The Evolution of Metabolisms that Shaped Life on Earth

The Evolution of Metabolisms that Shaped Life on Earth


Dr. Patricia Sánchez-Baracaldo (Geographical Sciences, University of Bristol) – Main contact Email:; Tel: +44 (0) 117 954 6858 Prof. John Huelsenbeck (Dept. of Integrative Biology, University of California, Berkeley)

The bacterial metabolisms of photosynthesis and nitrogen fixation have shaped life on our planet by contributing to the cycling of carbon and nitrogen in the Earth’s biosphere. While photosynthesis fixes carbon dioxide using different electron donors into carbohydrates, nitrogen fixation transforms atmospheric nitrogen into a bioavailable source such as ammonium. Geochemical and biological evidence suggests that photosynthesis (1-3) and nitrogen fixation (4,5) evolved shortly after life originated on our planet. Understanding how these metabolisms evolved through the bacterial domain will give insights into how these processes have shaped biogeochemical cycles. How can we study the evolution of
photosynthesis and nitrogen fixation given that they evolved billions of years ago? The evolution of these processes must be studied indirectly, through the phylogenetic comparison of a wide diversity of bacterial
lineages. Such an analysis can help elucidate the details of how these processes evolved and when they evolved. Lateral gene transfer — the transmission of genes between different bacterial lineages — has been used to explain the current distribution of these metabolisms on the bacterial tree of life. Alternative explanations might also be possible, such as the differential loss of genes involved in these metabolisms as
bacterial lineages diversified.

Using the bacterial tree of life, this project aims to study how and when these fundamental metabolisms evolve. We will use large genomic data sets to study: (1) the evolution of the bacterial linages and
(2) the evolutionary patterns for photosynthesis and nitrogen fixation (both vertical and horizontal) across bacterial groups. The Ph.D. student funded by this grant will also have the unique opportunity to not only collect the appropriate data but also to develop new phylogenetic methods.

This student would be co-advised by Dr. Patricia Sánchez-Baracaldo (University of Bristol) who is an expert in the biological/geological data and Prof. John Huelsenbeck (University of California, Berkeley)
who is an expert in the development of phylogenetic methods. This is a great opportunity for students interested in evolutionary biology, phylogenetic methods, bioinformatics, and the origin of life.

This is a four-year project funded by the University of Bristol (the host institution) with a stipend of £14,296 + fees for UK and EU students.

How to apply: Please make an online application for this project at Please select ‘Geographical Sciences: Physical (PhD)’ on the Programme Choice page and enter the title of the studentship project ‘The Evolution of Metabolisms that Shaped Life on Earth’ when prompted in the Funding and Research Details sections of the form.

Applications deadline:: 17 February 2017. Interviews are expected to be held in early March 2017

Candidate requirements: At least a 2.1 (Hons) degree or equivalent in a relevant quantitative subject, e.g. microbiology, bioinformatics, population genomics, environmental biotechnology, marine biology, plant
molecular biology, genetics, genomics, and computer science. For EU students, English Language IELTS scores of at least 6.5 (no less than 6.0 in any element). A Masters degree in a relevant subject would be
desirable but not essential. Computer programming skills in a relevant language, e.g. C/C++, Python, R or Matlab would be an advantage. The award is available for UK or EU students only.


1. Bell, E. A., Boehnke, P., Harrison,  T. M. & Mao, W. L. Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon. P Natl Acad Sci USA 112, 14518-14521, (2015).

2. Tice, M. M. & Lowe, D. R. Photosynthetic microbial mats in the 3,416-Myr- old ocean. Nature 431, 549-552, (2004).

3. Blankenship, R. E. Early evolution of photosynthesis. Plant Physiol 154, 434-438, (2010).
4. Thomazo, C., Ader, M. & Philippot, P. Extreme 15N-enrichments in 2.72-Gyr- old sediments: evidence for a turning point in the nitrogen cycle.Geobiology 9, 107-120, (2011).
5. Weiss, M. C. et al. The physiology and habitat of the last universal common ancestor. Nat Microbiol 1, 16116, (2016).

John Huelsenbeck
University of California, Berkeley
Department of Integrative Biology
3060 VLSB # 3140
Berkeley, CA 94720-3140

Phone: (510) 502-5887

John Huelsenbeck <>

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