Methods > Removing sampling signal from diversity curves
Removing sampling signal from diversity curves
To remove sampling from a diversity curve.
Time series of both diversity (taxonomic richness) and a sampling proxy (e.g. formations, map area) as well as dates for each time bin.
Although reconstructing estimates of past diversity is a central goal of palaeobiology raw data can be misleading due to sampling and other biases. Raup (1972) made an early tabulation of such biases and set out two major ways in which they might be corrected. The first was subsampling, which has been explored thoroughly by John Alroy (Alroy et al. 2001, 2008; Alroy 2010a,b,c). The second was modelling, which has received comparatively little attention. A key paper, then, was that of Smith and McGowan (2007) who introduced a new modelling technique that assumes true diversity is constant such that observed diversity is driven purely by sampling. When this modelled estimate is subtracted from actual observed diversity then the residuals can be thought to represent a sampling-free diversity curve. Barrett et al. (2009) added a rudimentary significance test to the Smith and McGowan (2007) approach by treating the standard deviation of the residuals as a kind of confidence interval. However, this is flawed as it does not take into account how well or poorly the model fits. Most recently, Lloyd (2012) overhauled the Smith and McGowan method, by allowing non-linear relationships between the sampling proxy and diversity, implememting a more informative significance test and introducing a hinged-regression line to the resulting time series to elucidate medium-term diversity trends. This refined method has been applied to dinosaurs Lloyd (2012) and coccolithophores (Lloyd et al. 2011). Here a function that automates the Lloyd (2012) approach has been produced for use in the freely available statistical progamming language R.
1. Install and run R (it's free!).
Alroy, J. 2010a. The shifting balance of diversity among major marine animal groups. Science, 329, 1191-1194.
Alroy, J. 2010b. Fair sampling of taxonomic richness and unbiased estimation of origination and extinction rates. In: Alroy J, Hunt G (eds.) Quantitative Methods in Paleobiology. The Paleontological Society; New Haven, USA. 55-80.
Alroy, J. 2010c. Geographical, environmental and intrinsic biotic controls on Phanerozoic marine diversification. Palaeontology, 53, 1211-1235.
Alroy, J., Marshall, C. R., Bambach, R. K., Bezusko, K., Foote, M., Fursich, F. T., Hansen, T. A., Holland, S. M., Ivany, L. C., Jablonski, D., Jacobs, D. K., Jones, D. C., Kosnik, M. A., Lidgard, S., Low, S., Miller, A. I., Novack-Gottshall, P. M., Olszewski, T. D., Patzowsky, M. E., Raup, D. M., Roy, K., Sepkoski, J. J., Sommers, M. G., Wagner, P. J. and Webber, A. 2001. Effects of sampling standardization on estimates of Phanerozoic marine diversification. Proceedings of the National Academy of Sciences of the United States of America, 98, 6261-6266.
Alroy, J., Aberhan, M., Bottjer, D. J., Foote, M., Fursich, F. T., Harries, P. J., Hendy, A. J. W., Holland, S. M., Ivany, L. C., Kiessling, W., Kosnik, M. A., Marshall, C. R., McGowan, A. J., Miller, A. I., Olszewski, T. D., Patzowsky, M. E., Peters, S. E., Villier, L., Wagner, P. J., Bonuso, N., Borkow, P. S., Brenneis, B., Clapham, M. E., Fall, L. M., Ferguson, C. A., Hanson, V. L., Krug, A. Z., Layou, K. M., Leckey, E. H., Nurnberg, S., Powers, C. M., Sessa, J. A., Simpson, C., Tomasovych, A. and Visaggi, C. C. 2008. Phanerozoic trends in the global diversity of marine invertebrates. Science, 321, 97-100.
Barrett, P. M., McGowan, A. J. and Page, V. 2009. Dinosaur diversity and the rock record. Proceedings of the Royal Society, London B, 276, 2667-2674.
Lloyd, G. T. 2012. A refined modelling approach to assess the influence of sampling on palaeobiodiversity curves: new support for declining Cretaceous dinosaur richness. Biology Letters, 8, 123-126.
Lloyd, G. T., Smith, A. B. and Young, J. R. 2011. Quantifying the deep sea rock and fossil record bias using coccolithophores. In: Comparing the Rock and Fossil Records: Implications for Biodiversity, McGowan, A. J. and Smith, A. B. (eds.). Geological Society Special Publication 358, 167-177.
Raup, D. M. 1972. Taxonomic diversity during the Phanerozoic. Science, 177, 1065-1071.
Smith, A. B. and McGowan, A. J. 2007. The shape of the Phanerozoic diversity curve. How much can be predicted from the sedimentary rock record of Western Europe? Palaeontology, 50, 765-777.
|Last updated 7th November 2008.|