Ancient and recent hybridization in the Oreochromis cichlid fishes

Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in th..., , , # Ancient and recent hybridization in the Oreochromis cichlid fishes

[https://doi.org/10.5061/dryad.p2ngf1w0c](https://doi.org/10.5061/dryad.p2ngf1w0c)

## Description of the data and file structure

All trees inferred, along with the dataset used to generate them, are available in the trees folder, for both M. zebra and O. niloticus mapping dataset.

Mzeb_nc_iqtree.min4.phy.treefile, Onil_nc_iqtree.min4.phy.treefile - The iqtree inferred phylogenetic trees for the nuclear genome (non-coding regions) inferred for the M. zebra (Mzeb) and O. niloticus (Onil) mapping datasets. respectively. Intermediate files generated are also available for the iqtree runs (Mzeb_nc_iqtree.min4.phy.bionj, Mzeb_nc_iqtree.min4.phy.ckp.gz, Mzeb_nc_iqtree.min4.phy.contree, Mzeb_nc_iqtree.min4.phy.log, Mzeb_nc_iqtree.min4.phy.mldist, Mzeb_nc_iqtree.min4.phy.model.gz, Mzeb_nc_iqtree.min4.phy.runtrees, Mzeb_nc_iqtree.min4.phy.splits.nex, Onil_nc_iqtree.min4.phy.bionj, Onil_nc_iqtree.min4.phy.ckp.gz, Onil_nc_iqtr...