Background

1. Future Science Directions Workshop Draft Report Brook Trout Strategic Science Plan for the Chesapeake Bay Watershed

2. Background • Two day workshop at USGS Leetown Science Center • Objective: develop a 5-year plan of USGS research activities to address key science questions related to brook trout conservation and management in the Chesapeake Bay watershed.

3. Workshop Participants USGS LSC • Bill Palmisano, Steve Faulkner, Tim King, Than Hitt, Kelly Maloney, Ben Letcher, John Young, Bruce Taggart,Vicki Blazer USGS Reston • Mark Hudy, Scott Phillips, Pete Murdoch, Glenn Holcomb, Cora Roig-Silva USGS VA WSC • Kurt McCoy, Dave Nelms USFWS • Jennifer Greiner, Michael Slattery, Bridgette Costanzo, Callie McMunigal

4. Workshop Summary Focused discussion coalesced around three broad themes: • The relative importance of evolutionary and ecological processes in regulating brook trout ecology and population dynamics • The conceptual strengths and weaknesses of alternative methodological approaches to assess trends in population viability • Specific priorities and strategies to address partner needs and advance scientific understanding of brook trout sustainability, resilience, and restoration

5. Research Priority 1:Refine and Develop Patch-prioritization Tools Based on Brook Trout Occupancy and Abundance Research approach • Refine and develop patch-prioritization tools (PPTs) based on patterns of abundance which precede changes in occupancy and should generate a more sensitive indicator compared to occupancy Products and benefits • Help managers assess metrics of brook trout abundance and identify areas for brook trout conservation and restoration (a) maps of potential brook trout habitat distributions within the Bay (b) probabilities of brook trout occupancy and abundance in response to simulated future scenarios of climate change, land use, and invasive species

6. Additional Research Priority A:Conduct New Sampling to Assess Brook Trout Habitat Suitability and Resilience Across Spatial Scales Research approach • Nested sampling design for air/stream temperature and fish • Fine-scale sampling nested within coarse-scale sampling among watersheds • Geologic evaluation, groundwater contribution to streamflowusing hydrograph separation techniques Products and benefits • Refine the PPTs described above by enabling estimates of brook trout habitat availability, occupancy, and abundance across spatial scales from reaches to catchments • Provide important new information on the role of groundwater for brook trout habitat and sensitivity to climate change • Provide a framework to evaluate the optimal spatial and temporal sampling designs for brook trout monitoring programs

7. Additional Research Priority B: Assess Adaptive Potential (Evolvability) for Brook Trout Populations Research approach • Sequence brook trout genome using a combination of state-of-the-art "next generation" technologies, • Generate comparative gene expression profiles from deep sequencing (RNA-Seq) to identify genes exhibiting baseline (control) differential expression in brook trout representing the three major life history forms (salter, coaster, and riverine) across the latitudinal and elevational distributions within the Chesapeake Bay Watershed Products and benefits • New assessment tools of population vulnerability based on adaptive potential (evolvability) • Incorporate evolutionary changes in physiological/metabolic and immunological systems into mechanistic models of species distributions • Incorporate heritable variation, selection intensity and demographic effects on genetic variance into mechanistic models • Assembled and annotated genome sequences, the entire mitochondrial genome sequence, single nucleotide polymorphisms (SNPs), and new microsatellite markers for brook trout will be made available • Improved understanding of the functional differences among ecophenotypic variants for the brook trout

8. Additional Research Priority C:Assess Effects of Unconventional Oil and Gas Development on Brook Trout Populations Research approach • Combine baseline distributional data with occupancy models developed in RP1 to develop region-wide assessments of pre-shale gas development conditions • Develop stressor-response relationships and metrics to predict responses to disturbances associated with shale-gas development • Gradient or paired designs (e.g., BACI studies) to determine the changes in water availability, water quality, brook trout populations, macro-invertebrate communities and periphyton communities for headwater streams that can be attributed to shale-gas development Products and benefits • Provide improved understanding of brook trout threshold responses to shale gas development • Help industry and resource managers identify areas of greatest conservation value and provide a tool to estimate the cumulative impact of proposed shale-gas development on brook trout headwater ecosystems • Improve precision of PPTs developed in Research Priority 1

9. Additional Research Priority D: Comprehensive Assessment of Brook Trout Health, Sublethal Effects, and Biological Endpoints Research approach • A battery of biomarkers, ranging from necropsy-based organism level to molecular, have been developed for use on a number of fish species in the Chesapeake Bay watershed • Histopathology, in combination with expression of genes for immune function, endocrine disruption, oxidative damage and various contaminant-induced enzymes, can be very powerful for assessing overall health • Comprehensive assessments for general and reproductive brook trout health will be conducted using these tools in collaboration with other brook trout studies, especially those related to changes in land use (e.g., unconventional oil and gas) and climate Products and benefits • Detect sublethal effects of endocrine disruptors, emerging and legacy contaminants on brook trout health and reproduction. • Identify potential pathogens/parasites that may affect brook trout abundance • Provide information on the current health of brook trout populations and science-based approaches for monitoring programs