To investigate major evolutionary trends and the importance of fossil data we need to be confident that both phylogenetic trees and fossil dates are reliable. Indices of stratigraphic congruence provide a way to quantify the fit between the fossil record and phylogeny, but appear to be subject to a number of putative biases. I used both simulated data and a large sample of empirical trees to determine the effect of these biases on the most widely used indices of stratigraphic congruence to determine. The GER* (the modified gap excess ratio) was the least sensitive and therefore recommended for use. I found that stratigraphic congruence varied significantly across higher taxa (for example, arthropods were less stratigraphically congruent than tetrapods), and also throughout the Phanerozoic (the last 540 million years), closely following the taxonomic composition of my sample. I focussed on data quality and in particular taxon sampling, homoplasy and tree support to investigate general trends across taxonomic groups. A novel script was developed to automatically carry out continuous taxon jackknifing to investigate the effect of taxon sampling on the stability of phylogenetic trees. While this is a computationally intensive process, I found that measures of homoplasy and support (which are much easier to calculate) could serve as partial indicators of whether a tree was likely to be sensitive to taxon sampling. There was no major variation in taxon sampling trends across higher taxa. A modified version of this script was then used to look at particular cases of conflicting phylogenetic hypotheses to determine how easy it would be to get a data set to generate a constraint topology with only small changes to the taxon sample. In almost every case, it required maximal removal of taxa from the data set in order to match the constraint topology, indicating that there were very different phylogenetic signals in the different data sets. The extent of trends across taxonomic groups and through time is variable. Although stratigraphic congruence varies significantly between groups and throughout the Phanerozoic, measures of homoplasy and support do not appear to be taxon dependent. Taxon sampling is an important consideration when designing phylogenetic analyses: denser taxon sampling can have a positive influence on estimates of phylogenetic accuracy and perturbations of the taxon sample can result in radically different evolutionary relationships.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:636514 |
| Date | January 2014 |
| Creators | O'Connor, Anne |
| Contributors | Wills, Matthew |
| Publisher | University of Bath |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
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