Building large phylogenies: the amphibian tree of life

Amphibian tree of life

Amphibian tree of life 

A central aim for this PhD project is to build the most-comprehensive phylogeny of amphibians to date, and to have it applied generally to any phylogenetic group.

The studentship is part of the Great Western Four+ Doctoral Training Partnership, funded by NERC and starts September 2018.

Apply for this course

Read the eligibility criteria and application guidance below, then send your application to postgradoffice@nhm.ac.uk.

Application deadline: 7 January 2018

Research focus

The aim is to build the most-comprehensive, well-supported, dated phylogeny of amphibians to date.

The student will be required to address at least three important and interrelated methodological questions:

  • how best to integrate data from morphology and molecules - which is especially important because data of only one type are available for some taxa.
  • how best to ensure effective overlap of data in practice
  • which approach is best suited to building large-scale phylogenies

It is now possible to envisage having a system in which the current tree for a group of taxa is continuously updated through the integration of additional data, including data from previously unsampled taxa, as and when that data becomes available on-line. 

The ultimate aim of this project is to build such a system/pipeline, most probably incorporating analyses in a Bayesian framework, that can be applied more generally to the phylogenetics of any group.

Training 

The student will receive advanced training in phylogenetic analyses.

This will include

  • combined and separate analyses of morphological and molecular data
  • use of relaxed clocks and alternative strategies for incorporating fossil data to build timetrees
  • bioinformatics skills - interrogating data bases, handling and analysing big data, scripting and automation 
  • amphibian anatomy and palaeontology.

Training will include experimental design and simulations, as well as skills in presentation and scientific writing. 

Methodology

The project will first address how best to integrate data from morphology (both discrete and continuous) and from molecules. This is especially important because data of only one type are available for some taxa.

Large-scale datasets tend to have large blocks of non-randomly distributed missing data which can manifest in problems of ineffective overlap of constituent data partitions. It will be necessary to address how best to ensure effective overlap in practice.

The project will provide the opportunity for a substantial empirical evaluation of which of the available approaches (i.e. supertree and supermatix) is best suited for the task of building large-scale phylogenies.

Finally it is now possible to envisage a system in which the current tree for a group of taxa is continuously updated through the integration of additional data - including data from previously unsampled taxa - as and when that data becomes available online.

Background

Given their importance in evolutionary biology, large scale, comprehensive phylogenies are a prized resource. However, building accurate phylogenies efficiently is a major challenge. Data for building big trees is increasingly available but opinions are divided on how best the available data should be analysed.

Amphibians

Amphibians are an important group in terms of understanding vertebrate evolution and there is considerable concern over modern amphibian population declines.

The 2004, IUCN Global Amphibian Assessment found that a third of the 6,000 species are threatened, and there has been increased efforts to build the tree of life for this group, resulting in much new data and much greater sampling than hitherto.  As one of the major groups of vertebrates, and because there have been several attempts to build large-scale phylogenies of this group from which to learn and improve upon, amphibians provide an excellent focus for research in large-scale phylogenetic inference.

Eligibility

This project would suit a computer literate candidate with an interest in vertebrate evolution, especially of amphibians, and in the development of methods.

Studentships are open to UK and other EU students. Other nationalities (eg EEA countries) may be eligible - students should enquire with the project's respective postgraduate administration to see if they qualify for home fee rates. Up to nine studentships are available to EU students who do not ordinarily reside in the UK. Please note that this may be subject to change pending post-EU referendum discussions. All applicants need to comply with the registered university's English-language requirements.

Applicants should have obtained or be about to obtain a First or Upper Second Class UK Honours degree, or equivalent qualifications gained outside the UK. Applicants with a Lower Second Class degree will be considered if they also have a master's degree. Applicants with a minimum Upper Second Class degree and significant relevant non-academic experience are encouraged to apply.

How to apply

Applications for the PhD are processed through the Natural History Museum.

To apply please send the following documents to the Postgraduate Office at postgradoffice@nhm.ac.uk:

  • Curriculum vitae.
  • Covering letter outlining your interest in the PhD position, relevant skills training, experience and qualifications for the research, and a statement of how this PhD project fits your career development plans.
  • Two academic referees.

The deadline for applications is 7 January 2018.

Any questions?

If you have any questions about the project please contact

Main supervisor: Dr Mark Wilkinson

Supervisors

University of Bristol

Schools of Biological and Earth Sciences

Co-supervisor: Prof Davide Pisani

Co-supervisor: Prof Mike Benton

References

Baker WJ.  et al. Complete generic level phylogenetic analyses of palms (Arecaceae) with comparisons of supertree and supermatrix approaches. Syst. Biol. 58: 240-256 (2009).

Siu-Ting K. et al. Concatabominations: identifying unstable taxa in morphological phylogenetics using a heuristic extension to safe taxonomic reduction. Syst. Biol. 6: 137-143 (2015).

Pyron RA and Wiens JJ. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians." Molecular Phylogenetics and Evolution 61: 543-583 (2011).

Great Western Four+ Doctoral Training Partnership

Joint PhD training partnerships between the Natural History Museum and the Great Western Four, Bath, Bristol, Cardiff and Exeter universities.

Funded by 

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