Genomes are key to unlocking life's evolutionary history. The presence and absence of certain genetic sequences and mutations can give us clues to the order in which species diverge. However, even state-of-the-art methods struggle to accurately map evolutionary events from hundreds of millions of years ago. Published in Current Biology, a new method from scientists at the Okinawa Institute of Science and Technology (OIST) harnesses 'jumping genes' to recreate the termite tree of life, showcasing a new way for researchers to solve ancient evolutionary mysteries.
"Phylogenetic trees, which map the relationships between different organisms, are pivotal to the field of evolutionary biology. They help us to understand the origins of modern biodiversity and inform conservation strategies", says Professor Thomas Bourguignon, author on the study and head of the OIST Evolutionary Genomics Unit . "However, challenges arise when trying to predict evolution across deep history. Phylogenetic signals are often weak, and radiation events, where species rapidly diversify over a short period, add complexity, making it difficult to identify the order that individual species emerged. Our new method supports researchers to tackle these tricky scenarios".
What makes a gene 'jump'? Transposons explained
Certain DNA sequences, called 'transposable elements', or 'transposons', can move from one place to another, causing mutations and increasing genetic variability. Transposons are abundant in the genomes of eukaryotes—organisms having cells with nuclei encapsulating their genomes, including animals, plants and fungi. In fact, they form up to 50% of human genomes, and more in some other eukaryotes.
Despite their abundance, transposons have been somewhat overlooked in favor of other DNA marker sequences for tree of life construction. "Until recent advances in sequencing technologies and bioinformatics annotation tools, transposon characterization at genome level was difficult," explains first author Cong Liu, PhD student at OIST. "Phylogenetics has tended to focus on conserved genes, such as those encoding proteins critical for life, which are common across different species. These usually only change slowly over time, so are good for examining changes over evolutionary timescales."
This slow rate of change comes with a downside; it can become difficult to resolve rapid radiation events, as there may be very limited differences in these conserved genes between species. In such cases, transposons may provide helpful information on species divergence, given their active movement across the genome.
A new way to build phylogenetic trees
To prove the usefulness of transposons, the team first had to collect data, sequencing 45 termite and two cockroach genomes. They selected a diverse range of species to represent the different families and subfamilies of the insect lineage, studying each genome carefully to identify almost 38,000 transposon families across the different species.
By analyzing the presence and absence of transposons across the 47 species, the team built a tree of life, mapping when each species seemed to diverge from earlier ancestors. They then compared their tree to previously published termite trees of life. "We achieved similar accuracy to trees built from thousands of protein marker sequence alignments." notes Prof. Bourguignon.
Overcoming DNA degradation challenges
Although this study used relatively rich genomic information, the methods may hold for more limited data, opening new possibilities for research based on older specimens such as historical museum collections.
"It's often not possible to get 'nice' genomic data," says Mr. Liu. "DNA degrades naturally over time, and faster in hotter and more humid climates, as many biodiversity hotspots tend to be. This can be a problem even in short timescales, just going from collecting a specimen to sequencing. But it's particularly an issue when working with historical samples from old collections."
Methods which work with more fragmented data are important in enabling researchers to extract useful information, supporting both evolutionary studies and biodiversity mapping efforts. Since transposons are very short sequences, they could even be retrieved from fragmented DNA samples.
Termites and beyond
The team isn't done studying termites and is using their genomic data to bring about new insights into termite physiology, social structures and even dietary evolution. However, they hope this study will inspire researchers across wider fields to explore biodiversity and evolution throughout the animal kingdom.
"Our methods are complementary to existing phylogenetic techniques. We hope to inspire others to look towards transposons to unlock new evolutionary information and clarify longstanding mysteries within trees of life", says Prof. Bourguignon.
