Session 3b, Biometrics

This session will be held in the Erskine Building, Room 445

13:10 — 13:30

Climate Reconstruction

Matthew R. Schofield
University of Otago

Richard J. Barker
University of Otago

The study of climatological data is inhibited by the availability of data. Inference about the climate over the past hundreds or thousands of years cannot be based on direct observations, which are only available for the past century or two. To obviate this problem proxies with many more observations, such as isotopes, tree rings and ice cores are used to predict the missing climate observations using calibration/inverse regression methods. In this talk we will investigate the assumptions and corresponding limitations of various calibration strategies and make suggestions about the use of such methods. If time permits, an example will also be given.

13:30 — 13:50

Who has mud on their hands? A bootstrapping technique for determining a fingerprint for sediment tracing in the Whangapoua Harbour

Judith L. McWhirter
University of Waikato

Brendan Roddy
University of Waikato

Removal of soil from the earth's surface by wind and water and subsequent delivery to streams and rivers is a natural process that operates over geological time scales. Human land use activities such as agriculture and silviculture hasten this process and can increase the erosion. The sediment is delivered to streams, where the suspended fraction is richly organic and also transports bound nutrients and chemical pollutants. These then impact plant, fish and invertebrate communities; the physical and chemical characteristics of the streams and estuaries; as well as the physical appearance of these water bodies. In the New Zealand context, estuaries are the most impacted of all coastal waters and have water quality issues relating from the surrounding land uses, but sediment fingerprinting has rarely been used to determine the source.

We discuss an innovative bootstrapping technique which allows for the fingerprinting of sediment samples to their source areas so that the relative importance of these sources can be determined. We report the results from a pilot study undertaken in 2006 where it was concluded that the technique of sediment fingerprinting could distinguish between source areas based on land use (native forest, exotic forest, agriculture) in the Waitakuri River catchment.

13:50 — 14:10

Case studies in association mapping.

Dr Roderick D. Ball
Ensis Wood Quality (NZ Forest Research Institute)

We discuss statistical analysis and experimental design for association mapping with reference to case studies from Chapters 7 and 8 of the book “Association Mapping in Plants”, Springer 2007.

Case studies include:

  • A case control test for an association between the HbS mutation and malaria.
  • Detectability of associations between the APOE locus and Alzheimer's disease from a whole genome scan of SNP.
  • Candidate gene-based associations in eucalyptus and maize.
  • Power of TDTQ1-QQ5 tests.

We re-analyse previous results using Bayesian methods. Equivalent Bayes factors are derived from published results and posterior probabilities for putative associations assessed. Bayes factors are derived for the common association tests: the chi-squared, Fisher's exact test, and the TDT and S-TDT tests for discrete and continuous traits. Various methods are used including direct integration, MCMC, and the Savage-Dickey density ratio.

A common theme is the inadequacy of p-values as a measure of evidence for testing scientific hypotheses as noted by Berger and Berry (1998). Higher sample sizes are needed to obtain respectable Bayes factors, and even higher sample sizes are needed to obtain sufficiently high Bayes factors to overcome low prior probabilities for genomic associations.


  • Berger, J.O. and Berry, D.A. (1988) "Statistical analysis and the illusion of objectivity," American Scientist 159-165.

Presentation Program