national fish and wildlife foundation...the smithsonian environmental research center conducted...

Easygrants ID: 45567National Fish and Wildlife Foundation NFWF Project ID: 0104.14.045567Keystone Initiative - Marine & Coastal - River Herring - Fall 2014 - Submit Final Programmatic Report (New Metrics)Grantee Organization: Smithsonian InstitutionProject Title: River Herring Spawning Run Monitoring in Chesapeake Bay (VA, MD)

Project Period 2/01/2015 - 1/31/2016Project Location Description (from Proposal)

Run counts will be conducted in the Choptank River (Lower Eastern Shore) and Deer Creek (Lower Susquehanna River). Habitat use surveys will be conducted in these and four other priority watersheds in Maryland and Virginia.

Project Summary (from Proposal)

Provide scientifically rigorous imaging sonar run counts of river herring in key Chesapeake Bay spawning streams. Project will augment run counts with watershed-scale habitat use surveys.

Summary of Accomplishments

The Smithsonian Environmental Research Center conducted river herring spawning run counts in two tributaries of Chesapeake Bay and habitat use surveys in five tributaries. Biological samples augmented run counts to provide information on species, sex, size, age, and spawning history composition, as well as mortality estimates, of each run. Watershed-scale habitat use surveys provided valuable information on the use of habitats for spawning, and will ultimately be incorporated into a habitat use model under development with separate funding. Engagement with citizen scientists has benefited from funding support for a citizen science coordinator and our project intern developed an environmental DNA (eDNA) assay that is yielding promising early results. We hosted the third annual Chesapeake Bay River Herring Workshop on 27 October 2016, have disseminated results to regional conservation associations and continued to promote improvements in river herring monitoring in the Chesapeake BayWatershed.

Lessons Learned Key lessons learned include the following:

1)Multi-beam imaging sonar (DIDSON or ARIS) is an effective tool for conducting river herring spawning run counts using the high resolution provided at a frequency of 1.8 MHz.

2) Combining run counts with biological sampling of otolith age and spawning history allows for estimation of population structure that accounts for changes in age distribution and run strength throughout the spawning season.

3) Age structure, sex ratio, size structure, spawning history structure, and mortality rates vary by year and spawning stream in Chesapeake tributaries, but are generally within the range of values observed for other parts of each species range.

4) Watershed-scale habitat use surveys are valuable tools for understanding the spatial distribution of spawning habitat. Preliminary analysis of presence/absence data indicates that the proportion of available habitat used in each tributary varies. For most Chesapeake Bay tributaries, data on spawning habitat use either do not exist or date to the 1960s-1980s.

5) Early results suggest that our eDNA assay is effective at identifying river herring presence/absence inhabitat use surveys, and is likely to be the most cost-effective and sensitive of the three sampling methods we are testing.

The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the opinions or policies of the National Fish and Wildlife Foundation. Mention of trade names or commercial products does not

constitute their endorsement by the National Fish and Wildlife Foundation.

Activities and Outcomes

Funding Strategy Planning, Research, MonitoringActivity / Outcome Herring - Research - # research studies completedRequired RecommendedDescription Enter the number of research studies completed

# research studies completed - Current 4.00# research studies completed - Grant Completion 6.00

Notes In this metric, we counted the number of research studies based on the number of watersheds where studies have been conducted. In 2013-2014, we conducted research studies in four watersheds (Choptank River, Marshyhope Creek, Mattawoman Creek, and Deer Creek). With this project, we expand to six total watersheds at which we have conducted river herring research studies during the period 2013-2015 (Choptank River, Deer Creek, Patapsco River, Mattawoman Creek, Pamunkey River, and Rappahannock River). In 2015, we conducted studies in 5 total watersheds (all ofthe watersheds listed above except Mattawoman Creek, which was sampled in 2013 for habitat use in collaboration with citizen scientists). Note that the Rappahannock River replaced the Chickahominy River that was included in the project proposal in response to a request by Virginia Department of Game and InlandFisheries. In 2016, we are sampling for habitat use in an additional 6 tributaries, which will bring the the total number of tributaries studied to 12 for the period 2013-2016 (from a proposed minimum of 10).

Funding Strategy Capacity, Outreach, IncentivesActivity / Outcome Citizen scientists trainedRequired OptionalDescription Other Metric

Other Metric - Description The number of citizen scientists participating each year will be recorded for each part of the project including the number of volunteers involved in field surveys (minimum of 15) and the number of high school and undergraduate interns trained (three). In addition to counts of volunteers participating, we will record the number of hours of volunteer participation in each of the above categories as part of SERC’s existing volunteer and citizen science programs.

Notes

Funding Strategy Planning, Research, MonitoringActivity / Outcome Planning workshopRequired OptionalDescription Other Metric

Other Metric - Description We will host one workshop to foster collaborative research and begin implementing the draft Chesapeake Bay River Herring Monitoring Plan in support of the river herring outcomes of the Business Plan for the Chesapeake Bay Stewardship Fund and the Chesapeake Bay Watershed Agreement.



Final Programmatic Report Narrative

Instructions: Save this document on your computer and complete the narrative in the format provided. The final narrative should not exceed ten (10) pages; do not delete the text provided below. Once complete, upload this document into the on-line final programmatic report task as instructed.

1. Summary of AccomplishmentsIn four to five sentences, provide a brief summary of the project’s key accomplishments and outcomes that were observed or measured.

We conducted river herring spawning run counts in two tributaries of Chesapeake Bay and habitat use surveys in five tributaries. Biological samples augmented run counts to provide information on species, sex, size, age, and spawning history composition, as well as mortality estimates, of each run. Watershed-scale habitat use surveys provided valuable information on the use of habitats for spawning, and will ultimately be incorporated into a habitat use model under development with separate funding. Engagement with citizen scientists has benefited from funding support for a citizen science coordinator and our project intern developed an environmental DNA assay that is yielding promising early results.We hosted the third annual Chesapeake Bay River Herring Workshop on 27 October 2016, have disseminated results to regional conservation associations and continued to promote improvements in river herring monitoring in the Chesapeake Bay Watershed.

2. Project Activities & Outcomes

Activities

Describe and quantify (using the approved metrics referenced in your grant agreement) the primary activities conducted during this grant.

Briefly explain discrepancies between the activities conducted during the grant and the activities agreed upon in your grant agreement.

Imaging sonar fish passage monitoringDIDSON imaging sonar units were deployed in the Choptank River (Upper Eastern Shore) from March 13, 2015 to June 4, 2015 and Deer Creek (Lower Susquehanna River) from March 19, 2015 to May 26, 2015. Sonar deployment was later than anticipated (March 1) due to an exceptionally cold late winter and early spring. At both sites, sonar units were deployed before any Alewife were detected in either stream in biological samples. Sampling continued in the Choptank until Blueback Herring declined to near zero. In Deer Creek, Blueback Herring never migrated upstream to the sonar location and sampling was ended when numbers declined at the tidal/non-tidal interface.

Biological samplingBoat electrofishing was conducted weekly in the Choptank River to sample the species composition of fish passing the sonar unit. Deer Creek was sampled using a combination of a fyke net and cast nets to collect a sufficient sample size for determining species composition. It is too shallow and rocky near the sonar site for boat electrofishing. Alewife and Blueback Herring collected during biological sampling have all been dissected and otoliths and scales have been processed for age and spawning marks. Otolith and scales samples are archived at SERC.

Habitat use surveyA spawning habitat use study was initiated in March and completed in May. We surveyed potential spawning habitat sitesin five Chesapeake tributary watersheds in Maryland and Virginia including Choptank River, Deer Creek, Patapsco River,Rappahannock River, and Pamunkey River. We had planned to sample along the Anacostia River near Washington DC but did not receive a response to repeated requests until early July 2015. Sampling consisted of three main data types: 1) adult fish presence assessed by visual, GoPro and cast net sampling, 2) ichthyoplankton sampling for eggs and larvae, and3) water samples for environmental DNA. Citizen scientists assisted with data collection in several watersheds and one of these citizens assisted with sorting and counting of ichthyoplankton samples, which is complete. Dr. Louis Plough at the The views and conclusions contained in this document are those of the authors and should not be interpreted as representing

the opinions or policies of the National Fish and Wildlife Foundation. Mention of trade names or commercial products does not constitute their endorsement by the National Fish and Wildlife Foundation.

University of Maryland Center of Environmental Science Horn Point Lab has developed and tested an eDNA probe for detecting river herring presence/absence using water samples. His graduate student Katie Hornick was the project intern and conducted much of the work developing and testing the eDNA methods.

A separate grant was obtained through the Smithsonian Institution Competitive Grants Program to conduct detailed spatialanalyses of the habitat survey data. The work will result in a predictive habitat model for river herring spawning and juvenile habitat use throughout the Chesapeake watershed. A postdoc was hired in June 2016 to conduct this analysis which will be conducted during the next two years. Separate SERC internship funds were also raised to hire a summer intern who conducted a pilot habitat use analysis on both historical (1980’s) and current habitat use in the Choptank River,Maryland.

Outcomes

Describe and quantify progress towards achieving the project outcomes described in your grant agreement. (Quantify using the approved metrics referenced in your grant agreement or by using more relevant metrics not included in the application.)

o We or our partners conducted baseline habitat use surveys in 5 of 5 watersheds (Choptank River, Deer Creek, Patapsco River, Rappahannock River, and Pamunkey River).

o DIDSON run counts and biological sampling were conducted for both Choptank River and Deer Creek.

o In 2015, 15 out of 15 citizen scientists and 3 of 3 interns participated in the project. Including SERC’s citizen science coordinator has been invaluable for identifying and recruiting project participants.

o We hosted the third annual Chesapeake Bay River Herring Workshop on 27 October 2015.o An eDNA assay was developed for documenting river herring presence from water samples.

Briefly explain discrepancies between what actually happened compared to what was anticipated to happen.

o In spring 2015, we conducted a baseline habitat use survey in the Rappahannock watershed instead of the Chicahominy watershed. This change was made to best coordinate with the efforts of Virginia Department of Game and Inland Fisheries which was also sampling several sites in the Rappahannock this year. Our proposal for spring 2016 includes a baseline habitat use survey for the Chicahominy. There was no change in the number of priority watersheds monitored.

o We were surprised to find that no blueback herring spawned at our DIDSON station in Deer Creek. In 2000, Maryland DNR documented >4,000 blueback herring exiting a fish ladder upstream of the sonar station. It is thought that flow was too low this spring for blueback herring to move more than a very short distance upstream in Deer Creek in 2015 as they were observed insome numbers at the confluence of the creek with Susquehanna River (Jim Thompson, Maryland DNR, personal communication).

o We contracted Tom Schultz at Duke University to analyze archived fin clip samples for population genetics. Sample analysis is complete. Data analysis is underway and will inform the number of streams and geographic areas for which run count data are needed to adequately assessriver herring population dynamics in Chesapeake Bay. Sufficient funds were available to complete analysis of additional samples.

Provide any further information (such as unexpected outcomes) important for understanding project activities and outcome results.

Chesapeake Bay River Herring Monitoring Plan – Since 2013 (project 34809) we have developed and tested methods for assessing river herring spawning runs in the Chesapeake Bay watershed. For project 40321 we drafted a bay-wide monitoring plan for river herring spawning runs that included the following four components. With proposal 45567 we initiated an anticipated two-year implementation process for the plan.

1) Sentinel run counts: Species-specific run counts conducted in five key spawning streams distributed regionally

within the Chesapeake Bay watershed. Sentinel run counts will provide rigorous spawning stock data for regional

and coast-wide stock assessment models.The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the opinions or policies of the National Fish and Wildlife Foundation. Mention of trade names or commercial products does not


2) Habitat use surveys: Broad-scale habitat use surveys based on presence/absence data and conducted in at least10

important spawning streams. Habitat use surveys will provide critical data on changes in habitat use over time and

species-specific habitat preferences. The surveys also provide opportunities to involve citizen scientists in river

herring monitoring.

3) Existing long term surveys: Several existing long-term data sets have the potential to provide important

information on changes in river herring stock status in Chesapeake Bay. These data sets include fishery landings

(note that all river herring fisheries are currently under moratoria in Chesapeake Bay), fish counts at Bosher’s and

Conowingo Dams, juvenile and adult abundance indices generated by state agencies, academic institutions, and

non-profit organizations, and time series of age structure. Supplementing these existing data sets with sentinel run

counts and habitat use surveys will provide the best possible data for assessing river herring stocks in Chesapeake

Bay.

4) Fish passage efficiency assessments: Directed studies of fish passage efficiency at key blockages in important

spawning streams. Passage efficiency assessments will be essential for evaluating, maximizing, and sustaining

fish passage at locations where dam removal is unlikely.

Implementation Strategy (linked to Proposal 45567)1. Establish two of five sentinel run counts in key spawning streams: Run counts were conducted in the Choptank

River on Maryland’s Eastern Shore and Deer Creek, a tributary of the Lower Susquehanna River.2. Conduct habitat use surveys in five out of ten important spawning streams: Habitat use surveys were conducted in

the Choptank River, Deer Creek, Patapsco River, Rappahannock River, and Pamunkey River. Surveys in Deer Creek and Patapsco River supplemented and expanded sampling programs conducted by Maryland Department ofNatural Resources.

Sentinel Run CountsSentinel run counts were conducted in the Choptank River and Deer Creek using Dual-Frequency Identification Sonar (DIDSON). DIDSON units were mounted on metal frames and installed in each stream for the duration of the spawning runs. Orange plastic construction fence was used to restrict the stream width to the 10-m viewing window of the DIDSONunits, and stream depth was such that the majority of the water column was imaged except during high water events. The DIDSON units were set to record one 10-min file for each hour, with a random start time during the hour. Data were processed manually to determine the number of fish within the 200-350 mm total length (TL) of river herring swimming upstream and downstream each hour. From these, species-specific run counts were generated using weekly species composition data collected by electrofishing (Choptank River) or fyke netting (Deer Creek). Two run count indices were

Table 1. Comparison of 2013-2015 species-specific estimated run counts from DIDSON data including upstream and net upstream migrants. Total days refers to the number of days each species was present when the sonar was deployed. Interpolated indicates the number of days out of the total that were interpolated to fill data gaps. Asterisks (*) indicate run counts that should be viewed with caution due to substantial data gaps at the beginning of or during the run. For Alewife in 2013, no recordings were made during the first few weeks of the run and these counts are likely under-estimates. Crosses (†) indicate run counts that should be viewed with caution because of exceptionally high occurrence of large schools of milling fish. The net upstream run count (Net) accounts for milling fish and is a better metric for comparison among sites than raw upstream counts because of different levels of milling behavior observed among sites. For some sites and years, high quality DIDSON data are not available (N/A).

Site Species Year Upstream Net Total days InterpolatedChoptank Alewife 2013 367,524* N/A 19 3

2014 577,825 460,762 57 02015 715,387 465,486 53 0

Choptank Blueback 2013 733,520* N/A 36 122014 726,450 551,939 53 02015 875,765† 454,517 45 0

Deer Creek Alewife 2015 888,210 348,630 64 5Deer Creek Blueback 2015 0 0 0 0Marshyhope Alewife 2013 295,828* 147,745 26 1

2014 N/A N/A N/A N/AMarshyhope Blueback 2013 505,374 227,975 27 4

2014 951,861† 333,872† 47 4The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the opinions or policies of the National Fish and Wildlife Foundation. Mention of trade names or commercial products does not


constructed for each species in each spawning stream (Table 1): 1) the sum of the total number of upstream migrants each hour and 2) the sum of the net number of upstream migrants calculated as the difference between upstream and downstream migrants each hour (hours with more downstream than upstream migrants were assigned a value of 0 upstream migrants). For Deer Creek, run count data had to be interpolated for five days due to high flow events that caused the DIDSON frame to shift and which prevented correction until flows declined to allow safe access for repositioning. Also, we were surprised to find that no Blueback Herring migrated upstream to our study site in Deer Creekdespite high abundances in the Susquehanna a few miles downstream of the site. Previous sampling by Maryland DNR indicated that substantial numbers of Blueback Herring occur upstream of our site at least in some years. Because of this, we do not intend to continue using this site for river herring run counts as it is apparently not a reliable site for studying both species in all years.

Sex ratio, size, age, and spawning history composition of biological samplesThe sex ratio of Alewife in the Choptank River reversed in 2015 to be dominated by females (60% of fish sampled), a substantial change from the previous two years (Table 2). In contrast, only 9% of Alewife sampled in Deer Creek were female. Mean total length (TL) increased relative to 2013-2014 at both Choptank River and Deer Creek and remained consistently greater for females than for males. Mean spawner age continued to decline except for males in Deer Creek, which have consistently been youngest on average. The percent of repeat spawners increased in the Choptank River and declined or remained the same in Deer Creek. Note that we are no longer sampling Marshyhope Creek, but data are included in Table 2 for comparison.

Table 2. Alewife sex ratio, mean total length (TL), and percent of repeat spawners by river and year for biological samples.

Female MaleSex ratio Marshyhope Choptank Deer Creek Marshyhope Choptank Deer Creek2013 46% 28% N/S 54% 72% N/S2014 44% 32% 39% 56% 68% 61%2015 N/S 60% 9% N/S 40% 91%

Mean TL (mm)2013 273 269 N/S 252 251 N/S2014 272 268 261 259 253 2502015 N/S 276 275 N/S 261 256

Mean age2013 4.6 4.2 N/S 4.0 3.9 N/S2014 4.6 3.9 4.1 3.6 3.5 3.22015 N/S 3.6 3.5 N/S 3.3 3.2

Repeat spawn2013 56% 62% N/S 36% 51% N/S2014 61% 60% 62% 62% 54% 57%2015 N/S 77% 45% N/S 72% 57%

The sex ratio of Blueback Herring in the Choptank River also reversed, with 58% of fish collected being female comparedto 17% in 2014 (Table 3). Mean TL and age decreased for females, but increased for males. In contrast, the proportion of repeat spawners was more variable than for Alewife, with the spawning run composed of as few as 37% and as many as 87% repeat spawners. Also unlike Alewife, there was a marked increase in the percent of repeat spawners from 2013 to 2015. It is unclear from these data whether the increase was due to higher survival of prior spawners, lower recruitment offirst-time spawners, or sampling artifacts. Note that no Blueback Herring migrated into our Deer Creek study site in 2015 despite their occurrence downstream where Deer Creek enters the Susquehanna River.

In general, the sex ratio, mean TL, age and percent of repeat spawners are within the range of observations in other regions of the US Atlantic coast. For repeat spawning in particular, the three locations sampled in this study were consistent with the relatively high rates of repeat spawning observed in fishery-dependent data from Maryland and North Carolina, as well as fishery-independent data from New Hampshire and Maine (ASMFC 2013). These rates were often substantially higher than those observed in Massachusetts, New York, and South Carolina.



Table 3. Blueback Herring sex ratio, mean total length (TL), and percent of repeat spawners by river and year.

Female MaleSex ratio Marshyhope Choptank Deer Creek Marshyhope Choptank Deer Creek2013 47% 31% N/S 53% 69% N/S2014 25% 17% 35% 75% 83% 65%2015 N/S 58% N/S N/S 42% N/S

Mean TL (mm)2013 273 267 N/S 255 248 N/S2014 272 271 257 246 248 2352015 N/S 264 N/S N/S 254 N/S

Mean age2013 5.1 4.5 N/S 4.4 3.9 N/S2014 4.5 4.2 4.4 3.7 3.6 3.72015 N/S 3.6 N/S N/S 3.9 N/S

Repeat spawn2013 69% 55% N/S 37% 50% N/S2014 87% 82% 67% 69% 66% 41%2015 N/S 58% N/S N/S 80% N/S

Age distributions and mortality ratesAge distributions for Choptank River (2014, 2015) and Deer Creek (2015) spawning runs were generated by combining weekly run count and otolith age data to quantify the number of fish in each age class. Combining weekly run count and age data provide a more robust age distribution because changes in run strength and age distribution over time are accounted for. Using these data, mean age of Alewife in 2015 in the Choptank River declined from 3.70 to 3.44 and of Blueback Herring increased from 3.45 to 3.77. For Deer Creek, the mean age of Alewife was 3.21. Age distributions werethen used to calculate total instantaneous mortality (Z) using the Chapman-Robson estimator. In the Choptank River, Z increased from 1.47 in 2014 to 1.93 in 2015 and from 1.91 to 2.55 for Blueback Herring. These instantaneous mortality rates are equivalent to annual survival rates in 2015 of 15% for Alewife and 8% for Blueback Herring for fully-recruited adults (age 4-5 and older). For Alewife in Deer Creek in 2015, Z=1.53 and annual survival was 22%. These rates are relatively high, but are within the range observed for river herring in other parts of their range.

Habitat Use SurveyWatershed-scale habitat use surveys were conduct in five Chesapeake Bay tributaries including the Choptank River, Deer Creek and Patapsco Rivers in Maryland and the Rappahannock and Pamunkey Rivers in Virginia (Figure 1). The number of sample sites varied depending on the area of each watershed accessible to river herring. Sampling sites were located at road crossings to facilitate easy access, and were general distributed in a way that allows for determination of how far upstream river herring travel in each major tributary as well as which of the smaller side tributaries are used. The survey goal was to collect three types of presence/absence data at each site in order to determine which will be most cost-effective for future monitoring. These data types were 1) presence of adult fish by visual survey, GoPro video and/or cast net, 2) 5-min ichthyoplankton samples following standard Maryland DNR protocols, and 3) environmental DNA (eDNA) in water samples. Following completion of sampling in a total of 10 tributaries in 2016 (project 050023), we will make a direct comparison of the cost-effectiveness of each sampling method. Ichthyoplankton sampling was more likely to detect fish presence, although it is not possible to differentiate eggs among river herring species or Hickory Shad without additional DNA barcoding to determine species composition of eggs. Based on our experiences and preliminary results from 2015 sampling, it is anticipated that the eDNA method will be most time and cost-effective for large-scale, long-term habitat use monitoring.



Figure 1. Maps of habitat use survey river herring presence data comparing ichthyoplankton and visual/cast net sampling. Note that river herring presence was more likely to be detected in ichthyoplankton samples.

Habitat use data were collected at 85 sites throughout the five watersheds, with three sampling events per site. We had initially intended to sample each site twice, once for Alewife and once for Blueback Herring, but after initial sampling indicated that the Alewife run was barely starting despite warming stream temperatures due to cold water temperatures in Chesapeake Bay, we conducted a second round of Alewife sampling for some sites. Visual/cast net and eDNA data were collected at all sites, along with water quality (temperature, salinity, conductivity, dissolved oxygen). Ichthyoplankton samples were collected at most sites, but could not be collected at a few sites due to very low flow or unsafe access to the stream. All visual/GoPro/cast net data, as well as ichthyoplankton samples, have been processed. See below for details on eDNA assay development and results.

Environmental DNA assayWe contracted with Dr. Louis Plough at the University of Maryland Center of Environmental Science Horn Point Laboratory to develop and test an environmental DNA (eDNA) assay for river herring. Our primary objective of the eDNA assay was to distinguish river herring DNA from other closely related species. Although species-specific assays would be preferable, our limited funding for eDNA analyses was insufficient for the development of species-specific assays.

Initially, we designed a probe-based quantitative PCR (qPCR) assay for the mitochondrial control region to amplify (and thus detect) river herring DNA from environmental water samples. Because the genus Alosa has a number of other closely related species (i.e. species that have high genetic or DNA sequence similarity) that co-occur in the same habitats, primers have to be very specific to the two river herring species and we expected the non-coding control region to have the greatest sequence and structural polymorphism compared with other coding mitochondrial genes, as it typically does in other taxa. After some optimization, the dual-labeled (internal) probe assay performed fairly well - all river herring samples produced positive assay results (i.e. amplification that produces fluorescence on the qPCR instrument) early in the PCR program (15-30 cycles) and most non-target fish, particularly Hickory and American Shad that are genetically most similar, produced only a very weak, or no fluorescence (amplification) signal. However, further optimization did not improve the specificity to where it needed to be for a reliable field assay (for example, Bay Anchovy consistently amplified weakly, or late in the PCR run), so we decided to start over and develop a probe assay with the Cytochrome The views and conclusions contained in this document are those of the authors and should not be interpreted as representing


Oxidase-1 (CO1) mitochondrial locus, a standard and robust species identification locus that has significantly more publicly available genetic data for assay design.

For the CO1 assay, we developed a molecular beacon probe, which has, in theory, greater specificity than the standard dual-labelled probe that was used for the control region assay. Testing the CO1 beacon assay with in vitro DNA samples (diluted and non-diluted fin clip DNA extractions) from the target herring species and a number of related and proximal non-target species (e.g. American and Hickory Shad, Menhaden, Gizzard Shad and Bay Anchovy), we were able to produce better specificity (less amplification of non-targets) than the control region probe. Specifically, Bay Anchovy is no longer amplified, and Gizzard Shad amplifies rarely and poorly, producing weak fluorescence only after the 40th cycle. Importantly, American and Hickory Shad, which commonly co-occur with river herring in spawning streams, produce no amplification, even after 40 or 50 cycles. Note that a late-cycle amplification of Gizzard Shad DNA is far less likely to occur in a qPCR assay from environmental samples, which have much reduced macrobial (e.g. cells, mitochondria from fish/invertebrates) DNA concentrations, compared with the high quality, high concentration fin-clip DNA that produced late amplifications in lab trials.

Detailed analysis of eDNA data from the habitat use survey has only been conducted to date on a small subset (N=22) of water samples. Of these, the one sample for which adult river herring were seen during sample collection was positive for river herring and had stronger fluorescence than diluted fin clip DNA extractions tested during assay development. Three other samples were positive for river herring, but with weaker fluorescence. All six sample controls tested came up negative, indicating that samples are not being contaminated during transport and storage. Controls were bottles of DI water kept with eDNA samples in the coolers during sampling and freezers during storage. These results are highly encouraging and indicate that eDNA analysis is likely to be an efficient, reliable, and cost-effective method for conductinglarge-scale habitat use studies of river herring. In addition, species-specific information can be obtained for samples that test positive using our probe by conducting standard DNA barcoding of the amplified DNA.

Population geneticsWith Dr. Thomas Schultz at the Duke University Marine Laboratory, we have completed the genotyping of 505 river herring samples at 14 microsatellite loci. The samples were collected from three locations in 2013 (project 34809) and three locations in 2014 (project 40321). From these results, population differentiation is observed for both Alewife and Blueback Herring in the Chesapeake, although further analyses are needed to refine the story. Next steps will be to incorporate data from other sites to further visualize and quantify the levels of genetic differentiation and diversity in these populations.

3. Lessons LearnedDescribe the key lessons learned from this project, such as the least and most effective conservation practices or notable aspects of the project’s methods, monitoring, or results. How could other conservation organizations adapt their projects to build upon some of these key lessons about what worked best and what did not?

Multi-beam imaging sonar (DIDSON or ARIS) is an effective tool for conducting river herring spawning run counts using the high resolution provided at a frequency of 1.8 MHz.

Combining run counts with biological sampling of otolith age and spawning history allows for estimation of population structure that accounts for changes in age distribution and run strength throughout the spawning season.

Age structure, sex ratio, size structure, spawning history structure, and mortality rates vary by year and spawning stream in Chesapeake tributaries, but are generally within the range of values observed for other parts of each species range.

Watershed-scale habitat use surveys are valuable tools for understanding the spatial distribution of spawning habitat. Preliminary analysis of presence/absence data indicates that the proportion of available habitat used in each tributary varies. For most Chesapeake Bay tributaries, data on spawning habitat use either do not exist or date to the 1960s-1980s.

Early results suggest that our eDNA assay is effective at identifying river herring presence/absence in habitat use surveys, and is likely to be the most cost-effective and sensitive of the three sampling methods we are testing.



4. DisseminationBriefly identify any dissemination of lessons learned or other project results to external audiences, such as the public or other conservation organizations.

Website

Information about our project, including photos and videos, is available on SERC’s website at http://www.serc.si.edu/labs/fish_invert_ecology/herring.aspx.

Workshops

Attendees of the 2015 Chesapeake Bay River Herring Workshop included representatives from NFWF, NOAA FWS, EPA, Maryland Department of Natural Resources, Virginia Department of Game and Inland Fisheries, Delaware Department of Natural Resources and Environmental Control, Mattawoman Watershed Society, Virginia Institute of Marine Science, District of Columbia, George Mason University, Interstate Commission on the Potomac River Basin, Atlantic States Marine Fisheries Commission, Metropolitan Washington Council of Governments, University of Maryland Center of Environmental Science, and American Rivers

Presentations

Monitoring river herring spawning habitat use. Presentation at the Maryland Water Monitoring Council Board of Directors Meeting, Edgewater, Maryland.

Setting baselines for River Herring conservation in Chesapeake Bay. Virginia Institute of Marine Science Biological Sciences Seminar, Gloucester Point, Virginia, Virginia Institute of Marine Sciences, Eastern Shore Laboratory, Wachapreague, Virginia. Smithsonian Environmental Research Center, Edgewater, Maryland.

Abundance, Demography and Environmental Drivers of River Herring Spawning Runs in Chesapeake Bay Tributaries. Poster presentation at the 2015 Annual Meeting of the American Fisheries Society, Portland, OR.

Conservation Organizations

The Virginia Department of Game and Inland Fisheries has expressed substantial interest in our habitat use surveyand is collaborating with us on sample collection in 2016.

Virginia Institute of Marine Sciences has adopted our imaging sonar run count methods and is conducting a 2016 run count on a tributary of the York River, Virginia ( project 046672).

The South Carolina Department of Natural Resources has adopted our imaging sonar run counts methods and is conducting a 2016 run count on the Cooper River (project 046640).

An updated presence/absence and run count GIS layer has been provided to The Nature Conservancy and AtlanticCoastal Fish Habitat Partnership to replace an outdated layer used in the Atlantic Coast Alosine Prioritization

A preliminary river herring spawning habitat use map has been provided to the NOAA Chesapeake Bay Office forconservation prioritization in the Choptank River component of the North Atlantic Habitat Focus Area

Publications

A manuscript “Establishing Baselines for River Herring Populations in Chesapeake Bay using Dual-Frequency Identification Sonar (DIDSON)” has been submitted to a scientific journal for peer-review.

5. Project DocumentsInclude in your final programmatic report, via the Uploads section of this task, the following:

2-10 representative photos from the project. Photos need to have a minimum resolution of 300 dpi and must be accompanied with a legend or caption describing the file name and content of the photos;

Ten representative photos were uploaded and should be credited to the Smithsonian Environmental Research Center (SERC). Filenames and captions are listed below.

1. DIDSON.jpg – SERC Co-PI Dr. Matt Ogburn prepares the Dual-Frequency Identification Sonar (DIDSON) for deployment in the Choptank River, Maryland.

2. Deer_Creek.jpg – The Dual-Frequency Identification Sonar (DIDSON) site in Deer Creek, Maryland. The DIDSON is mounted on the metal frame at right, with orange plastic fencing installed to prevent fish from swimming behind or directly in front of the sonar unit.

3. Fyke_Net – Fyke net used to collect fish for species, sex, age and spawning history composition in Deer Creek, Maryland.The views and conclusions contained in this document are those of the authors and should not be interpreted as representing


4. Alewife_Choptank_2015.jpg – Alewife (Alosa pseudoharengus) swimming in the Choptank River, Maryland.5. Alewife.jpg – An Alewife (Alosa pseudoharengus) caught during habitat sampling in the Choptank River,

Maryland.6. Choptank_Habitat_Sampling.jpg – Citizen scientists conducting habitat use sampling on the Choptank River,

Maryland.7. Citizen_Science.jpg – Alison Cawood, Citizen Science Coordinator at the Smithsonian Environmental Research

Center, and citizen scientist collecting an environmental DNA sample on the Patapsco River, Maryland.8. Ichthyoplankton.jpg – Kim Richie and Will McBurney, Smithsonian Environmental Research Center Biological

Technicians, collecting an ichthyoplankton sample in the Rappahannock River, Virginia.9. Herring_Workshop – Participants at the 2015 Chesapeake Bay River Herring Workshop at the Smithsonian

Environmental Research Center.

report publications, GIS data, brochures, videos, outreach tools, press releases, media coverage;

any project deliverables per the terms of your grant agreement.

POSTING OF FINAL REPORT: This report and attached project documents may be shared by the Foundation and anyFunding Source for the Project via their respective websites. In the event that the Recipient intends to claim that its final report or project documents contains material that does not have to be posted on such websites because it is protected from disclosure by statutory or regulatory provisions, the Recipient shall clearly mark all such potentially protected materials as “PROTECTED” and provide an explanation and complete citation to the statutory or regulatory source for such protection.

