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USGS2023

Obtaining and applying public data for training students in technical statistical writing: Case studies with data from U.S. Geological Survey and general ecological literature

Effective undergraduate statistical education requires training using real-world data. Textbook datasets seldom match the complexities and messiness of real-world data and finding these datasets can be challenging for educators. Consulting and industrial datasets often have nondisclosure agreements. Academic datasets often require subject area expertise beyond those of a general education or lack connections to real-world applications. Many governments, including the United States, now require the release of data from projects they directly complete or fund though grants and contracts. We show how statistical educators may find datasets and incorporate them into courses. Specifically, we use two examples from the U.S. Geological Survey (USGS) and one example from the ecology literature. We demonstrate the use of these datasets in an upper-level analysis of variance (ANOVA) class. In addition to describing how we found the datasets, we describe how to include them into course work and the course’s student assessments. We have used these datasets over multiple semesters and included student feedback from these courses. Although our examples focus on an ANOVA class, the general methods for finding data shared here could be used for statistical classes ranging from high school to graduate education. Supplementary materials for this article are available online.

Journal of Statistics and Data Science Education↗

USGS2017

Semipermanent GPS (SPGPS) as a volcano monitoring tool: Rationale, method, and applications

Semipermanent GPS (SPGPS) is an alternative to conventional campaign or survey-mode GPS (SGPS) and to continuous GPS (CGPS) that offers several advantages for monitoring ground deformation. Unlike CGPS installations, SPGPS stations can be deployed quickly in response to changing volcanic conditions or earthquake activity such as a swarm or aftershock sequence. SPGPS networks can be more focused or more extensive than CGPS installations, because SPGPS equipment can be moved from station to station quickly to increase the total number of stations observed in a given time period. SPGPS networks are less intrusive on the landscape than CGPS installations, which makes it easier to satisfy land-use restrictions in ecologically sensitive areas. SPGPS observations are preferred over SGPS measurements because they provide better precision with only a modest increase in the amount of time, equipment, and personnel required in the field. We describe three applications of the SPGPS method that demonstrate its utility and flexibility. At the Yellowstone caldera, Wyoming, a 9-station SPGPS network serves to densify larger preexisting networks of CGPS and SGPS stations. At the Three Sisters volcanic center, Oregon, a 14-station SPGPS network complements an SGPS network and extends the geographic coverage provided by 3 CGPS stations permitted under wilderness land-use restrictions. In the Basin and Range province in northwest Nevada, a 6-station SPGPS network has been established in response to a prolonged earthquake swarm in an area with only sparse preexisting geodetic coverage. At Three Sisters, the estimated precision of station velocities based on annual ~ 3 month summertime SPGPS occupations from 2009 to 2015 is approximately half that for nearby CGPS stations. Conversely, SPGPS-derived station velocities are about twice as precise as those based on annual ~ 1 week SGPS measurements. After 5 years of SPGPS observations at Three Sisters, the precision of velocity determinations is estimated to be 0.5 mm/yr in longitude, 0.6 mm/yr in latitude, and 0.8 mm/yr in height. We conclude that an optimal approach to monitoring volcano deformation includes complementary CGPS and SPGPS networks, periodic InSAR observations, and measurements from in situ borehole sensors such as tiltmeters or strainmeters. This comprehensive approach provides the spatial and temporal detail necessary to adequately characterize a complex and evolving deformation pattern. Such information is essential to multi-parameter models of magmatic or tectonic processes that can help to guide research efforts, and also to inform hazards assessments and land-use planning decisions.

Journal of Volcanology and Geothermal Research↗

USGS2023

Framework for facilitating mangrove recovery after hurricanes on Caribbean islands

Mangrove ecosystems in the Caribbean are frequently exposed to hurricanes, leading to structural and regenerative change that elicit calls for recovery action. For those mangroves unaffected by human modifications, recovery can occur naturally. Indeed, observable natural recovery after hurricanes is the genesis of the “disturbance adaptation” classification for mangroves; while structural legacies exist, unaltered stands often regenerate and persist. However, among the >7,000 islands, islets, and cays that make up the Caribbean archipelago, coastal alterations to support development affect mechanisms for regeneration, sediment distribution, tidal water conveyance, and intertidal mangrove transgression, imposing sometimes insurmountable barriers to natural post-hurricane recovery. We use a case study approach to suggest that actions to facilitate recovery of mangroves on Caribbean islands (and similar settings globally) may be more effective when focusing on ameliorating pre-existing anthropogenic stressors. Actions to clean debris, collect mangrove propagules, and plant seedlings are noble endeavors, but can be costly and fall short of achieving recovery goals in isolation without careful consideration of pre-hurricane stress. We update a procedural framework that considers six steps to implementing “Ecological Mangrove Restoration” (EMR), and we apply them specifically to hurricane recovery. If followed, EMR may expedite actions by suggesting immediate damage assessment focused on hydrogeomorphic mangrove type, hydrology, and previous anthropogenic (or natural) influence. Application of EMR may help to improve mangrove recovery success following catastrophic storms, and reduce guesswork, delays, and monetary inefficiencies.

Restoration Ecology↗

USGS2021

Brown treesnake mortality after aerial application of toxic baits

Quantitative evaluation of control tools for managing invasive species is necessary to assess overall effectiveness and individual variation in treatment susceptibility. Invasive brown treesnakes ( Boiga irregularis ) on Guam have caused severe ecological and economic effects, pose a risk of accidental introduction to other islands, and are the greatest impediment to the reestablishment of extirpated native fauna. An aerial delivery system for rodent-based toxic baits can reduce brown treesnake abundance and heterogeneity among individuals may influence bait attraction or toxicant susceptibility. Previous baiting trials have either been simulated aerial treatments or relied on slightly different bait capsule compositions and the results of aerial delivery of toxic baits under operational conditions may not be directly comparable. We monitored 30 radio-tagged adult snakes (990–1,265 mm snout-vent length) during an aerial baiting operation in a 55-ha area using transmitters equipped with accelerometers and receivers programed to display a status code indicating mortality if a snake failed to move for >24 hours. We used known-fate models to estimate mortality and evaluate a priori hypotheses explaining differences in mortality based on size, sex, and treatment effects. Eleven radio-tagged snakes died in the aerial baiting treatment period (0.37, 95% CI = 0.21–0.55) and no individuals (0.00, 95% CI = 0.00–0.04) died during the non-treatment period. Our data provide strong evidence for an additive size-based treatment effect on mortality, with smaller adults (0.59, 95% CI = 0.35–0.80) exhibiting higher mortality than larger snakes (0.14, 95% CI = 0.02–0.37) but did not support a sex effect on mortality. The high mortality of snakes during the treatment period indicates that aerial baiting can reduce brown treesnake abundance, but further refinement or use in combination with other removal tools may be necessary to overcome size-based differences in susceptibility and achieve eradication.

Journal of Wildlife Management↗

USGS2010

Multistate modeling of habitat dynamics: Factors affecting Florida scrub transition probabilities

Many ecosystems are influenced by disturbances that create specific successional states and habitat structures that species need to persist. Estimating transition probabilities between habitat states and modeling the factors that influence such transitions have many applications for investigating and managing disturbance-prone ecosystems. We identify the correspondence between multistate capture-recapture models and Markov models of habitat dynamics. We exploit this correspondence by fitting and comparing competing models of different ecological covariates affecting habitat transition probabilities in Florida scrub and flatwoods, a habitat important to many unique plants and animals. We subdivided a large scrub and flatwoods ecosystem along central Florida's Atlantic coast into 10-ha grid cells, which approximated average territory size of the threatened Florida Scrub-Jay (Aphelocoma coerulescens), a management indicator species. We used 1.0-m resolution aerial imagery for 1994, 1999, and 2004 to classify grid cells into four habitat quality states that were directly related to Florida Scrub-Jay source-sink dynamics and management decision making. Results showed that static site features related to fire propagation (vegetation type, edges) and temporally varying disturbances (fires, mechanical cutting) best explained transition probabilities. Results indicated that much of the scrub and flatwoods ecosystem was resistant to moving from a degraded state to a desired state without mechanical cutting, an expensive restoration tool. We used habitat models parameterized with the estimated transition probabilities to investigate the consequences of alternative management scenarios on future habitat dynamics. We recommend this multistate modeling approach as being broadly applicable for studying ecosystem, land cover, or habitat dynamics. The approach provides maximum-likelihood estimates of transition parameters, including precision measures, and can be used to assess evidence among competing ecological models that describe system dynamics. ?? 2010 by the Ecological Society of America.

Ecology↗

USGS2026

Connecting and coordinating conservation action across landscapes through regional planning processes and syntheses

Modern threats to conservation are often global; however, relevant conservation decisions and actions typically occur within local jurisdictions. The socio-ecological complexity of these problems requires collaboration across large landscapes, diverse community interests, and geopolitical boundaries, yet a lack of interoperability of planning products among decision makers, jurisdictions, and objectives impedes collaboration. Here, we provide a working model for the collaborative, iterative development of a landscape conservation design (LCD) in the Midwest region of the United States, the Midwest Conservation Blueprint, and demonstrate its applicability to the coordination of voluntary conservation actions and investments across jurisdictional boundaries. We used spatial prioritization software to synthesize over 20 datasets to develop a basemap of priority lands and waters for conservation across a diverse set of societal and ecological values (e.g., water quality, biodiversity, recreation). The Midwest Conservation Blueprint is a living plan, updated annually based on improvements in underlying data, understanding of local conditions, and public input. Landscape-scale planning is not designed to replace local knowledge or supersede decision-making authorities. However, by synthesizing existing data that represent diverse socio-ecological values and planning at a broader scale, the Midwest Conservation Blueprint documents where there are shared priorities and opportunities for collaborative landscape conservation.

Midwest↗

USGS1999

Techniques for restoration of disturbed coastal wetlands of the Great Lakes

A long history of human-induced degradation of Great Lakes wetlands has made restoration a necessity, but the practice of wetland restoration is relatively new, especially in large lake systems. Therefore, we compiled tested methods and developed additional potential methods based on scientific understanding of Great Lakes wetland ecosytems to providc an overview of approaches for restoration. We addressed this challenge by focusing on four general fields of science: hydrology, sedimentology, chemistry, and biology. Hydrologic remediation methods include restoring hydrologic connections between diked and hydrologically altered wetlands and the lakes, restoring water tables lowered by ditching, and restoring natural variation in lake levels of regulated lakes Superior and Ontario. Sedimentological remediation methods include management of sediment input from uplands, removal or proper management of dams on tributary rivers, and restoration of protective barrier beaches and sand spits. Chemical remediation methods include reducing or eliminating inputs of contaminants from point and non-pont sources, natural sediment remediation by biodegradation and chemical degradation, and active sediment remediation by removal or by in situ treatment Biological remediation methods include control of non-target organisms, enhancing populations of target organisms, and enhancing habitat for target organisms. Some of these method were used in three major restoration projects (Metzger Marsh on Lake Erie and Cootes Paradise and Oshawa Second Marsh on Lake Ontario), which are described as case studies to show practical applications of wetland restoration in the Great Lakes. Successful restoration techniques that do not require continued manipulation must be founded in the basic tenets of ecology and should mimic natural processes. Success is demonstrated by the sustainability, productivity, nutrient-retention ability, invasibility, and biotic interactions within a restored wetland.

Wetlands↗

USGS2005

Multi-stage sampling for large scale natural resources surveys: A case study of rice and waterfowl

Large-scale sample surveys to estimate abundance and distribution of organisms and their habitats are increasingly important in ecological studies. Multi-stage sampling (MSS) is especially suited to large-scale surveys because of the natural clustering of resources. To illustrate an application, we: (1) designed a stratified MSS to estimate late autumn abundance (kg/ha) of rice seeds in harvested fields as food for waterfowl wintering in the Mississippi Alluvial Valley (MAV); (2) investigated options for improving the MSS design; and (3) compared statistical and cost efficiency of MSS to simulated simple random sampling (SRS). During 2000–2002, we sampled 25–35 landowners per year, 1 or 2 fields per landowner per year, and measured seed mass in 10 soil cores collected within each field. Analysis of variance components and costs for each stage of the survey design indicated that collecting 10 soil cores per field was near the optimum of 11–15, whereas sampling >1 field per landowner provided few benefits because data from fields within landowners were highly correlated. Coefficients of variation (CV) of annual estimates of rice abundance ranged from 0.23 to 0.31 and were limited by variation among landowners and the number of landowners sampled. Design effects representing the statistical efficiency of MSS relative to SRS ranged from 3.2 to 9.0, and simulations indicated SRS would cost, on average, 1.4 times more than MSS because clustering of sample units in MSS decreased travel costs. We recommend MSS as a potential sampling strategy for large-scale natural resource surveys and specifically for future surveys of the availability of rice as food for waterfowl in the MAV and similar areas.

Arkansas, Kentucky, Louisiana, Mississippi, Missou↗

USGS2015

geoknife: Reproducible web-processing of large gridded datasets

Geoprocessing of large gridded data according to overlap with irregular landscape features is common to many large-scale ecological analyses. The geoknife R package was created to facilitate reproducible analyses of gridded datasets found on the U.S. Geological Survey Geo Data Portal web application or elsewhere, using a web-enabled workflow that eliminates the need to download and store large datasets that are reliably hosted on the Internet. The package provides access to several data subset and summarization algorithms that are available on remote web processing servers. Outputs from geoknife include spatial and temporal data subsets, spatially-averaged time series values filtered by user-specified areas of interest, and categorical coverage fractions for various land-use types.

Ecography↗

USGS2010

Development of standard weight equations for Caribbean and Gulf of Mexico amphidromous fishes

We collected and compiled length and weight information from four countries and one commonwealth to develop standard weight (W s ) equations for three amphidromous fish species native to the Caribbean and Gulf of Mexico regions: mountain mullet Agonostomus monticola (N = 9,768 individuals, 52 populations), river goby Awaous banana (N = 1,847 individuals, 62 populations), and bigmouth sleeper Gobiomorus dormitor (N = 2,983 individuals, 53 populations). Linear and quadratic W s equations for three quartiles (25%, median, 75%) are presented for these three species. The length-weight relationship from eight lentic bigmouth sleeper populations was significantly different from that of lotic populations, reflecting higher weights of juvenile fish (< 70 mm total length) in lentic environments. Thus, independent W(s) equations were developed for lotic populations of bigmouth sleepers. W(s) equations were not developed from lentic bigmouth sleeper populations alone due to the low number of applicable populations caused by life history constraints; the equation from combined lentic and lotic populations is suggested for application to lentic bigmouth sleeper populations. These morphometric relationships for amphidromous fishes may improve the ability to assess existing and potential sport fisheries and allow ecological assessment based on fish condition.

North American Journal of Fisheries Management↗

USGS2002

Use of sediment quality guidelines and related tools for the asssessment of contaminated sediments: Executive summary sooklet of a SETAC Pellston Workshop

This publication summarizes the results of a Pellston Workshop sponsored by the Society of Environmental Toxicology and Chemistry (SETAC), held 17-22 August 2002 in Fairmont, Montana, USA. The full technical proceedings of the workshop will be published separately by SET AC in 2003. Previous SETAC workshops have focused on sediment ecological risk assessment (ERA) (Dickson et al. 1987; Ingersoll et al. 1997) and porewater toxicity testing (Carr and Nipper 2003). Another recent workshop addressed the application of weight-of-evidence (WOE) methods in ERA (Burton et al. 2002). These previous workshops focused on how, when, and why ERAs are needed in sediment assessments. However, more focused discussion among scientists, environmental regulators, and environmental managers is now needed to build on this previous work. Specifically, additional guidance is needed on procedures that can be used to integrate the information derived from multiple chemical and biological lines of evidence (LOE). These LOE, which are developed through the application of different assessment tools, often include the use of chemically based sediment quality guidelines (SQGs) to evaluate sediment contamination and to help practitioners in sediment assessment and management formulate risk management decisions. This workshop focused on evaluation of the scientific foundations supporting different chemically based numeric SQGs and methods to improve the integration of SQGs into different sediment quality assessment frameworks that include information derived from multiple chemical and biological LOE.

SETAC Pellston Workshop↗

USGS2024

Molecular sexing of birds using quantitative PCR (qPCR) of sex-linked genes and logistic regression models

The ability to sex individuals is an important component of many behavioural and ecological investigations and provides information for demographic models used in conservation and species management. However, many birds are difficult to sex using morphological characters or traditional molecular sexing methods. In this study, we developed probabilistic models for sexing birds using quantitative PCR (qPCR) data. First, we quantified distributions of gene copy numbers at a set of six sex-linked genes, including the sex-determining gene DMRT1 , for individuals across 17 species and seven orders of birds ( n = 150). Using these data, we built predictive logistic models for sex identification and tested their performance with independent samples from 51 species and 13 orders ( n = 209). Models using the two loci most highly correlated with sex had greater accuracy than models using the full set of sex-linked loci, across all taxonomic levels of analysis. Sex identification was highly accurate when individuals to be assigned were of species used in model building. Our analytical approach was widely applicable across diverse neognath bird lineages spanning millions of years of evolutionary divergence. Unlike previous methods, our probabilistic framework incorporates uncertainty around qPCR measurements as well as biological variation within species into decision-making rules. We anticipate that this method will be useful for sexing birds, including those of high conservation concern and/or subsistence value, that have proven difficult to sex using traditional approaches. Additionally, the general analytical framework presented in this paper may also be applicable to other organisms with sex chromosomes.

Molecular Ecology Resources↗

USGS2003

The effect of stochiastic technique on estimates of population viability from transition matrix models

Population viability analysis is an important tool for conservation biologists, and matrix models that incorporate stochasticity are commonly used for this purpose. However, stochastic simulations may require assumptions about the distribution of matrix parameters, and modelers often select a statistical distribution that seems reasonable without sufficient data to test its fit. We used data from long-term (5–10 year) studies with 27 populations of five perennial plant species to compare seven methods of incorporating environmental stochasticity. We estimated stochastic population growth rate (a measure of viability) using a matrix-selection method, in which whole observed matrices were selected at random at each time step of the model. In addition, we drew matrix elements (transition probabilities) at random using various statistical distributions: beta, truncated-gamma, truncated-normal, triangular, uniform, or discontinuous/observed. Recruitment rates were held constant at their observed mean values. Two methods of constraining stage-specific survival to ≤100% were also compared. Different methods of incorporating stochasticity and constraining matrix column sums interacted in their effects and resulted in different estimates of stochastic growth rate (differing by up to 16%). Modelers should be aware that when constraining stage-specific survival to 100%, different methods may introduce different levels of bias in transition element means, and when this happens, different distributions for generating random transition elements may result in different viability estimates. There was no species effect on the results and the growth rates derived from all methods were highly correlated with one another. We conclude that the absolute value of population viability estimates is sensitive to model assumptions, but the relative ranking of populations (and management treatments) is robust. Furthermore, these results are applicable to a range of perennial plants and possibly other life histories.

Ecology↗

USGS2015

State-space modeling to support management of brucellosis in the Yellowstone bison population

The bison ( Bison bison ) of the Yellowstone ecosystem, USA, exemplify the difficulty of conserving large mammals that migrate across the boundaries of conservation areas. Bison are infected with brucellosis ( Brucella abortus ) and their seasonal movements can expose livestock to infection. Yellowstone National Park has embarked on a program of adaptive management of bison, which requires a model that assimilates data to support management decisions. We constructed a Bayesian state-space model to reveal the influence of brucellosis on the Yellowstone bison population. A frequency-dependent model of brucellosis transmission was superior to a density-dependent model in predicting out-of-sample observations of horizontal transmission probability. A mixture model including both transmission mechanisms converged on frequency dependence. Conditional on the frequency-dependent model, brucellosis median transmission rate was 1.87 yr −1 . The median of the posterior distribution of the basic reproductive ratio ( R 0 ) was 1.75. Seroprevalence of adult females varied around 60% over two decades, but only 9.6 of 100 adult females were infectious. Brucellosis depressed recruitment; estimated population growth rate λ averaged 1.07 for an infected population and 1.11 for a healthy population. We used five-year forecasting to evaluate the ability of different actions to meet management goals relative to no action. Annually removing 200 seropositive female bison increased by 30-fold the probability of reducing seroprevalence below 40% and increased by a factor of 120 the probability of achieving a 50% reduction in transmission probability relative to no action. Annually vaccinating 200 seronegative animals increased the likelihood of a 50% reduction in transmission probability by fivefold over no action. However, including uncertainty in the ability to implement management by representing stochastic variation in the number of accessible bison dramatically reduced the probability of achieving goals using interventions relative to no action. Because the width of the posterior predictive distributions of future population states expands rapidly with increases in the forecast horizon, managers must accept high levels of uncertainty. These findings emphasize the necessity of iterative, adaptive management with relatively short-term commitment to action and frequent reevaluation in response to new data and model forecasts. We believe our approach has broad applications.

Wyoming↗

USGS2011

Growth rate and age distribution of deep-sea black corals in the Gulf of Mexico

Black corals (order Antipatharia) are important long-lived, habitat-forming, sessile, benthic suspension feeders that are found in all oceans and are usually found in water depths greater than 30 m. Deep-water black corals are some of the slowest-growing, longest-lived deep-sea corals known. Previous age dating of a limited number of black coral samples in the Gulf of Mexico focused on extrapolated ages and growth rates based on skeletal 210 Pb dating. Our results greatly expand the age and growth rate data of black corals from the Gulf of Mexico. Radiocarbon analysis of the oldest Leiopathes sp. specimen from the upper De Soto Slope at 300 m water depth indicates that these animals have been growing continuously for at least the last 2 millennia, with growth rates ranging from 8 to 22 µm yr –1 . Visual growth ring counts based on scanning electron microscopy images were in good agreement with the 14 C-derived ages, suggestive of annual ring formation. The presence of bomb-derived 14 C in the outermost samples confirms sinking particulate organic matter as the dominant carbon source and suggests a link between the deep-sea and surface ocean. There was a high degree of reproducibility found between multiple discs cut from the base of each specimen, as well as within duplicate subsamples. Robust 14 C-derived chronologies and known surface ocean 14 C reservoir age constraints in the Gulf of Mexico provided reliable calendar ages with future application to the development of proxy records.

Marine Ecology Progress Series↗

USGS2009

Applications of a broad-spectrum tool for conservation and fisheries analysis: Aquatic gap analysis

Natural resources support all of our social and economic activities, as well as our biological existence. Humans have little control over most of the physical, biological, and sociological conditions dictating the status and capacity of natural resources in any particular area. However, the most rapid and threatening influences on natural resources typically are anthropogenic overuse and degradation. In addition, living natural resources (i.e., organisms) do not respect political boundaries, but are aware of their optimal habitat and environmental conditions. Most organisms have wider spatial ranges than the jurisdictional boundaries of environmental agencies that deal with them; even within those jurisdictions, information is patchy and disconnected. Planning and projecting effects of ecological management are difficult, because many organisms, habitat conditions, and interactions are involved. Conservation and responsible resource use involves wise management and manipulation of the aspects of the environment and biological communities that can be effectively changed. Tools and data sets that provide new insights and analysis capabilities can enhance the ability of resource managers to make wise decisions and plan effective, long-term management strategies. Aquatic gap analysis has been developed to provide those benefits. Gap analysis is more than just the assessment of the match or mis-match (i.e., gaps) between habitats of ecological value and areas with an appropriate level of environmental protection (e.g., refuges, parks, preserves), as the name suggests. Rather, a Gap Analysis project is a process which leads to an organized database of georeferenced information and previously available tools to examine conservation and other ecological issues; it provides a geographic analysis platform that serves as a foundation for aquatic ecological studies. This analytical tool box allows one to conduct assessments of all habitat elements within an area of interest. Aquatic gap analysis naturally focuses on aquatic habitats. The analytical tools are largely based on specification of the species-habitat relations for the system and organism group of interest (Morrison et al. 2003; McKenna et al. 2006; Steen et al. 2006; Sowa et al. 2007). The Great Lakes Regional Aquatic Gap Analysis (GLGap) project focuses primarily on lotic habitat of the U.S. Great Lakes drainage basin and associated states and has been developed to address fish and fisheries issues. These tools are unique because they allow us to address problems at a range of scales from the region to the stream segment and include the ability to predict species specific occurrence or abundance for most of the fish species in the study area. The results and types of questions that can be addressed provide better global understanding of the ecological context within which specific natural resources fit (e.g., neighboring environments and resources, and large and small scale processes). The geographic analysis platform consists of broad and flexible geospatial tools (and associated data) with many potential applications. The objectives of this article are to provide a brief overview of GLGap methods and analysis tools, and demonstrate conservation and planning applications of those data and tools. Although there are many potential applications, we will highlight just three: (1) support for the Eastern Brook Trout Joint Venture (EBTJV), (2) Aquatic Life classification in Wisconsin, and (3) an educational tool that makes use of Google Earth (use of trade or product names does not imply endorsement by the U.S. Government) and Internet accessibility.

Gap Analysis Bulletin↗

USGS2026

Epigenetics in captivity: Restoring wild phenotypes in captive-reared salmonids

Captive rearing is a common practice for the stocking, conservation, and supplementation of fish species worldwide, but captive-reared fish can exhibit altered phenotypes leading to reduced fitness in nature compared to wild conspecifics. In salmonids, certain studies have found limited genetic differentiation between wild and captive-reared fish. However, documented changes in gene expression in hatchery fish have led scientists to investigate epigenetic mechanisms, such as DNA methylation, as a source of these differences. In this binational collaborative piece, we synthesize the knowledge and efforts of academics and government scientists to highlight how interactions between captive rearing and the epigenome elicit parallel phenotypic changes across salmonid species. We examine the known and potential links between DNA methylation and the phenotypic effects of captive rearing including changes in behavior, color, gut microbiomes, and developmental abnormalities. We review efforts to minimize these phenotypic and epigenetic effects including attempts to modify the hatchery environment and rearing protocols. We provide a framework to integrate epigenetic considerations into hatchery rearing protocols by weighing the heritable nature of DNA methylation with the goals of different captive rearing programs and explore whether minimizing the phenotypic and epigenetic effects of captive rearing is worthwhile. We examine heritability and persistence of epigenetic effects, and we propose the exploitation of heritable bet-hedging as an epigenetic buffer to increase post-release survival. We also suggest novel applications of epigenomic biomarkers as a non-lethal method for post-release monitoring. Ultimately, collaborative multi-disciplinary research across species is needed to understand the comprehensive effects of captive rearing, reduce the ecological impacts of captive fish in the wild, and increase population resilience. Integrating epigenetics into fish hatchery management will provide new opportunities for optimizing and improving captive rearing.

Evolutionary Applications↗

USGS2020

Ecological interfaces between land and flowing water: Themes and trends in riparian research and management

This paper provides an overview of past, present and future themes for research and management of riparian zones, often relating to papers within this Wetlands Special Feature. Riparian research expanded in the United States around 1980 with themes that recognized (1) damage from excessive livestock, or (2) damage from river damming and diversion, and (3) the beneficial capacity of riparian buffers to intercept and assimilate nutrients and other water contaminants. Research expanded globally in the 1990s, with themes including (4) plant life history requirements and (5) reliance on fluvial geomorphic dynamics that enable riparian rejuvenation. Resource managers recognized that riparian areas provide (6) rich wildlife habitats (7) along with valued ecosystem services, (8) which encouraged conservation and restoration initiatives, (9) including environmental flow regimes. Floodplains are (10) vulnerable to invasive plants and management has included biocontrol such as for Tamarix in the American Southwest. Into the twenty-first century, (11) climate change is advancing, and riparian ecosystems may be especially impacted due to the compound challenges from increasing water demand and declining summer flows. As an emerging opportunity, (12) while reservoirs submerge floodplain vegetation, reservoir deltas may support compensatory riparian wetlands. (13) Studies increasingly utilize remote sensing tools including satellite imagery, LiDAR and unmanned aircraft systems, and (14) the coordination of large data sets invites digital ecology, including artificial intelligence and machine learning. Since riparian zones are centres for human activities, (15) there are opportunities for citizen science, social media and internet applications, which will increasingly democratize riparian research and management.

Wetlands↗