Most species, extinct or extant, are unknown. And even known species are typically absent from evolutionary analyses. These "ghost lineages" can strongly bias the study of horizontal processes such as endosymbiosis, horizontal gene transfer, or introgression, since these lineages may act as donors or recipients of gene flow. Yet, their impact has been largely overlooked. We quantified how ghost lineages affect common gene flow detection methods. We show that, when unsampled taxa vastly outnumber sampled ones - which is more than likely -, both donors and recipients of gene flow are often misidentified, potentially leading to incorrect or reversed conclusions.

On a more optimistic note, I will highlight recent findings showing that ghost lineages do not simply mislead gene flow detection methods; they may also leave detectable signatures in phylogenetic trees, allowing us to predict, along the branches of a species tree, the abundance of these unseen (ghost) lineages. This offers a unique opportunity to explore extinct species that do not fossilize.