Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes

Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding of the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled “ghost” extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modeling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic..., We performed population genomics analysis based on RAD sequence data (279 individuals from 21 populations, and one outgroup individual) and whole genome resequencing data (18 individuals from three populations and one outgroup individual) for Chaenogobius annularis, a coastal goby species inhabiting the Japanese archipelago. Our analyses included repeat annotation, gene annotation, population recombination rate estimation, estimation of potential deleterious mutations, population genetic analysis, test for hybridization, PSMC analysis, fastsimcoal2-based demographic modeling, SLiM-based forward simulation, sliding window analysis, and permutation-based characterization of introgression landscapes., , # Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes

[https://doi.org/10.5061/dryad.7wm37pw09](https://doi.org/10.5061/dryad.7wm37pw09)

## **Brief description of the data and file structure**

### scripts.tar.gz

#### **Note:** **\"scripts.tar.gz\" can be obtained from the Zenodo link (https://doi.org/10.5281/zenodo.10048869) tied to this Dryad page** (see \"Related works\" section in the upper right corner). **To get the script only, please visit this Zenodo link**.
#### For your convenience, we have changed the \"scripts.tar.gz\" file to be available directly from Data files in this page as well (added on 12/18/2023).

The scripts used in this study (bash, python, R).
These scripts are categorized into the following 10 contents, which are hierarchized within each directory.
1\. ddRAD\-seq genotyping
2\. WGS \(whole genome resequencing\) genotyping
3\. repeats and gene annotation
4\. population recombination r...