Archaeogenomic analysis of Chesapeake Atlantic sturgeon illustrates shaping of its populations in recovery from severe overexploitation

Atlantic sturgeon (Acipenser oxyrinchus ssp. oxyrinchus) has been a food
resource in North America for millennia. However, industrial-scale fishing
activities following the establishment of European colonies led to
multiple collapses of sturgeon stocks, driving populations such as those
in the Chesapeake area close to extinction. While recent conservation
efforts have been successful in restoring census numbers, little is known
regarding genomic consequences of the population bottleneck. Here, we
characterise its effect on present-day population structuring and genomic
diversity in James River populations. To establish a pre-collapse
baseline, we collected genomic data from archaeological remains from
Middle Woodland Maycock’s Point (c. 200-900 CE), as well as Jamestown and
Williamsburg colonial sites. Demographic analysis of recovered mitogenomes
reveals a historical collapse in effective population size, also reflected
in diminished present-day mitogenomic diversity and structure. We infer
that James River fall and spring spawning populations likely took shape in
recent years of population recovery, where genetic drift enhanced the
degree of population structure. The mismatch of mitogenomic lineages to
geographical-seasonal groupings implies that despite their homing instinct
and differential adaptation to season-specific behaviour, colonisation of
new rivers has been a key ecological strategy for Atlantic sturgeon over
evolutionary timescales.