Alosine Genetic Stock Identification and Tissue Repository
American Shad (Alosa sapidissima), Blueback Herring (Alosa aestivalis), and Alewife (Alosa pseudoharengus; collectively “alosines”) once supported large fisheries along the U.S. Atlantic Coast. However, impassable migration barriers, declines in habitat quality, and exploitation have led to declines in many spawning populations. Substantial resources have been invested to support the recovery of alosine populations, yet results have been mixed. For example, some fish passage projects have resulted in large increases in populations, whereas others have had disappointing results – suggesting that other factors may be inhibiting recovery.
Alosine Genetic Stock Identification and Tissue Repository
As anadromous fishes, alosines spend much of their life history in estuarine and marine environments, where they may form mixed stock aggregations and where they are sometimes captured as bycatch in other fisheries. There is a critical need to be able to distinguish among populations or management units when individuals are encountered away from natal areas. An enhanced understanding of stock composition will provide critical information on the status and trends of specific populations and offer much needed insight into how fisheries bycatch may be impacting recovery efforts.
As part of the Eastern Ecological Science Center’s initiative to increase science support for the Atlantic States Marine Fisheries Commission (ASMFC), the center started an alosine genomics program in 2020. This effort is under the direction of Research Fish Biologist Dr. David Kazyak and Research Biologist Dr. Miluska Olivera-Hyde.
The first objective of the project is to establish a tissue repository for shad and river herring, which will be an essential resource to support mixed stock analysis at the USGS and other institutions. We are working with partners along the Atlantic coast to obtain tissue samples from different locations to augment current genetic baselines and to date have received samples from more than 10 agencies. We are now working with the New Jersey Division of Fish and Wildlife on an effort to characterize the stock composition of American Shad captured in Delaware Bay. We are also working with the Northeast Fisheries Observer Program to obtain samples from shad and river herring that are incidentally captured in commercial fisheries for Atlantic Herring and Atlantic Mackerel. Bycatch associated with these fisheries is a management concern, in part because impacts to coastal populations are poorly understood.
Another objective of the project is to support the development of genomic baselines for shad and river herring. Through partnerships with outside groups (e.g., Cornell University), we are helping to develop or improve panels for shad and river herring, including the establishment of efficient approaches to screen large numbers of samples across many loci.
Sample Submission Protocol
All sample information received is entered into the EESC alosine tissue repository. If you can collect tissue samples and would like to support the project, please contact Miluska Olivera Hyde at mhyde@usgs.gov.
Below, you can find the protocol for fresh samples collection. In addition, collaborators are encouraged to download and fill out the data sheet form.
Protocol for fresh samples – (preservation in RNAlater)
Once sampling has been completed, please mail samples to:
Miluska Olivera-Hyde
U.S. Geological Survey
Eastern Ecological Science Center at the Leetown Research Laboratory
11649 Leetown Road
Kearneysville, WV 25430
A template of the spreadsheet will be included with each sampling kit, which contains pre-labeled tubes. Each spreadsheet is prepared for its specific sampling kit and includes unique IDs that correspond to the sampling kits. Please fill out the spreadsheet and send it electronically to mhyde@usgs.gov along with the corresponding IDs from the sampling kit.
This information will be leveraged to:
- Assess population genetics at local, regional, and range-wide scales by estimating genetic diversity, effective population size, and gene flow among populations, and
- Determine the composition of mixed-stock aggregations, such as those that occur in fisheries bycatch. Our genomic baselines will also allow us to identify the populations that may be most vulnerable (small effective population size, low diversity, and/or extensive family structure) as well as those that are most robust. Moreover, the genomics data we generate may help identify populations suitable as broodstock sources for restoration efforts. This information will support the management needs of the Atlantic States Marine Fisheries Commission and fisheries management agencies.
American Shad (Alosa sapidissima), Blueback Herring (Alosa aestivalis), and Alewife (Alosa pseudoharengus; collectively “alosines”) once supported large fisheries along the U.S. Atlantic Coast. However, impassable migration barriers, declines in habitat quality, and exploitation have led to declines in many spawning populations. Substantial resources have been invested to support the recovery of alosine populations, yet results have been mixed. For example, some fish passage projects have resulted in large increases in populations, whereas others have had disappointing results – suggesting that other factors may be inhibiting recovery.
Alosine Genetic Stock Identification and Tissue Repository
As anadromous fishes, alosines spend much of their life history in estuarine and marine environments, where they may form mixed stock aggregations and where they are sometimes captured as bycatch in other fisheries. There is a critical need to be able to distinguish among populations or management units when individuals are encountered away from natal areas. An enhanced understanding of stock composition will provide critical information on the status and trends of specific populations and offer much needed insight into how fisheries bycatch may be impacting recovery efforts.
As part of the Eastern Ecological Science Center’s initiative to increase science support for the Atlantic States Marine Fisheries Commission (ASMFC), the center started an alosine genomics program in 2020. This effort is under the direction of Research Fish Biologist Dr. David Kazyak and Research Biologist Dr. Miluska Olivera-Hyde.
The first objective of the project is to establish a tissue repository for shad and river herring, which will be an essential resource to support mixed stock analysis at the USGS and other institutions. We are working with partners along the Atlantic coast to obtain tissue samples from different locations to augment current genetic baselines and to date have received samples from more than 10 agencies. We are now working with the New Jersey Division of Fish and Wildlife on an effort to characterize the stock composition of American Shad captured in Delaware Bay. We are also working with the Northeast Fisheries Observer Program to obtain samples from shad and river herring that are incidentally captured in commercial fisheries for Atlantic Herring and Atlantic Mackerel. Bycatch associated with these fisheries is a management concern, in part because impacts to coastal populations are poorly understood.
Another objective of the project is to support the development of genomic baselines for shad and river herring. Through partnerships with outside groups (e.g., Cornell University), we are helping to develop or improve panels for shad and river herring, including the establishment of efficient approaches to screen large numbers of samples across many loci.
Sample Submission Protocol
All sample information received is entered into the EESC alosine tissue repository. If you can collect tissue samples and would like to support the project, please contact Miluska Olivera Hyde at mhyde@usgs.gov.
Below, you can find the protocol for fresh samples collection. In addition, collaborators are encouraged to download and fill out the data sheet form.
Protocol for fresh samples – (preservation in RNAlater)
Once sampling has been completed, please mail samples to:
Miluska Olivera-Hyde
U.S. Geological Survey
Eastern Ecological Science Center at the Leetown Research Laboratory
11649 Leetown Road
Kearneysville, WV 25430
A template of the spreadsheet will be included with each sampling kit, which contains pre-labeled tubes. Each spreadsheet is prepared for its specific sampling kit and includes unique IDs that correspond to the sampling kits. Please fill out the spreadsheet and send it electronically to mhyde@usgs.gov along with the corresponding IDs from the sampling kit.
This information will be leveraged to:
- Assess population genetics at local, regional, and range-wide scales by estimating genetic diversity, effective population size, and gene flow among populations, and
- Determine the composition of mixed-stock aggregations, such as those that occur in fisheries bycatch. Our genomic baselines will also allow us to identify the populations that may be most vulnerable (small effective population size, low diversity, and/or extensive family structure) as well as those that are most robust. Moreover, the genomics data we generate may help identify populations suitable as broodstock sources for restoration efforts. This information will support the management needs of the Atlantic States Marine Fisheries Commission and fisheries management agencies.