Sean M. Murphy

United States Geological Survey | USGS · Western Ecological Research Center

Concerns over red wolf (Canis rufus) extinction caused by hybridization with coyotes (C. latrans) led to the capture and removal of remnant wild wolves from southwestern Louisiana and southeastern Texas, United States, during the 1970s. Here we show that despite decades of unmitigated hybridization, and declaration of endangered red wolves as funct...

Obtaining reliable population density estimates for pumas (Puma concolor) and other cryptic, wide-ranging large carnivores is challenging. Recent advancements in spatially explicit capture-recapture models have facilitated development of novel survey approaches, such as clustered sampling designs, which can provide reliable density estimation for e...

Habitat loss and overexploitation extirpated American black bears (Ursus americanus) from most of the Central Appalachians, USA, by the early 20th Century. To attempt to restore bears to the southwestern portion of this region, 2 reintroductions that used small founder groups (n = 27 and 55 bears), but different release methods (hard vs. soft), wer...

Range-wide status assessments of wildlife are critical to effective species conservation and management. Reliability of these assessments is contingent on having accurate and precise demographic estimates for local populations, but for large carnivores, such estimates are often biased, imprecise, or unavailable. Despite being the most widely distri...

The last known red wolves were captured in southwestern Louisiana and eastern Texas in 1980 to establish a captive breeding population. Before their extirpation, gene flow with coyotes resulted in the persistence of endangered red wolf genetic variation in local coyote populations. We assessed genomic ancestry and morphology of coyotes in southwest...

Identifying population-level relationships between predators and their prey is often predicated on having reliable population estimates. Camera-trapping is effective for surveying terrestrial wildlife, but many species lack individually unique natural markings that are required for most abundance and density estimation methods. Analytical approache...

A significant effort in biomedical sciences has been made to examine relationships between sex and the mechanisms underlying various disease states and behaviors, including sleep. Here, we investigated biological sex differences in sleep using male and female C57BL/6J mice (n = 267). Physiological parameters were recorded for 48-h using non-invasiv...

Mental health conditions and concussion history reported by a collegiate athlete may contribute to prolonged recovery and symptom severity after concussion. This work examined the potential associations among concussion history, pre-existing conditions, and sex relative to initial symptom severity and recovery duration following sport-related concu...

Background Sport-related concussion (SRC) is a heterogenous injury that often presents with varied symptoms and impairment. Recently, research has focused on identifying subtypes, or clinical profiles of concussion to be used in assessing and treating athletes with SRC. The purpose of this study was to investigate sex differences in clinical profil...

Soybean (Glycine max) is among the most important field crops in the world, and the USA is a top global producer, but USA soybean losses have increased because of multitude of factors, including wildlife damage. Although small, terrestrial rodents (Order: Rodentia) are capable of causing substantial damage to soybean and other field crops. Conseque...

Traumatic brain injury (TBI) disrupts the blood–brain barrier (BBB), which may exacerbate neuroinflammation post-injury. Few translational studies have examined BBB dysfunction and subsequent neuroinflammation post-TBI in juveniles. We hypothesized that BBB dysfunction positively predicts microglial activation and that vulnerability to BBB dysfunct...

Traumatic brain injury (TBI) can damage the hypothalamus and cause improper activation of the growth hormone (GH)-axis, leading to growth hormone deficiency (GHD). GHD is one of the most prevalent endocrinopathies following TBI in adults; however, the extent to which GHD affects juveniles remains understudied. We used post-natal day 17 rats (n = 83...

To investigate microglial mechanisms in central and peripheral inflammation after experimental traumatic brain injury (TBI), we inhibited the colony-stimulating factor-1 receptor (CSF-1R) with PLX5622 (PLX). We hypothesized that microglia depletion would attenuate central inflammation acutely with no effect on peripheral inflammation. After randomi...

Wildlife species are often used as bioindicators to evaluate the extent and severity of environmental contamination and the effectiveness of remediation practices. A common approach for investigating population- or community-level impacts on bioindicators compares demographic parameter estimates (e.g., population size or density) between sites that...

Microglial morphology is used to measure neuroinflammation and pathology. For reliable inference, it is critical that microglial morphology is accurately quantified and that results can be easily interpreted and compared across studies and laboratories. The process through which microglial morphology is quantified is a key methodological choice and...

The microglial response to a pathological microenvironment is hallmarked by a change in cellular morphology. Following a pathological stimulus, microglia become reactive and simultaneously divide to create daughter cells. Although a wide array of microglial morphologies has been observed, the exact functions of these distinct morphologies are unkno...

Microglia play a critical role in the neuroimmune response, but little is known about the role of microglia in sleep following an inflammatory trigger. Nevertheless, decades of research have been predicated on the assumption that an inflammatory trigger increases sleep through microglial activation. We hypothesized that mice (n = 30) with depleted...

Dryland rivers often harbor abundant populations of nonnative species that threaten native fauna and negatively alter ecosystem structure and function. Native semiaquatic carnivores, such as river otters (Lontra canadensis), that could predate nonnative fauna have been extirpated from many dryland rivers. During 2008-2010, river otters were reintro...

Common ravens (Corvus corax) inhabited much of the eastern United States prior to European colonization but were nearly extirpated by the mid‐1900s. Although remnant raven populations have since begun recolonizing portions of their historic range in the eastern United States, the extent of recovery remains largely unknown because of the species' el...

The objective of this study was to determine the prevalence of sleep-wake disturbances (SWD) following pediatric traumatic brain injury (TBI), and to examine characteristics of TBI and patient demographics that might be predictive of subsequent SWD development. This single-institution retrospective study included patients diagnosed with a TBI durin...

Few translational studies have examined how age-at-injury affects the glial response to traumatic brain injury (TBI). We hypothesized that rats injured at post-natal day (PND) 17 would exhibit a greater glial response, that would persist into early adulthood, compared to rats injured at PND35. PND17 and PND35 rats (n = 75) received a mild to modera...

Wildlife managers require defensible and transparent population estimates to justify species management. Statistical population reconstruction (SPR) is being widely adopted to estimate wildlife population sizes from hunter harvest data. We assessed factors influencing variation in SPR population estimates produced for bobcats in Wyoming, USA. Speci...

Monitoring the demographics and genetics of reintroduced populations is critical to evaluating reintroduction success, but species ecology and the landscapes that they inhabit often present challenges for accurate assessments. If suitable habitats are restricted to hierarchical dendritic networks, such as river systems, animal movements are typical...

Although least chipmunks (Neotamias minimus) are a widely distributed North American species of least concern, the southernmost population, N. m. atristriatus (Peñasco least chipmunk), is imperiled and a candidate for federal listing as a subspecies. We conducted a phylogeographic analysis across the N. minimus range to assess genomic differentiati...

Domestic violence (DV) is a chronic societal epidemic that often involves physical assault to the head, neck, and face, which increases the risk of traumatic brain injuries (TBIs) in DV victims. However, epidemiological data on the extent of TBI-DV at the population scale remain sparse. We performed a statewide, multi-institution, retrospective rev...

Elderly populations (≥65 years old) have the highest risk of developing Alzheimer's disease (AD) and/or obtaining a traumatic brain injury (TBI). Using translational mouse models, we investigated sleep disturbances and inflammation associated with normal aging, TBI and aging, and AD. We hypothesized that aging results in marked changes in sleep com...

Monitoring the ecological impacts of environmental pollution and the effectiveness of remediation efforts requires identifying relationships between contaminants and the disruption of biological processes in populations, communities, or ecosystems. Wildlife are useful bioindicators, but traditional comparative experimental approaches rely on a stau...

Identifying differential responses between sexes following traumatic brain injury (TBI) can elucidate the mechanisms behind disease pathology. Peripheral and central inflammation in the pathophysiology of TBI can increase sleep in male rodents, but this remains untested in females. We hypothesized that diffuse TBI would increase inflammation and sl...

Invited Article for Wild Felid Monitor. Available at: https://www.wildfelid.org/monitor.php.

Recently introduced unmarked spatial capture–recapture (SCR), spatial mark–resight (SMR), and 2‐flank spatial partial identity models (SPIMs) extend the domain of SCR to populations or observation systems that do not always allow for individual identity to be determined with certainty. For example, some species do not have natural marks that can re...

Supplement to: Murphy, SM; Wilckens, DT; Augustine, BC; Peyton, MA; Harper, GC (2019) Improving estimation of puma (Puma concolor) population density: clustered camera-trapping, telemetry data, and generalized spatial mark-resight models. Scientific Reports, 9, 4590, https://doi.org/10.1038/s41598-019-40926-7. This dataset consists of a .zip folder...

Wildlife management relies heavily on high quality field data to analyze and predictively model animal population dynamics, evaluate population viability, and ultimately inform management decisions. During 2011–2015, we conducted a study to investigate survival and cause-specific mortality of male and female elk Cervus canadensis in a harvested pop...

Chronic neurological impairments can manifest from repetitive traumatic brain injury (rTBI), particularly when subsequent injuries occur before the initial injury completely heals. Herein, we apply post-traumatic sleep as a physiological biomarker of vulnerability, hypothesizing that a second TBI during post-traumatic sleep worsens neurological and...

Multiple small populations of American black bears Ursus americanus, including the recently delisted Louisiana black bear subspecies U. a. luteolus, occupy a fragmented landscape in the Lower Mississippi Alluvial Valley, USA (LMAV). Populations include bears native to the LMAV, bears translocated from Minnesota during the 1960s, and recently reintr...

Spatial capture–recapture models can produce unbiased estimates of population density, but sparse detection data often plague studies of social and territorial carnivores. Integrating multiple types of detection data can improve estimation of the spatial scale parameter (σ), activity center locations, and density. Noninvasive genetic sampling is ef...

Published in International Bear News (ISSN #1064-1564) by the International Association for Bear Research and Management. Article available at: https://www.bearbiology.org/wp-content/uploads/2018/08/272_Summer2018_small.pdf

A flood event in 2011 had minor impacts on apparent survival and movement probabilities of a small, isolated population of Louisiana black bears (Ursus americanus luteolus) in the Upper Atchafalaya River Basin, Louisiana, USA. However, the potential effects of the flood on recruitment of juveniles into the population, then listed as threatened unde...

Recently introduced unmarked spatial capture-recapture (SCR), spatial mark-resight (SMR), and 2-flank spatial partial identity models (SPIM) extend the domain of SCR to populations or observation systems that do not always allow for individual identity to be determined with certainty. For example, some species do not have natural marks that can rel...

Toxoplasma gondii is an important protozoan parasite of mammals that impacts wildlife and human health and behavior. Although this parasite has been documented in several mammalian wildlife species, relatively little is known about T. gondii impacts on North American elk (wapiti, Cervus canadensis) or American black bears (Ursus americanus), both o...

During the 1990s, two American black bear (Ursus americanus) reintroductions using small founder groups occurred along the Kentucky-Virginia and Kentucky-Tennessee borders in the Central Appalachians, USA, which established 2 relatively small, allopatric populations by 2012 (N = 482 and 228 bears, respectively). Late autumn (Nov.–Dec.) legal harves...

Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agri...

Data, noninvasive genetic capture-recapture hair trap detections and corresponding trap locations for Florida black bears in the Highlands-Glades subpopulation during 2010–2012. (DOCX)

Data, microsatellite genotypes for individual Florida black bears detected in the Highlands-Glades subpopulation via noninvasive genetic capture-recapture hair trap sampling during 2004–2005 and 2010–2012. (DOCX)

The Highlands–Glades subpopulation (HGS) of Florida, USA, black bears (Ursus americanus floridanus) is small, genetically depauperate, and resides primarily within the endangered Lake Wales Ridge ecosystem, which has lost >85% of native habitat to land development. Habitat loss can reduce availability of critical natural foods and cause bears to in...

We assessed Toxoplasma gondii seroprevalence in 53 free-ranging American black bears (Ursus americanus) in the Central Appalachians, USA. Seroprevalence was 62.3% with no difference between males and females or ages. Wildlife agencies should consider warnings in hunter education programs to reduce the chances for human infection from this source.

Toxoplasma gondii is an important protozoan parasite of mammals that impacts animal health and behavior. Although this parasite has been documented in several cervid species, including red deer (Cervus elaphus) in Europe, little is known about T. gondii impacts on the closely related North American counterpart, the elk (wapiti, Cervus canadensis),...

New Mexico Department of Game and Fish (NMDGF) will surgically sterilize coyotes (Canis latrans) at Fort Stanton, New Mexico to attempt to reduce coyote predation of neonate pronghorns (Antilocapra americana). Potential for this novel method to also decrease coyote density (D) exists, but such a hypothesis has not been explicitly evaluated using ri...

Many large carnivores are recolonizing range as a result of improved management and conservation policy, habitat restoration, and reintroduction programs. American black bears (Ursus americanus) are projected to recolonize portions of the United States, but few studies have characterized or provided practical methods for monitoring this process. We...

Reintroduction is a useful tool for restoring imperiled large carnivores, and long-term demographic monitoring is critical for evaluating reintroduction success. During 2001-2009, federally threatened adult female (n = 48) Louisiana black bears (Ursus americanus luteolus) and their dependent cubs (n = 104) were reintroduced to a portion of indigeno...

Reintroduced populations are vulnerable to demographic and environmental stochasticity, deleterious genetic effects, and reduced population fitness, all of which can increase extinction probability. Population viability is principle to determining the status of reintroduced populations and for guiding management decisions. To attempt to reestablish...

Habitat fragmentation caused by natural and anthropogenic disturbances can have deleterious effects on the demographics and genetics of wildlife populations. By 1999, the Tensas River Basin subpopulation (TRB) of Louisiana black bears (Ursus americanus luteolus) was subdivided at Interstate 20 into 2 isolated segments (Deltic and Tensas) that exper...

Animal reintroductions are important tools of wildlife management to restore species to their historical range, and they can also create unique opportunities to study population dynamics and genetics from founder events. We used non-invasive hair sampling in a systematic, closed-population capture-mark-recapture (CMR) study design at the Big South...

Human-bear conflicts have become more common in North America as bear populations have increased commensurate with human populations. Multiple methods of conflict abatement are used by natural resources managers, but recent research has indicated that many of these methods may be ineffective and that lethal removal of habitual conflict bears may be...

Human-bear conflict has increased in frequency in many regions of North America during recent decades. The frequency of bear attacks on humans has increased temporally as well, and the availability of anthropogenic foods to bears has been identified as a factor in some attacks. Mitigating bear access to anthropogenic foods is therefore important fo...

The history and heritage of Louisiana has always been closely associated with its natural resources. Since establishment of this state more than two centuries ago, generations of Louisianans have used wildlife resources to provide food and clothing for their families, for economic benefit, and for outdoor recreation. These close ties to the land an...

Once abundant in Kentucky, Ursus americanus (American Black Bear) were extirpated from the state by the late 19th century because of overharvest and habitat alteration. Regenerating deciduous forests, increased human tolerance, and source population growth and expansion in neighboring states have facilitated Black Bear recolonization in parts of so...