1. Where did retroviruses come from: exogenous viruses or endogenous retroelements?

Retroviruses are best known as infectious viruses that spread between cells and individuals. However, vertebrate genomes also contain numerous retrovirus-like sequences known as endogenous retroviruses (ERVs). These sequences are usually interpreted as remnants of ancient infections in which retroviruses entered the germline and became permanently incorporated into the host genome, allowing them to be inherited by subsequent generations.

But could the evolutionary history of retroviruses be more complicated? What if some retroviral lineages have survived primarily as mobile genetic elements within host genomes, rather than through repeated cycles of infection between individuals?

Our preliminary comparative genomic analyses suggest that many vertebrate ERV lineages exhibit long-term evolutionary associations with their hosts, potentially spanning tens to hundreds of millions of years. These observations raise the possibility that some ERVs have persisted and diversified through mechanisms resembling those of other retrotransposons. If so, endogenous retroviruses may represent not merely the remnants of past infections, but an important and potentially continuing phase of retroviral evolution.

In this project, we aim to investigate the evolutionary origins and long-term persistence of vertebrate retroviruses. By systematically identifying retrovirus-like elements across a diverse range of vertebrate genomes, we will reconstruct their evolutionary relationships and compare them with the evolutionary histories of their hosts. We will also examine retroelement diversity, genomic copy numbers, integration patterns and the preservation of viral genes to explore whether particular lineages have expanded predominantly through vertical inheritance, amplification within genomes, or recurrent exogenous infection.

A complementary part of the project may focus on the koala retrovirus (KoRV), which offers a rare opportunity to study retroviral endogenisation on a contemporary evolutionary timescale. Subject to the availability of suitable samples and genomic data, we aim to characterise KoRV insertion sites across koala individuals and populations. By examining which insertions are shared, inherited or polymorphic, we will investigate how retroviral copies accumulate and spread within natural populations, and what these patterns reveal about the transition between infectious viruses and heritable retroelements.

Ultimately, this research seeks to address a fundamental question in evolutionary biology: did retroviruses diversify primarily as infectious agents that occasionally entered host genomes, or could long-term endogenous propagation have played a much greater role in their evolutionary history than previously recognised?

Techniques: Comparative genomics, genome sequencing, bioinformatics, identification and annotation of retroviral sequences, phylogenetic analysis, evolutionary reconstruction, and analysis of genomic insertion polymorphisms.