Lorraine Maceda

Conservation of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus: delineation of stock structure and distinct population segments

The anadromous Atlantic sturgeon Acipenser oxyrinchus oxyrinchus, a wide-ranging species along the Atlantic Coast of North America, is being considered for federal listing under the U.S. Endangered Species Act. Identification of distinct population segments (DPS) is necessary but problematic for highly vagile species such as Atlantic sturgeon which may spend a high proportion of their lives outside of their natal estuaries. Characterization of genetic differentiation and estimates of gene flow provide a quantitative measure of the number of DPS into which species could be divided over their distribution and the reproductive independence of each unit. We sequenced a portion of the mitochondrial DNA control region to characterize population structure and gene flow across all naturally reproducing populations from which specimens could be obtained. We then considered these genetic data along with ancillary information on life history characteristics, historical fisheries data, and trajectories of abundance to determine the number of DPS into which this species should be divided. Our results suggest that philopatry is high for Atlantic sturgeon and that each U.S. estuary analyzed hosts genetically distinct populations of Atlantic sturgeon. We conclude that at least nine DPS of Atlantic sturgeon exist along the Atlantic Coast of the U.S. In contrast, the Atlantic Sturgeon Status Review Team has proposed a five DPS scheme for this subspecies based largely on results from nuclear DNA microsatellites, but with fewer populations represented and lower samples sizes. These different conclusions illustrate the somewhat arbitrary nature of the DPS concept, at least as applied to Atlantic sturgeon.

Use of mitochondrial DNA polymorphisms to estimate the relative contributions of the Hudson River and Chesapeake bay striped bass stocks to the mixed fishery on the Atlantic coast

Abstract Restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) was used to characterize stocks of striped bass Morone saxatilis and to estimate their relative contributions during the fall of 1989 to the mixed coastal fishery at eastern Long Island, New York. Mitochondrial DNA was obtained from reference samples of striped bass collected during the spring of 1989 from the Hudson River, New York, and four spawning areas of the Chesapeake Bay (Choptank, Rappahannock, and Potomac rivers and the upper Chesapeake Bay). Five mtDNA major length genotypes were detected in these fish, and significant differences in their frequencies were observed between the Hudson River and Chesapeake Bay samples. An mtDNA minor length genotype found in some fish (13%) from the Chesapeake Bay and absent from all Hudson River samples provided a second discriminatory character. By using a constrained generalized least squares approach, we estimated that the Hudson River and Chesapeake Bay stocks cont...

Stock Identification of Atlantic Cod in U.S. Waters Using Microsatellite and Single Nucleotide Polymorphism DNA Analyses

Abstract Management of Atlantic cod Gadus morhua in U.S. waters is based on a two-stock model composed of stocks from (1) the Gulf of Maine (GOM) and (2) Georges Bank (GB) and areas south; however, evidence suggests a more fine-scale structuring. We used microsatellite and single nucleotide polymorphism (SNP) analyses to investigate the stock structure of Atlantic cod in U.S. waters. In year 1, we analyzed microsatellite loci in larvae from GB, age-0 juveniles from multiple locations in the GOM, and adults of unknown maturity from GB, Jeffreys Ledge, and the Great South Channel (GSC). In year 2, Atlantic cod collected from spawning aggregations in Ipswich Bay in the spring and at GB, Stellwagen Bank, Chatham, and Ipswich Bay in the winter, along with adults of unknown maturity from Long Island, New York, were surveyed at a modified battery of microsatellites and three SNPs. In year 1, we saw no significant differences in allelic frequencies between our composite sample of adult and juvenile cod from the G...

An evaluation of introgression of Atlantic coast striped bass mitochondrial DNA in a Gulf of Mexico population using formalin-preserved museum collections

Striped bass Morone saxatilis populations in drainages along the Gulf of Mexico coast (Gulf) were depleted in the 1950s and 1960s, probably because of anthropogenic influences. It is believed that only the Apalachicola‐Chattahoochee‐Flint (A‐C‐F) river system continually supported a naturally reproducing population of Gulf lineage. Striped bass juveniles of Atlantic coast (Atlantic) ancestry were introduced to restore population abundances in the A‐C‐F from the late 1960s to the mid 1970s and in many other Gulf rivers from the 1960s to the present. We previously identified mtDNA polymorphisms that were unique to ≊ 60% of striped bass from the A‐C‐F and which confirmed the continued successful natural reproduction of striped bass of Gulf maternal ancestry within the system. However, the genetic relatedness of the extant A‐C‐F population to ‘pure’ Gulf striped bass was not addressed. In this study, we determined the frequency of a diagnostic mtDNA XbaI polymorphism in samples of ‘pure’ Gulf striped bass that were collected from the A‐C‐F prior to the introduction of Atlantic fish, that were obtained from museum collections, and that were originally preserved in formalin. PCR primers were developed that allowed for amplification of a 191‐bp mtDNA fragment that contained the diagnostic XbaI restriction site. Using RFLP and direct sequence analyses of the PCR amplicons, we found no significant differences in mtDNA XbaI genotype frequencies between the archived samples and extant A‐C‐F samples collected over a 15‐year period. This indicates that significant maternally mediated introgression of Atlantic mtDNA genomes into the A‐C‐F gene pool has not occurred. Additionally, we found no evidence of the unique Gulf mtDNA genotype in striped bass from extant populations in Texas, Louisiana and the Mississippi River. These results highlight the importance of the A‐C‐F as a repository of striped bass to restore extirpated Gulf populations and the potential use of museum collections in retrospective population studies.

Stock Origin of Migratory Atlantic Sturgeon in Minas Basin, Inner Bay of Fundy, Canada, Determined by Microsatellite and Mitochondrial DNA Analyses

Abstract Five distinct population segments of Atlantic sturgeon Acipenser oxyrinchus were recently listed (April 2012) as endangered or threatened under the U.S. Endangered Species Act. Atlantic sturgeon are anadromous, spawning occurs in rivers from the St. Lawrence River, Quebec, to the Satilla River, Georgia, and subadults and adults undertake extensive coastal migrations. Bycatch of Atlantic sturgeon in coastal fisheries may have resulted in the slowed or failed rebuilding of many populations despite the imposition of a U.S. federal moratorium on their harvest in 1998. Canadas Bay of Fundy hosts weir and trawl fisheries which bycatch Atlantic sturgeon of unknown origin. Additionally, tidal power development projects for the Bay of Fundy have been proposed which could detrimentally impact migratory sturgeon. We hypothesized that the Atlantic sturgeon that occur in Minas Basin in the Bay of Fundy are of local Saint John River, New Brunswick, origin with little or no U.S. contribution. We used microsate...

Population origin of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus by-catch in U.S. Atlantic coast fisheries

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 NOAAs 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.

Origin of Atlantic Sturgeon Collected off the Delaware Coast during Spring Months

AbstractAtlantic 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 referen...

Origin and Movements of Young-of-the-Year Striped Bass in the Southern Gulf of St. Lawrence, New Brunswick

Abstract Young-of-the-year (age-0) striped bass Morone saxatilis have been observed during late summer and fall in southern Gulf of St. Lawrence estuaries that may not support striped bass spawning. In this study, we tested the hypothesis that age-0 striped bass in the Richibucto and Kouchibouguac rivers disperse there from the Miramichi River, which is located approximately 35 km north of the Kouchibouguac River and 55 km north of the Richibucto River. Beach seining of the coastline between these three rivers during summer in 1997 and 1998 confirmed the presence of age-0 striped bass in the latter half of August but not before. Age-0 fish distributions over time were consistent with movement from the Miramichi River to the Kouchibouguac and Richibucto estuaries. Microsatellite nuclear DNA and mitochondrial DNA analyses were performed to determine the genetic relatedness among striped bass from these estuaries. Age-0 striped bass from the Shubenacadie River population in the Bay of Fundy, which is known t...

Coastwide Stock Structure of Winter Flounder Using Nuclear DNA Analyses

AbstractMany 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. ...

Introgression of Nuclear DNA (nDNA) Alleles of Stocked Atlantic Coast Striped Bass with the Last Remaining Native Gulf of Mexico Population

Abstract Since the 1960s, only the Apalachicola–Chattahoochee–Flint (ACF) river system has continually supported a naturally reproducing population of striped bass Morone saxatilis of Gulf of Mexico (Gulf) lineage. Striped bass fry and fingerlings of Atlantic ancestry (from the Santee– Cooper system) were introduced into the ACF from the late 1960s to 1977. Genotypes were previously identified that were unique to fish from the ACF and that confirmed the continued natural reproduction of striped bass of Gulf ancestry within that population. Also, no significant difference in haplotype frequencies between “pure” archived ACF and extant ACF samples was found at an Xba I mitochondrial DNA (mtDNA) restriction site that is diagnostic in distinguishing extant ACF from extant Atlantic specimens. This suggested that significant maternally mediated introgression of Atlantic mtDNA genomes has not occurred. However, because mtDNA is maternally inherited, the introgression of paternally derived nuclear DNA alleles int...