VCF for neutral data set and potential connectivity matrices of Harpagifer antarcticus, along the Western Antarctic Peninsula

Connectivity is a fundamental process of population dynamics in marine ecosystems. In the last decade, with the emergence of new methods, combining different approaches to understand the patterns of connectivity among populations and their regulation has become increasingly feasible. The Western Antarctic Peninsula (WAP) is characterized by complex oceanographic dynamics, where local conditions could act as barriers to population connectivity. Here, the notothenioid fish Harpagifer antarcticus, a demersal species with a complex life cycle (adults with poor swim capabilities and pelagic larvae), was used to assess connectivity along the WAP by combining biophysical modeling and population genomics methods. Both approaches showed congruent patterns. Areas of larvae retention and low potential connectivity, observed in the biophysical model output, coincide with four genetic groups within the WAP: (1) South Shetland Islands, (2) Bransfield Strait, (3) the central, and (4) the southern area..., Biophysical model
An implementation of the Regional Ocean Modeling System (ROMS; Haidvogel et al. 2008) was used to simulate ocean circulation along the WAP. To estimate the potential role of the ocean as an advective mechanism, Lagrangian particle tracking simulations were implemented to determine the potential dispersal of H. antarcticus larvae. The implementation of ROMS for the WAP (Hudson et al., 2021) has 1.5 km horizontal resolution and 24 vertical sigma layers. It includes a dynamic sea ice model (Budgell, 2005) and the interaction between floating ice shelves and oceanographic conditions (Holland and Jenkins, 1999; Dinniman et al., 2011). Atmospheric forcing is from archived forecasts from the Antarctic Mesoscale Prediction System (Powers et al., 2012), tidal forcing was added at the model lateral boundaries using tidal sea surface height and velocity from the CATS2008 regional Antarctic tidal model (Padman et al., 2002).
The model was run from November to May of years 2008-200..., , # VCF for neutral SNPs and connectivity matrices of Harpagifer antarcticus, along the Western Antarctic Peninsula

[https://doi.org/10.5061/dryad.b5mkkwhjk](https://doi.org/10.5061/dryad.b5mkkwhjk)

This is a dataset containing first a vcf of 20778 neutral SNPs (obtained through Genotyping-by-Sequencing method ) of 143 adult individuals of Harpagifer antarcticus, from 11 localities along the Western Antarctic Peninsula (WAP), between 60.72ºS, 45.66ºW and 67.89ºS, 67.40ºW. DNA extractions were done using the DNeasy Blood® and Tissue Kit (QIAGEN®, USA). The GBS method was performed at the Biotechnology Center of the University of Wisconsin, using (after optimization) the ApeKI restriction enzyme. The second dataset 

## Description of the data and file structure

The SNP-calling for this dataset was carried out with the pipeline Universal Network-Enabled Analysis Kit (UNEAK) in Tassel v. 3 software (Lu et al., 2013). The SNPs were filtered using a site minimum call rate of 0.75, a minimum...