Data from: 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 glaciations.
Both species showed evidence of declines over the past thousand years,
potentially reflecting anthropogenic pressures with the recent decline
indicating an accelerated process. Analysis of Runs of Homozygosity (ROH)
showed low but non-trivial inbreeding, with FROH from 0.012 to 0.063 in
long-tailed duck and ranged from 0 to 0.047 in velvet scoter. Lengths of
ROH suggested that this was due to ongoing background inbreeding rather
than recent declines. Overall, despite demographically important declines
this has not yet led to strong inbreeding and genetic erosion, and the
most pressing conservation concern may be the risk of density dependent
 (Allee) effects. We recommend monitoring of inbreeding using ROH
analysis as a cost-efficient method to track future developments to
support effective conservation of these species.