Species long-term persistence is to a great extent contingent on the ability of populations to mount variable responses to perturbations; the breadths of which are largely dependent on the amount of heritable variation present at the population level. However, populations are not necessarily equivalent in their amount of genetic variation, or in their responses to future environmental conditions, and information about the magnitude and spatial distribution of intraspecific genetic variation is integral to conservation planning, and preserving species evolutionary potential. Using neutral molecular markers, I demonstrate that latitude is an important determinant of the amount and spatial distribution of genetic variation within and among Nearctic fishes. Latitudinal declines observed among species were mirrored by declines within species, and encourage a cautionary approach for interspecific comparisons and inferences of broad spatial patterns of genetic variation when data for individual species are obtained from only a portion of their range. I subsequently examined the magnitude and spatial distribution of microsatellite based variation for 33 spawning runs from across the range of American shad (Alosa sapidissima). Sequential reductions of intraspecific genetic variation with latitude were observed among spawning runs from formerly glaciated regions; consistent with stepwise post-glacial range expansion, and successive population founder events. Canadian populations exhibited temporally stable genetic differentiation characterized by a significant pattern of isolation by distance, and exhibited evidence of metapopulation structure. Although isolation by distance was observed among U.S. spawning runs, population structure was comparatively weak; a possible consequence of increased levels of gene flow (human-mediated or natural). Different spatial patterns of population structure were detected across the species’ range, but are not likely due to alternative reproductive strategies (iteroparity vs. semelparity). Rather, these different patterns probably reflect different management strategies in Canada (no stocking) and the United States (stocking), alternative glacial histories, or combinations thereof. Reciprocal patterns of genetic diversity and differentiation observed across the species’ range suggests that U.S spawning runs contribute more to diversity and less to differentiation than Canadian spawning runs. These results have implications for future shad restoration efforts, and the long-term persistence of the species.

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Smallmouth bass (Micropterus dolomieu) were collected from a reach of the James River, Virginia undergoing American shad (Alosa sapidissima) restoration and fish passage projects. Diet and growth of these specimens were compared to specimens collected prior (1987-1990) to American shad restoration and fish passage. The Piedmont James River was stocked with >5 million American shad larvae annually since 1995 and was re-opened to migratory fish in 1999. Mean lengths-at-age (ages 1-4) were back-calculated from scales and compared using the Mann-Whitney Test. Smallmouth bass collected in 2002 had a significantly lower mean length-at-age for age 2 specimens compared to 1987-1989 smallmouth bass (P=0.04). Stomach contents were placed into four major categories (fish, crayfish, aquatic insects, terrestrial insects) and compared using Schoener's Diet Overlap Index. Schoener's Index produced a score of 0.94; indicating very high diet overlap. In 2002, Centrachidae was the dominant fish prey family and redbreast sunfish (Lepomis auritus) was the dominant species. American shad was not observed in stomach samples during 1987-1990, but was the second most common fish species prey species identified in 2002. Recovery of American shad from smallmouth bass indicates smallmouth bass are utilizing forage produced by restoration stockings. No semi-migratory fish species using new fish passage structures were recovered fiom smallmouth bass stomachs. Fish prey was measured by weight, number of items, and by occurrence; and placed in six family categories for comparison. Schoener's Index produced scores ranging from 0.26 for prey weight to 0.40 for prey occurrence, indicating low fish prey diet overlap. These data indicate that smallmouth bass are utilizing new forage resulting from restoration activities, but growth rates have not changed significantly. Smallmouth bass may not be forage-limited in the study area.

The American shad Alosa sapidissima has experienced severe declines throughout its native range due to habitat degradation, fragmentation, and over-fishing. Hatchery supplementation is often used for stock restoration, but the effects of supplementation on population structure and genetic diversity are rarely assessed. This study employed molecular markers to evaluate how supplementation of the James River American shad population with Pamunkey River origin larvae since 1994 has impacted genetic diversity and population structure. Population genetic parameters of other major Chesapeake Bay tributaries (Susquehanna, Rappahannock, Potomac, and Nanticoke) also were characterized. Prior to stocking, the James and Pamunkey populations exhibited subtle genetic differentiation, which was absent among post-supplementation samples, presumably due to the stockings. A similar situation was observed among other shad populations of Chesapeake Bay tributaries which were subtly differentiated in the 1990s but lacked any credible among-population differentiation among contemporary samples. Genetic diversity of the James River shad population was high prior to stocking, and remained high throughout years of intensive supplementation, yet the current population decline suggests that the James River shad population still has not recovered. Despite harvest curtailment, elimination of the ocean intercept fishery, and widespread supplementation efforts, Chesapeake Bay tributary American shad populations are collectively at their lowest levels in recorded history. Therefore, success of other restoration goals such as creation of fish passage in James River was investigated in a concurrent radio telemetry study to assess passage at Bosher's Dam fishway. Ninety-four American shad were radio-tagged on the spawning grounds below Bosher's Dam. Approximately one-half of the tagged shad were detected at the escapement receiver within 24 hours after tagging, and the average residence times of remaining shad were approximately one week. No tagged shad were detected above Bosher's Dam. These results imply that restricted passage through Bosher's Dam fishway may be an important factor in the failure of James River American shad to recover. Therefore, improving passage at migratory barriers such as Bosher's Dam, in conjunction with a continued Bay-wide fishing moratorium, may be more beneficial to shad restoration efforts in James and other Chesapeake Bay tributaries than continued supplementation.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references (p. 188-204). / Geochemical signatures in the otoliths of diadromous fishes may allow for retrospective analyses of natal origins. In an assessment of river-specific signatures in American shad (Alosa sapidissima), an anadromous clupeid native to the Atlantic coast of North America, stable isotope and elemental ratios in otoliths of juvenile American shad produced accurate natal tags from 12 rivers. Significant inter-annual variability in geochemical signatures from several rivers was detected, due largely to differences in 8180 values among years. The database was further expanded to include 20 rivers from Florida to Quebec, encompassing all major spawning populations. This task was accomplished by collecting juvenile otoliths along with water samples from rivers where juveniles were not sampled. Regressions between otolith and water chemistry for those rivers where both were collected showed significant relationships for Sr:Ca, Ba:Ca, 86180, and 87Sr:86Sr ratios but not for Mg:Ca or Mn:Ca. Despite reducing the combined signature to only four chemical ratios, cross-validated classification accuracies of known-origin juveniles averaged 93%. Ground-truthed signatures were used to classify migrants of unknown origins. Adults returning to spawn in the York River were classified according to their otolith composition. / (cont.) Only 6% of spawners originated from rivers other than the York, supporting the hypothesis that most American shad spawn in their natal river. Of remaining spawners, 79% originated from the Mattaponi River and 21% from the Pamunkey River. The results suggested that while most American shad home to their natal river there is less fidelity to individual tributaries, allowing subsidies to subpopulations with persistent recruitment failure. Otolith signatures were also used in mixed-stock analyses of immature migrants along the coast of Maine in the spring and Minas Basin in the summer. Mixed-stock compositions showed remarkably low diversity and were dominated by fish from the Shubenacadie and Hudson rivers, with an increasing proportion of Potomac River fish over time. In contrast to results from adult tagging studies, southern stocks were virtually absent. These data suggest ontogenetic shifts in migratory behavior. The thesis concludes with a report that water contributed 83% of Sr and 98% of Ba in the otoliths of a marine fish. / by Benjamin Walther. / Ph.D.