Genetic stock composition of marine bycatch reveals disproportional impacts on depleted river herring genetic stocks

Abstract

Bycatch of mid-trophic-level anadromous fishes that connect marine and freshwater ecosystems is a growing conservation concern. Anadromous alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis) are important components of coastal freshwater and marine food webs, but have experienced dramatic declines in the abundances of spawning adults. Freshwater-focused restoration efforts have yielded few consistent signs of recovery, raising concerns that bycatch in Northwest Atlantic commercial fisheries may be negating these conservation actions. Using data from 15 microsatellites genotyped for baseline populations and bycatch, we conducted genetic stock identification to understand how bycatch was partitioned among previously identified regional genetic stocks. We then combined this information with fishery observer data to estimate genetic stock-specific bycatch mortality for the southern New England Atlantic herring fishery (2012–2013). Bycatch overall, but especially in the Atlantic herring fishery, was disproportionately assigned to the most severely depleted genetic stocks (alewife southern New England stock — 70% of assignments; blueback herring mid-Atlantic stock — 78% of assignments). These genetic stocks overlap in the region surrounding Long Island Sound, suggesting that bycatch taken from this area in recent years may be negatively impacting recovery efforts in this region. Our study suggests that mitigating bycatch on the southern New England fishing grounds may benefit recovery efforts for alewife and blueback herring genetic stocks that have experienced the greatest declines in spawning adult abundances.

Genotyping‐by‐sequencing of genome‐wide microsatellite loci reveals fine‐scale harvest composition in a coastal Atlantic salmon fishery

“…With this increased resolution, assignment accuracy has remained high, averaging 88%–91% for individual assignment or mixture analysis, respectively, on par with previous estimates of regional assignment accuracy in salmon populations in eastern North America (Bradbury et al., ; Gauthier‐Ouellet et al., ; Moore et al., ). Notwithstanding the high overall accuracy reported here, slight systematic biases either upward or downward were detected in assignment among a few reporting groups as has been noted elsewhere (Hasselman et al., ), but these biases seem to have minimal impact on the levels of overall accuracy.…”

“…Hasselman et al. () have shown that use of the parametric bootstrap correction as implemented in RUBIAS reduces biases in mixed‐stock estimates by >50%. For each fishery sample, we estimate the proportion contributed from each reporting unit, and the 95% credible interval from MCMC samples of the mixing proportions of the posterior probability distribution.…”

Discovery and characterization of single nucleotide polymorphisms in two anadromous alosine fishes of conservation concern

“…Generating these markers using high‐throughput sequencing of genomic DNA enhances our ability to confidently distinguish populations of alewife and blueback herring that are genetically distinct across both species’ ranges. This ability to identify stock of origin for fish caught at sea is critical for management of populations experiencing diminished spawning returns and of increasing conservation concern (Hasselman et al., ). Using these new tools, samples from mixed‐stock assemblages can be quickly and efficiently genotyped, allowing new insights into marine movement patterns and impacts of marine fisheries.…”

“…Hasselman et al. () also found that these same data had sufficient statistical power to confidently assign river herring bycatch in commercial fisheries to regional genetic stocks. Given their propensity for natal philopatry, the conservation and management of river herring requires a “population‐level” approach, and there is a need for molecular tools that can resolve population genetic structure at spatial scales finer than regional genetic stock.…”

“…Recent genetic studies of alewife and blueback herring used polymorphic microsatellite markers to resolve the spatial scale of population genetic structure (McBride, Willis, Bradford, & Bentzen, ; Palkovacs et al., ), examine range‐wide patterns of hybridization (Hasselman et al., ), assess the influence of stocking activities on genetic structure (McBride, Hasselman, Willis, Palkovacs, & Bentzen, ), and determine the origin of river herring bycatch in commercial fisheries (Hasselman et al., ). Palkovacs et al.…”