Gene flow can reveal ghost lineages

Abstract Ghost species, encompassing extinct, unknown, and unsampled taxa, vastly outnumber those typically included in phylogenetic analyses. This hidden diversity has been shown to influence the study of horizontal gene flow (e.g. introgression and horizontal gene transfer) by complicating the phylogenetic signals commonly used for their detection. In this work, we explore the potential of horizontal gene transfer (HGT) detection methods based on phylogenies (i.e. reconciliation methods) to detect and quantify ghost diversity. We briefly outline the theoretical framework underpinning our approach. Then, using simple simulations and empirical data from Cyanobacteria, we show that HGT signals, as interpreted by reconciliation methods, can reveal the presence and phylogenetic position of ghost clades, despite the absence of genomic data for these taxa. We anticipate possible limitations and difficulties in using HGT detection to explore ghost diversity and suggest promising approaches to address or circumvent them. Altogether, this proof of concept opens new lines of research for the future: a scarce fossil record and a large proportion of unknown lineages, especially in Archaea and Bacteria, do not equate to an absence of information for evolutionary studies.