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 (<i>Clangula hyemalis</i>) and velvet scoter (<i>Melanitta fusca</i>) 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 <i>C</i>. <i>hyemalis</i> to show more historical demographic stability, whereas <i>M. fusca</i> was affected particularly by the Last (Weichselian) Glaciation. This likely reflects <i>C</i>. <i>hyemalis</i> 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 <i>M. fusca</i> would lead to significant range contraction during glaciations. Both species showed evidence of declines over the past thousands of years, potentially reflecting anthropogenic pressures with the recent decline indicating an accelerated process. Analysis of runs of homozygosity (ROH) showed low but nontrivial inbreeding, with <i>F</i> _ROH from 0.012 to 0.063 in <i>C</i>. <i>hyemalis</i> and ranging from 0 to 0.047 in <i>M. fusca</i>. 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.