Faculty Bibliography

Atlantic sturgeon Acipenser oxyrinchus surfacing behaviour was investigated in Minas Basin (45° 20' N; 64° 00' W) and the Bay of Fundy with pop-up satellite archival tags (MiniPAT) measuring physical variables (pressure, temperature, light). Of six tags deployed during June and July, five provided pop-up locations and two were recovered after c. 4 months. Analysis of recovered archival data revealed that the frequency of surfacing events was highest (78·9%) when A. oxyrinchus were in Minas Basin at depths <10 m. Surfacing frequency decreased substantially when fish migrated into greater depths of the Bay of Fundy (>40 m). The tidal cycle in Minas Basin had a significant relationship to surfacing frequency, with the most surfacing events (49·5%) occurring on the flood tide, from mid- to high-tide. Surfacing events ranged from 0-12 a day and the maximum number occurred between 2300 and 0300 hours. Maximum surfacing ascent speeds ranged from 0·50 to 4·17 m s^-1and maximum descent speeds ranged from 0·17 to 3·17 m s^-1. Buoyancy control, by gulping air to inflate the gas bladder, is proposed as the main reason for surfacing behaviour in A. oxyrinchus.

Atlantic sturgeon and shortnose sturgeon co-occur in many estuaries along the Atlantic Coast of North America. Both species are protected under the U.S. Endangered Species Act and internationally on the IUCN Red list and by CITES. Early life-stages of both sturgeons may be exposed to persistent aromatic hydrocarbon contaminants such as PCBs and PCDD/Fs which are at high levels in the sediments of impacted spawning rivers. Our objective was to compare the PCBs and TCDD sensitivities of both species with those of other fishes and to determine if environmental concentrations of these contaminants approach those that induce toxicity to their young life-stages under controlled laboratory conditions. Because our previous studies suggested that young life-stages of North American sturgeons are among the more sensitive of fishes to coplanar PCB and TCDD-induced toxicities, we were interested in identifying the molecular bases of this vulnerability. It is known that activation of the aryl hydrocarbon receptor 2 (AHR2) in fishes mediates most toxicities to these contaminants and transcriptional activation of xenobiotic metabolizing enzymes such as cytochrome P4501A (CYP1A). Previous studies demonstrated that structural and functional variations in AHRs are the bases for differing sensitivities of several vertebrate taxa to aromatic hydrocarbons. Therefore, in this study we characterized AHR2 and its expression in both sturgeons as an initial step in understanding the mechanistic bases of their sensitivities to these contaminants. We also used CYP1A expression as an endpoint to develop Toxicity Equivalency Factors (TEFs) for these sturgeons. We found that critical amino acid residues in the ligand binding domain of AHR2 in both sturgeons were identical to those of the aromatic hydrocarbon-sensitive white sturgeon, and differed from the less sensitive lake sturgeon. AHR2 expression was induced by TCDD (up to 6-fold) and by three of four tested coplanar PCB congeners (3-5-fold) in Atlantic sturgeon, but less so in shortnose sturgeon. We found that expression of AHR2 and CYP1A mRNA significantly covaried after exposure to TCDD and PCB77, PCB81, PCB126, but not PCB169 in both sturgeons. We also determined TEFs for the four coplanar PCBs in shortnose sturgeon based on comparison of CYP1A mRNA expression across all doses. Surprisingly, the TEFs for all four coplanar PCBs in shortnose sturgeon were much higher (6.4-162 times) than previously adopted for fishes by the WHO.

Atlantic tomcod in the Hudson River Estuary bioaccumulate high hepatic burdens of environmental toxicants. Previously, we demonstrated that Hudson River tomcod developed resistance to TCDD and PCB toxicity probably through strong natural selection during their early life-stages for a variant of the Aryl Hydrocarbon Receptor2 (AHR2). Here, we evaluated the genomic consequences of the resistant genotype by comparing global gene expression in larval tomcod from the Hudson River with expression in larvae from a nearby sensitive population (Shinnecock Bay). We developed an annotated draft tomcod genome to explore the effects of multigenerational exposure to toxicants and a functionally impaired AHR2 on the transcriptome. We used the tomcod genome as a reference in RNA-Seq to compare global gene expression in tomcod larvae from the Hudson River and Shinnecock Bay after experimental exposure of larvae to graded doses of TCDD. We found dramatic differences between offspring from the two populations in the number of genes that were differentially expressed at all doses (0.01, 0.1, and 1 ppb) and even in the vehicle controls. At the two lowest TCDD doses, 250 and 1,141 genes were differentially expressed in Shinnecock Bay larvae compared with 14 and 12, respectively, in Hudson River larvae. At the highest dose (1.0 ppb), 934 genes were differentially expressed in Shinnecock Bay larvae and 173 in Hudson River larvae, but only 28 (16%) of affected genes were shared among both populations. Given the large difference between the two populations in the number and identity of differentially expressed genes, it is likely that the AHR2 pathway interacts directly or indirectly with many genes beyond those known in the AHR2 battery and that other regulatory systems may also respond to TCDD exposure. The effects of chronic multi-generational exposure to environmental toxicants on the genome of Hudson River tomcod are much greater than previously expected.

Natural mortality of Atlantic sturgeon (Acipenser oxyrinchus) has been determined to be low (M = 0.07). Reported herein is the mortality by beach stranding of 11 Atlantic sturgeon in Scot's Bay, part of the inner Bay of Fundy in Nova Scotia, Canada on 22 June 2014. Genetic analyses, histological analysis and age determination were performed to determine origin, maturity stage and age of the stranded Atlantic sturgeon. Microsatellite and mitochondrial DNA analyses indicated that four of the Atlantic sturgeon (2 males and 2 females) were from the Saint John River, NB population, which was designated as threatened by the Committee on the Status of Endangered Wildlife in Canada. Seven Atlantic sturgeon (1 male, 5 females, 1 unknown) were from the Kennebec River, Maine population, that was listed as threatened under the Endangered Species Act in the U. S. Ageing of A. oxyrinchus by pectoral fin spine analysis determined that the mean age of the individuals from the Saint John River ( [Formula: see text] years, sd = 5.0) and the Kennebec River ( [Formula: see text] years, sd = 3.5) were not significantly different. This is the first report of a stranding event of Atlantic sturgeon, and describes a source of natural mortality affecting populations of concern in both Canada and the U. S.

Atlantic Sturgeon is listed under the U.S. Endangered Species Act as five Distinct Population Segments (DPS). The "endangered" New York Bight (NYB) DPS is thought to only harbor two populations; one in the Hudson River and a second smaller one in the Delaware River. Historically, the Connecticut River probably supported a spawning population of Atlantic Sturgeon that was believed extirpated many decades ago. In 2014, we successfully collected pre-migratory juvenile specimens from the lower Connecticut River which were subjected to mitochondrial DNA (mtDNA) control region sequence and microsatellite analyses to determine their genetic relatedness to other populations coastwide. Haplotype and allelic frequencies differed significantly between the Connecticut River collection and all other populations coastwide. Sibship analyses of the microsatellite data indicated that the Connecticut River collection was comprised of a small number of families that were likely the offspring of a limited number of breeders. This was supported by analysis of effective population size (Ne) and number of breeders (Nb). STRUCTURE analysis suggested that there were 11 genetic clusters among the coastwide collections and that from the Connecticut River was distinct from those in all other rivers. This was supported by UPGMA analyses of the microsatellite data. In AMOVA analyses, among region variation was maximized, and among population within regions variation minimized when the Connecticut River collection was separate from the other two populations in the NYB DPS indicating the dissimilarity between the Connecticut River collection and the other two populations in the NYB DPS. Use of mixed stock analysis indicated that the Connecticut River juvenile collection was comprised of specimens primarily of South Atlantic and Chesapeake Bay DPS origins. The most parsimonious explanation for these results is that the Connecticut River hosted successful natural reproduction in 2013 and that its offspring were descendants of a small number of colonizers from populations south of the NYB DPS, most notably the South Atlantic DPS. Our results run contrary to the belief that re-colonizers of extirpated populations primarily originate in proximal populations.

Phragmites australis is a perennial grass that has invaded wetlands of the northeastern United States over the past century. The Hudson River Estuary and surrounding watersheds are no exception in that populations of P. australis have spread dramatically along its shores and tributaries in the past 40 years. Recent studies have shown that genetically variable populations of P. australis can spread by seed dispersal in addition to clonal mechanisms. It is important to characterize the genetic variation of Hudson River populations as part of a management strategy for this species to determine the mechanisms by which its spreads and colonizes new habitats, particularly those with frequent anthropogenic disturbances. The goals of this study were to quantify levels of genetic variation and structuring in Hudson River populations of P. australis using microsatellite DNA analysis. A total of 354 culms of P. australis were collected from nine locations ranging from Albany, New York to Staten Island, New York in the summers of 2004 (N = 174) and 2011 (N = 180). Microsatellite data from eight loci indicated that the Hudson River Estuary has some of the highest levels of genetic variation of all U. S. Atlantic Coast regions containing P. australis. Gene diversity (Hs) across all loci in the 2004 collection was 0.45 (+/- 0.02) and that of the 2011 collection was 0.47 (+/- 0.07). Patches within sample sites were rarely monoclonal and had multiple genetic phenotypes. Moran's Identity tests indicated that individuals within a patch were closely related, whereas little genetic relatedness was evident among individuals from sample sites &gt; 1 km apart. Spatial structuring was also not evident in autospatial correlation and principle coordinate analyses. These findings suggest that genetic diversity is maintained within stands by sexual reproduction and that seeds are important in dispersal of P. australis across the Hudson River Estuary. Ample habitats are available for establishment of new Phragmites stands due to high levels of anthropogenic disturbance from populations living along the Estuary. Wildlife managers should focus on monitoring habitats that provide seedbed for Phragmites and promote land use practices that prevent soil disturbance and establishment of new stands.

The Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus is an important component of biodiversity along the Atlantic coast of North America, but most populations have been decimated by habitat degradation and chronic overfishing. Historically, spawning populations existed in all major Atlantic coast rivers from the St. Lawrence River, Quebec, to the St. Johns River, Florida, but fisheries surveys conducted in the past two decades suggest that several populations at the southern extent of this range are now extirpated or have declined to remnant status. Our objective was to assess the abundance and genetic character of Atlantic Sturgeon in the Satilla River, Georgia. Using entanglement gears, we expended over 2,800 h of sampling effort and captured a total of 193 Atlantic Sturgeon in tidally influenced reaches of the river during 2008-2010. Of the 157 fish that were collected in 2010, 72 were identified as river-resident juveniles (ages 0-1). Genetic analyses of a subset (n = 61) of these juveniles revealed (1) depauperate levels of mitochondrial DNA (mtDNA) haplotype diversity and (2) the presence of large family units based on microsatellite DNA multilocus genotypes, collectively suggesting that very few parents produced the 2008 year-class. The mtDNA and microsatellite analyses both indicated that juveniles in the Satilla River population were genetically distinct from other populations in the South Atlantic Distinct Population Segment. Atlantic Sturgeon life history characteristics and the present results suggest that sampled juveniles from the 2008 year-class were the offspring of a small remnant pool of Satilla River adults; however, a full description of the population's genetic character and origin will require additional juvenile samples from future year-classes.

American mink Neovison vison may be particularly vulnerable to toxicities of persistent contaminants such as PCBs because of their aquatic-based diet, position near the top of the food web, and small deme sizes. Furthermore, ranched mink are sensitive to reproductive toxicities of fish diets from PCB-polluted sites. The upper Hudson River is highly contaminated with PCBs and previous studies have shown elevated hepatic burdens of total and coplanar PCBs in mink collected near the river compared with those from more distant locales in New York and elsewhere. We hypothesized that bioaccumulation of PCBs in Hudson River mink has reduced their levels of genetic diversity or altered their genetic population structure. To address this, we conducted microsatellite DNA analysis on collections made in proximity to and from more distant locales in the Hudson River watershed, elsewhere in New York State, and at other sites in eastern North America including New Brunswick, four locales in Ontario, multiple drainages in Maine, and two ecoregions in Rhode Island. We did not find reduced genetic diversity at the individual or population levels in mink collected near (<6 km) to PCB hotspots in the Hudson River nor evidence of altered population structure. Consistent with their distribution in small localized and isolated demes, we did find significant genetic population structure among many mink collections in New York State and elsewhere. Depending on the analytical approach used, genetically distinct populations numbered between 16 when using STRUCTURE to 19-20 when using Exact G tests, F ST, or AMOVA analyses. Genetically distinct population units were found among major ecoregions and minor ecoregions in New York State, among different hydrologic subunits within the Hudson River watershed, among spatially separate locales in Ontario, and among most watersheds in Maine. However, despite this localization and potential heightened impact of stressors, genetic diversity and genetic population structure in mink does not seem to be affected by their bioaccumulation of high levels of PCBs of Hudson River origin.

BACKGROUND: Large epidemiologic studies have the potential to make valuable contributions to the assessment of gene-environment interactions because they prospectively collected detailed exposure data. Some of these studies, however, have only serum or plasma samples as a low quantity source of DNA. METHODS: We examined whether DNA isolated from serum can be used to reliably and accurately genotype single nucleotide polymorphisms (SNPs) using Sequenom multiplex SNP genotyping technology. We genotyped 81 SNPs using samples from 158 participants in the NYU Women's Health Study. Each participant had DNA from serum and at least one paired DNA sample isolated from a high quality source of DNA, i.e. clots and/or cell precipitates, for comparison. RESULTS: We observed that 60 of the 81 SNPs (74%) had high call frequencies (>/=95%) using DNA from serum, only slightly lower than the 85% of SNPs with high call frequencies in DNA from clots or cell precipitates. Of the 57 SNPs with high call frequencies for serum, clot, and cell precipitate DNA, 54 (95%) had highly concordant (>98%) genotype calls across all three sample types. High purity was not a critical factor to successful genotyping. CONCLUSIONS: Our results suggest that this multiplex SNP genotyping method can be used reliably on DNA from serum in large-scale epidemiologic studies.

Microsatellite DNA and mitochondrial DNA control-region sequence analyses were used to determine the population and distinct population segment (DPS) origin of 173 Atlantic sturgeon Acipenser oxyrinchus oxyrinchus encountered from the Gulf of Maine to Cape Hatteras, North Carolina, in NOAA's Northeast Fisheries Observer Program. It was found that the Hudson River was by far the greatest contributor to this coastal by-catch, with 42.2-46.3% of specimens originating there. Generally, specimens represented the geographic province of the river in which they were spawned, but some specimens, particularly those originating in the South Atlantic DPS, moved to great distances. Genetic mixed-stock analyses provide an accurate approach to determine the DPS and population origin of A. o. oxyrinchus by-catch in coastal waters, but most informative management requires that these results be partitioned by locale, season, target fishery and gear type.