RT Journal Article SR Electronic T1 Ghost lineages highly influence the interpretation of introgression tests JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.03.30.437672 DO 10.1101/2021.03.30.437672 A1 Théo Tricou A1 Eric Tannier A1 Damien M. de Vienne YR 2021 UL http://biorxiv.org/content/early/2021/10/21/2021.03.30.437672.abstract AB Most species are extinct; those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, introgression and admixture, are therefore likely to involve “ghosts”, i.e. extinct, unknown or unsampled lineages. The existence of these ghost lineages is widely acknowledged, but their possible impact on the detection of gene flow and on the identification of the species involved is largely overlooked. It is generally considered as a possible source of error that, with reasonable approximation, can be ignored. We explore the possible influence of absent species on an evolutionary study by quantifying the effect of ghost lineages on introgression as detected by the popular D-statistic method. We show from simulated data that under certain frequently encountered conditions, the donors and recipients of horizontal gene flow can be wrongly identified if ghost lineages are not taken into account. In particular, having a distant outgroup, which is usually recommended, leads to an increase in the error probability and to false interpretations in most cases. We conclude that introgression from ghost lineages should be systematically considered as an alternative possible, even probable, scenario.Competing Interest StatementThe authors have declared no competing interest.