The direct sequencing of PCR products from diploid organisms is problematic because of ambiguities associated with phase inference in multi-site heterozygotes. Several molecular methods such as cloning, SSCP, and DGGE have been developed to empirically reduce diploid sequences to their constitutive haploid components, but in theory these empirical approaches can be supplanted by analytical treatment of diploid sequences. Analytical approaches are more desirable than molecular methods because of the added time and expense required to generate molecular data. A variety of analytical methods have been developed to address this issue, but few have been rigorously evaluated with empirical data. Furthermore, they all assume that the sequences under consideration are evolving in a neutral fashion and assume a moderate number of heterozygous sites. Here, we use non-neutral major histocompatibility complex (MHC) sequences comprised of large numbers of heterozygous sites that are under strong balancing selection to evaluate the performance of the popular Bayesian algorithm implemented by the program PHASE. Our results suggest that PHASE performs admirably with non-neutral sequences of moderate length with numerous heterozygous sites typical of MHC class II sequences. We conclude that analytical approaches to haplotype inference have great potential in large-scale population genetic assays, but recommend groundtruthing analytical results using empirical (molecular) approaches at the outset of population-level analyses.

Concern over the impacts of incidental catches of Alewife, Alosa pseudoharengus and Blueback Herring, A. aestivalis (collectively managed as ‘river herring’) in the commercial Atlantic Herring (Clupea harengus) and Atlantic Mackerel (Scomber scombrus) fisheries has resulted in the recent implementation of river herring incidental catch limits. These incidental catches are highly variable in frequency and magnitude, and the environmental conditions associated with these catches are poorly understood. We used generalized additive models (GAMs) to describe habitat associations of Alewife, Blueback Herring, Atlantic Herring, and Atlantic Mackerel. Bottom temperature, bottom depth, bottom salinity, solar azimuth and elevation, and region of the Northeast U.S. continental shelf were all significant in the habitat models; GAMs explained 25.2, 16.9, 18.9, and 20.6% of the deviance observed for the presence/absence of Alewife, Blueback Herring, Atlantic Herring, and Atlantic Mackerel. A subset of the data was omitted from the model and the probability of presence was compared with observations; 66–77% of observations were correctly predicted. The individual probabilities of presence were used to quantify and evaluate the accuracy of modelled overlap of Alewife and Blueback Herring with Atlantic Herring (68–72% correct predictions) and Alewife and Blueback Herring with Atlantic Mackerel (57–69% correct predictions). Our findings indicate that environmental gradients influence the distributions and overlap of Alewife, Blueback Herring, Atlantic Herring, and Atlantic Mackerel, and with further testing and refinement these models could be developed into a tool to aid industry in reducing incidental catches of river herring.

Juvenile habitat use and early life migratory behaviors of successfully recruited adult fish provide unique insight into critical habitats for a population, and this information allows restoration plans to be tailored to maximize benefits. Retrospective analysis of adult otolith chemistry combined with fish-otolith growth models were used to assess juvenile nursery habitat selection and size at egress to adult habitats (marine waters) for anadromous alewife and blueback herring from 20 rivers throughout the eastern US. Between-species differences in the size of emigrants were small, with blueback herring found in freshwater nurseries ~ 8% more frequently than alewives, and alewives using a combination of freshwater and estuarine nurseries ~ 9% more than bluebacks. Estuarine nursery use was more common in populations at lower latitudes. No clear trends in sizes of emigrants or habitat use were observed between the species in watersheds where both co-occur. Principal component analysis of latitude, watershed area, estuary area, accessible river kilometers, and percentage of the watershed in urban use indicated that the combined effects of these watershed characteristics were correlated with size at egress. These results highlight the considerable plasticity in early life habitat use among populations of anadromous fishes as well as the effect of watershed characteristics on early life migration timing and strategies.