Demographic history and inbreeding in two declining sea duck species inferred from whole genome sequence data

Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (Clangula hyemalis) and velvet scoter (Melanitta fusca) were once important quarry sea duck species in NW Europe, but recent declines resulted in their reclassification as Vulnerable on the IUCN Red List. We sequenced and assembled genomes for both species and resequenced 15 individuals of each. Using analyses based on site frequency spectra and sequential Markovian coalescence, we found long-tailed duck to show more historical demographic stability, whereas velvet scoter was affected particularly by the Last (Weichselian) Glaciation. This likely reflects long-tailed duck breeding continuously across the Arctic, with cycles of glaciation primarily shifting breeding areas south or north without major population declines, whereas the more restricted southern range of velvet scoter would lead to significant range contraction during glaciat..., A. Sampling
A total of 16 individuals were sampled of each species in overwintering areas in Denmark, in each case encompassing 13 males and three females. The sampled individuals were obtained in Denmark from Danish hunters between December 2017 and January 2019, during the open hunting seasons as part of a separate study run by the Danish Hunters’ Association and Aarhus University on the distribution and feeding ecology of C. hyemalis and M. fusca. Individuals were stored at -18°C and kept frozen until samples of muscle tissue were collected. Tissue samples were then stored in 96% ethanol at -18°C until DNA extraction.
B. DNA extraction and whole genome resequencing
DNA was extracted from 15 individuals of each species using the E.Z.N.A.® Tissue DNA Kit (OMEGA, Bio-tek, CA, USA) following the manufacturer's recommendations. Whole genome resequencing was outsourced to BGI and involved 150 bp paired-end sequencing on the DNBseq platform, aimed at providing sequencing depths of 20X.
C. M..., , # Data from: Demographic history and inbreeding in two declining sea duck species inferred from whole genome sequence data

[https://doi.org/10.5061/dryad.w3r22810z](https://doi.org/10.5061/dryad.w3r22810z)

## Description of the data and file structure

The data encompasses multiple VCF files generated from whole-genome resequencing of two sea duck species, the velvet scoter *(Melanitta fusca)* and long-tailed duck *(Clangula hyemalis).*

**1A) LTD_raw.vcf.gz**
Raw variant calls from WGS data from long-tailed duck.

**2A) LTD.filtered.max2.QUAL30.minDP10.minGQ15.miss0.9.variant.sansSexChr.HWE.vcf**
Variant calls from file 1A) filtered based on quality, depth, missing data and HWE. Contains only bi-allelic SNPs of QUAL>30, only genotypes with read depth >10 and genotype quality >15, and only sites in Hardy-Weinberg equilibrium, located on autosomal scaffolds and with <10% missing data and pooled read depth >250 and <470.

**3A) LTD.filtered.max2.QUAL30.minDP10.minGQ15....