PhD: Convergent genome evolution in the conquest of land by animals

The colonisation of land by life is one of the major evolutionary transitions in the history of the planet which dramatically shaped modern terrestrial ecosystems (Figure 1). Despite its key ecological and evolutionary importance, the genetic and cellular basis of terrestrialisation and its timing(s) are not well understood. This project brings together a team of expert zoologists, palaeontologists, genome biologists, and developmental biologists. Our main objective is to apply an integrative approach based on the “from genes to ecosystems” framework to understand the genetic and cellular basis, as well as the environmental factor underpinning the adaptation of animal life on land. We will use the latest genomic approaches and comparative methods to disentangle the multiple transitions from water to land in animals.

Project Aims and Methods

Following the “from genes to ecosystems” integrative philosophy and exploting available data (Figure 2), we will identify the genome-wide gene changes, their biological functions, and their mode of evolution (gene gains, losses, horizontal genetic transfer, etc) during terrestrialisation, and reconstruct a precise timescale of the transitions to land to identify the speed of these transitions as well as their ecoenvironmental contexts.

We will apply an evolutionary genomics pipeline developed in the host lab, published in Current Biology, Nature Communications, and Nature Ecology and Evolution, to infer the node of origin of a gene family. The biological function of genes of interest (e.g., gained during terrestrialisation) will be interrogated via Gene Ontology. For molecular dating, the gene family members will be aligned with MAFFT, ambiguous regions will be trimmed with BMGE, and trees will be inferred with Phylobayes. Molecular dating of the trees, using fossils and geological events to define soft minimum and maximum constraints, will be done with MCMCTree within PAML. Environmental conditions for the different dates will be mined from the literature. The student will contribute to the execution of these analyses and the overall design of the project, bringing in their own ideas and inform the research direction.

Candidate requirements

The candidate should have a deep interest in evolutionary biology, and an eagerness to learn computational methods and programming. Knowledge of molecular biology, invertebrate diversity, or palaeontology would be advantageous but is not required. We welcome and encourage student applications from under-represented groups. We value a diverse research environment.

Project partners

This project has an exciting partner in the Natural History Museum (NHM). The NHM is a research institution with international reputation that hosts over 350 scientists. Its researchers hold unique expertise in evolutionary biology, biodiversity and phylogenetics, supported by the Museum's core research labs and vast biological collections. An acclaimed research institution, the NHM publishes over 700 scientific papers a year with international collaborators. The collections hold 80 million objects that span 4.5 billion years, from the formation of the solar system to the present day. The student will work closely with Dr Greg Edgecombe FRS, who will provide opportunities to access collections and collaborate and network with other researchers in the NHM.

Training

You will be working at the forefront of an actively area of research and will be trained in phylogenetics, phylogenomics, comparative genomics, and animal evolution. You will learn how to generate, analyse, and interpret datasets using cutting edge sequencing methods and computational techniques. Finally, you will learn how to present challenging ideas to the scientific community and the public through the publication of articles in scientific journals and presenting your work at international conferences. All these are extremely valuable transferrable skills, and you will be fully equipped for a career in both the academia and the private sector.