Geology topics

Michael E. Colvin

Publications and source records attributed to Michael E. Colvin.

31 records · Page 2Linked to original sources

USGS2017

Dietary plasticity in a nutrient-rich system does not influence brown bear (Ursus arctos) body condition or denning

Behavioral differences within a population can allow use of a greater range of resources among individuals. The brown bear ( Ursus arctos ) is a generalist omnivore that occupies diverse habitats and displays considerable plasticity in food use. We evaluated whether brown bear foraging that resulted in deviations from a proposed optimal diet influenced body condition and, in turn, denning duration in Lake Clark National Park and Preserve, Alaska. To assess assimilated diet, we used sectioned guard hair samples ( n = 23) collected in autumn to determine stable carbon and nitrogen isotope ratios. To index proportional contributions of meat and vegetation to assimilated diets, we compared the carbon (δ 13 C) and nitrogen (δ 15 N) values of hair samples with the values identified for major food categories. We then compared percentage body fat and body mass in relation to the proportion of assimilated meat in the diet using linear models. We also examined the influence of autumn percentage body fat and mass on denning duration. Percentage body fat was not influenced by the proportion of assimilated meat in the diet. Additionally, percentage body fat and body mass did not influence denning duration. However, body mass of bears assimilating proportionately more meat was greater than bears assimilating less meat. Our results provide support for previous findings that larger bears consume higher amounts of protein to maintain their body size and therefore forage further from the proposed optimal diet. Additionally, our results demonstrate that individuals can achieve similar biological outcomes (e.g., percentage body fat) despite variable foraging strategies, suggesting that individuals within generalist populations may confer an adaptive advantage through behavioral plasticity.

Alaska↗

USGS2017

Assessment of adult pallid sturgeon fish condition, Lower Missouri River—Application of new information to the Missouri River Recovery Program

During spring 2015, Nebraska Game and Parks Commission (NGPC) biologists noted that pallid sturgeon (Scaphirhynchus albus) were in poor condition during sampling associated with the Pallid Sturgeon Population Assessment Project and NGPC’s annual pallid sturgeon broodstock collection effort. These observations prompted concerns that reduced fish condition could compromise reproductive health and population growth of pallid sturgeon. There was a further concern that compromised condition could possibly be linked to U.S. Army Corps of Engineers management actions and increase jeopardy to the species. An evaluation request was made to the Missouri River Recovery Program and the Effects Analysis Team was chartered to evaluate the issue. Data on all Missouri River pallid sturgeon captures were requested and received from the National Pallid Sturgeon Database. All data were examined for completeness and accuracy; 12,053 records of captures between 200 millimeters fork length (mm FL) and 1,200 mm FL were accepted. We analyzed condition using (1) the condition formula (Kn) from Shuman and others (2011); (2) a second Kn formulation derived from the 12,053 records (hereafter referred to as “Alternative Kn”); and (3) an analysis of covariance (ANCOVA) approach that did not rely on a Kn formulation. The Kn data were analyzed using group (average annual Kn) and individual (percentage in low, normal, and robust conditions) approaches. Using the Shuman Kn formulation, annual mean Kn was fairly static from 2005 to 2011 (although always higher in the upper basin), declined from 2012 to 2015, then remained either static (lower basin) or increasing (upper basin) in 2016. Under the Alternative Kn formulation, the upper basin showed no decline in Kn, whereas the lower basin displayed the same trend as the Shuman Kn formulation. Using both formulations, the individual approach revealed a more complex situation; at the same times and locations that there are fish in poor condition, there are nearby fish in normal or robust condition. The ANCOVA approach revealed that fish condition at size changed between 400 and 600 mm and that some of the apparent trend in low condition was caused by differences in sample size across the size range of the population (that is, greater catch of intermediate-sized fish compared to large fish). We examined basin, year, origin (hatchery compared to wild), segment, and size class for effects on condition and concluded that, since 2012, there has been an increase in the percentage of pallid sturgeon in low condition. There are basin, year, and segment effects; origin and size class do not seem to have an effect. The lower basin, in particular segment 9 (Platte River to Kansas River), had a high percentage of low-condition fish. Within the segment, there were bend-level effects, but the bend effect was not spatially contiguous. We concluded that existing data confirm concerns about declining fish condition, especially in the segments between Sioux City, Iowa, and Kansas City, Missouri. Although the evidence is strong that fish condition has been in decline from 2011 to 2015, additional analysis of individual fish histories may provide more confidence in this conclusion; such analysis was beyond the scope of this effort but is part of our recommendations. The most recent data in 2016 indicate that decline of condition may have leveled off; however, the length of record is insufficient to determine whether recent declines are within the background range of variation. We recommend that monitoring of fish condition should be increased and enhanced with additional health metrics. We also recommend that, should condition continue to decline, processes are deployed to bring low-condition adult fish into the hatchery to improve nutrition and condition. We could not determine the cause of declining fish condition with available data, but we compiled information on several dominant hypotheses in two main categories: inter- or intraspecific competition for resources and habitat conditions. Data are insufficient to indicate a specific causation or solution, and it is possible that multiple causes apply. We make recommendations for additional research that can be pursued to address uncertainties in trends in fish health as well as potential causes.

Missouri River↗

USGS2017

A hidden-process model for estimating prespawn mortality using carcass survey data

After returning to spawning areas, adult Pacific salmon Oncorhynchus spp. often die without spawning successfully, which is commonly referred to as prespawn mortality. Prespawn mortality reduces reproductive success and can thereby hamper conservation, restoration, and reintroduction efforts. The primary source of information used to estimate prespawn mortality is collected through carcass surveys, but estimation can be difficult with these data due to imperfect detection and carcasses with unknown spawning status. To facilitate unbiased estimation of prespawn mortality and associated uncertainty, we developed a hidden-process mark–recovery model to estimate prespawn mortality rates from carcass survey data while accounting for imperfect detection and unknown spawning success. We then used the model to estimate prespawn mortality and identify potential associated factors for 3,352 adult spring Chinook Salmon O. tshawytscha that were transported above Foster Dam on the South Santiam River (Willamette River basin, Oregon) from 2009 to 2013. Estimated prespawn mortality was relatively low (≤13%) in most years (interannual mean = 28%) but was especially high (74%) in 2013. Variation in prespawn mortality estimates among outplanted groups of fish within each year was also very high, and some of this variation was explained by a trend toward lower prespawn mortality among fish that were outplanted later in the year. Numerous efforts are being made to monitor and, when possible, minimize prespawn mortality in salmon populations; this model can be used to provide unbiased estimates of spawning success that account for unknown fate and imperfect detection, which are common to carcass survey data.

Oregon↗

USGS2016

Preparing future fisheries professionals to make good decisions

Future fisheries professionals will face decision-making challenges in an increasingly complex field of fisheries management. Though fisheries students are well trained in the use of the scientific method to understand the natural world, they are rarely exposed to structured decision making (SDM) as part of an undergraduate or graduate education. Specifically, SDM encourages users (e.g., students, managers) to think critically and communicate the problem and then identify specific, measurable objectives as they relate to the problem. Next, users must think critically and creatively about management alternatives that can be used to meet the objectives—there must be more than one alternative or there is no decision to be made. Lastly, the management alternatives are evaluated with regard to how likely they are to succeed in terms of multiple, possibly completing, objectives, such as how stakeholder groups value outcomes of management actions versus monetary cost. We believe that exposure to SDM and its elements is an important part of preparing future fisheries professional to meet the challenges they may face. These challenges include reduced budgets, the growth of potentially competing natural resource interest groups, and stakeholder desire to be involved in management decisions affecting public trust resources, just to name a few.

Fisheries↗

USGS2016

Missouri River Scaphirhynchus albus (pallid sturgeon) effects analysis—Integrative report 2016

The Missouri River Pallid Sturgeon Effects Analysis was designed to carry out three components of an assessment of how Missouri River management has affected, and will affect, population dynamics of endangered Scaphirhynchus albus (pallid sturgeon): (1) collection of reliable scientific information, (2) critical assessment and synthesis of available data and analyses, and (3) analysis of the effects of actions on listed species and their habitats. This report is a synthesis of the three components emphasizing development of lines of evidence relating potential future management actions to pallid sturgeon population dynamics. We address 21 working management hypotheses that emerged from an expert opinion-based filtering process. The ability to quantify linkages from abiotic changes to pallid sturgeon population dynamics is compromised by fundamental information gaps. Although a substantial foundation of pallid sturgeon science has been developed during the past 20 years, our efforts attempt to push beyond that understanding to provide predictions of how future management actions may affect pallid sturgeon responses. For some of the 21 hypotheses, lines of evidence are limited to theoretical deduction, inference from sparse empirical datasets, or expert opinion. Useful simulation models have been developed to predict the effects of management actions on survival of drifting pallid sturgeon free embryos in the Yellowstone and Upper Missouri River complex (hereafter referred to as the “upper river”), and to assess the effects of flow and channel reconfigurations on habitat availability in the Lower Missouri River, tributaries, and Mississippi River downstream of Gavins Point Dam (hereafter referred to as the “lower river”). A population model also has been developed that can be used to assess sensitivity of the population to survival of specific life stages, assess some hypotheses related to stocking decisions, and explore a limited number of management scenarios. Consideration of lines of evidence for each of the 21 hypotheses includes a discussion of how the degree of uncertainty and risk associated with each hypothesis may guide science and implementation strategies. Implementation strategies include full implementation in the field, limited implementations as field-scale experiments, or (in the case of greatest uncertainty) implementation as learning actions, including research and opportunistic experiments or field-based gradient studies. Given the substantive uncertainties associated with pallid sturgeon population dynamics and the need to continually assimilate and assess new information, we proposed that an Effects Analysis-like process should be considered an integral part of ongoing Missouri River adaptive management.

Missouri↗

USGS2016

Science information to support Missouri River Scaphirhynchus albus (pallid sturgeon) effects analysis

The Missouri River Pallid Sturgeon Effects Analysis (EA) was commissioned by the U.S. Army Corps of Engineers to develop a foundation of understanding of how pallid sturgeon ( Scaphirhynchus albus ) population dynamics are linked to management actions in the Missouri River. The EA consists of several steps: (1) development of comprehensive, conceptual ecological models illustrating pallid sturgeon population dynamics and links to management actions and other drivers; (2) compilation and assessment of available scientific literature, databases, and models; (3) development of predictive, quantitative models to explore the system dynamics and population responses to management actions; and (4) analysis and assessment of effects of system operations and actions on species’ habitats and populations. This report addresses the second objective, compilation and assessment of relevant information. Scientific information on pallid sturgeon and its environment has grown substantially during the last decade. Presently available (2015) information indicates that stocked sturgeon are surviving and growing, and that wild and hatchery sturgeon are spawning in the wild. However, natural recruitment to age-1 and older has not been detected since systematic sampling began in 2005. Population models indicate the sensitivity of population growth to certain demographic variables, in particular early-life stage survival and perhaps adult fecundity. This report documents the existing population models for the pallid sturgeon, and the substantial quantities of information developed through the Pallid Sturgeon Population Assessment Program (PSPAP), the Habitat Assessment and Monitoring Program (HAMP), the Comprehensive Sturgeon Research Project (CSRP), range-wide genetics databases, and related research studies. The reference database compiled for the EA consists of over 190 peer-reviewed documents specifically related to pallid sturgeon and over 12,000 references on the Missouri River system and related species. Notwithstanding the large quantity of information available, the EA faces challenges in synthesizing the information into useful, quantitative models. In particular, critical demographic parameters for population models remain uncertain and the functional relationships between the two main categories of physical management action—changes in flow regime and reengineering channel form—and pallid sturgeon survival responses are obscure. In addition, there is an overarching uncertainty about how physical management actions interact with propagation management actions in view of evolving understanding of genetic structuring of the pallid sturgeon population. Synthesis efforts are also challenged by the fragmentation of information sources among projects and agencies; one objective of this report is to facilitate future assessments by providing documentation of what information is available and where.

Iowa, Kansas, Missouri, Montana, Nebraska, North D↗

USGS2016

Development of working hypotheses linking management of the Missouri River to population dynamics of Scaphirhynchus albus (pallid sturgeon)

This report documents a process of filtering of hypotheses that relate Missouri River Scaphirhynchus albus (pallid sturgeon) population dynamics to management actions including flow alterations, channel reconfigurations, and pallid sturgeon population augmentation. The filtering process was a partnership among U.S. Geological Survey, U.S. Army Corps of Engineers, and U.S. Fish and Wildlife Service to contribute to the Missouri River Recovery Management Plan process. The objective of the filtering process was to produce a set of hypotheses with high relevance to pallid sturgeon population dynamics and decision making on the Missouri River. The Missouri River Pallid Sturgeon Effects Analysis team filtered hundreds of potential hypotheses implicit in conceptual ecological models to develop a set of 40 candidate dominant hypotheses that were identified by experts as being important in pallid sturgeon population dynamics. Using a modified Delphi process and additional expert opinion, the team reduced this set of hypotheses to 23 working dominant hypotheses. We then matched the 23 hypotheses with management actions that could influence the biotic outcomes, resulting in as many as 176 potential effects between management actions and pallid sturgeon in the Missouri River. This number was consolidated to a candidate set of 53 working management hypotheses because some management actions applied to multiple life stages of the pallid sturgeon. We used an additional round of expert surveys to identify a set of 30 working management hypotheses. Finally, the set of working management hypotheses was filtered by the U.S. Army Corps of Engineers, Missouri River Recovery Program for actions that were within the agency’s authority and jurisdiction. This round resulted in a set of 21 hypotheses for initial modeling of linkages from management to pallid sturgeon population responses. The initial set of candidate hypotheses provides a useful starting point for quantitative modeling and adaptive management of the river and species. We anticipate that hypotheses will change from the set of working management hypotheses as adaptive management progresses. More importantly, hypotheses that have been filtered out of our multistep process are still being considered. These filtered hypotheses are archived and if existing hypotheses are determined to be inadequate to explain observed population dynamics, new hypotheses can be created or filtered hypotheses can be reinstated.

Missouri River Basin↗

USGS2016

Innate and adaptive immune responses in migrating spring-run adult chinook salmon, Oncorhynchus tshawytscha

Adult Chinook salmon ( Oncorhynchus tshawytscha ) migrate from salt water to freshwater streams to spawn. Immune responses in migrating adult salmon are thought to diminish in the run up to spawning, though the exact mechanisms for diminished immune responses remain unknown. Here we examine both adaptive and innate immune responses as well as pathogen burdens in migrating adult Chinook salmon in the Upper Willamette River basin. Messenger RNA transcripts encoding antibody heavy chain molecules slightly diminish as a function of time, but are still present even after fish have successfully spawned. In contrast, the innate anti-bacterial effector proteins present in fish plasma rapidly decrease as spawning approaches. Fish also were examined for the presence and severity of eight different pathogens in different organs. While pathogen burden tended to increase during the migration, no specific pathogen signature was associated with diminished immune responses. Transcript levels of the immunosuppressive cytokines IL-10 and TGF beta were measured and did not change during the migration. These results suggest that loss of immune functions in adult migrating salmon are not due to pathogen infection or cytokine-mediated immune suppression, but is rather part of the life history of Chinook salmon likely induced by diminished energy reserves or hormonal changes which accompany spawning.

Oregon↗

USGS2015

Occupancy modeling for improved accuracy and understanding of pathogen prevalence and dynamics

Most pathogen detection tests are imperfect, with a sensitivity < 100%, thereby resulting in the potential for a false negative, where a pathogen is present but not detected. False negatives in a sample inflate the number of non-detections, negatively biasing estimates of pathogen prevalence. Histological examination of tissues as a diagnostic test can be advantageous as multiple pathogens can be examined and providing important information on associated pathological changes to the host. However, it is usually less sensitive than molecular or microbiological tests for specific pathogens. Our study objectives were to 1) develop a hierarchical occupancy model to examine pathogen prevalence in spring Chinook salmon Oncorhynchus tshawytscha and their distribution among host tissues 2) use the model to estimate pathogen-specific test sensitivities and infection rates, and 3) illustrate the effect of using replicate within host sampling on sample sizes required to detect a pathogen. We examined histological sections of replicate tissue samples from spring Chinook salmon O. tshawytscha collected after spawning for common pathogens seen in this population: Apophallus/ echinostome metacercariae, Parvicapsula minibicornis, Nanophyetus salmincola/ metacercariae, and Renibacterium salmoninarum . A hierarchical occupancy model was developed to estimate pathogen and tissue-specific test sensitivities and unbiased estimation of host- and organ-level infection rates. Model estimated sensitivities and host- and organ-level infections rates varied among pathogens and model estimated infection rate was higher than prevalence unadjusted for test sensitivity, confirming that prevalence unadjusted for test sensitivity was negatively biased. The modeling approach provided an analytical approach for using hierarchically structured pathogen detection data from lower sensitivity diagnostic tests, such as histology, to obtain unbiased pathogen prevalence estimates with associated uncertainties. Accounting for test sensitivity using within host replicate samples also required fewer individual fish to be sampled. This approach is useful for evaluating pathogen or microbe community dynamics when test sensitivity is <100%.

PLoS ONE↗

USGS2015

A food web modeling analysis of a Midwestern, USA eutrophic lake dominated by non-native Common Carp and Zebra Mussels

Food web modeling is recognized as fundamental to understanding the complexities of aquatic systems. Ecopath is the most common mass-balance model used to represent food webs and quantify trophic interactions among groups. We constructed annual Ecopath models for four consecutive years during the first half-decade of a zebra mussel invasion in shallow, eutrophic Clear Lake, Iowa, USA, to evaluate changes in relative biomass and total system consumption among food web groups, evaluate food web impacts of non-native common carp and zebra mussels on food web groups, and to interpret food web impacts in light of on-going lake restoration. Total living biomass increased each year of the study; the majority of the increase due to a doubling in planktonic blue green algae, but several other taxa also increased including a more than two-order of magnitude increase in zebra mussels. Common carp accounted for the largest percentage of total fish biomass throughout the study even with on-going harvest. Chironomids, common carp, and zebra mussels were the top-three ranking consumer groups. Non-native common carp and zebra mussels accounted for an average of 42% of the total system consumption. Despite the relatively high biomass densities of common carp and zebra mussel, food web impacts was minimal due to excessive benthic and primary production in this eutrophic system. Consumption occurring via benthic pathways dominated system consumption in Clear Lake throughout our study, supporting the argument that benthic food webs are significant in shallow, eutrophic lake ecosystems and must be considered if ecosystem-level understanding is to be obtained.

Iowa↗

USGS2015

Development of conceptual ecological models linking management of the Missouri River to pallid sturgeon population dynamics

This report documents the process of developing and refining conceptual ecological models (CEMs) for linking river management to pallid sturgeon ( Scaphirhynchus albus ) population dynamics in the Missouri River. The refined CEMs are being used in the Missouri River Pallid Sturgeon Effects Analysis to organize, document, and formalize an understanding of pallid sturgeon population responses to past and future management alternatives. The general form of the CEMs, represented by a population-level model and component life-stage models, was determined in workshops held in the summer of 2013. Subsequently, the Missouri River Pallid Sturgeon Effects Analysis team designed a general hierarchical structure for the component models, refined the graphical structure, and reconciled variation among the components and between models developed for the upper river (Upper Missouri & Yellowstone Rivers) and the lower river (Missouri River downstream from Gavins Point Dam). Importance scores attributed to the relations between primary biotic characteristics and survival were used to define a candidate set of working dominant hypotheses about pallid sturgeon population dynamics. These CEMs are intended to guide research and adaptive-management actions to benefit pallid sturgeon populations in the Missouri River.

Missouri River, Yellowstone River↗

USGS2012

Strategies to control a common carp population by pulsed commercial harvest

Commercial fisheries are commonly used to manage nuisance fishes in freshwater systems, but such efforts are often unsuccessful. Strategies for successfully controlling a nuisance population of common carp Cyprinus carpio by pulsed commercial harvest were evaluated with a combination of (1) field sampling, (2) population estimation and CPUE indexing, and (3) simulation using an exponential semidiscrete biomass dynamics model (SDBDM). The range of annual fishing mortalities ( F ) that resulted in successful control ( F = 0.244–0.265) was narrow. Common carp biomass dynamics were sensitive to unintentional underharvest due to high rates of surplus production and a biomass doubling time of 2.7 years. Simulations indicated that biomanipulation never achieved successful control unless supplemental fishing mortality was imposed. Harvest of a majority of annual production was required to achieve successful control, as indicated by the ecotrophic coefficient (EC). Readily available biomass data and tools such as SDBDMs and ECs can be used in an adaptive management framework to successfully control common carp and other nuisance fishes by pulsed commercial fishing.

North American Journal of Fisheries Management↗

USGS2012

Semi-discrete biomass dynamic modeling: an improved approach for assessing fish stock responses to pulsed harvest events

Continuous harvest over an annual period is a common assumption of continuous biomass dynamics models (CBDMs); however, fish are frequently harvested in a discrete manner. We developed semidiscrete biomass dynamics models (SDBDMs) that allow discrete harvest events and evaluated differences between CBDMs and SDBDMs using an equilibrium yield analysis with varying levels of fishing mortality ( F ). Equilibrium fishery yields for CBDMs and SDBDMS were similar at low fishing mortalities and diverged as F approached and exceeded maximum sustained yield ( F MSY ). Discrete harvest resulted in lower equilibrium yields at high levels of F relative to continuous harvest. The effect of applying harvest continuously when it was in fact discrete was evaluated by fitting CBDMs and SDBDMs to time series data generated from a hypothetical fish stock undergoing discrete harvest and evaluating parameter estimates bias. Violating the assumption of continuous harvest resulted in biased parameter estimates for CBDM while SDBDM parameter estimates were unbiased. Biased parameter estimates resulted in biased biological reference points derived from CBDMs. Semidiscrete BDMs outperformed continuous BDMs and should be used when harvest is discrete, when the time and magnitude of harvest are known, and when F is greater than F MSY .

Canadian Journal of Fisheries and Aquatic Sciences↗