PhD: Tests of Phylogenetic Accuracy using the Temporal and Biogeographical Distributions of Fossils

What is the best way to use fossil dates and biogeographical data to test the accuracy of evolutionary trees?

Phylogenetic (evolutionary) trees for living and fossil species are routinely inferred from both morphological and molecular sequence data. Different data sets and different inference methods often result in mutually incompatible trees and sometimes radically different hypotheses of relationships. Historically, maximum parsimony has been the method of choice for morphological data, but systematists are increasingly analysing their characters using likelihood and Bayesian frameworks. Choosing between these hypotheses requires some independent source of data on the evolutionary history of the constituent species. First fossil occurrence data is one such resource and the palaeobiogeographical distribution of species is another. Neither temporal nor spatial data are routinely Incorporated into the process of tree building.

There are a number of indices that quantify the congruence between the branching order of a cladogram and the sequence of first fossil occurrences. Unfortunately, all are subject to various biases relating to the size and balance (pectinate versus symmetrical) of the tree and distribution of first fossil occurrence dates. Indices have been refined (O’Connor et al., 2011; O’Connor & Wills, 2016), but all operate within a parsimony framework. In the same way that likelihood and Bayesian approaches are being applied to the inference of phylogeny from morphological and molecular data, This project will explore Bayesian and other methods for measuring stratigraphic congruence.

The biogeographical distributions of species were instrumental in the formulation of ideas on natural selection for both Charles Darwin and Alfred Russell Wallace. Nonetheless, spatial distribution patterns are rarely used to inform inferences of phylogeny: Hence they can be used as an independent test. Both phylogenetic hypotheses and patterns of spatial relationships can be analysed as networks, and the project will further explore ways in which their consilience might constitute a test of phylogenetic accuracy.

This project is most suitable for a student with a background in mathematics or mathematical biology. Some knowledge of scripting would be beneficial.

Applicants should hold, or expect to receive, a First Class or good Upper Second Class Honours degree, or the equivalent from an overseas university. A master’s level qualification would also be advantageous.

Informal enquiries should be directed to Prof Matthew Wills (m.a.wills@bath.ac.uk).

Formal applications should be made via the University of Bath’s online application form for a PhD in Biology:
https://www.bath.ac.uk/samis/urd/sits.urd/run/siw_ipp_lgn.login?process=...

More information about applying for a PhD at Bath may be found here:
http://www.bath.ac.uk/guides/how-to-apply-for-doctoral-study/

Anticipated start date: 1 October 2018

O’Connor A, Wills MA. 2016. Measuring stratigraphic congruence across trees, higher taxa and time. Systematic Biology, DOI: 10.1093/sysbio/syw039

O'Connor A, Moncrieff C, Wills, MA. 2011. Variation in stratigraphic congruence (GER) through the Phanerozoic and across higher taxa is partially determined by sources of bias. Geological Society Special Publication 358, 31-52.