Northeast Fishery Center
Northeast Region
 

Recent Projects of the Population Ecology Branch

 

Annual Genetic Characterization of Atlantic Salmon broodstock at Craigbrook National Fish Hatchery

2005 Pedigree Line for the Pleasant River Broodstock at Craigbrook National Fish Hatchery

Genetic Characterization of an Isolated Population of Northern Plymouth Red-bellied Cooter (Pseudemys rubriventris) in Massachusetts

Genetic Characterization of two Northern Riffleshell (Epioblasma torulosa rangiana) population in the Allegheny River

Evaluation of Genetic Diversity and Relatedness for Atlantic Sturgeon (Acipenser oxyrinchus) captively held by Maryland DNR

Genetics Assessment of Susquehanna River Shad

Juvenile Atlantic Sturgeon Sampling in the Hudson River, NY

Mortality Associated with Catch and Release Angling of Striped Bass in the Hudson River

An age-structured population model for horseshoe crabs in the Delaware Bay area to assess harvest and egg availability for shorebirds

Evaluation of Removal Sampling for Basin-wide Assessment of Atlantic Salmon

Assessment of Thermal Habitat for Maine’s DPS Atlantic Salmon

Assessment of Watershed Scale Habitat Features on the Survival of Juvenile Atlantic Salmon

Tagging Adult Atlantic Sturgeon in the Hudson River with Sonic and Pop-off Archival Tags

Monitoring Brook Trout Populations in the Sinnemahoning Creek Watershed, Pennsylvania

 

Annual Genetic Characterization of Atlantic Salmon broodstock at Craigbrook National Fish Hatchery

Processing Genetic Samples

USFWS biologist processing gentics samples. (Photo Credit: USFWS - NEFC)

 

Atlantic salmon broodstock management incorporates the use of genetic characterization of all potential broodstock. Genetic characterization is used to track changes in estimates of genetic diversity, monitor for evidence of artificial selection, and manage the future spawning stock to maintain genetic diversity over time. Genetic data is used to identify optimal spawning pairs, assess recovery of stocked juveniles, and screen for potential aquaculture escapees. Characterization is completed annually for adult salmon returning to the Veazie Dam on the Penobscot River. Genetic characterization and monitoring of the broodstocks follows recommendations described in the CBNFH Broodstock Management Plan, and the Recovery Plan for Atlantic Salmon.

Back to top

2005 Pedigree Line for the Pleasant River Broodstock at Craigbrook National Fish Hatchery

salmon smolts

Atlantic salmon smolts. (Photo Credit: USFWS - CBNFH)

 

Due to a small broodstock population size and poor recovery of stocked hatchery juveniles, a pedigree line was established for the Pleasant River, ME. To ensure adequate numbers of individuals in the broodstock, the use of a pedigree line was implemented for the offspring from the 2003 spawning year for the Pleasant River. A pedigree line is composed of two parts, where fry from all families are mixed, and half of the juveniles are retained in the hatchery (domestic portion), and the other half are stocked in the river according to stocking practices (captive portion). Following collection of the captive portion from the river as parr, all individuals from both portions are genotyped to determine the familial representation within each group. Individual familial contribution is equalized using individuals from both groups, and then surplus individuals (to broodstock needs) are stocked into the river as smolts.

Back to top

Genetic Characterization of an Isolated Population of Northern Plymouth Red-bellied Cooter (Pseudemys rubriventris) in Massachusetts

Red-bellied Cooter Photo

Red-bellied cooter.

 

The northern red-bellied cooter is a turtle species that is currently listed as endangered in Massachusetts. There is some discussion regarding whether or not the Massachusetts population is a subspecies, or represents a single isolated population. Because the Massachusetts population is isolated and its status is supplemented by a head-start hatching program, there are additional concerns about the genetic diversity and long-term viability of the population, particularly through high levels of inbreeding. The goal of this project is to characterize the genetic diversity observed in the Massachusetts population relative to populations observed in other parts of its range. Information about the genetic diversity observed in the Massachusetts population will be used by agencies to revise management and conservation strategies as needed.

Back to top

Genetic Characterization of two Northern Riffleshell (Epioblasma torulosa rangiana) population in the Allegheny River

Northern Riffleshell mussel

Northern Riffleshell. Courtesy of USFWS Region 3 Division of Endangered Species

 

The northern rifflleshell (Epioblasma torulosa rangiana) is a mussel that is currently listed as an endangered species. Two isolated populations are thought to be the only population of northern riffleshell remaining in the Allegheny River. The two populations in the Allegheny River are currently threatened by road construction projects. To prevent potential harm to the population due to increased sedimentation, both groups of mussels will be temporarily removed from the area and housed at the USFWS White Sulphur Springs mussel culture facility. The use of refugia and captive propagation for mussel culture presents unique opportunities to obtain genetic material from mussels. This study will characterize estimates of genetic variation in each of the populations to determine genetic viability of each population. Additionally captive breeding protocols will be developed to ensure long-term maintenance of genetic diversity of this species.

Back to top

Evaluation of Genetic Diversity and Relatedness for Atlantic Sturgeon (Acipenser oxyrinchus) captively held by Maryland DNR

Atlantic sturgeon

Atlantic sturgeon. Courtesy of Duane Raver, USFWS.

 

Hatchery supplementation has often been used as a tool in fisheries management to restore declining populations, supplement existing populations, or introduce new species. An important component of hatchery supplementation is broodstock management. The primary goals of captive broodstock management for restoration or recovery of declining populations include minimizing inbreeding potential and maintaining genetic diversity. To minimize inbreeding and maintain genetic diversity, the primary broodstock techniques focus on the number of adults used for spawning and the mating strategy used for propagation. Maryland Department of Natural Resources (MDDNR) currently maintains a captive broodstock for Atlantic sturgeon. Offspring resulting from captive broodstock propagation would be incorporated into a stocking program for the greater Chesapeake Bay area. Microsatellite DNA markers were used to estimate measures of genetic diversity for individuals from both the wild caught and captively bred groups of Atlantic sturgeon to be used as broodstock by MDDNR. This information will be used to develop a broodstock management plan and spawning design for the Maryland captive sturgeon.

Back to top

Genetics Assessment of Susquehanna River Shad

American shad

American shad. Courtesy of Duane Raver, USFWS.

 

Hatchery propagation and stocking of American shad represent a large component of restoration efforts in the Susquehanna River. In a subsample of the returning adult population at Conowingo Dam in 2003, approximately 26% of the adults were of wild origin, and 74% wer of hatchery origin. The Susquehanna River Anadromous Fish Restoration Committee (SRAFRC) collects shad eggs from two locations on the Susquehanna River, and from the Hudson and Delaware rivers for stocking in the Susquehanna River. If possible, determination of the source of wild origin shad in the Susquehanna that successfully retun as adults (as the marked individuals) and produce offspring that return as adults (unmarked) will aid in restoration efforts through the targetting of those stocks for stocking efforts. We are conducting genetic investigations of the adult shad that returned to the Lapidum area and to Conowingo Dam in the spring 2005 to identify the source of wild-origin adult shad. Comparisons of estimates of genetic diversity between shad of hatchery origin may identify which introduced stocks were successful in establishing reproducing populations. Additionally, characterizing shad utilizing different sections of river may adid in the understanding of life history characteritics and behavior.

Back to top

Juvenile Atlantic Sturgeon Sampling in the Hudson River, NY

Releasing juvenile sturgeon

Releasing a juvenile Atlantic Sturgeon in Haverstraw Bay of the Hudson River, NY (Photo Credit: USFWS - NEFC)

 

Atlantic sturgeon Acipenser oxyrinchus populations have greatly declined along the east coast of North America. Atlantic sturgeon are a long-lived species with a complex life history, making population assessment difficult. We collaborated with New York State Department of Envronmental Conservation (NYSDEC) staff to determine seasonal habitat use by juvenile Atlantic sturgeon in the Hudson River estuary and to provide recommendations for future population monitoring. Our study focused on Newburgh and Haverstraw bays of the Hudson River, as these are areas of known juvenile concentrations. Habitat within each bay was coarsely stratified according to substrate (hard versus soft) and depth (deep versus shallow). Sampling occurred during fall 2003, spring 2004, fall 2004, spring 2005, and fall 2005. Fall sampling occurred from October through November and spring sampling occurred from March through April. We used anchored gill nets of 76, 102, and 127 mm stretch mesh. A total of 562 individual juvenile Atlantic sturgeon were captured during the course of this study (14 were captured more than once), with the majority (90%) coming from Haverstraw Bay. Soft/deep areas of Haverstraw Bay consistently yielded the greatest frequency of catches, the highest mean catch-per-unit-effort (CPUE), and lowest variance on CPUE. Catch-per-unit-effort was highest during spring seasons in soft/deep areas of Haverstraw Bay. These results suggest that future population monitoring should focus sampling effort in soft/deep areas of Haverstraw Bay in order to have the greatest statistical power in detecting population trends.

Back to top

Mortality Associated with Catch and Release Angling of Striped Bass in the Hudson River

Striped Bass

USFWS biologists holding a striped bass from the Hudson River, NY (Photo Credit: USFWS - NEFC)

 

Catch-and-release fishing commonly occurs in recreational fisheries, including those for striped bass Morone saxatilis of the Atlantic coast. The contribution of catch-and-release practices to the overall fishing mortality is often not estimated. In conjunction with NYSDEC and the help of volunteer anglers, we estimated the catch-and-release mortality for the Hudson River spawning stock of striped bass in 2001. Volunteer anglers caught striped bass between April 30 and May 16, 2001. Fish were transferred to transport boats in lice wells and placed in one of nine 15,000-L land-based holding tanks. Control fish were collected by electrofishing and otherwise handled similarly. Treatment and control fish were uniquely tagged and held together for 5 days. Hooking mortality was estimated via conditional rate and additive rates. These two estimation techniques partitioned total observed mortality into hooking mortality and handling mortality, the latter being estimated from control fish. Catch-and-release mortality for striped bass averaged 16% for traditional J hooks and 5% for circle hooks over the entire period. Hook location and the occurrence of bleeding were the most influential variables in determining the probability of death. Mortality rate increased when water temperatures reached 16oC. THis mortality rate is significant and should be considered when accounting for Hudson River striped bass removals from their spawning population.

Back to top

An age-structured population model for horseshoe crabs in the Delaware Bay area to assess harvest and egg availability for shorebirds

Graphic of horseshoe crab population growth

An example of simulated spawning female horseshoe crab population growth under the conditions of harvest occuring before the spawn, harvest of 50,000 females per year, and medium egg mortality.

 

The objective of this computer simulation study was to create an age-structured population model for horseshoe crabs (Limulus polyphemus) in the Delaware Bay region using best available estimates of age-specific mortality and recent harvest levels. Density dependence was incorporated using a spatial model relating egg mortality with abundance of spawning females. Combinations of annual female harvest (0, 50, 100, and 200 thousand), timing of female harvest (before or after spawning), and three levels of density dependent egg mortality were simulated. The probability of the population increasing was high (>80%) with low and medium egg mortality and harvest less than 200 thousand females per year. Under the high egg mortality case, the probability of the population increasing was <50% regardless of harvest. Harvest occurring after spawning increased the probability of population growth. The number of eggs available to shorebirds was highest when egg mortality was lowest and female abundance was at its highest levels. Although harvest and egg mortality influenced population growth and food availability to shorebirds, sensitivity and elasticity analysis showed that early-life stage mortality, age 0 mortality in particular, was the most important parameter for population growth. Our modeling results suggest that future research and management actions should be directed at the early juvenile stages of horseshoe crabs in the Delaware Bay. NEFC staff were aided in this study by the expertise of USGS - Leetown Science staff.

Back to top

Evaluation of Removal Sampling for Basin-wide Assessment of Atlantic Salmon

Backpack Electrofishing

USFWS and biologists electrofishing Atlantic salmon parr (Photo Credit: USFWS - CBNFH)

Removal estimators for stream fish abundance are widely used, but can result in biased population estimates at the site level. NEFC, National Marine Fisheries Service (NMFS), and Maine Atlantic Salmon Commission (MEASC) biologists conducted computer simulations to examine how the Carle and Strub (1978) estimator coupled with variation in catchability influences the accuracy of population estimates at the site level. Site level population estimates were then used to examine what effect potential bias in the population estimate at a site had on basin-wide abundance estimates. Historic Atlantic salmon Salmo salar electrofishing data from the Narraguagus River, ME was used as baseline data for the construction of these simulations. At the site level, mean percent bias of population estimates was -23% when catchability was low (0.30 – 0.40) and the true population was low (1 – 20 fish). Bias was reduced as the true population size increased and catchability increased. The negative bias at the site level affected total population estimates for the entire river basin. Under current sampling methodology in the Narraguagus River, basin-wide population estimates are likely 11 - 17% lower than the true population. Confidence intervals (95%) would be expected to cover the true population between 65 - 79% of the time. Increasing the amount of sampling had little effect on the negative bias of basin-wide population estimates, but did reduce the error about the estimate as expected. These results should serve as a reference point to gauge the effectiveness of current sampling efforts in providing reliable estimates of Atlantic salmon parr in the Narraguagus River. The methodology employed by this simulation study can also be applied to other Atlantic salmon rivers to evaluate current sampling programs.

Back to top

Assessment of Thermal Habitat for Maine’s DPS Atlantic Salmon

Map of temperature in the Narraguagus River, ME

Example map of mainstem Narraguagus River temperatures.

 

Physical habitat in Maine Atlantic salmon distinct population segment (DPS) rivers has been mapped, classified, and quantified. However, less is known about thermal habitat. Physical habitat may be adequate for spawning and juvenile rearing, but may still be limiting due to elevated temperature. Also, elevated stream temperatures may be more suitable for invasive species such as smallmouth bass, which tend to have higher thermal preferences (and tolerances). The objectives of this study were to use historical temperature logger data obtained by the MEASC to: (1) determine trends in summer temperature regimes, (2) create maps of suitable thermal habitat and compare these to maps of physical habitat, and (3) compare thermal habitat suitability of Atlantic salmon parr vs. non-native smallmouth bass. The current study focused on the Sheepscot and Narraguagus Rivers because these rivers currently have the greatest spatial and temporal coverage by temperature loggers. Daily summer temperatures (May 1 – Sept 10) from 2001 – 2004 were averaged on a weekly basis and GIS techniques were used to interpolate stream temperatures between logger sites. Interpolated temperatures were overlaid on maps of rearing habitat and classified according to the potential for growth based on a bioenergetics model for Atlantic salmon parr. Comparison of Atlantic salmon and smallmouth bass bioenergetics models suggests that relative growth potential is greater for smallmouth bass when temperatures exceed 20 oC. Using 20 oC as a threshold, maps were created showing the species most suited for temperatures during each week of the summer. Long-term datasets showed temperatures significantly increased through time. However, temperatures of rearing habitat remained within the range of temperatures required for parr growth. Stream temperatures exceeded 20 oC over nearly all portions of the Sheepscot and Narraguagus rivers during the middle of summer, and although this may still be conducive for Atlantic salmon parr growth, smallmouth bass may be better adapted to temperature regimes during this portion of the summer. Our mapping of temperature regimes in these rivers will aid managers in prioritizing fry stocking and habitat restoration efforts. Future analysis will include earlier years of data, and expand to other rivers as data becomes available.

 

Back to top

Assessment of Watershed Scale Habitat Features on the Survival of Juvenile Atlantic Salmon

 

Sheepscot Genetics Group Map

Location of genetic groups of Atlantic salmon fry stocked in the Sheepsoct River, ME in 2005.

 

 

Current Atlantic salmon recovery efforts rely heavily on the stocking of juvenile Atlantic salmon with the majority of fish being stocked as fry. In order for recovery efforts to be successful there is a need to identify areas of watersheds that yield the greatest fry to parr survival and contribute most to the outmigrating smolt population. Identification of such areas will allow managers to refine fry stocking practices to increase survival to the parr stage and optimize the number of outmigrating smolts per the number of fry stocked. Also, identification of critical juvenile Atlantic salmon production areas will help guide future salmon habitat enhancement and restoration efforts. The objectives of this study are: (1) determine quantitative relationships between inter-stage survival of juvenile Atlantic salmon and macrohabitat variables such as watershed area, temperature, pH/Alkalinity, stream gradient, abundance of non-salmon species, and abundance of predatory species, and (2) use genetically marked fry to identify the rearing locations of outmigrating Atlantic salmon smolts and assess relative survival to the smolt stage from various stocking locations. Sheepscot River 2004 broodstock at Craig Brook National Fish Hatchery were genotyped using highly polymorphic microsatellite DNA markers. Using genetic parentage analysis as a “mark”, we will be able to identify stocking location, and use the recapture and abundance of the marked fish to evaluate survival. Within a given river reach, a single genetic group of fry was stocked in May 2005. Estimation of survival to parr stages began in the September 2005. Age-0 parr survival was assessed at 27 electrofishing sites throughout the watershed by NEFC and MEASC staff. A subsample of parr had a fin clip taken for genetic analysis to determine the degree of immigration from fish stocked in other river reaches. Abundance of non-salmon species was also estimated at each electrofishing site. Survival of age-0 parr to the age-1 parr stage will be assessed during the early fall of 2006 in the same manner. Survival to the smolt stage will be assessed using a rotary screw trap near the Head Tide Dam on the mainstem of the Sheepscot River in the spring 2007. Upon collection, smolts will have a fin clip taken for parentage analysis which will identify the location of stocking as fry. Multiple regression analysis will be used to determine relationships between site level survival to each lifestage and macrohabitat features such as watershed area, stream gradient, temperature (proportion of time within the range for positive salmon growth), minimum and mean pH/Alkalinity, and biological components such as the abundance and biomass of non-salmon species and predatory species.

 

Back to top

Tagging Adult Atlantic Sturgeon in the Hudson River with Sonic and Pop-off Archival Tags

Release of tagged adult sturgeon

Release of an Adult Atlantic sturgeon tagged with a sallelite pop-off archival tag in the Hudson River, NY. (Photo Credit: USFWS - NEFC)

 

Atlantic sturgeon in the Hudson river are severely depressed and the species is protected internationally. All catch of Atlantic sturgeon in U.S. waters has been banned. Population declines are due to overfishing, dam construction that prevented access to spawning grounds, and deteriorating water quality. Knowledge of the spawning habitats, movements, and migratory patterns of adult Atlantic sturgeon is required to be able to appropriately monitor their abundance and assess the efficacy of management actions for restoration. The objective of this study is to tag adult Atlantic sturgeon entering the Hudson River in order to locate spawning grounds and track offshore movements. This knowledge will allow us to protect habitats crucial for Atlantic sturgeon restoration. In cooperation with the New York State Department of Envronmental Conservation (NYSDEC) and Wildlife Conservation Society (WCS) we captured adult Atlantic sturgeon by gill netting in the spring and summer of 2006 and 2007. Adult sturgeon were tagged with sonic transmitters and satellite pop-off archival tags which record depth, temperature, and light level data. The sonic tags are bieng used by NYSDEC staff to track in-river movements with the goal of identifying additional spawning areas. The pop-off archical tags are programed to release from the fish at pre-determined dates. The tags then float to the surface and transmit recorded data to a satellite which can then be downloaded by biologists. These data can then be used to infer when the fish left the river and where it migrated in the ocean.

 

Back to top

Monitoring Brook Trout Populations in the Sinnemahoning Creek Watershed

Brook Trout

Pennsylvania brook trout (Photo Credit: USFWS - NEFC)

 

 

Brook trout have been extirpated from many streams and their overall distribution has been reduced throughout the eastern United States. Much effort is being put forth by federal, state, and non-governmental organizations to restore brook trout throughout the species historic range. Evaluation of these restoration efforts is difficult because brook trout populations show a high degree of inter-annual variation and population targets are rarely established. The purpose of this study is to establish a long-term brook trout monitoring program in tributaries of the Sinnemahoning Creek watershed in north-central Pennsylvania. Information gained through this monitoring program will help refine brook trout monitoring protocols, establish reference conditions for which to compare ongoing restoration efforts in other stream systems, and determine the relative influences of density-dependent and density-independent factors on brook trout population dynamics.

 

Back to top

 

Last updated: July 23, 2012
Northeast Region Fisheries Home
Northeast Region Home


U.S. Fish and Wildlife Service Home Page | Department of the Interior  | USA.gov  | About the U.S. Fish and Wildlife Service  | Accessibility  | Privacy  | Notices  | Disclaimer  | FOIA