Research themes
Our goal is to develop innovative approaches to marine and freshwater ecosystem management.  We integrate quantitative science + ecology + socioeconomic research to advance solutions to natural resource management problems spanning from local case studies to seascape scales.  Research in our group spans a set of core themes:

Quantitative tool development
A core of our research group centers on quantitative ecological methodology development.  We work across applied statistics, ecological modeling, and genetics to advance the set of tools available to observe and manage ecosystems.

Fisheries: Combining many different fisheries surveys to inform marine species distributions at ecologically relevant scales
Marine species’ ranges are extensive, typically spanning across fisheries jurisdictional boundaries. Thus a common challenge in fisheries assessments is making inference about fish populations from multiple different surveys. Visiting Fulbright Scholar from Ulster University, Meadhbh Moriarty, is leading a project to investigate statistical approaches to combining different trawl surveys in European waters to provide information on the spatial ecology of marine species.

Fisheries: Novel survival modeling using small acoustic tag technology to assess juvenile fish survival
We are developing novel statistical models for tagged fish survival estimation.  Results will provide a general survival model that can accommodate three phases of the tagging process for individually-tracked animals: mortality upon tag deployment, mortality during recovery from tagging, and transition to ‘natural mortality’ regimes after recovery from tagging. As a test case, we will apply these models to estimate survival of juvenile fish stocked into lakes using novel small acoustic tags.

Genetics: Close kin mark recapture unlocks new opportunities for fisheries assessments
Mark recapture methods provide a mainstay in assessing fish populations.  Yet, these methods have rather rigid sampling requirements and suffer from ever present ‘capture heterogeneity’ problems which can bias abundance estimates.  Novel close-kin mark recapture methods provide an exciting new approach to population assessments, utilizing relationship states as the population statistic of interest, as opposed to capture histories under traditional mark recapture.  As a result, close kin mark recapture can circumvent many capture heterogeneity problems and open up new opportunities to utilize mark recapture sampling, such as achieving single-occasion abundance estimates! PhD student (Kraft/Sullivan lab) Ben Marcy-Quay is leading a collaboration to compare close kin mark recapture for brook trout against traditional mark recapture sampling.

Genetics: DNA mixtures for ecology
Mixtures of DNA from multiple individuals are commonly found in the environment and may provide information useful to inform population ecology.  We are developing a likelihood based model to infer the number of contributors to a DNA mixture for ecological applications.  Initial simulation and laboratory results look promising, with mixtures of up to 10 or more individuals successfully resolved with reasonable sized marker panels.  Looking forward, we hope to be able to apply this model to a range of field settings including diet analysis and environmental DNA sampling.

Genetics: Genetic mark recapture population assessment of Pacific Walrus 
Pacific Walrus are a culturally important marine mammal in the arctic seas.  In a project lead by the Alaska US Fish and Wildlife Service, we’re conducting a multi-year genetic mark recapture project using crossbow dart biopsied sample collection in the Bering and Chukchi seas to assess survival and abundance of Pacific Walrus.

Stream ecology: Are remotely sensed thermal products useful for stream fisheries ecology? (MS project at Alaska Pacific University: R. Murphy, J. Hagan)
Remotely sensed thermal information provides large scale and relatively easy to collect information on surface temperatures.  In this project, the accuracy and precision of remotely sensed Landsat thermal data is being compared to instream water temperature measurements along the Kenai Peninsula in southcentral Alaska.  While at the forefront of climate change, subarctic and arctic systems are typically remote and difficult to access.  In this project supported by NASA, the Western AK Landscape Conservation Cooperative, and Pollock Conservation Cooperative funding, we hope to assess whether remotely sensed data might provide information useful for assessing temporal or spatial changes in stream temperatures.

Computational sustainability: Minimizing ecosystem impacts from planned hydropower expansion in the Amazon
Over 350 large hydropower dams have been proposed for construction in the Andean Amazon region.  Hydropower dams can produce energy benefits, however, they also impact ecosystem services.  In this international project led by Alex Flecker and Carla Gomes at Cornell with support from the Atkinson Center for a Sustainable Future, we are collaborating across ecology, computer science, economics, hydrology, and geology to develop a computational sustainability framework for siting hydropower dams on large river systems while minimizing negative ecosystem service impacts.  Additional information can be found at the project website.

Recent papers:
Remote sensing: Machine learning to identify ghost dams
Remote sensing: Can Landsat thermal imagery and environmental data accurately estimate water temperatures in small streams?
Fisheries: acoustic tag retention in juvenile salmonines
Genetics: population genetics with eDNA!
Fisheries: Close kin mark recapture modeling for inland fish population abundance and survival
Computational sustainability: minimizing GHG emissions from Amazon hydropower
Genetics: DNA mixtures for ecology
Fisheries: combining many surveys to inform marine species distribution modeling
Fisheries: application of dynamic occupancy modeling to assess marine fish ecology
Fisheries: PSATs provide information on bycaught Pacific Halibut survival
Computation sustainability: High value of ecological information for river connectivity restoration.
Fisheries: New statistical approach to handle missing data at fish weirs.
Fisheries: Novel use of finite mixture models to age juvenile fish with length measurements.

Ecology and demography to support ecosystem management
Information on food webs, the interaction between individuals and their environment, and population demography is central to informing natural resource and conservation planning decisions.

Fisheries: Stock assessment and predator prey modeling to develop control rules for Pacific Salmon management in Lake Ontario (PhD project: K. Fitzpatrick)
In this collaboration with the NY State Department of Environmental Conservation, we’ll be developing a portfolio of projects to assess Chinook and alewife population dynamics in Lake Ontario.  We seek to develop tools to assist managers in coping with shocks to the predator-prey system and develop guidance for appropriate stocking or harvest strategies.  The project will incorporate structured conceptual modeling with stakeholders, empirical work to assess predator and/or prey abundances or demographic rates, and population dynamics simulations, building from a legacy of strong predator-prey work in the Great Lakes science community.

Fisheries restoration: Population re-introduction of Cisco in the Finger Lakes (PhD student project)
Coregonines such as Cisco (C. artedi) used to range throughout cold water lakes in the Northeast, serving an important role as both predator and prey.  Decades of water quality degradation, overfishing, and invasive species introductions have constricted the range of these native species and led to extirpations in many waterbodies.  In this project, we are working with State and Federal collaborators to reintroduce Cisco to Keuka lake in an effort to re-establish native forage fish resources and improve lake resiliency.  Utilizing state of the art small acoustic tags, our group is monitoring the movement and survival of stocked Cisco, providing key information needed to guide Cisco population restoration practices in the Great Lakes basin.

Fisheries: Spatial ecology of juvenile Coregonines in the Great Lakes (MS/PhD project: Taylor Brown)
Taylor will explore early life stage ecology of Coregonines in Lake Ontario. In a joint collaboration with Brian Weidel at the USGS Great Lakes Science Center and Lars Rudstam at Cornell, we seek to advance understanding about the spatiotemporal habitat use of Coregonines at lake-wide scales.  This work will support long term monitoring and restoration management options for this important native fish complex across the Great Lakes.

Fisheries: Cisco spawning ecology in the Great Lakes (MS project: M. Paufve)
Cisco, Coregonus artedi, a native coregonine in the Great Lakes was once highly abundant and supported large commercial fisheries.  Combinations of overfishing, changing lake productivity, pollution, and invasive species led to wide-scale stock collapses of Cisco and other coregonines. With support from the Great Lakes Research Institute, we are working with Brian Lantry at the USGS Lake Ontario Biological Field Station to assess habitat use by Cisco in upper Great Lakes with remnant spawning populations.  Ultimately, information gained in the upper Lakes will be used to inform restoration efforts in Lake Ontario.

Recent papers:
Marine mammal ecology: the Pacific Walrus abundance estimate
Fisheries assessments: the Lake Ontario Chinook salmon stock assessment
Fisheries ecology: Aquatic connectivity to lentic habitats are a conservation priority for Coho salmon
Marine mammal ecology: panmixia describes Pacific Walrus population structure
Apex carnivore ecology: Novel use of satellite-collar fix success to infer canid parturition.
Marine mammal ecology: Spatial ecology of Beluga whales inferred from novel use of industry-lea aerial survey data.
Fisheries ecology: Do radio tags affect swimming performance of Chum salmon?
Fisheries ecology: Dynamic occupancy to learn about habitat use and foraging behavior of marine fish species.

Response of ecosystems to anthropogenic x natural disturbance
Understanding the response of ecosystems to human and natural disturbances is needed to design solutions to address stressors as well as set expectations about the range of future variability with which managers must cope.

Fisheries: Modeling tradeoffs between marine reserves versus fishing gear modification to manage seafloor impacts for Gulf of Alaska and Bering Sea fisheries (PhD project: S. Smeltz)
In this project, we’re implementing recovery-decay models for seascape-scale simulations to explore potential benthic impacts from commercial fishing gear.  Ultimately, we seek to develop tools for policy makers to compare commercial fishing gear modification (‘gear conservation’) tools with spatial closures (‘marine reserves’) in managing habitat impacts from fishing.  This work is highly relevant to the U.S. Federal fishery management councils as they develop tools to assess and manage Essential Fish Habitat. Project supported by a grant from the Atkinson Center for a Sustainable Future.

Invasive fish ecology: defining the ecological niche of Round goby on the inland temperate lake invasion front
A relatively recent arrival to the NE region, round goby are now found throughout the Great Lakes basin. This benthic fish may negatively impact native species in the Great Lakes via habitat and food competition, and by predation on native fish eggs and larvae. Conversely, gobies prey on invasive Dreissenid mussels and themselves may be viable prey for adult native Great Lakes fish. Information on the distribution and ecology of goby is a top priority for understanding ecosystem-level impacts from this rapidly expanding invader. In this collaboration between Cornell, NY Sea Grant, and the NY State Department of Environmental Conservation, we are using benthic videography and sound recording to assess the distribution and biomass of round goby in heavily infested Cayuga Lake as a mesocosm relevant for Great Lakes waters.

Ecosystem transformation: Guiding principles for managing transforming ecosystems
Ecosystem transformation involves the emergence of a self-organizing, self-sustaining, social-ecological system that deviates, sometimes irreversibly, from prior ecosystem structure and function. These dramatic transformations are occurring with increasing frequency across the globe as a result of rapid changes in climate, land use, and prevalence of introduced species. Consequently, a dynamic view of ecosystem processes that accommodates rapid and potentially irreversible change will be critical for effectively conserving fish, wildlife, and other species. The American Fisheries Society and The Wildlife Society have organized a joint synthesis team to identify steps forward to manage ecosystem under dramatic transformations.  In this project involving managers and ecologists spanning from terrestrial to marine systems, we will explore a simple trichotomy of management approaches to cope with ecosystem transformation: resist, accept, or direct change.

Recent papers:
Ecosystem management: Fisheries management options under transforming marine ecosystems
Fisheries: Life history consequences of stream connectivity loss for salmon
Ecosystem management: Resist, Accept, or Direct ecosystem transformation
Aquatic invasives: Lake depth mediates the potential for invasive round goby impacts
Fisheries: seascape scale habitat impacts modeling to assess bottom tendered fishing impacts
Marine ecology: Assessment of press versus pulse disturbances on rocky shore communities.
Aquatic invasives: Rapid response for invasive waterweeds at the arctic invasion front — assessment of collateral impacts from herbicide treatments.
Aquatic invasives: Review of invasive aquatic plants in high latitude systems and identification of a novel “remote area invasion ratchet” process.
Fisheries: Identification of the top knowledge needs to inform best practices for trawl-based fisheries.

Social-ecological systems management
Natural resource management problems involve a combination of social and ecological processes, and thus effective management need address both systems.

Fisheries: Climate ready fishing communities
Climate change is advancing rapidly, particularly in high latitude oceans leading to shifting marine species distributions, and impacting fish population productivity and variability. As a result, fishing communities face increasing threats to local economies and cultural heritage as they bear risk of losing fishing access under changing marine ecosystems. In this project we seek to address a key sustainability challenge for fisheries-reliant communities: How can communities maintain access to commercial fishing resources in the face of climate-driven ocean changes? In this interdisciplinary collaboration, we will work across fisheries science, climate science, and computer science to identify optimal fishing portfolios robust to climate change. Finally, we seek to ‘close the loop’ on climate adaptation strategies by identifying finance needs to support fishers and fishing communities adaptation actions.

Fisheries: Alternative income generating activities to wild capture fisheries in the Philippines
Fisheries in many regions operate under weak or non-existent governance.  As a result, these systems are characterized by severe overfishing and declining marine ecosystem integrity.  Without the prospect of central ‘command and control’ governance, economic alternatives to fishing may be a necessary component of fisheries reform for many communities.  In this project, we are quantifying the impact of marine ecotourism as an ‘alternative income generating activity’ to fishing in Moalboal, a Philippines fishing commmunity.  The Moalboal community currently hosts a thriving marine ecotourism diving industry which provides local incomes and jobs, integrates fishers, and aligns incentives for marine ecosystem conservation.  In this collaboration between Cornell, Environmental Defense Fund, and Stonybrook, we seek to understand the Moalboal system as an example case study of what works and what doesn’t for implementing marine ecotourism as an alternative to wild capture fishing for marine communities.

Fisheries: Advancing conservation finance opportunities for fisheries 
While many commercial fisheries are sustainably managed, overfishing, bycatch, gear-related habitat damage, and profit dissipation remain a problem in some regions.  The pace of reform is slow, and some countries do not have adequate regulatory resources to implement sustainable fisheries management.  Private investment capital presents a potentially large opportunity to fund the transition to sustainable fisheries management, aligning investor return opportunities with environmental and social performance goals.  In this joint collaboration between the Environmental Defense Fund and Atkinson Center at Cornell, we seek to help accelerate the pace of conservation investments in fisheries by addressing key information gaps.  We are exploring more mature conservation finance sectors to develop understanding about the necessary conditions for viable fishery investment opportunities which can satisfy investor risk-return expectations while improving fisheries socioecological performance.

Fisheries: Wild x aquaculture fisheries food production systems 
Many communities rely on wild capture fisheries as a primary source of nutrition and livelihoods. Yet, rapidly transforming ecosystems and mounting anthropogenic impacts on marine and aquatic ecosystems are stressing wild fish resources.  In a set of projects, we are exploring opportunities, costs, and interactions among wild-capture and aquaculture-based fishery resources as food systems. Currently our work is focusing on wild versus aquaculture fishery resources in the Amazon basin. Looking forward, we are also designing proposals for projects to assess the potential to divert commercial fisheries wastes towards aquaculture feeds.

Recent papers:
Conservation finance: a state of the sector survey, identifying flows and obstacles
Fisheries socioecological systems: ecotourism as a source of alternative income to fishing
Fisheries food systems: Declining diversity of wild-caught species puts dietary nutrient supplies at risk
Fisheries food systems: Substitution of inland fisheries with aquaculture and chicken undermines human nutrition in the Peruvian Amazon
Conservation finance: financing nature
Conservation finance: catalyzing investments in fisheries conservation
Fisheries socioecological systems: Development of quantitative metrics to monitor fishing communities.
Fisheries socioecological systems: Examination of the relationship between Alaskan fishing community fishing portfolios and community revenue risk.