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At least 109 records · Page 6Linked to original sources
USGS2024

Designing count-based studies in a world of hierarchical models

Advances in hierarchical modeling have improved estimation of ecological parameters from count data, especially those quantifying population abundance, distribution, and dynamics by explicitly accounting for observation processes, particularly incomplete detection. Even hierarchical models that account for incomplete detection, however, cannot compensate for data limitations stemming from poorly planned sampling. Ecologists therefore need guidance for planning count-based studies that follow established sampling theory, collect appropriate data, and apply current modeling approaches to answer their research questions. We synthesize available literature relevant to guiding count-based studies. Considering the central historical and ongoing contributions of avian studies to ecological knowledge, we focus on birds as a case study for this review, but the basic principles apply to all populations whose members are sufficiently observable to be counted. The sequence of our review represents the thought process in which we encourage ecologists to engage 1) the research question(s) and population parameters to measure, 2) sampling design, 3) analytical framework, 4) temporal design, and 5) survey protocol. We also provide 2 hypothetical demonstrations of these study plan components representing different research questions and study systems. Mirroring the structure of hierarchical models, we suggest researchers primarily focus on the ecological processes of interest when designing their approach to sampling, and wait to consider logistical constraints of data collection and observation processes when developing the survey protocol. We offer a broad framework for researchers planning count-based studies, while pointing to relevant literature elaborating on particular tools and concepts.

Journal of Wildlife Management↗
USGS2012

Nonsteroidal anti-inflammatory drugs in raptors

The use of analgesia has become standard, and appropriate, practice in avian medicine. As in mammals, pain control in avian patients is usually accomplished with opioids and nonsteroidal anti-inflammatory drugs (NSAIDs) used singly or in combination for a multimodal approach. Despite their usefulness, widespread use, and relative safety in clinical use, few controlled studies in birds have been conducted on efficacy, safety, and dosing. The guidelines for the use of NSAIDs in raptors and other birds have mainly been empirical. More recently, NSAIDs in free-living raptors have emerged as a major conservation issue with the discovery that diclofenac sodium was responsible for the population crash of three species of Gyps vultures in southern Asia. In this context, residues of veterinary NSAIDs in domestic animals are now considered environmental contaminants that can be significantly toxic to vultures and possibly other avian scavengers. Ironically, the disaster with Asian vultures has led to a considerable body of research on NSAIDs in raptors to the benefit of clinicians who now have scientific information available to help assess dosing, safety, toxicity, and pharmacokinetics of NSAIDs in their raptor patients.

Book chapter↗
USGS2005

Long-term effects of precommercial thinning on small mammals in northern Maine

Precommercial thinning (PCT) is being practiced increasingly throughout the Acadian forest of eastern North America to meet silvicultural objectives; however, effects of this practice on wildlife, both immediately and several years post-treatment are not well understood. Forest dependent small mammals have ecological roles as prey for numerous avian and mammalian predators, dispersers of seeds, fruit, and spores, and contribute to nutrient cycling. Researchers in the northwestern USA have suggested that thinning of young, regenerating clearcuts may increase the abundance and diversity of some forest-dependent small mammals by increasing rates of forest development and enhancing the ecological representation of mid-successional stands across managed landscapes. We examined the effects of PCT within conifer-dominated forest stands 1-, 6-, 11-, and 16-years post-treatment, on abundances of mice, voles, and shrews, and on within-stand structure in the commercially managed, Acadian forests of northern Maine. We live-trapped small mammals on 24 herbicide-treated clearcuts treated with PCT and on 13 similar, unthinned stands during summers of 2000 and 2001. Thinning of mid-successional conifer stands resulted in increased abundances, (red-backed voles, Clethrionomys gapperi, P = 0.008; masked shrews, Sorex cinereus, P < 0.001) or had no detectable effect on (deer mice, Peromyscus maniculatus, P = 0.544; short-tailed shrews, Blarina brevicauda, P = 0.517) the 4 most common species of Muridae and Soricidae in northern Maine. In general, abundance of deer mice responded more positively to increasing development class and to the number of years since thinning than other species of small mammals. Several within-stand habitat characteristics associated with stand maturity, such as larger stem diameters and a partially open canopy, occurred in thinned stands. Thus, PCT may accelerate the development of habitat attributes typical of mid-successional conifer stands in intensively managed stands within the Acadian Forest. PCT may increase abundances of small mammal species associated with mid-seral forest conditions at the scale of the forest stand. ?? 2004 Elsevier B.V. All rights reserved.

Forest Ecology and Management↗
USGS2016

Synthesis of juvenile lamprey migration and passage research and monitoring at Columbia and Snake River Dams

We compiled and summarized previous sources of data and research results related to the presence, numbers, and migration timing characteristics of juvenile (eyed macropthalmia) and larval (ammocoetes) Pacific lamprey Entosphenus tridentatus, in the Columbia River basin (CRB). Included were data from various screw trap collections, data from historic fyke net studies, catch records of lampreys at JBS facilities, turbine cooling water strainer collections, and information on the occurrence of lampreys in the diets of avian and piscine predators. We identified key data gaps and uncertainties that should be addressed in a juvenile lamprey passage research program. The goal of this work was to summarize information from disparate sources so that managers can use it to prioritize and guide future research and monitoring efforts related to the downstream migration of juvenile Pacific lamprey within the CRB. A common finding in all datasets was the high level of variation observed for CRB lamprey in numbers present, timing and spatial distribution. This will make developing monitoring programs to accurately characterize lamprey migrations and passage more challenging. Primary data gaps centered around our uncertainty on the numbers of juvenile and larval present in the system which affects the ability to assign risk to passage conditions and prioritize management actions. Recommendations include developing standardized monitoring methods, such as at juvenile bypass systems (JBS’s), to better document numbers and timing of lamprey migrations at dams, and use biotelemetry tracking techniques to estimate survival potentials for different migration histories.

Report↗
USGS2014

Nutritional stress affects corticosterone deposition in feathers of Caspian tern chicks

Stressful environmental conditions affect the adrenocortical function of developing animals, which can have consequences for their fitness. Discovery of the avian stress hormone corticosterone (CORT) in feathers has the potential to broaden the application of endocrine research in ecological and evolutionary studies of wild birds by providing a long-term measure of CORT secretion. Mechanisms of CORT deposition in feathers are not well known and few studies have related feather CORT to circulating plasma CORT during feather growth. Our objective was to experimentally test the validity of using feather CORT as a measure of CORT secretion in developing birds experiencing nutritional stress. Caspian tern Hydroprogne caspia chicks were fed ad libitum or restricted (35% less than ad libitum) diets for four weeks. We measured CORT in feathers from these chicks to examine the relationship between feather CORT concentrations and nutritional limitation, circulating plasma CORT, and feather development. We found that feather CORT was higher in controls fed ad libitum than in restricted individuals, despite higher levels of plasma CORT in restricted chicks compared to controls. Feather mass and growth rates were strongly and positively related to feather CORT concentrations in both treatments. This is the first experimental study to show that feather CORT concentrations can be lower in response to nutritional stress, even when plasma CORT concentrations are elevated. Our results indicate that CORT deposition in feathers may be confounded when feather mass and growth rates are compromised by nutritional stress. We conclude that feather CORT can be used for assessing nutritional stress in growing birds, but the direction of response depends on how strongly stress affects feather development.

Journal of Avian Biology↗
USGS2020

Research priorities for migratory birds under climate change—A qualitative value of information assessment

The mission of the U.S. Geological Survey National Climate Adaptation Science Center is to provide actionable, management-relevant research on climate change effects on ecosystems and wildlife to U.S. Department of the Interior bureaus. Providing this kind of useful scientific information requires understanding how natural-resource managers make decisions and identifying research priorities that support those decision-making processes. Migratory bird management and conservation of migratory bird habitat are central components of the U.S. Department of the Interior’s mission. In particular, the U.S. Fish and Wildlife Service has an intensive, complex decision-making process for identifying high-priority parcels of land that will contribute to migratory bird conservation through permanent acquisition or easement. Climate change introduces several uncertainties into this decision-making process, and additional climate change research should help to support more informed decision making regarding habitat acquisition. Not all climate change related uncertainties, however, will have a meaningful effect on acquisition decisions; therefore, understanding which uncertainties have the most potential to alter decision making is crucial. This document summarizes a multiyear effort to clarify the major sources of climate change uncertainty that affect migratory bird management and to articulate related research priorities. We worked with U.S. Fish and Wildlife Service staff to assess the primary ways in which climate change is likely to affect migratory birds and their habitats; to clarify uncertainties surrounding these effects; and to assess how uncertainties may affect habitat acquisition decisions. Using a modified structured decision-making approach, we assessed a set of hypotheses about how climate change will affect migratory birds and their habitats. Then, we used a qualitative value of information assessment to rank the most important topics for future research. The ranking process was built on an assessment of three primary characteristics: the magnitude of uncertainty, the topic’s relevance to habitat acquisition decision making, and the feasibility of reducing the uncertainty. Based on the results of this process, high-priority topics for future research include the following: The effects of rising temperatures on spatial distributions of migratory birds during the breeding and nonbreeding seasons; Climate-driven changes to avian community composition through homogenization and loss of specialists; The effects of decreased precipitation on abundance in the breeding season; and The effects of rising temperatures on abundance in the nonbreeding season. In addition to describing high-priority research needs, this document provides a summary of the methodology used to identify, assess, and rank uncertainties. This method was developed for a climate change related topic where a full quantitative value of information approach may not be feasible. The results and methodology described here may be useful for U.S. Geological Survey and other science-funding agencies interested in improving the applicability of their research to natural-resource management decision making.

Circular↗
USGS2002

Large scale wildlife monitoring studies: Statistical methods for design and analysis

Techniques for estimation of absolute abundance of wildlife populations have received a lot of attention in recent years. The statistical research has been focused on intensive small-scale studies. Recently, however, wildlife biologists have desired to study populations of animals at very large scales for monitoring purposes. Population indices are widely used in these extensive monitoring programs because they are inexpensive compared to estimates of absolute abundance. A crucial underlying assumption is that the population index ( C ) is directly proportional to the population density ( D ). The proportionality constant, β , is simply the probability of 'detection' for animals in the survey. As spatial and temporal comparisons of indices are crucial, it is necessary to also assume that the probability of detection is constant over space and time. Biologists intuitively recognize this when they design rigid protocols for the studies where the indices are collected. Unfortunately, however in many field studios the assumption is clearly invalid. We believe that the estimation of detection probability should be built into the monitoring design through a double sampling approach. A large sample of points provides an abundance index, and a smaller sub-sample of the same points is used to estimate detection probability. There is an important need for statistical research on the design and analysis of these complex studies. Some basic concepts based on actual avian, amphibian, and fish monitoring studies are presented in this article.

Environmetrics↗
USGS2022

Changes in waterfowl migration phenologies in central North America: Implications for future waterfowl conservation

Globally, migration phenologies of numerous avian species have shifted over the past half-century. Despite North American waterfowl being well researched, published data on shifts in waterfowl migration phenologies remain scarce. Understanding shifts in waterfowl migration phenologies along with potential drivers is critical for guiding future conservation efforts. Therefore, we utilized historical (1955–2008) nonbreeding waterfowl survey data collected at 21 National Wildlife Refuges in the mid- to lower portion of the Central Flyway to summarize changes in spring and autumn migration phenology. We examined changes in the timing of peak abundance from survey data at monthly intervals for each refuge and species (or species group; n = 22) by year and site-specific temperature for spring (Jan–Mar) and autumn (Oct–Dec) migration periods. For spring ( n = 187) and autumn ( n = 194) data sets, 13% and 9% exhibited statistically significant changes in the timing of peak migration across years, respectively, while the corresponding numbers for increasing temperatures were 4% and 9%. During spring migration, ≥80% of significant changes in the timing of spring peak indicated advancements, while 67% of significant changes in autumn peak timing indicated delays both across years and with increasing temperatures. Four refuges showed a consistent pattern across species of advancing spring migration peaks over time. Advancements in spring peak across years became proportionally less common among species with increasing latitude, while delays in autumn peak with increasing temperature became proportionally more common. Our study represents the first comprehensive summary of changes in spring and autumn migration phenology for Central Flyway waterfowl and demonstrates significant phenological changes during the latter part of the twentieth century.

Kansas, Nebraska, New Mexico, Oklahoma, Texas↗
USGS2001

Neuroendocrine and behavioral implications of endocrine disrupting chemicals in quail

Studies in our laboratory have focused on endocrine, neuroendocrine, and behavioral components of reproduction in the Japanese quail. These studies considered various stages in the life cycle, including embryonic development, sexual maturation, adult reproductive function, and aging. A major focus of our research has been the role of neuroendocrine systems that appear to synchronize both endocrine and behavioral responses. These studies provide the basis for our more recent research on the impact of endocrine disrupting chemicals (EDCs) on reproductive function in the Japanese quail. These endocrine active chemicals include pesticides, herbicides, industrial products, and plant phytoestrogens. Many of these chemicals appear to mimic vertebrate steroids, often by interacting with steroid receptors. However, most EDCs have relatively weak biological activity compared to native steroid hormones. Therefore, it becomes important to understand the mode and mechanism of action of classes of these chemicals and sensitive stages in the life history of various species. Precocial birds, such as the Japanese quail, are likely to be sensitive to EDC effects during embryonic development, because sexual differentiation occurs during this period. Accordingly, adult quail may be less impacted by EDC exposure. Because there are a great many data available on normal development and reproductive function in this species, the Japanese quail provides an excellent model for examining the effects of EDCs. Thus, we have begun studies using a Japanese quail model system to study the effects of EDCs on reproductive endocrine and behavioral responses. In this review, we have two goals: first, to provide a summary of reproductive development and sexual differentiation in intact Japanese quail embryos, including ontogenetic patterns in steroid hormones in the embryonic and maturing quail. Second, we discuss some recent data from experiments in our laboratory in which EDCs have been tested in Japanese quail. The Japanese quail provides an excellent avian model for testing EDCs because this species has well-characterized reproductive endocrine and behavioral responses. Considerable research has been conducted in quail in which the effects of embryonic steroid exposure have been studied relative to reproductive behavior. Moreover, developmental processes have been studied extensively and include investigations of the reproductive axis, thyroid system, and stress and immune responses. We have conducted a number of studies, which have considered long-term neuroendocrine consequences as well as behavioral responses to steroids. Some of these studies have specifically tested the effects of embryonic steroid exposure on later reproductive function in a multigenerational context. A multigenerational exposure provides a basis for understanding potential exposure scenarios in the field. In addition, potential routes of exposure to EDCs for avian species are being considered, as well as differential effects due to stage of the life cycle at exposure to an EDC. The studies in our laboratory have used both diet and egg injection as modes of exposure for Japanese quail. In this way, birds were exposed to a specific dose of an EDC at a selected stage in development by injection. Alternatively, dietary exposure appears to be a primary route of exposure; therefore experimental exposure through the diet mimics potential field situations. Thus, experiments should consider a number of aspects of exposure when attempting to replicate field exposures to EDCs.

Hormones and Behavior↗
USGS2010

Estimating length of avian incubation and nestling stages in afrotropical forest birds from interval-censored nest records

In the East Usambara Mountains in northeast Tanzania, research on the effects of forest fragmentation and disturbance on nest survival in understory birds resulted in the accumulation of 1,002 nest records between 2003 and 2008 for 8 poorly studied species. Because information on the length of the incubation and nestling stages in these species is nonexistent or sparse, our objectives in this study were (1) to estimate the length of the incubation and nestling stage and (2) to compute nest survival using these estimates in combination with calculated daily survival probability. Because our data were interval censored, we developed and applied two new statistical methods to estimate stage length. In the 8 species studied, the incubation stage lasted 9.6-21.8 days and the nestling stage 13.9-21.2 days. Combining these results with estimates of daily survival probability, we found that nest survival ranged from 6.0% to 12.5%. We conclude that our methodology for estimating stage lengths from interval-censored nest records is a reasonable and practical approach in the presence of interval-censored data. ?? 2010 The American Ornithologists' Union.

The Auk↗
USGS2026

Biological, environmental, and geomorphological factors influencing reach-specific survival of spring Chinook Salmon smolts upstream of the Columbia–Snake River hydrosystem

Objective Pacific salmon Oncorhynchus spp. are exhibiting catastrophic declines throughout much of the Pacific Northwest, and juvenile mortality contributions are disproportionately high. Many Pacific salmon smolt populations are exhibiting high natal stream mortality; however, detailed natal stream reach-specific survival knowledge is lacking. Our objectives were to estimate natal stream reach-specific survival and identify influential covariates for spring Chinook Salmon O. tshawytscha smolts. An additional objective was to evaluate (i.e., estimate postrestoration cumulative survival) a novel and strategic large-scale river restoration approach (i.e., stream confluence restoration) in two Pacific Northwest spring Chinook Salmon natal streams. Methods Using radiotelemetry techniques during March–June (2011–2017), we estimated natal stream reach-specific survival for spring Chinook Salmon smolts in Catherine Creek and the Grande Ronde River, northeast Oregon. We examined the interrelated influences of temporal, biological, environmental, and geomorphological covariates on the behavior, travel time, and reach-specific survival of spring Chinook Salmon smolts that were emigrating through two hydrologically altered natal streams in the interior Columbia River basin. For each natal stream smolt tag-group, Cormack–Jolly–Seber reach-specific survival estimates that were adjusted for premature tag failure (i.e., bias-corrected) were generated. Subsequently, smolt effects were estimated using reach-specific travel times and survival estimates coupled with individual time-varying covariates from radio-tagged smolts and occupied reaches using an existing predator–prey model (i.e., mean free-path length [ XT ] model). Complementary population-specific principal coordinate analyses (PCoAs) were conducted to facilitate visualization of multicovariate resemblances in ordination space. Last, we employed our best-fitting XT model to model cumulative changes in smolt survival that were associated with a large-scale stream channel restoration scenario (i.e., restoration of the historical Catherine Creek and Grande Ronde River confluence). Results In aggregate, Catherine Creek smolts exhibited high mortality throughout Catherine Creek but near-100% survival upon entering the Grande Ronde River. In contrast, Grande Ronde River smolts generally exhibited low mortality upstream from the Grande Ronde Valley and high mortality throughout the Grande Ronde Valley. Our best-fitting XT model indicated that smolt survival was positively correlated with discharge, body size, and current velocity but negatively correlated with avian predation. Natural-origin smolts from Catherine Creek displayed higher λ-values (i.e., distance between predator–prey encounters) than their significantly larger and faster emigrating hatchery conspecifics, indicating that hatchery smolts may be more susceptible to predation. Our population-specific PCoAs further revealed that novel water (i.e., unique water chemistry) and emigration rate were the strongest predictors of reach occupancy in multivariate ordination space. Under a stream restoration scenario of restoring the historical hydrological template (i.e., restored channel configuration), our best-fitting XT model predicted changes in population-specific cumulative survivals to the lower Grande Ronde Valley (Imbler, Oregon) ranging from −38.4% to 69.0% for Grande Ronde River and Catherine Creek spring Chinook Salmon smolts, respectively. Conclusions Our best-fitting XT model and PCoAs identified the relative importance of biological, environmental, and geomorphological factors to both natural- and hatchery-origin Chinook Salmon smolt survival in two neighboring interior natal streams in the Columbia River basin. Our research indicates that concurrent habitat restoration and fish management strategies, including focused attention on smolt-rearing nursery habitat restoration, piscivorous avian control plans, adaptive management strategies for hatchery smolt releases, and discharge and novel water regime restoration projects, may yield survival benefits to “in-basin” Chinook Salmon smolts. Our research can inform origin-type-specific Chinook Salmon smolt management, habitat restoration, and future research decisions throughout the upper Grande Ronde River subbasin and potentially the Pacific Northwest.

Oregon, Washington↗
USGS2010

Embryo malposition as a potential mechanism for mercury-induced hatching failure in bird eggs

We examined the prevalence of embryo malpositions and deformities in relation to total mercury (THg) and selenium (Se) concentrations in American avocet ( Recurvirostra americana ), black‐necked stilt ( Himantopus mexicanus ), and Forster's tern ( Sterna forsteri ) eggs in San Francisco Bay (CA, USA) during 2005 to 2007. Overall, 11% of embryos were malpositioned in eggs ≥18 d of age ( n = 282) and 2% of embryos were deformed in eggs ≥13 d of age ( n = 470). Considering only those eggs that failed to hatch ( n = 62), malpositions occurred in 24% of eggs ≥18 d of age and deformities occurred in 7% of eggs ≥13 d of age. The probability of an embryo being malpositioned increased with egg THg concentrations in Forster's terns, but not in avocets or stilts. The probability of embryo deformity was not related to egg THg concentrations in any species. Using a reduced dataset with both Se and THg concentrations measured in eggs ( n = 87), we found no interaction between Se and THg on the probability of an embryo being malpositioned or deformed. Results of the present study indicate that embryo malpositions were prevalent in waterbird eggs that failed to hatch and the likelihood of an embryo being malpositioned increased with egg THg concentrations in Forster's terns. We hypothesize that malpositioning of avian embryos may be one reason for mercury‐related hatching failure that occurs late in incubation, but further research is needed to elucidate this potential mechanism.

Environmental Toxicology and Chemistry↗
USGS1978

Wildlife and electric power transmission

Hundreds of thousands of miles of transmission lines have been introduced into our natural environment. These lines and their corridors can be damaging or beneficial to wildlife communities depending on how they are designed, where they are placed, and when they are constructed and maintained. With the current trend toward UHV systems, new problems (associated with additional increments in audible noise, electric and magnetic force fields, etc.) must be addressed. We recommend the following areas for careful study: (1) the response of wilderness species to transmission lines and line construction and maintenance activities (2) the magnitude of bird collision and electrocution mortality, (3) the response of power corridor and power tower in habiting wildlife to laboratory and field doses of electro-chemical oxidants, corona noise, electric and magnetic fields, etc., (4) the productivity of tower inhabiting birds compared with nearby non-tower nesters, and (5) the influence of powerline corridors on mammalian and avian migration patterns. It is our hope that the questions identified in this study will help stimulate further research so that we can maximize wildlife benefits and minimize wildlife detriments.

Book chapter↗
USGS2010

Effects of lipid extraction on stable isotope ratios in avian egg yolk: Is arithmetic correction a reliable alternative?

Many studies of nutrient allocation to egg production in birds use stable isotope ratios of egg yolk to identify the origin of nutrients. Dry egg yolk contains >50% lipids, which are known to be depleted in 13 C. Currently, researchers remove lipids from egg yolk using a chemical lipid-extraction procedure before analyzing the isotopic composition of protein in egg yolk. We examined the effects of chemical lipid extraction on ?? 13 C, ?? 15 N, and ?? 34 S of avian egg yolk and explored the utility of an arithmetic lipid correction model to adjust whole yolk ?? 13 C for lipid content. We analyzed the dried yolk of 15 captive Spectacled Eider (Somateriafischeri) and 20 wild King Eider (S. spectabilis) eggs, both as whole yolk and after lipid extraction with a 2:1 chloroform:methanol solution. We found that chemical lipid extraction leads to an increase of (mean ?? SD) 3.3 ?? 1.1% in ?? 13 C, 1.1 ?? 0.5% in ?? 15 N, and 2.3 ?? 1.1% in ?? 34 S. Arithmetic lipid correction provided accurate values for lipid-extracted S13C in captive Spectacled Eiders fed on a homogeneous high-quality diet. However, arithmetic lipid correction was unreliable for wild King Eiders, likely because of their differential incorporation of macronutrients from isotopically distinct environments during migration. For that reason, we caution against applying arithmetic lipid correction to the whole yolk ?? 13 C of migratory birds, because these methods assume that all egg macronutrients are derived from the same dietary sources. ?? 2010 The American Ornithologists' Union.

The Auk↗
USGS2025

The scientific benefits of a statewide, standardized, coastal wetland monitoring program in Hawaiʻi

In this viewpoint, we provide a scientific justification for a statewide, standardized, coastal wetland monitoring program for Hawaiʻi, USA. Hawaiian coastal wetlands provide important habitat for endangered waterbirds, invertebrates, plants, and the Hawaiian hoary bat (ʻōpeʻapeʻa; Lasiurus semotus ) as well as support Indigenous food systems. Currently, numerous agencies and groups in Hawaiʻi collect data on coastal wetlands, but information is not typically shared and methods are not standardized. A statewide, standardized, coastal wetland monitoring program with a centralized database would allow managers to keep better track of progress toward restoration goals, population changes of conservation-reliant species, outbreaks and impacts of avian botulism, rates of coastal salinization, and many other critical issues across space and time. Monitoring combined with targeted research could fill critical knowledge gaps about the types, functions, values, and biodiversity of Hawaiian coastal wetlands. Ultimately, the improved knowledge gained from long-term coastal wetland monitoring could inform landscape-scale restoration actions and adaptive management of coastal wetlands under sea-level rise and climate change.

Hawaii↗
USGS2016

A field ornithologist’s guide to genomics: Practical considerations for ecology and conservation

Vast improvements in sequencing technology have made it practical to simultaneously sequence millions of nucleotides distributed across the genome, opening the door for genomic studies in virtually any species. Ornithological research stands to benefit in three substantial ways. First, genomic methods enhance our ability to parse and simultaneously analyze both neutral and non-neutral genomic regions, thus providing insight into adaptive evolution and divergence. Second, the sheer quantity of sequence data generated by current sequencing platforms allows increased precision and resolution in analyses. Third, high-throughput sequencing can benefit applications that focus on a small number of loci that are otherwise prohibitively expensive, time-consuming, and technically difficult using traditional sequencing methods. These advances have improved our ability to understand evolutionary processes like speciation and local adaptation, but they also offer many practical applications in the fields of population ecology, migration tracking, conservation planning, diet analyses, and disease ecology. This review provides a guide for field ornithologists interested in incorporating genomic approaches into their research program, with an emphasis on techniques related to ecology and conservation. We present a general overview of contemporary genomic approaches and methods, as well as important considerations when selecting a genomic technique. We also discuss research questions that are likely to benefit from utilizing high-throughput sequencing instruments, highlighting select examples from recent avian studies.

The Auk↗
USGS2010

Validation of a real-time reverse transcriptase-PCR assay for the detection of H7 avian influenza virus

This report describes the validation of an avian influenza virus (AIV) H7 subtype-specific real-time reverse transcriptasePCR (rRT-PCR) assay developed at the Southeast Poultry Research Laboratory (SEPRL) for the detection of H7 AI in North and South American wild aquatic birds and poultry. The validation was a collaborative effort by the SEPRL and the National Veterinary Services Laboratories. The 2008 H7 rRT-PCR assay detects 10 1 50% embryo infectious doses per reaction, or 10 3 10 4 copies of transcribed H7 RNA. Diagnostic sensitivity and specificity were estimated to be 97.5% and 82.4%, respectively; the assay was shown to be specific for H7 AI when tested with >270 wild birds and poultry viruses. Following validation, the 2008 H7 rRT-PCR procedure was adopted as an official U.S. Department of Agriculture procedure for the detection of H7 AIV. The 2008 H7 assay replaced the previously used (2002) assay, which does not detect H7 viruses currently circulating in wild birds in North and South America. ?? 2010 American Association of Avian Pathologists.

Avian Diseases↗