Image credit: Luke Lythgoe, Wellcome Sanger Institute
From sex-changing fish to asexual lizards, these and many more species will be captured in a new sex database made possible by the Wellcome Sanger Institute’s powerful genomic resources.
Thirteen years ago, a group of scientists came together to talk about sex. They were interested in how different species across the tree of life pass DNA onto the next generation. They dubbed their project the Tree of Sex.
The work culminated in a database capturing the reproductive strategies of over 22,000 species. A community formed, ideas were exchanged, and several highly influential papers were published, including one entitled ‘Sex Determination: Why So Many Ways of Doing It?’ in 2014.
In the years since, scientists continued their research - somewhere between 200 and 300 papers have been published every year on sex chromosomes alone. At the same time, genomic technology leapt forward. Many believed the time was now ripe for a Tree of Sex v2.0.
Since the last Tree of Sex, a genomic revolution has occurred. DNA sequencing technologies have become more sophisticated, their yields have increased, and costs have come down. Along with several other biodiversity genomics consortia, the Sanger Institute’s Tree of Life Programme has begun producing top-quality reference genomes for all kinds of species, something that new long-read DNA sequencing technology has only made possible in the last few years.
“When we integrate all these new data, we can ask new questions that we couldn’t ask with the previous data that were available,” explains Sanger Group Leader, Dr Kamil Jaron, who sits on the new Tree of Sex organisational committee. “We need to compile all of this information in one place so that it is accessible, scalable and sustainable. This is where Sanger and the Tree of Life Programme come in, because there aren’t that many places in the world that can do this so comprehensively.”
Over one hundred scientists researching diversity of reproduction attended the Tree of Sex v2.0 ‘kick-off’ at the Sanger Institute. Much of this meeting focused on outlining a new Tree of Sex database for a new genomic age, attempting to capture the dizzying variety of ways in which sex is determined throughout the natural world.
Tree of Sex 2.0 group photo
Tree of Sex 2.0 Conference members. Photo by Luke Lythgoe, Wellcome Sanger Institute
Tree of Life, Tree of Sex
Much of the required infrastructure for Tree of Sex v2.0 is already being built and tested, thanks to global genomics initiatives under the Earth BioGenome Project. The aim of this international network is to produce whole reference genomes for all 1.8 million named species of animal, plant, fungi and protist on the planet, a feat which requires huge data processing and storage capacity. The Sanger Institute is at the forefront of this effort, with the Tree of Life Programme nearing a milestone of 1,000 genomes completed.
Some of the tools developed by the Tree of Life will provide a useful basis for the Tree of Sex. In particular the database Genomes on a Tree (GoaT), which essentially acts like a huge search engine for the latest genomic information being produced across the world. The GoaT model is interesting for its ability to handle huge amounts of genomic data which can then be queried by users. GoaT will also index the data from the new database connecting together sequenced genomes and the reproductive features of the species.
“Longevity, inclusivity and adaptability are what we are interested in now,” says Dr Cibele Sotero-Caio, GoaT’s Curator based at Sanger. “The vision that we have for the Tree of Sex is not only to create a database, but also a knowledge base. We want access to information that is not specifically entered, but that can be inferred by looking at the relationships in the data. And we want to create something that will last as long as people are interested in pursuing these questions.”
This vision was forming in several minds simultaneously. It was the summer of 2021 when Dan Jeffries first discussed the idea of rebooting the Tree of Sex with Tatiana Giraud and Paul Jay, after a small conference in Paris. The idea quickly gained momentum and there was clearly ample support from the research community. Fast forward to the summer of ’22, where Dan presented a poster advertising the new initiative at the Congress of the European Society for Evolutionary Biology in Prague. It was here that he bumped into Kamil, who, having recently started his post at the Sanger Institute's Tree of Life programme, had also already been planning to restart the Tree of Sex. At the very same event, Cibele was presenting a poster on GoaT and revealed that original Tree of Sex data were already being incorporated into that project. It was clear that the Sanger institute was the best home for the new Tree of Sex database, and so, Dan, Paul, Tatiana, Kamil and Cibele joined forces. Several weeks later Lukáš Kratochvíl, and Sònia Garcia were added to the committee, to round out its expertise across the vast field of reproductive evolution
Tree of Sex Organisational Committee
Sònia Garcia
Institut Botanic de Barcelona
Spain
Tatiana Giraud
Université Paris-Saclay
France
Kamil Jaron
Wellcome Sanger Institute
UK
Paul Jay
University of California, Berkeley
USA
Dan Jeffries
University of Bern
Switzerland
Lukáš Kratochvíl
Charles University
Czech Republic
Cibele Sotero-Caio
Tree of Life, Wellcome Sanger Institute
UK
Reproducing the Tree of Sex
For all its innovation, the new Tree of Sex is undoubtedly the direct descendant of the original. Much of the earlier project’s DNA has been inherited, including many of the scientists involved between 2010 and 2014.
The main idea behind the project is also similar: to compile as much data as possible to help paint the bigger picture. How does reproductive diversity look not just within small groups, but across all life?
Many of the same questions will be asked, but with the answers now enhanced by cutting-edge genomic technology. Why are separate sexes common in some groups of organisms but not others? How do different sex determination mechanisms evolve, are there common genetic or ecological factors? How stable are different strategies over time, are they under the same evolutionary pressures? And, ultimately, why are there so many ways of doing it?
The original Tree of Sex was a great success. These pioneering researchers brought together a global community of like-minded researchers, compiled a sizeable and diverse database of the reproductive information that existed at that time, and facilitated a big step forward in the thinking in the field.
The lessons learned from this project are now being shared, from the Tree of Sex veterans of v1.0, to their colleagues in the new v2.0 consortium - the official membership of which currently stands at 85 researchers from 72 institutions in 16 different countries. Importantly, with the stable funding and infrastructure at the Sanger Institute, this new version will not represent just a snapshot of our knowledge but will be a resource that will be maintained, updated, and adapted as the field progresses into the future.
As Kamil puts it: “Even now, current knowledge gives us just a glimpse of the reproductive diversity in nature. The knowledge will evolve, the amount of data will increase. We need to think ahead of time. We need to future-proof our records today if they are going to also work tomorrow.”
