Sea otter sequence capture project data files

Extinction or severe population contractions are rarely uniform across an
entire species. However, because of the rapid onset of the fur trade in
the 18th and 19th centuries, sea otters (Enhydra lutris) were
systematically hunted to near extinction across their entire Northern
Pacific range. Many sea otter populations were driven fully extinct, and
the populations that survived suffered a rapid decline from 10-20,000
individuals per population to fewer than one hundred survivors. Each
surviving remnant sea otter population represents a replicate of an
extreme population bottleneck event impacting genetic diversity and
fitness into the future. Here, we designed sequence capture probes of the
sea otter exome and neutral regions to examine the population structure
and demographic history of five surviving sea otter populations from
throughout the species’ former range, including three ancient Californian
samples from ~1500 and ~200 years ago. We show that southern sea otters in
California are the last survivors of a divergent lineage that has been
isolated from northern and Asian populations for thousands of years,
highlighting the need for their separate conservation. We detect a signal
of extreme population decline in every surviving sea otter population and
use simulations to demonstrate that these contractions may have lowered
the fitness of recovering populations. However, we also infer historically
low effective population sizes prior to the fur trade bottleneck which
paradoxically could have led to the purging of highly deleterious
mutations and mitigated the effects of population decline on the burden of
harmful genetic variants, countering the conventional wisdom that large
populations are most robust to decline. Nonetheless, future bottlenecks
caused by existing external threats may act to maintain the negative
genetic impacts of the fur trade for hundreds of generations, illustrating
how human exploitation can leave a species vulnerable long after its
nominal recovery.