James E Hines

• BS, Math, Univ. of MD
• United States Geological Survey

Objective We identified spatial and temporal variation in population trends for Gulf Sturgeon Acipenser desotoi (previously known as Acipenser oxyrinchus desotoi) across the species’ range to inform recovery strategies. We also assessed whether adult survival or recruitment more strongly influences population change. Methods We analyzed adult Gulf...

Understanding mechanisms underlying coexistence among potential competitors, and between predators and prey, is a persistent challenge in community ecology. Using 6 years (2013–2018) of camera‐trapping data and species interaction models, we investigated the spatiotemporal patterns of inter‐ and intra‐guild interspecific interactions in a diverse t...

The richness and composition of a small mammal community inhabiting semiarid California oak woodland may be changing in response to climate change, but we know little about the causes or consequence of these changes. We applied a capture‐mark‐recapture model to 17 years (1997–2013) of live trapping data to estimate species‐specific abundances. The...

Some mammal species inhabiting high-latitude biomes have evolved a seasonal moulting pattern that improves camouflage via white coats in winter and brown coats in summer. In many high-latitude and high-altitude areas, the duration and depth of snow cover has been substantially reduced in the last five decades. This reduction in depth and duration o...

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...

Estimates of demographic parameters based on capture–mark–recapture (CMR) methods may be biased when some individuals in the population are temporarily unavailable for capture (temporary emigration). We estimated snowshoe hare abundance, apparent survival, and probability of temporary emigration in a population of snowshoe hares (Lepus americanus E...

The occurrence, density and survival of a species often depend on various aspects of the habitat that it occupies including patch size and disturbance. The demography of most threatened tropical species largely remain unstudied but could provide valuable information about their biology and insights for their conservation. Our study examined the eff...

In semi-arid environments, aperiodic rainfall pulses determine plant production and resource availability for higher trophic levels, creating strong bottom-up regulation. The influence of climatic factors on population vital rates often shapes the dynamics of small mammal populations in such resource-restricted environments. Using a 21-year biannua...

Poaching is a pervasive threat to wildlife, yet quantifying the direct effect of poaching on wildlife is rarely possible because both wildlife and threat data are infrequently collected concurrently. In this study, we used poaching data collected through the Management Information System (MIST) and wildlife camera trap data collected by the Tropica...

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...

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....

The moose (Alces alces) is a charismatic species in decline across much of their southern distribution in North America. In the northeastern United States, much of the reduction has been attributed to winter tick (Dermacentor albipictus) infestations. Winter ticks are fairly immobile throughout all life stages, and therefore their distribution patt...

In semi-arid environments, aperiodic rainfall pulses determine cycles of plant production and resource availability for higher trophic levels, creating strong bottom-up regulation. The influence of climatic factors on population vital rates often shapes the dynamics of small mammal populations in such resource-restricted environments. Using a 21-ye...

Increases in apex predator abundance can influence the behavior of sympatric species, particularly when the available habitat and/or resources are limited. We assessed the temporal and spatiotemporal interactions between Florida panthers (Puma concolor coryi) and six focal sympatric species in South Florida, where Florida panther abundance has incr...

Given the public health, economic and conservation implications of zoonotic diseases, their effective surveillance is of paramount importance. The traditional approach to estimating pathogen prevalence as the proportion of infected individuals in the population is biased because it fails to account for imperfect detection. A statistically robust wa...

Tiger populations are declining globally, and depletion of major ungulate prey is an important contributing factor. To better understand factors affecting prey distribution in Thailand’s Western Forest Complex (WEFCOM), we conducted sign surveys for gaur (Bos gaurus), banteng (Bos javanicus), and sambar (Rusa unicolor) along 3,517 1-km transects an...

Abstract Cyclic fluctuations in abundance exhibited by some mammalian populations in northern habitats (“population cycles”) are key processes in the functioning of many boreal and tundra ecosystems. Understanding population cycles, essentially demographic processes, necessitates discerning the demographic mechanisms that underlie numerical change...

Cyclic fluctuations in abundance exhibited by some mammalian populations in northern habitats (“population cycles”) are key processes in the functioning of many boreal and tundra ecosystems. Understanding population cycles, essentially demographic processes, necessitates discerning the demographic mechanisms that underlie numerical changes. Using m...

Exploring trends in species richness and the distribution of individual species over time as well as the factors affecting these trends informs conservation priorities in protecting species and ecosystems as a whole. We used data from 41 park‐wide line transect surveys in 2009 and 2014 and multi‐season occupancy models with multi‐species data to ex...

• Despite conservation efforts, large mammals such as tigers (Panthera tigris) and their main prey, gaur (Bos gaurus), banteng (Bos javanicus), and sambar (Rusa unicolor), are highly threatened and declining across their entire range. The only large viable source population of tigers in mainland Southeast Asia occurs in Thailand's Western Forest Co...

For species that exist at low abundance or are otherwise difficult to study, it is challenging to estimate vital rates such as survival and fecundity and common to assume that survival rates are constant across ages and sexes. Population assessments based on overly simplistic vital rates can lead to erroneous conclusions. We estimated sex- and leng...

Understanding the relative impact of climate change and land cover change on changes in avian distribution has implications for the future course of avian distributions and appropriate management strategies. Due to the dynamic nature of climate change, our goal was to investigate the processes that shape species distributions, rather than the curre...

The California mouse (Peromyscus californicus) inhabits semiarid oak (Quercus spp.) woodlands and shrublands of California's southern Coast Ranges and lower slopes of the western Sierra Nevada. From 1993 to 2014, we studied the demography of California mice in semiarid oak woodland in coastal-central California. Using capture-mark-recapture (CMR) m...

The metapopulation paradigm has been central to improve the conservation and management of natural populations. However, despite the large number of studies on metapopulation dynamics, the overall support for the relationships on which the paradigm is based has not been strong. Here, we studied the occupancy dynamics of two Neotropical fishes (i.e....

Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence, Second Edition, provides a synthesis of model-based approaches for analyzing presence-absence data, allowing for imperfect detection. Beginning from the relatively simple case of estimating the proportion of area or sampling units occupied at the time of surve...

Poaching is one of the greatest threats to wildlife conservation world‐wide. However, the spatial and temporal patterns of poaching activities within protected areas, and the effectiveness of ranger patrols and ranger posts in mitigating these threats, are relatively unknown. We used 10 years (2006–2015) of ranger‐based monitoring data and dynamic...

Nutria (Myocaster coypus), invasive, semi-aquatic rodents native to South America, were introduced into Maryland near Blackwater National Wildlife Refuge (BNWR) in 1943. Irruptive population growth, expansion, and destructive feeding habits resulted in the destruction of thousands of acres of emergent marshes at and surrounding BNWR. In 2002, a par...

Organochlorine pesticides disrupted reproduction and killed many raptorial birds, and contributed to population declines during the 1940s-1970s. We sought to discern whether and to what extent territory occupancy and breeding success changed from the pesticide era to recent years in a resident population of Peregrine Falcons Falco peregrinus in sou...

We used 22 yr of capture–mark–reencounter (CMR) data collected from 1988 to 2009 on about 12,500 birds at what went from three to five coastal colony sites in Massachusetts, New York, and Connecticut, United States, to examine spatial and temporal variation in breeding dispersal/fidelity rates of adult Roseate Terns (Sterna dougallii). At the start...

There is intense interest in basic and applied ecology about the effect of global change on current and future species distributions. Projections based on widely used static modeling methods implicitly assume that species are in equilibrium with the environment and that detection during surveys is perfect. We used multiseason correlated detection o...

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...

Although the Middle East supports a high level of avian biodiversity, the ecology of relatively few species that use the region has been studied in detail. Despite its restricted breeding distribution in the Middle East, and apparent unfavorable conservation status, little is known about the population ecology of the Sooty Falcon (Falco concolor),...

The Endangered snow leopard Panthera uncia occurs in the Central Asian Mountains, which cover c. 2 million sq km. Little is known about its status in the Kyrgyz Alay Mountains, a relatively narrow stretch of habitat connecting the southern and northern global ranges of the species. In 2010 we gathered information on current and past (1990, the last...

The population of Common Terns (Sterna hirundo) in Barnegat Bay, New Jersey, USA, has recently experienced poor productivity with complete or near-complete breeding failure at multiple colonies, and the number of breeding pairs has declined. Adult Common Terns were captured and banded at Pettit Island from 2010 through 2014 and at four additional i...

Selective logging is pervasive in the tropics and is among the most urgent threats to tropical biodiversity. The vast areas of logged tropical forest are often vulnerable to relogging, clear‐felling, burning or conversion to plantations, despite evidence that logged forests retain a large proportion of tropical forest species at high abundances com...

Many reptile species are in decline and turtles are especially susceptible. In Massachusetts, eastern box turtle (Terrapene carolina carolina) population densities are critically low, and they are listed as a Species of Special Concern. To aid in the conservation of this species, we developed a statewide population monitoring program to track large...

With ongoing climate change, many species are expected to shift their spatial and temporal distributions. To document changes in species distribution and phenology, detection/non‐detection data have proven very useful. Occupancy models provide a robust way to analyse such data, but inference is usually focused on species spatial distribution, not p...

Population models are essential components of large-scale conservation and management plans for the federally endangered Golden-cheeked Warbler (Setophaga chrysoparia; hereafter GCWA). However, existing models are based on vital rate estimates calculated using relatively small data sets that are now more than a decade old. We estimated more current...

Many pest species exhibit huge fluctuations in population abundance. Understanding their large-scale and long-term dynamics is necessary to develop effective control and management strategies. Occupancy models represent a promising approach to unravel interactions between environmental factors and spatiotemporal dynamics of outbreaking populations....

Birds and their population dynamics are often used to understand and document anthropogenic effects on biodiversity. Nest success is a critical component of the breeding output of birds in different environments; but to obtain the complete picture of how bird populations respond to perturbations, we also need an estimate of nest abundance or densit...

Occupancy surveys collecting data from adjacent (sometimes correlated) spatial replicates have become relatively popular for logistical reasons. Hines et al . ( ) presented one approach to modelling such data for single‐season occupancy surveys. Here, we present a multiseason analogue of this model (with corresponding software) for inferences about...

Aim Much research in conservation biogeography is fundamentally dependent on obtaining reliable data on species distributions across space and time. Such data are now increasingly being generated using various types of public surveys. These data are often integrated with occupancy models to evaluate distributional patterns, range dynamics and conse...

Metapopulation ecology is a field that is richer in theory than in empirical results. Many existing empirical studies use an incidence function approach based on spatial patterns and key assumptions about extinction and colonization rates. Here we recast these assumptions as hypotheses to be tested using 18 years of historic detection survey data c...

The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition's importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading s...

Estimates of band reporting probabilities are used for managing North American waterfowl to convert band recovery probabilities into harvest probabilities, which are used to set harvest regulations. Band reporting probability is the probability that someone who has shot and retrieved a banded bird will report the band. This probability can vary rel...

Adult survival, an important fitness component, is usually 1) lower in lighter individuals due to their reduced ability to survive winter conditions compared to heavier ones, especially in resident species at northern temperate latitudes and 2) lower in females compared with males due to higher reproductive costs incurred by females. In this paper,...

A decline in species richness moving from equatorial regions to polar regions is a common, but not universal, macroecological pattern. Many studies have focused on this pattern, but few have focused on how the vital rates responsible for species richness patterns, local rates of species extinction and turnover, vary with latitude. We examine patter...

Range performance is often the key requirement around which electro-optical and infrared camera systems are designed. This work presents an objective framework for evaluating competing range performance models. Model selection based on the Akaike's Information Criterion (AIC) is presented for the type of data collected during a typical human observ...

Many industrial and agricultural activities involve wildlife fatalities by colli- sion, poisoning or other involuntary harvest: wind turbines, highway network, utility network, tall structures, pesticides, etc. Impacted wildlife may bene�t from o�cial protection, including the requirement to monitor the impact. Car- cass counts can often be conduct...

Collision of birds and bats with turbines in utility‐scale wind farms is an increasing cause of concern. Carcass counts conducted to quantify the ‘take’ of protected species need to be corrected for carcass persistence probability (removal by scavengers and decay) and detection probability (searcher efficiency). These probabilities may vary with ti...

Many species are found today in the form of fragmented populations occupying patches of remnant habitat in human‐altered landscapes. The persistence of these population networks requires a balance between extinction and colonization events assumed to be primarily related to patch area and isolation, but the contribution of factors such as the chara...

To offer a test of expert knowledge about rarity of twenty Amazon forest bird species following an approach that equates rarity with low site occupancy and formally accounts for imperfect species detection. We define ten pairs of closely related species, each pair with one hypothetically common and one hypothetically rare species. Our null hypothes...

Large-scale presence-absence monitoring programs have great promise for many conservation applications. Their value can be limited by potential incorrect inferences owing to observational errors, especially when data are collected by the public. To combat this, previous analytical methods have focused on addressing non-detection from public survey...

Occupancy statistical models that account for imperfect detection have proved very useful in several areas of ecology, including species distribution and spatial dynamics, disease ecology, and ecological responses to climate change. These models are based on the collection of multiple samples at each of a number of sites within a given season, duri...

The advent of spatially explicit capture–recapture models is changing the way ecologists analyse capture–recapture data. However, the advantages offered by these new models are not fully exploited because they can be difficult to implement. To address this need, we developed a user‐friendly software package, created within the R programming environ...

The eastern indigo snake (Drymarchon couperi) is a federally listed species, most recently threatened by habitat loss and habitat degradation. In an effort to estimate snake survival, a total of 103 individuals (59 males, 44 females) were followed using radio-tracking from January 1998 to March 2004 in three landscape types that had increasing leve...

The upper Hudson River basin in east central New York, USA, is highly contaminated, primarily with polychlorinated biphenyls (PCBs). Reduced adult survival has been documented in tree swallows (Tachycineta bicolor) at a similarly PCB-contaminated river system in western Massachusetts. The purpose of the present study was to assess whether adult sur...

In this paper, we modify dynamic occupancy models developed for detection‐nondetection data to allow for the dependence of local vital rates on neighborhood occupancy, where neighborhood is defined very flexibly. Such dependence of occupancy dynamics on the status of a relevant neighborhood is pervasive, yet frequently ignored. Our framework permit...

1. Ecologists have long been interested in the processes that determine patterns of species occurrence and co-occurrence. Potential short-comings of many existing empirical approaches that address these questions include a reliance on patterns of occurrence at a single time point, failure to account properly for imperfect detection and treating the...

Development and use of multistate mark-recapture models, which provide estimates of parameters of Markov processes in the face of imperfect detection, have become common over the last 20 years. Recently, estimating parameters of hidden Markov models, where the state of an individual can be uncertain even when it is detected, has received attention....

Background/Question/Methods We demonstrate an approach to both modeling and inference that deals simultaneously with the dynamics of a focal species, habitat state, and predators of the focal species. We used site occupancy models to construct a Markov-chain model that projects annual changes in occupancy of the southwest arroyo toad, availabilit...

Metapopulation ecology has historically been rich in theory, yet analytical approaches for inferring demographic relationships among local populations have been few. We show how reverse-time multi-state capture-recapture models can be used to estimate the importance of local recruitment and interpopulation dispersal to metapopulation growth. We use...

Understanding how events during one period of the annual cycle carry over to affect survival and other fitness components in other periods is essential to understanding migratory bird demography and conservation needs. Previous research has suggested that western Atlantic red knot (Calidris canutus rufa) populations are greatly affected by horsesho...

1. Relationships between animal populations and their habitats are well known and commonly acknowledged to be important by animal ecologists, conservation biologists and wildlife managers. Such relationships are most commonly viewed as static, such that habitat at time t is viewed as a determinant of animals present at that same time, t, or sometim...

Data from mark-recapture studies are used to estimate population rates such as exploitation, survival, and growth. Many of these applications assume negligible tag loss, so tag shedding can be a significant problem. Various tag shedding models have been developed for use with data from double-tagging experiments, including models to estimate consta...

We estimated laying dates, clutch sizes, and nest success rates of sympatrically breeding populations of American black ducks (Anas rubripes) and mallards (Anas platyrhynchos) on Chesapeake Bay islands between 1986 and 1989. Neither average laying date nor clutch size differed between black ducks and mallards. Nest success rates were higher for mal...

The possible impact on Microtus pennsylvanicus of ground applications of Orthene® insecticide was investigated in old-field habitats in northern Maryland during 1982 and 1983. The treatment grids in 1982 and 1983 were sprayed at 0.62 and 0.82 kg active ingredient/ha, respectively. A capture–recapture design robust to unequal capture probabilities w...

The distribution patterns during winter of American black ducks (Anas rubripes) were compared among age – sex classes using band recovery data. In addition, fidelity to wintering areas was compared between sexes and between coastal and inland wintering sites. We did not find evidence of age- or sex-specific differences in distribution patterns (P >...

Corridors are critical elements in the long-term conservation of wide-ranging species like the jaguar (Panthera onca). Jaguar corridors across the range of the species were initially identified using a GIS-based least-cost corridor model. However, due to inherent errors in remotely sensed data and model uncertainties, these corridors warrant field...

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...

Global and regional species conservation efforts are hindered by poor distribution data and range maps. Many Indian primates face extinction, but assessments of population status are hindered by lack of reliable distribution data. We estimated the current occurrence and distribution of 15 Indian primates by applying occupancy models to field data f...