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Total evidence in phylogentic inference: a test of principle using the Crustacea

Reference	BB/C006682/1
Principal Investigator / Supervisor	Professor Matthew Wills
Co-Investigators / Co-Supervisors	Professor Richard Ffrench-Constant, Professor Laurence Hurst
Institution	University of Bath
Department	Biology and Biochemistry
Funding type	Research
Value (£)	259,740
Status	Completed
Type	Research Grant
Start date	09/05/2005
End date	08/09/2008
Duration	40 months

Abstract

The need for large, well supported phylogenies as the basis for rigorous comparative, biodiversity and evolutionary analyses has never been greater. There are principally two methods for improving the scope and or robustness of trees. Supertree methods combine trees rather than raw data, each tree the product of an independent parsimony or likelihood analysis. Total evidence, by contrast, derives a supermatrix that can comprise raw data from many molecules and morphology, and subjects this to a single tree-building analysis. The topologies resulting may differ from any of those derived from the investigation of subsets of the data, and branch support values are often significantly enhanced. Another compelling defence of total evidence centres on its purported ability to recover weak phylogenetic signals and improve resolution at multiple levels. Examples in the literature are usually of a limited scale, and often derive a stable topology when data from a small number of sources are combined. We will attempt a proof of principle here by applying total evidence to one of the most recalcitrant phylogenetic problems within the Metazoa: the relationships of crustaceans. In this group, the piecemeal addition of data from new molecules and from additional taxa has thus far only served to muddy the water. Rather than reinforcing support and converging on a single resolution, there is now uncertainty concerning the monophyly or paraphyly of the group, the integrity of most orders and nearly all inter-ordinal relationships. What is needed is markedly more diverse character and taxon sampling throughout the crustaceans and their closest relatives. We will greatly improve coverage down to the subordinal level for six established phylogenetic markers: 18S, 28S, 16S, COI, Elongation factor 1 alpha, RNA Polymerase II. We will also generate important new data for five hitherto underutilised phylogentic markers: G3PDH, PEPCK, Enolase, Elongation factor 2, alpha-Tubulin 1. We will collate and extend existing morphological data sets, and include data on important fossil genera. When complete, this will represent the largest and most diverse phylogenetic character set ever complied for the crustaceans. Partitions of the data will be analysed independently to compare their signals. All data will be analysed simultaneously using parsimony and likelihood approaches, and the robustness of the resulting trees will be assessed using bootstrapping and branch support indices. Results from total evidence analyses will be compared with supertrees.

Summary

unavailable

Committee	Closed Committee - Genes & Developmental Biology (GDB)
Research Topics	X – not assigned to a current Research Topic
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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