblages to global warming since the Last Glacial Maximum"

Harmonized data and R code for "Coherent response of zoo- and phytoplankton assemblages to global warming since the Last Glacial Maximum"
by Tonke Strack, Lukas Jonkers, Marina C. Rillo, Karl-Heinz Baumann, Helmut Hillebrand and Michal Kucera (submitted to Global Ecology and Biogeography, 2024).

STRUCTURED ABSTRACT
Aim: We use the fossil record of different marine plankton groups to determine how their biodiversity changed during past climate warming comparable to projected future warming.
Location: North Atlantic Ocean and adjacent seas. Time series cover a latitudinal range of 75°N to 6°S.
Time period: Past 24,000 years, i.e., from the Last Glacial Maximum (LGM) to the current warm period covering the last deglaciation.
Major taxa studied: Planktonic foraminifera, dinoflagellates and coccolithophores.
Methods: We analyse time series of fossil plankton communities using principal component analysis and generalised additive models to estimate the overall trend of temporal compositional change in each plankton group and identify periods of significant change. We further analyse local biodiversity change by analysing species richness, species gains and losses, and the effective number of species in each sample and compare alpha diversity to the LGM mean.
Results: All plankton groups show remarkably similar trends in the rates and spatio-temporal dynamics of local biodiversity change and a pronounced non-linearity with climate change in the current warm period. Assemblages of planktonic foraminifera and dinoflagellates started to significantly change with the onset of global warming around 15,500 to 17,000 years ago and continued to change at the same pace during the current warm period until at least 5,000 years ago, while coccolithophores assemblages changed at a constant rate throughout the past 24,000 years seemingly irrespective of the prevailing temperature change.
Main conclusions: The climate change during the transition from the LGM to the current warm period led to a long-lasting reshuffling of the zoo- and phytoplankton assemblages likely associated with the emergence of new ecological interactions and possibly a shift in the dominant drivers of plankton assemblage change from more abiotic-dominated causes during the last deglaciation to more biotic-dominated causes with the onset of the Holocene.

CONTENT
This dataset includes the harmonized assemblage data of the three investigated plankton groups (planktonic foraminifera, dinoflagellates and coccolithophores) as well as all the R code needed to re-produce the results of this study and it's main figures.

Scripts written by Tonke Strack

DATA SOURCES
1)  GMST: Osman, M. B. et al. Globally resolved surface temperatures since the Last Glacial Maximum. 
          Nature 599, 239-244, doi:10.1038/s41586-021-03984-4 (2021).
2) WOA18: Locarnini, R. A. et al. World Ocean Atlas 2018, Volume 1: Temperature. A. Mishonov, Technical Editor. 
          NOAA Atlas NESDIS 81, 52 (2019).
3) plankton assemblage data: individual data references provided in CoreList.csv

DATA
1. Harmonized assemblage data*: FullDataTable_PF_harmonized.txt
2. Core list of additional information on time series: CoreList.csv
3. Reference lists for species names names: ReferenceList_PlanktonicForaminifera.csv, ReferenceList_Dino.csv, ReferenceList_Cocco.csv

CODE
1. 01_LoadData.R: loads harmonized assemblage data from planktonic foraminifera, dinocyst and coccolithophores
2. 02_GMST_import.R: loads loads the globally resolved surface temperature since the LGM from Osman et al. (2011)
3. 03_DataAnalysis_PCA_GAM.R:  PCA/GAM analysis on the plankton assemblage data (results shown in Figure 2 and 3), sensititvity analysis (results shown in Figure 4), and some summary statistics
4. 04_DataAnalysis_MH_GAM_AlternativeApproach.R: alternative GAM approach using Morisita-Horn index (results shown in Figure S2, S3 and S4)
5. 05_DataAnalysis_BiodiversityChange.R: local biodiversity change analysis of individual time series  (results shown in Figure 5, 6 and S9)

*Assemblage data of individual time series were manually downloaded, quality checked, taxonomically harmonized, and combined into one data file.
Planktonic foraminifera data were harmonized following Siccha and Kuchera (2017). We merged Globigerinoides ruber ruber and Globigerinoides ruber 
albus, because some studies only reported them together as Globigerinoides ruber. Also, P/D intergrades (an informal category of morphological
intermediates between Neogloboquadrina incompta and Neogloboquadrina dutertrei) were merged with Neogloboquadrina incompta.
Dinocyst taxonomy was harmonized following de Vernal et al. (2020) with slight additions following Zonneveld et al. (2013). Names that could not be
resolved using synonym lists and assigned a harmonized name following de Vernal et al. (2020) and Zonneveld et al. (2013) were treated as unidentified
specimens and were excluded from the assemblage analyses. These specimens were present in 4 time series and were rare taxa (relative abundances < 3%).
The protoperidinoids were also excluded from further assemblage analyses as this category includes all unidentified brownish cysts (de Vernal et al., 2020).
Coccolithophore taxonomy follows Young et al. (2003) and coccolith countings were conducted on a scanning-electron microscope (SEM) to ensure that all
specimens are resolved to the species level. We merged Coccolithus pelagicus subspecies, because they were not distinguished in all studies. 
Species not reported in the time series data were assumed to be absent (that is, zero abundance) which is in accordance with the completeness of the counts
reported in the original studies. The original data were either given in absolute or relative abundances, and after excluding unnecessary columns
(unidentified or rare taxa that could not be harmonised) the abundances were recalculated to 100 %. In total, 41 species of planktonic foraminifera,
30 species of coccolithophores and 53 species of organic-walled dinocysts were observed in our study.

REFERENCES
de Vernal, A., Radi, T., Zaragosi, S., Van Nieuwenhove, N., Rochon, A., Allan, E., . . . Richerol, T. (2020). Distribution of common modern dinoflagellate cyst taxa in surface sediments of the Northern Hemisphere in relation to environmental parameters: The new n=1968 database. Mar. Micropaleontol., 159. doi:10.1016/j.marmicro.2019.101796
Siccha, M. & Kucera, M. ForCenS, a curated database of planktonic foraminifera census counts in marine surface sediment samples. Sci. Data 4, 170109, doi:10.1038/sdata.2017.109 (2017).
Young, J. R., Geisen, M., Cros, L., Kleijne, A., Sprengel, C., Probert, I., & Østergaard, J. B. (2003). A guide to extant coccolithophore taxonomy. Journal of Nannoplankton Research Special Issue, 1, 1-125. doi:10.58998/jnr2297
Zonneveld, K. A. F., Marret, F., Versteegh, G. J. M., Bogus, K., Bonnet, S., Bouimetarhan, I., . . . Young, M. (2013). Atlas of modern dinoflagellate cyst distribution based on 2405 data points. Rev. Palaeobot. Palynol., 191, 1-197. doi:10.1016/j.revpalbo.2012.08.003