Numbers of wild anadromous Atlantic salmon (Salmo salar) have declined demonstrably throughout their native range. The current status of runs on rivers historically supporting salmon indicate widespread declines and extirpations in Europe and North America primarily in southern portions of the range. Many of these declines or extirpations can be attributed to the construction of mainstem dams, pollution (including acid rain), and total dewatering of streams. Purported effects on declines during the 1960s through the 1990s include overfishing, and more recently, changing ocean conditions, and intensive aquaculture. Most factors affecting salmon numbers do not act singly, but rather in concert, which masks the relative contribution of each factor. Salmon researchers and managers should not look for a single culprit in declining numbers of salmon, but rather, seek solutions through rigorous data gathering and testing of multiple effects integrated across space and time.

We examined the effects of low-head dams on aquatic biota, habitat, and water quality in a 171-km reach of a midwestern warmwater river that was fragmented by 15 dams into a series of free-flowing and impounded habitats. Dams impounded 55% of the river's surface area within the study reach and influenced distributions of 30 species of fish by restricting upstream movements. Values for the Illinois index of biotic integrity (IBI) were higher in free-flowing areas (mean IBI ϭ 46 out of a possible 60 at below-dam and midsegment free-flowing locations) than impounded areas (mean IBI Ͻ 31 for above-dam and midsegment impounded locations). Likewise, scores from a macroinvertebrate condition index (MCI) were higher at stations in free-flowing reaches (mean MCI Ͼ 415 out of a possible 700) than in nearshore areas of impounded reaches (mean MCI Ͻ 210). Ponar dredge samples taken only from open-water impounded areas showed an offshore invertebrate community that consisted almost entirely of tolerant oligochaetes and chironomid larvae. Qualitative habitat evaluation index (QHEI) scores indicated good-quality habitat in free-flowing areas (mean QHEI Ͼ 70 out of a possible 100) and severely degraded habitat at impounded sites (mean QHEI Ͻ 45). In impounded reaches, dissolved oxygen and pH showed wide daily fluctuations (2.5-18.0 mg/L and 7.0-9.4 units) and often failed to meet Illinois water quality standards. In free-flowing portions of river, fluctuations in these parameters were less extreme and water quality standards typically were met. We found little evidence of cumulative effects of dams; however, our data suggest that low-head dams adversely affect warmwater stream fish and macroinvertebrate communities by degrading habitat and water quality and fragmenting the river landscape. These results should aid river managers and stakeholders in determining appropriate restoration practices (i.e., dam removal versus fish passage structures) for warmwater rivers and streams that contain low-head dams.

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A major challenge in conservation biology is the need to broadly prioritize conservation efforts when demographic data are limited. One method to address this challenge is to use population genetic data to define groups of populations linked by migration and then use demographic information from monitored populations to draw inferences about the status of unmonitored populations within those groups. We applied this method to anadromous alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), species for which long-term demographic data are limited. Recent decades have seen dramatic declines in these species, which are an important ecological component of coastal ecosystems and once represented an important fishery resource. Results show that most populations comprise genetically distinguishable units, which are nested geographically within genetically distinct clusters or stocks. We identified three distinct stocks in alewife and four stocks in blueback herring. Analysis of available time series data for spawning adult abundance and body size indicate declines across the US ranges of both species, with the most severe declines having occurred for populations belonging to the Southern New England and the Mid-Atlantic Stocks. While all alewife and blueback herring populations deserve conservation attention, those belonging to these genetic stocks warrant the highest conservation prioritization.

The Connecticut River historically represented the southernmost extent of the North American range of Atlantic salmon (Salmo salar), but the native population was extirpated 200 years ago by dam construction. An extensive restoration effort has relied upon stock transfers from more northerly rivers, especially the Penobscot River (Maine). Recent work has shown differences in age structure between donor and derivative populations. Here we focus on a related life-history trait, the timing of the adult migration. We examined 23 years of migration timing data collected at two capture locations in the Connecticut River drainage. We found that both dates of first capture and median capture dates have shifted significantly earlier by about 0.5 days·year–1. To conclude whether this is a consequence of local adaptation or a coast-wide effect, we also quantified changes in migration timing of more northerly stocks (in Maine and Canada). We found that the changes in migration timing were not unique to the Connecticut River stock and instead observed coherent patterns in the shift towards earlier peak migration dates across systems. These consistent shifts are correlated with long-term changes in temperature and flow and may represent a response to global climate change.

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.

The recent increase in river restoration projects is altering habitat connectivity for many aquatic species, increasing the chance that previously isolated populations will come into secondary contact. Anadromous and landlocked alewife (Alosa pseudoharengus) are currently undergoing secondary contact as a result of a fishway installation at Rogers Lake in Old Lyme, Connecticut. To determine the degree of prezygotic isolation and potential for hybridization between alewife life history forms, we constructed spawning time distributions for two anadromous and three landlocked alewife populations using otolith‐derived age estimates. In addition, we analyzed long‐term data from anadromous alewife migratory spawning runs to look for trends in arrival date and spawning time. Our results indicated that anadromous alewife spawned earlier and over a shorter duration than landlocked alewife, but 3%–13% of landlocked alewife spawning overlapped with the anadromous alewife spawning period. The degree of spawning time overlap was primarily driven by annual and population‐level variation in the timing of spawning by landlocked alewife, whereas the timing and duration of spawning for anadromous alewife were found to be relatively invariant among years in our study system. For alewife and many other anadromous fish species, the increase in fish passage river restoration projects in the coming decades will re‐establish habitat connectivity and may bring isolated populations into contact. Hybridization between life history forms may occur when prezygotic isolating mechanisms are minimal, leading to potentially rapid ecological and evolutionary changes in restored habitats.

Hybridization between Atlantic salmon Salmo salar and brown trout S. trutta is frequently reported, and the role of mature male Atlantic salmon parr has been suspected but never proven. Salmon fry were stocked into a headwater tributary stream of the Connecticut River, where no adult salmon are present. The stream has a self‐sustaining population of brown trout. Enzyme electrophoresis revealed the presence of one hybrid (0.81% of the sampled population). The maternal species was identified as brown trout; therefore, the only possibility for the male parent was that it was a mature male Atlantic salmon parr. This is the first direct evidence of parr producing hybrid offspring in a totally natural setting and in the absence of any sea‐return salmon.