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.

This dataset comprises the intermediary files obained from bioinformatic processing of raw DNA sequnces obtained through high throughput sequencing of Atlantic sturgeon (AS). Sources of modern AS data: fin clips from James River (Chesapeake DPS) fall and spring populations; Great PeeDee River (South Carolina DPS) fall and spring populations. Sources of archaeological AS data: remains in the form of bones and scutes from Jamestown Colony, Williamsburg Colony and Maycock's point (Middle Woodland site).

Specifically, the datasets produced are based on variants called from target captured exonic DNA and mitogenomes sequenced with the aid of target capture. The population genomic and phylogenomic analytical steps conducted in the publication are outlined here.