Journal of Paleolimnology

, Volume 39, Issue 4, pp 551–566 | Cite as

A Bayesian palaeoenvironmental transfer function model for acidified lakes

  • Philip B. Holden
  • Anson W. MackayEmail author
  • Gavin L. Simpson
Original Paper


A Bayesian approach to palaeoecological environmental reconstruction deriving from the unimodal responses generally exhibited by organisms to an environmental gradient is described. The approach uses Bayesian model selection to calculate a collection of probability-weighted, species-specific response curves (SRCs) for each taxon within a training set, with an explicit treatment for zero abundances. These SRCs are used to reconstruct the environmental variable from sub-fossilised assemblages. The approach enables a substantial increase in computational efficiency (several orders of magnitude) over existing Bayesian methodologies. The model is developed from the Surface Water Acidification Programme (SWAP) training set and is demonstrated to exhibit comparable predictive power to existing Weighted Averaging and Maximum Likelihood methodologies, though with improvements in bias; the additional explanatory power of the Bayesian approach lies in an explicit calculation of uncertainty for each individual reconstruction. The model is applied to reconstruct the Holocene acidification history of the Round Loch of Glenhead, including a reconstruction of recent recovery derived from sediment trap data.

The Bayesian reconstructions display similar trends to conventional (Weighted Averaging Partial Least Squares) reconstructions but provide a better reconstruction of extreme pH and are more sensitive to small changes in diatom assemblages. The validity of the posteriors as an apparently meaningful representation of assemblage-specific uncertainty and the high computational efficiency of the approach open up the possibility of highly constrained multiproxy reconstructions.


Environmental reconstruction Transfer functions Bayesian model selection Diatoms Acidification 



We are grateful to Devinder Sivia, John Birks and Richard Telford for useful discussions. We are additionally grateful for the constructive comments of both referees which have substantially improved the paper.


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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Philip B. Holden
    • 1
  • Anson W. Mackay
    • 1
    Email author
  • Gavin L. Simpson
    • 1
  1. 1.Environmental Change Research Centre, Department of GeographyUniversity College LondonLondonUK

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