Pruning the Tree of Life

Dr Tom WIlliams

Anyone who has studied biology has seen an image of the tree of life in the text books.  Most of us think of this as being set in stone, one of the rock solid foundations on which evolutionary biology is built.  However, all is not quite as settled as it seems.  Recently, a Nature article from the laboratory of ICaMB’s Professor Martin Embley challenges the traditional three domain structure of the root of life.  Here, first author on the paper, Dr Tom Williams, tells us the story.

By Dr Tom Williams

Our modern understanding of the tree of life began in 1977 when Carl Woese and his colleagues discovered the Archaea, a group of prokaryotes originally isolated from extremely hot or salty environments. Although Archaea looked indistinguishable from Bacteria under the microscope, their gene sequences were at least as different to those of Bacteria as from the eukaryotes – the group of organisms, including fungi, animals and plants, whose cells contain a mitochondrion and a nucleus. According to these analyses, living cells should be classified into three main groups: Bacteria, Archaea and eukaryotes – rather than the two (prokaryotes and eukaryotes) that had previously been established based on cell structure. In 1990, Woese and his colleagues published another seminal paper in which they argued for this “three domains” classification. This three-domains tree has become an iconic image in biology, and is often found in the popular science literature, as well as many textbooks – you’ve probably seen it before. Here it is from a 1997 review by Norman Pace:

The traditional 3 domain Tree of Life. From: A molecular view of diversity and the biosphere. Pace NR Science (1997) 276: 734-740


Professor Martin Embley

This was certainly the tree of life that I was familiar with, first as an undergrad and later as a Ph.D. student at Trinity College Dublin. So I was surprised and very intrigued when a certain Martin Embley came to talk at an Irish bioinformatics meeting, claiming that support for the three-domains tree was not as strong as you might expect. New work from his lab instead favoured the “eocyte tree”, in which the eukaryotes (or, at least, some of their genes) actually evolved from within the Archaea. If true, this tree would imply that there were originally only two types of cells – Bacteria and Archaea – and that the eukaryotes (i.e., us!) originated later in a partnership between the two primary domains.

The new model of the Tree of Life proposed by the Embley lab

Fast-forward a couple of years, and I was thinking about where I wanted to do my postdoc. I remembered Martin not only from that talk, but also from some interesting work (2nd link) he had done on a group of parasitic fungi called Microsporidia. I joined his group and began working on microsporidians, but I was still very interested in the tree of life and the origin of eukaryotes. In the meantime, DNA sequencing technology had been improving, and microbial ecologists were beginning to publish genomes from new groups of Archaea that could not be grown in the lab, and so had never been studied before. One of the really exciting findings from these studies was that some Archaea contained genes that looked very similar to fundamental components of our own cells, such as actin and tubulin – two proteins that help to define the microscopic “skeleton” of eukaryotic cells. When we added these new genomes to our analyses, we found even stronger support for the eocyte tree; those findings were reported last year in Proceedings B. At about the same time, a number of other researchers were reporting something similar: as our view of archaeal biodiversity increased, support for the three-domains tree was on the wane. Given the prominent position of the three-domains tree in the literature, and the importance of this question for understanding early life on Earth, we decided to write a review summarizing these recent developments in the field – it came out in Nature this week, and it’s the reason for this blog post!

As we delved back into the 30 years of literature on the molecular tree of life, one of the most interesting discoveries for me was a seam of eocyte literature that I hadn’t been aware of previously. Although many analyses over the past three decades have recovered the three-domains tree, and it appears in all the textbooks, the literature has actually never been unanimous in its support. Nonetheless, it is only in the last five years or so that support for the eocyte hypothesis has reached critical mass, perhaps due to improvements in our statistical methods and, more recently, sampling of archaeal biodiversity.

The Embley lab: Back row, left-to-right: Kacper Sendra, Martin Embley, Tom Williams, Robert Hirt. Front row: Shaojun Long, Ekaterina Kozhevnikova, Andrew Watson, Paul Dean, Maxine Geggie,Alina Goldberg-Cavalleri, Sirintra Nakjang.

Of course, our latest work is almost certainly not going to be the last word on the relationship between eukaryotes and other cells. Our methods are getting better – in part thanks to the statisticians we are collaborating with here in Newcastle – but there is much room for improvement, and so much about the microbial world that we still have to discover. Still, if the eocyte tree is correct – and it appears to be the best-supported tree on the current evidence – then that has important implications for how we understand early life on Earth and the origin of our own cells. For one thing, it rules out the eukaryotes as a primordial cellular lineage, as old as the Bacteria and Archaea. Instead, it suggests that the Bacteria and Archaea were established and diversifying on Earth before the origin of eukaryotes, resurrecting the concept of an “Age of Prokaryotes” on the early Earth. Of course, when you think about the phenomenal number of Bacteria and Archaea that live in your own body, never mind the wider environment, you might well argue that it never ended…

This work was supported by a Marie Curie postdoctoral fellowship to Tom Williams. Martin Embley acknowledges support from the European Research Council Advanced Investigator Programme and the Wellcome Trust.


The Nature Article:

The Proceedings B paper:

The Embley lab website:

Microsporidia papers:

Careers PAN!C

by PAN!C committee

PAN!C committee

Last Tuesday marked the biggest PAN!C event to date: the Careers PAN!C Postgraduate Symposium. Like many postgraduate research students, it’s likely you’ve been subjected to those pesky lab bench shackles, leaving you little time to give a second thought for what may lay beyond the dreaded viva! There are so many career paths that lay open to you, but it’s difficult to make a start with career planning when it seems like such a distant and sometimes scarily unattainable goal. Can you keep up with the endless pressure of lab confinement with the small chance of attaining an academic professorship (since only 0.45% of PhDs become professors)? After such specific research training is it all a massive waste to move to a different field or change careers? And how the heck can a family life fit in with career success?

After being awarded the Innovation Funding in June, which was an important milestone for PAN!C, the committee were able to organise a half day symposium to showcase the vast array of career options available to PhD students and make the haze of career planning a little clearer.

The symposium hosted 12 insightful career development talks with speakers giving their account of a career path in a range of professions including academia, industry, recruitment, teaching, journalism and patent law. There were also useful stalls from Bionow, SRG and the NHS as well as information from Covance and the Careers Service providing.

The common theme from the speakers was about having passion and enthusiasm for science and research, a notion we can all relate to in our PhDs. This motivation is sure to carry us in good stead to be able choose pretty much any science-related career out there. In short, we chose a good starting point!

Another useful point from the day is that it’s important for postgraduate students to identify and reflect upon their transferable skills and not only to recognise careers where they are likely to succeed but also to fully demonstrate their ability to a potential new employer. Honing this skill will facilitate the diversification to other fields by acknowledging the valuable skill set we gain over our postgraduate studies.

An important take home message from many of the speakers is that determination and drive are so important whatever career you choose. As Ed Yong mentioned, play the long game with your career, it takes much time and effort to build but ultimately it’s worth it. You’ll need to push yourself hard, especially early on, to aid your career progression and rise to a position of responsibility. Often those with successful careers attribute this in part to ‘being in the right place at the right time’ but it’s also about creating opportunities for yourself and being prepared for those make or break situations when they come around. Professor Judith Howard mentioned that it is important to find your inspiration, whether it be a figure or an experience that motivates you or even just a field you really enjoy. Be sure of what you want to do then get out there and just do it. Success doesn’t come easy, but it’s certainly within reach.

PAN!C would like to thank the Postgraduate Innovation Fund for financial backing of the symposium and future academic events, and ICaMB for continued support of PAN!Cs endeavours. Of course, the rapidly growing numbers of postgraduate students getting involved with our events also deserve a massive thank you. Over 60 attended the symposium and the day was a huge success, with 100% of feedback stating it was good or excellent! Such enthusiasm and input from students over the last year has really helped PAN!C become established and have an impact both within ICaMB and recently other institutes across FMS, so much so that we see this as only the beginning of the PAN!C community!

The day ended with refreshments and wine for all and a well-deserved stint in the pub for the committee!


If you are interested in joining the PAN!C committee and furthering your organisational and networking skills, please get in touch. We’re always keen for new members and new ideas, the more the merrier!