Description
In recent years, ghost lineages have emerged as a research topic in its own right. Multiple articles have contributed to shaping this field and have explored not only the impact of ghost lineages on the study of gene flow (introgression and horizontal gene transfer), but also new approaches to detect or unveil them (see a non-exhaustive list of references below).The idea that horizontal evolutionary events may involve unseen (extinct or extant) lineages is not new, but the fact that these ghost lineages can be explicitly considered when detecting gene flow and can be characterized through these events has become a central question. Ghost lineages are now starting to be given the place they deserve in evolutionary biology: a central object to study, not a simple source of noise in analyses.
This mailing list aims to build a community around ghost lineages, to share ideas, map the state of the art, and explore future directions.
Two non-exclusive activities are envisioned:
- A first meeting (online or in-person) to discuss current work and define the contours of this emerging field (Autumn 2026 as a target).
- A collective review article (or book) to synthesize origins, advances, and future directions of ghost lineage research.
References
- Durvasula, A. & Sankararaman, S. (2020). Recovering signals of ghost archaic introgression in African populations. Sci Adv 6, eaax5097.
- Kato, S., Arakaki, S., Nagano, A.J., Kikuchi, K., Hirase, S. (2024). Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes. Molecular Ecology 33, e17216.
- Ottenburghs, J. (2020). Ghost introgression: spooky gene flow in the distant past. BioEssays 42, 2000012.
- Pang, X.-X. et al. (2023). Impact of ghost introgression on coalescent-based species tree inference and estimation of divergence time. Systematic Biology 72, 35–49.
- Pang, X.-X. & Zhang, D.-Y. (2024). Detection of ghost introgression requires exploiting topological and branch length information. Systematic Biology 73, 207–222.
- Szöllősi, G.J. et al. (2013). Lateral gene transfer from the dead. Systematic Biology 62, 386–397.
- Zhang, W.-P. et al. (2024). Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species. The Plant Journal 119, 1386–1399.
- Tolman, E.R. & Suvorov, A. (2025). GhostParser: a highly scalable phylogenomic approach for the identification of ghost introgression. bioRxiv. https://doi.org/10.1101/2025.08.21.671585
- Tricou, T., Marsot, E., Boussau, B., Tannier, E., de Vienne, D.M. (2025). Gene flow can reveal ghost lineages. Evolutionary Journal of the Linnean Society 4(1), kzaf014.
- Tannier, E., Tricou, T., Benali, S., de Vienne, D.M. (2025). HGTs are not SPRs: in the presence of ghost lineages, series of horizontal gene transfers do not result in series of subtree pruning and regrafting. Molecular Biology and Evolution 42(6), msaf128.
- Tricou, T., Tannier, E., de Vienne, D.M. (2024). Response to “On the impact of incomplete taxon sampling on the relative timing of gene transfer events.” PLOS Biology 22(3), e3002557.
- Tricou, T., Tannier, E., de Vienne, D.M. (2022a). Ghost lineages highly influence the interpretation of introgression tests. Systematic Biology 71, 1147–1158.
- Tricou, T., Tannier, E., de Vienne, D.M. (2022b). Ghost lineages can invalidate or even reverse findings regarding gene flow. PLOS Biology 20, e3001776.
- Davín, A.A., Tricou, T., Tannier, E., de Vienne, D.M., Szöllősi, G.J. (2019). Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages. Bioinformatics 36(4), 1286–1288.
- Fournier, G.P., Huang, J., Gogarten, J.P. (2009). Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Phil. Trans. R. Soc. B 364, 2229–2239.
- Andam, C.P., Gogarten, J.P. (2011). Biased gene transfer in microbial evolution. Nature Reviews Microbiology 9(7), 543–555.
- Kuhlwilm, M. et al. (2019). Ancient admixture from an extinct ape lineage into bonobos. Nature Ecology & Evolution 3, 957–965.
- Zhang, D. et al. (2019). Ghost introgression as a cause of deep mitochondrial divergence in a bird species complex. Molecular Biology and Evolution 36(11), 2375–2386.
- Shen, C.C. et al. (2025). Exploring mitonuclear discordance: ghost introgression from an ancient extinction lineage in the Odorrana swinhoana complex. Molecular Ecology 34(10), e17763.