Alan B. Franklin

United States Department of Agriculture | USDA · National Wildlife Research Center

Ecology Letters (2010) 13: 659–674 Analytical methods accounting for imperfect detection are often used to facilitate reliable inference in population and community ecology. We contend that similar approaches are needed in disease ecology because these complicated systems are inherently difficult to observe without error. For example, wildlife dise...

In this chapter, we provide a general framework for developing strategies to mitigate the contamination of agricultural operations with pathogens carried by wildlife. As part of this framework, we present adaptive management as a viable approach to developing these strategies to reduce the uncertainty over time as to whether management methods are...

There is evidence that the current outbreak of the novel coronavirus SARS-CoV-2, which causes COVID-19, is of animal origin. As with a number of zoonotic pathogens, there is a risk of spillover into novel hosts. Here, we propose a hypothesized conceptual model that illustrates the mechanism whereby the SARS-CoV-2 could spillover from infected human...

The northern spotted owl (Strix occidentalis caurina) inhabits older coniferous forests in the Pacific Northwest and has been at the center of forest management issues in this region. The immediate threats to this federally listed species include habitat loss and competition with barred owls (Strix varia), which invaded from eastern North America....

Waterfowl infected with avian influenza A viruses (IAVs) shed infectious virus into aquatic environments, providing a mechanism for transmission among waterfowl, while also exposing the entire aquatic ecosystem to the virus. Aquatic invertebrates such as freshwater snails are likely exposed to IAVs in the water column and sediment. Freshwater snail...

New tools and techniques offer insight into the lives of these secretive birds.

We conducted a range‐wide investigation of the dynamics of site‐level reproductive rate of northern spotted owls using survey data from 11 study areas across the subspecies geographic range collected during 1993–2018. Our analytical approach accounted for imperfect detection of owl pairs and misclassification of successful reproduction (i.e., at le...

Birds are known to carry pathogens affecting human and agricultural health. Conversely, agricultural operations can serve as sources of pathogens that affect wild bird populations. In this chapter, we provide guidelines to identify focal avian species that frequently use agricultural operations. We couple this with identifying host types, such as m...

Significance Invasive species can cause extinctions of native species and widespread biodiversity loss. Invader removal is a common management response, but the use of long-term field experiments to characterize effectiveness of removals in benefitting impacted native species is rare. We used a large-scale removal experiment to investigate the demo...

Anthropogenic inputs into the environment may serve as sources of antimicrobial resistant bacteria and alter the ecology and population dynamics of synanthropic wild animals by providing supplemental forage. In this study, we used a combination of phenotypic and genomic approaches to characterize antimicrobial resistant indicator bacteria, animal t...

Western North American forest ecosystems are experiencing rapid changes in disturbance regimes because of climate change and land use legacies (Littell et al. 2018). In many of these forests, the accumulation of surface and ladder fuels from a century of fire suppression, coupled with a warming and drying climate, has led to increases in the number...

Emerging diseases of wildlife origin are increasingly spilling over into humans and domestic animals. Surveillance and risk assessments for transmission between these populations are informed by a mechanistic understanding of the pathogens in wildlife reservoirs. For avian influenza viruses (AIV), much observational and experimental work in wildlif...

In 2015, the mcr-1 gene was discovered in Escherichia coli in domestic swine in China that conferred resistance to colistin, an antibiotic of last resort used in treating multi-drug resistant bacterial infections in humans. Since then, mcr-1 was found in other human and animal populations, including wild gulls. Because gulls could disseminate the m...

A method was developed and validated for the detection of colistin-resistant Escherichia coli containing mcr-1 in the feces of feral swine. Following optimization of an enrichment method using EC broth supplemented with colistin (1 μg/mL) and vancomycin (8 μg/mL), aliquots derived from 100 feral swine fecal samples were spiked with of one of five d...

Influenza A viruses (IAVs) are a public-health, veterinary, and agricultural concern. Although wild birds are considered the primary reservoir hosts for most IAVs, wild-bird IAV strains are known to spill over into poultry, domestic or wild mammals, and humans. Occasionally, spillover events may result in adaptation or reassortment with other strai...

Slow ecological processes challenge conservation. Short‐term variability can obscure the importance of slower processes that may ultimately determine the state of a system. Furthermore, management actions with slow responses can be hard to justify. One response to slow processes is to explicitly concentrate analysis on state dynamics. Here, we focu...

Using data on waterfowl band recoveries, we identified spatially‐explicit hotspots of concentrated waterfowl movement to predict occurrence and spatial spread of a novel influenza A virus (clade 2.3.4.4) introduced from Asia by waterfowl from an initial outbreak in North America in November 2014. In response to the outbreak, the hotspots of waterfo...

Conservation biology is a value-laden discipline predicated on conserving biodiversity (Soulé 1985), a mission that does not always sit easily with objective science (Lackey 2007; Pielke 2007; Scott et al. 2007). While some encourage scientists to be responsible advocates for conservation (Garrard et al. 2016), others worry that objectivity in cons...

Inbreeding has been difficult to quantify in wild populations because of incomplete parentage information. We applied and extended a recently developed framework for addressing this problem to infer inbreeding rates in Northern Spotted Owls (Strix occidentalis caurina) across the Pacific Northwest, USA. Using pedigrees from 14,187 Northern Spotted...

This protocol demonstrates a customized bioaerosol sampling method for viruses. In this system, anion exchange resin is coupled with liquid impingement-based air sampling devices for efficacious concentration of negatively-charged viruses from bioaerosols. Thus, the resin serves as an additional concentration step in the bioaerosol sampling workflo...

Porcine epidemic diarrhea virus, a pathogen first detected in US domestic swine in 2013, has rapidly spilled over into feral swine populations. A better understanding of the factors associated with pathogen emergence is needed to better manage, and ultimately prevent, future spillover events from domestic to nondomestic animals.

Objective Marijuana (Cannabis spp.) growing operations (MGO) in California have increased substantially since the mid-1990s. One environmental side-effect of MGOs is the extensive use of anticoagulant rodenticides (AR) to prevent damage to marijuana plants caused by wild rodents. In association with a long-term demographic study, we report on an ob...

Abstract Live bird markets are common in certain regions of the U.S. and in other regions of the world. We experimentally tested the ability of a wild bird influenza A virus to transmit from index animals to naı¨ve animals at varying animal densities in stacked cages in a simulated live bird market. Two and six mallards, five and twelve quail, and...

Migratory waterfowl are often viewed as vehicles for the global spread of influenza A viruses (IAVs), with mallards (Anas platyrhynchos) implicated as particularly important reservoir hosts. The physical demands and energetic costs of migration have been shown to influence birds’ body condition; poorer body condition may suppress immune function an...

The detection of aerosolized viruses can serve as an important surveillance and control tool in agriculture, human health, and environmental settings. Here, we adapted an anion exchange resin-based method, initially developed to concentrate negatively charged viruses from water, to liquid impingement-based bioaerosol sampling. In this method, aeros...

Ecological disturbances shape and maintain natural communities, but climate change and human land use can alter disturbance regimes and affect population persistence and vital rates in unpredictable ways. Species inhabiting landscapes shaped by wildfire have evolved mechanisms allowing them to persist under this dynamic disturbance type, which crea...

Estimates of species' vital rates and an understanding of the factors affecting those parameters over time and space can provide crucial information for management and conservation. We used mark–recapture, reproductive output, and territory occupancy data collected during 1985–2013 to evaluate population processes of Northern Spotted Owls (Strix oc...

Following a 2008 outbreak of North American low-pathogenic H5N8 influenza A virus at an upland gamebird farm, we sero-sampled rock doves (pigeons, Columba livia) at the outbreak site and conducted experimental inoculations of wild-caught pigeons using the H5N8 virus and another low-pathogenic virus (H4N6). While 13 % of pigeons at the outbreak site...

The potential role of wild mammals in avian influenza A virus (IAV) transmission cycles has received some attention in recent years and cases where birds have transmitted IAV to mammals have been documented. However, the contrasting cycle, wherein a mammal could transmit an avian IAV to birds, has been largely overlooked. We experimentally tested t...

The range of the barred owl (Strix varia) has expanded westward over the past century and now entirely overlaps the range of the federally threatened northern spotted owl (S. occidentalis caurina) in the Pacific Northwest. We compared Haemoproteus blood parasite assemblages among northern spotted owls in their native range and barred owls in both t...

Background Cottontails (Sylvilagus spp.) are common mammals throughout much of the U.S. and are often found in peridomestic settings, potentially interacting with livestock and poultry operations. If these animals are susceptible to avian influenza virus (AIV) infections and shed the virus in sufficient quantities they may pose a risk for movement...

Background Wild raccoons have been shown to be naturally exposed to avian influenza viruses (AIV). However, the mechanisms associated with these natural exposures are not well-understood. Methodology/Principal Findings We experimentally tested three alternative routes (water, eggs, and scavenged waterfowl carcasses) of AIV transmission that may ex...

As an invasive species, feral swine (Sus scrofa) are a classic example of a species that can profoundly influence ecological communities and ecosystems. They alter environments through a suite of well-known traits: rooting behaviors that alter soil properties and disturb plant communities; a generalist diet that can encompass seeds, crops, and anim...

Wild birds are the primary source of genetic diversity for influenza A viruses that eventually emerge in poultry and humans. Much progress has been made in the descriptive ecology of avian influenza viruses (AIVs), but contributions are less evident from quantitative studies (e.g. those including disease dynamic models). Transmission between host s...

Striped skunks (Mephitis mephitis) are susceptible to infection with some influenza A viruses. However, the viral shedding capability of this peri-domestic mammal and its potential role in influenza A virus ecology are largely undetermined. Striped skunks were experimentally infected with a low pathogenic (LP) H4N6 avian influenza virus (AIV) and m...

In 2008, children playing on a soccer field in Colorado were sickened with a strain of Shiga toxin-producing Escherichia coli (STEC) O157:H7, which was ultimately linked to feces from wild Rocky Mountain elk. We addressed whether wild cervids were a potential source of STEC infections in humans and whether STEC was ubiquitous throughout wild cervid...

Abstract In aquatic bird populations, the ability of avian influenza (AI) viruses to remain infectious in water for extended periods provides a mechanism that allows viral transmission to occur long after shedding birds have left the area. However, this also exposes other aquatic organisms, including freshwater invertebrates, to AI viruses. Previou...

Abstract Highly pathogenic avian influenza virus A/H5N1 has been reported in 11 African countries. Migratory waterbirds have the potential of introducing A/H5N1 into east Africa through the Rift Valley of Kenya. We present the results of a wild bird surveillance system for A/H5N1 and other avian influenza viruses based on avian fecal sampling in Ke...

Pour basic control strategies mitigate the risks to aviation caused by wildlife at airports: (1) aircraft flight schedule modification (primarily at military air· bases) and enhancement of aircraft visibility to avoid interactions with wildlife (e.g., Blackwell et a1. 2009b, 2012); (2) habitat modification and elimination of food, water, and cover...

A United States interagency avian influenza surveillance plan was initiated in 2006 for early detection of highly pathogenic avian influenza viruses (HPAIV) in wild birds. The plan included a variety of wild bird sampling strategies including the testing of fecal samples from aquatic areas throughout the United States from April 2006 through Decemb...

Low-pathogenicity avian influenza viruses (LPAIV) can lead to epizootics that cause economic losses in poultry or the emergence of human-infectious strains. LPAIVs experience a complex immunity landscape since they are endemic in multiple host species and many antigenically-distinct strains co-circulate. Prevention and control of emergence of detri...

Abstract We report experimental evidence for bioconcentration of a low-pathogenicity avian influenza virus (H6N8) in the tissue of freshwater clams. Our results support the concept that freshwater clams may provide an effective tool for use in the early detection of influenza A viruses in aquatic environments.

Many bird species do not make their own nests; therefore, selection of existing sites that provide adequate microclimates is critical. This is particularly true for owls in north temperate climates that often nest early in the year when inclement weather is common. Spotted owls use three main types of nest structures, each of which are structurally...

Avian influenza viruses are known to productively infect a number of mammal species, several of which are commonly found on or near poultry and gamebird farms. While control of rodent species is often used to limit avian influenza virus transmission within and among outbreak sites, few studies have investigated the potential role of these species i...

European starlings (Sturnus vulgaris) are a known risk factor for the occurrence of microorganisms that are pathogenic to cattle and humans in concentrated animal feeding operations (CAFOs). Starling use of CAFOs is known to vary in response to weather; starling control operations on CAFOs often are timed to coincide with favorable environmental co...

The northern spotted owl (Strix occidentalis caurina) is a controversial species in the Pacific Northwest that is listed as threatened under the Endangered Species Act. The barred owl (Strix varia), a species historically restricted to eastern North America, has recently expanded its range to completely overlap that of the northern spotted owl. Rec...

1. Characterizing and mitigating the disease risks associated with wildlife use of concentrated animal feeding operations (CAFOs) can reduce the spread of micro-organisms throughout the environment while increasing agricultural productivity. To better understand the disease risks associated with bird use of CAFOs, we assessed the capacity of Europe...

We used data from 11 long-term studies to assess temporal and spatial patterns in fecundity, apparent survival, recruitment, and annual finite rate of population change of Northern Spotted Owls (Strix occidentalis caurina) from 1985 to 2008. Our objectives were to evaluate the status and trends of the subspecies throughout its range and to investig...

The California spotted owl ( Strix occidentalis occidentalis ) is the only spotted owl subspecies not listed as threatened or endangered under the United States Endangered Species Act despite petitions to list it as threatened. We conducted a meta‐analysis of population data for 4 populations in the southem Cascades and Sierra Nevada, California, U...

An investigation was performed to describe the responses of naturally acquired antibodies to influenza A virus in raccoons (Procyon lotor) over time. Seven wild raccoons, some of which had been exposed to multiple subtypes of influenza A virus, were held in captivity for 279 days, and serum samples were collected on 10 occasions during this interva...

To characterize the responses of raccoons to West Nile virus (WNV) infection, we subcutaneously exposed them to WNV. Moderately high viremia titers (≤ 10(4.6) plaque forming units [PFU]/mL of serum) were noted in select individuals; however, peak viremia titers were variable and viremia was detectable in some individuals as late as 10 days post-ino...

Wild mallards (Anas platyrhychos) are considered one of the primary reservoir species for avian influenza viruses (AIV). Because AIV circulating in wild birds pose an indirect threat to agriculture and human health, understanding the ecology of AIV and developing risk assessments and surveillance systems for prevention of disease is critical. In th...

Equine influenza A virus (EIV) is a highly infectious respiratory pathogen of horses (Hannant and Mumford 1996, Palese and Shaw 2007). The illness is characterised by an abrupt onset of fever, depression, coughing and nasal discharge, and is often complicated by secondary bacterial infections that can lead to pneumonia and death. Two subtypes of EI...

INFLUENZA A virus (IAV) (family Orthomyxoviridae) is a highly infectious respiratory pathogen of birds and mammals, including human beings and horses (Palese and Shaw 2007). The virus is classified into different subtypes based on the antigenic properties of the haemagglutinin (HA) and neuraminidase (NA) proteins. Sixteen HA subtypes (H1 to H16) an...

As part of the USA's National Strategy for Pandemic Influenza, an Interagency Strategic Plan for the Early Detection of Highly Pathogenic H5N1 Avian Influenza in Wild Migratory Birds was developed and implemented. From 1 April 2006 through 31 March 2009, 261,946 samples from wild birds and 101,457 wild bird fecal samples were collected in the USA;...

An epitope-blocking enzyme-linked immunosorbent assay (bELISA) was developed for the detection of antibodies to influenza A virus in taxonomically diverse domestic and wild vertebrate species. In contrast to the bELISAs published previously that require reagent production, manipulation by the end-user, or have not been evaluated for use with both m...