Faculty Bibliography

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.

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.

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 > 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.

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.

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.

Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus was federally listed under the U.S. Endangered Species Act as five distinct population segments (DPS). Currently, at least 18 estuaries coastwide host spawning populations and the viability of these vary, requiring differing levels of protection. Subadults emigrate from their natal estuaries to marine waters where they are vulnerable to bycatch; one of the major threats to the rebuilding of populations. As a result, identifying the population origin of Atlantic Sturgeon in coastal waters is critical to development of management plans intended to minimize interactions of the most imperiled populations with damaging fisheries. We used mitochondrial DNA control region sequencing and microsatellite DNA analyses to determine the origin of 261 Atlantic Sturgeon collected off the Delaware coast during the spring months. Using individual-based assignment (IBA) testing and mixed stock analysis, we found that specimens originated from all nine of our reference populations and the five DPSs used in the listing determination. Using IBA, we found that the Hudson River population was the largest contributor (38.3%) to our coastal collection. The James (19.9%) and Delaware (13.8%) river populations, at one time thought to be extirpated or nearly so, were the next largest contributors. The three populations combined in the South Atlantic DPS contributed 21% of specimens; the Altamaha River, the largest population in the South Atlantic DPS, only contributed a single specimen to the collection. While the origin of specimens collected on the Delaware coast was most likely within rivers of the New York Bight DPS (52.1%), specimens that originated elsewhere were also well represented. Genetic analyses provide a robust tool to identify the population origin of individual sturgeon outside of their natal estuaries and to determine the quantitative contributions of individual populations to coastal aggregations that are vulnerable to bycatch and other anthropogenic threats. C1 Wirgin, Isaac; NYU, Dept Environm Med, Sch Med, 57 Old Forge Rd, Tuxedo Pk, NY 10987 USA

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.

Many Winter Flounder Pseudopleuronectes americanus populations have declined dramatically. In U.S. waters, Winter Flounder are managed as three stocks: Gulf of Maine, southern New England-Mid-Atlantic Bight, and Georges Bank. Historically, it was believed that the spawning of inshore stocks occurs exclusively within natal estuaries. Based on the supposition of estuary-specific spawning, we hypothesized that Winter Flounder exhibit greater stock structure than predicted by the three-stock model and, in fact, that they exhibit genetic differentiation at the level of individual estuaries. We tested this hypothesis by conducting microsatellite DNA analysis at 12 loci and single-nucleotide polymorphism analysis at 4 loci on young-of-the year and adult Winter Flounder collected from 27 estuaries from Newfoundland to Delaware as well as from Georges Bank. We found highly significant coastwide genetic stock structure among Winter Flounder; however, there was little evidence of estuary-specific structure. Pooled collections from north and south of Cape Cod were genetically distinct, as were many individual collections compared between these two regions. However, there was little genetic heterogeneity among estuarine collections within either of these major geographic regions. The two Canadian collections from the Miramichi River and Newfoundland were genetically distinct from those in the Gulf of Maine. Our collection from Georges Bank was marginally distinct from the inshore collections from north and south of Cape Cod. Overall, our genetic results support the three-stock model used to manage Winter Flounder in U.S. waters and indicate the presence of at least two genetic stocks in Canadian waters (the Miramichi River in the Gulf of St. Lawrence and Passamaquoddy Bay in the Bay of Fundy). Furthermore, our data suggest that the spawning of Winter Flounder in nearshore coastal waters is more extensive than previously thought or that homing is weaker, contributing to the absence of genetic differentiation!

American Shad Alosa sapidissima in the Hudson River, New York, and coastwide have shown major long-term declines. A possible contributing factor is commercial fisheries that harvest this population outside of the Hudson River estuary. Using previously published and new reference microsatellite data from 33 baseline populations, our goals were (1) to estimate the proportion of Hudson River American Shad contributing to the two remaining major mixed-stock fisheries along the Atlantic coast in Delaware Bay and the Bay of Fundy and (2) to estimate the proportions of other American Shad stocks contributing to these two fisheries at the highest level of stock specificity. Stock composition estimates for 2009 and 2010 Delaware Bay collections were made using three models that ranged from the most simple question (Hudson River and Delaware Bay populations) to one with all 33 baseline populations included. In all cases, a Hudson River contribution nearly equal to that of the Delaware Bay contribution was observed, indicating a substantial take on the otherwise protected Hudson River population. When all baseline populations were included for the larger 2010 Delaware Bay collection, 19 showed nonzero contributions, largely drawn from mid-Atlantic U.S. rivers. The 2009 Bay of Fundy collection showed contributions from across most of the species' range but was dominated by northern populations. Mixed-stock analyses of collections from the two sites together indicate that these estuarine fisheries harvested not only proximal populations but those originating from a wide latitudinal range.