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Pollen data from four European sequences the Neotoma database (Goring et al., 2015)

Source: R/example_data.R
example_data.Rd

Taxa were standardised to the taxonomically highest pollen morphotype (Level = MHVar2) using the pollen harmonisation table in Giesecke et al. (2019). Age-depth models were developed using the pre-selected radiometric control points provided in Giesecke et al. (2014) and calibrated the radiocarbon dates using the IntCal13 Northern Hemisphere calibration curve (Reimer et al., 2013). For each sequence, an age-depth model was constructed using the Bchron R package (Haslett & Parnell, 2008) to generate 1000 possible age predictions (i.e. age uncertainties) for all levels. We calculated the median of all the uncertainties for each level to give the most probable age (default age) in calibrated years before present (cal yr BP, where 0 = 1950 CE). In each sequence, we excluded all levels that contained less than 150 pollen grain counts of the terrestrial taxa, and all levels beyond a 3000-years extrapolation of the oldest chronological control point. In addition, we excluded all levels with an age older than 8500 cal yr BP to focus on the period of most substantial human impact.

Usage

example_data

Format

A data.frame with columns:

  • dataset.id - Neotoma unique number for each sequence

  • collection.handle - Neotoma sequence name aberration

  • lat - Latitude (degrees)

  • long - Longitude (degrees)

  • pollen_data - Data.frame contain pollen counts of taxa in each level.

  • sample_age - Data.frame including estimated ages for each level

  • age_uncertainty - Matrix with age uncertainties from age-depth model

Source

https://www.neotomadb.org/

Details

We obtained pollen data from the Neotoma database (Williams, Grimm, et al., 2018) using the Neotoma R package (Goring et al., 2015). We chose four European sequences (A - D). I each sequence, taxa were standardised to the taxonomically highest pollen morphotype (Level = MHVar2) using the pollen harmonisation table in Giesecke et al. (2019). To develop age-depth models, we used the pre-selected radiometric control points provided in Giesecke et al. (2014) and calibrated the radiocarbon dates using the IntCal13 Northern Hemisphere calibration curve (Reimer et al., 2013). For each sequence, we constructed an age-depth model using the Bchron R package (Haslett and Parnell, 2008) to generate 1000 possible age estimates for all sample depths at the original sampling resolution of the original pollen sequences. We used these 1000 draws to build posterior estimates of age uncertainty. We calculated the median age estimate for each sample depth to obtain the default age used in following analyses. In each sequence, we excluded all levels that contained less than 150 pollen counts of terrestrial taxa, and all levels beyond a 3000-years extrapolation of the oldest chronological control point. In addition, we excluded all levels with an age older than 8500 cal yr BP to ensure focus on the period with substantial human impact.

References

Giesecke, T., Davis, B., Brewer, S., Finsinger, W., Wolters, S., Blaauw, M., de Beaulieu, J.L., Binney, H., Fyfe, R.M., Gaillard, M.J., Gil-Romera, G., van der Knaap, W.O., Kunes, P., Kuhl, N., van Leeuwen, J.F.N., Leydet, M., Lotter, A.F., Ortu, E., Semmler, M., Bradshaw, R.H.W., 2013. Towards mapping the late Quaternary vegetation change of Europe. Veg. Hist. Archaeobot. 23, 75-86.

Giesecke, T., Wolters, S., van Leeuwen, J.F.N., van der Knaap, P.W.O., Leydet, M., Brewer, S., 2019. Postglacial change of the floristic diversity gradient in Europe. Nat. Commun. 10.

Goring, S., Dawson, A., Simpson, G.L., Ram, K., Graham, R.W., Grimm, E.C., Williams, J.W., 2015. Neotoma: A programmatic interface to the Neotoma paleoecological database. Open Quat. 1, 1-17.

Haslett, J., Parnell, A., 2008. A simple monotone process with application to radiocarbon-dated depth chronologies. J. R. Stat. Soc. Ser. C Appl. Stat. 57, 399-418.

Reimer, P.J., Bard, E., Bayliss, A., Beck, J.W., Blackwell, P.G., Ramsey, C.B., Buck, C.E., Cheng, H., Edwards, R.L., Friedrich, M., Grootes, P.M., Guilderson, T.P., Haflidason, H., Hajdas, I., Hatte, C., Heaton, T.J., Hoffmann, D.L., Hogg, A.G., Hughen, K.A.,

Kaiser, K.F., Kromer, B., Manning, S.W., Niu, M., Reimer, R.W., Richards, D.A., Scott, E.M., Southon, J.R., Staff, R.A., Turney, C.S.M., van der Plicht, J., 2013. IntCal13 and Marine13 Radiocarbon Age Calibration Curves 0-50,000 years cal BP. Radiocarbon 55, 1869-1887.

Examples

if (FALSE) {
data(example_data)
}