PhD: Molecules and Mass Extinction: Using Molecular Clocks to Understand Recovery from Mass Extinction

Introduction

Darwin thought that evolution proceeded by the gradual action of everyday processes, over vast spans of time. But can rare, extreme events- catastrophes- play a role? Palaeontology suggests that biodiversity has been shaped by mass extinctions- rapid, global, and severe losses of diversity, wiping out >50% of the species on Earth. Fossils document five major extinctions, and many lesser events(1). The most recent of the ‘Big Five’ is the Cretaceous-Paleogene (K-Pg) extinction, which eliminated the dinosaurs and 80-90% of all species on Earth(2). The Eocene-Oligocene (E-O) climactic event, the most severe global cooling event of the Cenozoic, was less severe but nevertheless drove turnover on land and in the seas.
Fossils are rare, however, particularly for small or soft-bodied animals. It is therefore unclear how mass extinctions affected many organisms. But extinctions leave other traces, written into the survivors’ DNA. After each extinction, diversity rebounded as the survivors evolved to occupy vacant niches. These recoveries can be reconstructed with molecular clocks.
After speciation, the genes of the two daughter species evolve. If we know how fast mutations accumulate, we can use the degree of divergence to estimate how long ago speciation occurred: DNA acts as a molecular clock. Mass extinctions should be followed by bursts of speciation, with multiple speciation events occurring in rapid succession(3,4,5) In principle, the molecular clock is simple, but until recently, molecular models disagreed with patterns observed in the fossils. Now, recent advances, including Bayesian relaxed-clock models, more rigorous fossil calibration approaches, new calibration strategies, and the widespread availability of genomic data have made molecular clocks far more accurate, and they are finally a practical tool to study mass extinction(3,4,5).

Aims and Methods
The project aim is to use molecular clocks to study mass extinction, focusing on clades with limited fossil records such as lizards, fish, insects, and crustaceans. The student will focus on major questions including:

1. To what extent is modern biodiversity the result of post-extinction radiation?
Are mammals and birds unusual in showing post-extinction radiations, or is this pattern ubiquitous in nature? The student will produce gene alignments, reconstruct phylogenies, and employ Bayesian relaxed-clock models (PhyloBayes) to test for the existence of post-extinction radiation in a diverse range of organisms.

2. How did survivors radiate to occupy new niches?
Ancestral state reconstruction, using likelihood-based approaches and other models, will be used to infer the evolution of ecological traits including body size, diet, habitat, and breeding biology. This will enable the student to explore whether organisms rapidly radiated into new niches, or whether niche occupation increased over tens of millions of years, suggesting a prolonged ecological recovery.

3. How does mass extinction affect biogeography?
Biogeographic analytic tools such as BioGeoBEARS will be used to test evolutionary scenarios of dispersal and biogeography. The candidate will examine hypotheses such as the idea that the biogeography of groups such as lizards was driven by Cenozoic dispersal(3), not Mesozoic continental drift.
Candidate
The project is part of a 5-year, Leverhulme-funded research project to study mass extinction and recovery. To build our team, we seek students who are hardworking, curious, creative, and collaborative. Applicants should have a strong research background; publications and a master’s degree are desirable. Palaeontological experience is not necessary but students should have a background in quantitative science, e.g. statistics, scripting, R, and ideally phylogenetics. This PhD is fully funded for 4 years. We also assist students seeking external funding. Please contact Nick Longrich (nrl22@bath.ac.uk) with any questions.

Training
Your project is designed to result in published papers in major journals and prepare you to pursue a research career. The student will be trained in sequence alignment, molecular phylogenetic analysis, molecular divergence dating, and biogeographic tools. We will develop your oral and written work and help you turn your science into academic publications. You will also become part of the University of Bath’s Palaeontology Group which is young but rapidly growing. We currently have three faculty members, Dr. Nicholas Longrich, Professor Matt Wills and Dr. Daniel Field, the palaeontology group is in turn a central part of Bath’s new Milner Centre for Evolution, a unique research centre focused on fundamental research on major problems in evolutionary biology and training the next generation of evolutionary biologists.

1. Sepkoski Jr., J.J., Bambach, R.K., Raup, D.M., Valentine, J.M., 1981. Phanerozoic marine diversity and the fossil record. Nature 293, 435-537.
2. Longrich, N.R., Scriberas, J., Wills, M.A., 2016. Severe extinction and rapid recovery of mammals across the Cretaceous‐Paleogene boundary, and the effects of rarity on patterns of extinction and recovery. Journal of evolutionary biology DOI: 10.1111/jeb.12882.
3. Longrich, N.R., Vinther, J., Pyron, A., Pisani, D., Gauthier, J.A., 2015. Biogeography of worm lizards (Amphisbaenia) driven by end-Cretaceous mass extinction. Proceedings of the Royal Society of London B: Biological Sciences 202, 20143034.
4. Prum RO, et al. (2015) A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature.
5. dos Reis M, et al. (2012) Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proceedings of the Royal Society B 279:3491-3500.