Anadromous river herring (alewife and blueback herring) persist at historically low abundances and are caught as bycatch in commercial fisheries, potentially preventing recovery despite conservation efforts. We used newly established single-nucleotide polymorphism genetic baselines for alewife and blueback herring to define fine-scale reporting groups for each species. We then determined the occurrence of fish from these reporting groups in bycatch samples from a Northwest Atlantic fishery over four years.Within sampled bycatch events, the highest proportions of alewife were from the Block Island (34%) and Long Island Sound (22%) reporting groups, while for blueback herring the highest proportions were from the Mid-Atlantic (47%) and Northern New England (24%) reporting groups. We then quantified stock-specific mortality in a focal geographic area (~3500 km² including Block Island Sound) of high bycatch incidence and sampling effort, where the most accurate estimates of mortality could be made. During this period, we estimate that bycatch took about 4.6 million alewife and 1.2 million blueback herring, highlighting the need to reduce bycatch mortality for the most depleted river herring stocks.

The data uploaded for this project includes the SNP genotyped baselines for alewife and blueback herring as well as the genotyped bycatch of alewife and blueback herring. The methods are described in the manuscript.

We have provided the R-code for simulations to estimate the accuracy of RG for alewife and blueback herring and to estimate mixing proportion estimates for alewife and blueback herring bycatch.