Inversions dominate evolution in the European Sardine (Sardina pilchardus) amid strong gene flow

This dataset contains genomic resources associated with a study of chromosomal inversions and population structure in the European sardine (Sardina pilchardus). It includes whole-genome resequencing data, variant call files (VCFs), inferred genotypes for structural variants, and associated metadata across multiple populations spanning the species’ range. These data were used to identify large chromosomal inversions and assess their role in maintaining genetic differentiation amid high gene flow. The resources support future analyses of structural variation, local adaptation, and demographic history in marine fishes., 2.1 | Sampling, DNA Extraction, Library Preparation and Sequencing
European sardines were collected from across the Atlantic and Mediterranean species' range between 2019 and 2021 (Table 1). Samples were obtained during annual research surveys conducted in the eastern North and Central Atlantic using small pelagic trawls, except for samples from the Aegean, Ionian, and Adriatic Seas obtained from local fishermen. Wherever possible, two samples were obtained per location: one sample of 25 juveniles and another of 25 adult individuals. Given the variability in size at maturity throughout the species ́range and the marked differences between Atlantic and Mediterranean sardines (e.g., Dimarchopoulou and Tsikliras 2022; Silva et al. 2006), individuals were categorised as juveniles or adults using location-specific cutoff values of size at 50% maturity (L50): 18cm for Atlantic samples, and 16cm for Mediterranean samples. The final sample set comprised 13 juvenile and 21 adult samples (Table ..., , # Inversions Dominate Evolution in the Highly Admixed European Sardine (*Sardina pilchardus*)

Dryad: [https://doi.org/10.5061/dryad.vmcvdnd3f](https://doi.org/10.5061/dryad.vmcvdnd3f)

###### Principle Investigator Contact Information

```
Name: Stephen J. Sabatino
Institution: CIBIO - BIOPOLIS
Email: [e-mail]
```

###### Alternate Contact Information

```
Name: Ana Veríssimo
Institution: CIBIO - BIOPOLIS
Email: [e-mail]
```

## Dataset Overview

This dataset contains the data and code required to replicate analyses in Sabatino et al., using whole-genome sequencing to investigate the influence of inversions on the population genomics of the r-selected European sardine (*Sardina pilchardus*). Samples include genomic DNA extracted from 25 individuals (pooled males and females) from each of 33 locations in the Northeastern Atlantic and Mediterranean Sea covering most of the species distribution range. Genetic data include the following datasets of single nucleotide...,