A big data-model integration approach for predicting epizootics and population recovery in a keystone species

Infectious diseases pose a significant threat to global health and biodiversity. Yet, predicting the spatiotemporal dynamics of wildlife epizootics remains challenging. Disease outbreaks result from complex nonlinear interactions among a large collection of variables that rarely adhere to the assumptions of parametric regression modeling. We adopted a nonparametric machine learning approach to model wildlife epizootics and population recovery, using the disease system of colonial black-tailed prairie dogs (BTPD, Cynomys ludovicianus) and sylvatic plague as an example. We synthesized colony data between 2001 and 2020 from eight USDA Forest Service National Grasslands across the range of BTPDs in central North America. We then modeled extinctions due to plague and colony recovery of BTPDs in relation to complex interactions among climate, topoedaphic variables, colony characteristics, and disease history. Extinctions due to plague occurred more frequently when BTPD colonies were spatially clustered, in closer proximity to colonies decimated by plague during the previous year, following cooler than average temperatures the previous summer, and when wetter winter/springs were preceded by drier summers/falls. Rigorous cross-validations and spatial predictions indicated that our final models predicted plague outbreaks and colony recovery in BTPD with high accuracy (e.g., AUC generally >0.80). Thus, these spatially explicit models can reliably predict the spatial and temporal dynamics of wildlife epizootics and subsequent population recovery in a highly complex host-pathogen system. Our models can be used to support strategic management planning (e.g., plague mitigation) to optimize benefits of this keystone species to associated wildlife communities and ecosystem functioning. This optimization can reduce conflicts among different landowners and resource managers, as well as economic losses to the ranching industry. More broadly, our big data-model integration approach provides a general framework for spatially explicit forecasting of disease-induced population fluctuations for use in natural resource management decision-making.

Assembling a safe and effective toolbox for integrated flea control and plague mitigation: Fipronil experiments with prairie dogs

Background

Plague, a widely distributed zoonotic disease of mammalian hosts and flea vectors, poses a significant risk to ecosystems throughout much of Earth. Conservation biologists use insecticides for flea control and plague mitigation. Here, we evaluate the use of an insecticide grain bait, laced with 0.005% fipronil (FIP) by weight, with black-tailed prairie dogs (BTPDs, Cynomys ludovicianus). We consider safety measures, flea control, BTPD body condition, BTPD survival, efficacy of plague mitigation, and the speed of FIP grain application vs. infusing BTPD burrows with insecticide dusts. We also explore conservation implications for endangered black-footed ferrets (Mustela nigripes), which are specialized predators of Cynomys.

Principal findings

During 5- and 10-day laboratory trials in Colorado, USA, 2016–2017, FIP grain had no detectable acute toxic effect on 20 BTPDs that readily consumed the grain. During field experiments in South Dakota, USA, 2016–2020, FIP grain suppressed fleas on BTPDs for at least 12 months and up to 24 months in many cases; short-term flea control on a few sites was poor for unknown reasons. In an area of South Dakota where plague circulation appeared low or absent, FIP grain had no detectable effect, positive or negative, on BTPD survival. Experimental results suggest FIP grain may have improved BTPD body condition (mass:foot) and reproduction (juveniles:adults). During a 2019 plague epizootic in Colorado, BTPDs on 238 ha habitat were protected by FIP grain, whereas BTPDs were nearly eliminated on non-treated habitat. Applications of FIP grain were 2–4 times faster than dusting BTPD burrows.

Significance

Deltamethrin dust is the most commonly used insecticide for plague mitigation on Cynomys colonies. Fleas on BTPD colonies exhibit the ability to evolve resistance to deltamethrin after repeated annual treatments. Thus, more tools are needed. Accumulating data show orally-delivered FIP is safe and usually effective for flea control with BTPDs, though potential acute toxic effects cannot be ruled out. With continued study and refinement, FIP might be used in rotation with, or even replace deltamethrin, and serve an important role in Cynomys and black-footed ferret conservation. More broadly, our stepwise approach to research on FIP may function as a template or guide for evaluations of insecticides in the context of wildlife conservation.

Oral Sylvatic Plague Vaccine Does Not Adequately Protect Prairie Dogs (Cynomys spp.) for Endangered Black-Footed Ferret (Mustela nigripes) Conservation

The plague bacterium Yersinia pestis is lethal to endangered black-footed ferrets (Mustela nigripes, BFF) and the prairie dogs (Cynomys spp., PD) on which they depend for habitat and prey. We assessed the effectiveness of an oral sylvatic plague vaccine delivered in baits to black-tailed PD (Cynomys ludovicianus, BTPD) from 2013 to 2017 on the Charles M. Russell National Wildlife Refuge (CMR) in northcentral Montana. We permanently marked BTPD on four paired vaccine (N = 1,349 individuals) and placebo plots (N = 926; 7,027 total captures). We analyzed capture–recapture data under a Cormack–Jolly–Seber model to estimate annual apparent survival. Overall, survival averaged 0.05 lower on vaccine plots than on paired placebo plots. Immediately before noticeable die-offs and detecting plague on pairs CMR1 and CMR2, 89% of BTPD sampled on vaccine plots had consumed at least one bait and the immune systems of 40% were likely boosted by consuming baits over multiple years. Survival to the following year was 0.16 and 0.05 on the vaccine plots and 0.19 and 0.06 on the placebo plots for pairs CMR1 and CMR2, respectively. These rates were markedly lower than 0.63, the overall average estimate on those same plots during the previous 3 years. PD populations subjected to such large die-offs would not be expected to sustain a BFF population. An overriding limitation to achieving sufficient protection rests with vaccine delivery constraints. Late summer/fall bait distribution results in the highest bait uptake rates. However, the PD birth pulse each spring can double the size of populations in most years, greatly reducing the proportion of vaccinates in populations and diminishing potential herd immunity benefits. In addition to nonvaccinated juveniles and PD that do not consume bait, incomplete vaccine protection and time required for immunity to develop leaves a large majority of PD populations vulnerable to plague for 6–7 months or more each year.

Utah prairie dog population dynamics on the Awapa Plateau: precipitation, elevation, and plague

Utah prairie dogs (UPDs, Cynomys parvidens) are colonial, herbivorous rodents listed under the Endangered Species Act as threatened. Little is known about UPD population dynamics at higher elevations in the species’ range. From 2013 through 2016, we studied UPDs on five colonies at 2,645 to 2,873 m elevation on the Awapa Plateau, Utah, USA. Primary production increases with precipitation and precipitation increases with elevation on the plateau. We hypothesized that UPD body condition, reproduction, survival, and population growth all would vary directly with precipitation and elevation. Each year, we live-trapped UPDs from late-Jun through Aug, weighing each UPD, aging it as adult or pup, measuring its right hind foot, marking it for unique identification, and releasing it at point of capture. Fleas from live-trapped UPDs and opportunistically collected rodent carcasses, and rodent carcasses themselves, were tested for the agent of sylvatic plague (Yersinia pestis), a lethal invasive pathogen. Adult UPD body condition (mass:foot) increased with elevation. In addition, UPD reproduction (pups:adults) and population growth (λ) increased with precipitation. Annual survival declined from 0.49 in 2013–2014 to 0.24 in 2015–2016. We captured 421 UPDs in 2013 but only 149 in 2016. Sylvatic plague may have contributed to population declines. Notwithstanding, plague detection (yes/no by colony and year) had no statistical effect on population growth or annual survival, raising suspicion about the predictive value of binary plague detection variables. Generally speaking, efforts to conserve UPDs may benefit from the restoration and preservation of large colonies at mesic sites.

Plague transforms positive effects of precipitation on prairie dogs to negative effects

Rodents characteristically benefit from increased precipitation, especially in typically dry habitats; “good years” of high precipitation improve their forage and water balance. However, Yersinia pestis (plague), a flea-borne pathogen of mammals that was introduced to western North America, has the greatest negative impact on at least some species of rodents during years of above-average precipitation. In the absence of plague mitigation, negative effects of plague in wet years might overwhelm the otherwise beneficial effects of increased moisture. In Montana and Utah, USA, where plague now occurs enzootically, we investigated the influence of precipitation on finite rates of annual population change (2000–2005) for 3 species of prairie dogs (Cynomys spp.) in replicated plots treated with deltamethrin dust and in non-treated plots for paired comparisons. There was a significant interaction between precipitation and treatment. When we reduced plague vector fleas, prairie dog visual counts tended to increase with increasing precipitation. Simultaneously, there was a negative relationship between counts and precipitation on paired plots where plague was not managed, suggesting that plague transformed and reversed the otherwise beneficial effect of increased precipitation. Are the good years gone for prairie dogs? Even if the good years are not gone, they are perhaps relatively scarce compared to historic times prior to the invasion of plague. This scenario might apply to other ecosystems and may pose broad conservation challenges in western North America.

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Negative plague effects overwhelm positive precipitation effects on prairie dogs.

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“Good years” of primary production may be gone in the introduced ranges of plague.

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Plague management with flea-control addresses this conservation challenge.

Drought-mediated changes in black-tailed prairie dog colonies in the Northern Great Plains

Populations of many mammal species living in grassland ecosystems across North America have been reduced greatly over the past 200 years due to conversion of native prairie to human-related uses. Foremost among these species is the black-tailed prairie dog (Cynomys ludovicianus), populations of which have declined an estimated 98% during that time. In addition to anthropogenic factors including plague, black-tailed prairie dog populations can vary in size in response to grazing by native ungulates, fire, and precipitation. Colonies in the Northern Great Plains have expanded and contracted during dry and wet periods, respectively. Drought reduces vegetation height; tall vegetation is known to limit colony expansion, possibly due to increased predation risk. We used mixed-effects models to analyze data sets of colony areas of black-tailed prairie dogs spanning 16–22 years and 983 total colony counts, from 142 unique colonies at Badlands National Park and Wind Cave National Park, South Dakota, United States, and Scotts Bluff National Monument, Nebraska, United States, to relate areal dynamics of colonies over time to total annual precipitation, drought stress, and plague. We also analyzed the relationship between active-burrow densities and precipitation and drought stress using 7 years of data from 271 colony counts at Badlands National Park. Black-tailed prairie dog colonies expanded in response to drought conditions in all three national parks, with colonies in Wind Cave National Park exhibiting a time-delayed response. In addition, colony area was negatively related to total accumulated precipitation for the preceding 12 months for Scotts Bluff National Monument. Active-burrow density at Badlands National Park decreased in response to drought stress with a time lag of 24–36 months. Plague first was reported at Badlands National Park in 2008 and colony areas decreased dramatically and rapidly during plague epizootic events. Our results support observations that black-tailed prairie dog colonies in the Northern Great Plains expand and contract in response to drought stress and wet weather. Furthermore, our findings provide new insights into the role of climate on a keystone species of conservation importance and demonstrate the value of collecting long-term ecological data.

Predictors of nestling survival during harsh weather events in an aerial insectivore, the Tree Swallow (Tachycineta bicolor)

Extreme weather events influence the population dynamics of wild animals. For organisms whose food source is affected by environmental conditions, such as aerial insectivorous birds, periods of inclement weather can have devastating effects. Here, we examine predictors of survival of individual nestlings and whole broods in Tree Swallows (Tachycineta bicolor (Vieillot, 1808)) during an extreme, 2-day harsh weather event in central British Columbia, Canada, which co-occurred with experimental reduction of nest ectoparasite loads using an antiparasite drug (ivermectin) or heat-treating nests. A curvilinear relationship existed between survival and brood age such that middle-aged broods were least likely to survive. Survival of broods and nestlings was higher when raised by males with bluer plumage, whereas nestling survival was lower when female parents had brighter and more UV-reflective plumage. Within broods, smaller nestlings had a lower chance of surviving than their larger siblings. Nestlings in broods where half of the offspring received ivermectin injections had significantly higher chances of surviving than nestlings from nonexperimental broods, suggesting that parasite loads can influence survival during inclement weather. Our results identify several factors influencing resiliency of nestlings to harsh weather and are particularly relevant in the context of declining aerial insectivorous bird populations and climate change.

Environmental determinants of activity variation of an overlooked burrowing rodent: the Indian crested porcupine

A study of the activity patterns, time allocation for each activity and variations in activities due to environmental alterations are necessary for understanding the biology of any species. This study investigates the relationship of micro-habitat and environmental conditions with seasonal and temporal activities of Indian crested porcupines (ICP) around their burrows in Keoladeo National Park (KNP), India. This species is considered as a problem species, often ignoring its ecological importance as an ecosystem engineer. Of the 39 sampled burrows, 58.97%, 38.46% and 83.78% were occupied in winter, summer and monsoon, respectively. The estimated porcupine density was 3.21±1.32SD individuals/km2, accounting for a population size of 65.89±27.15SD individuals. A seasonal shift in rate of emergence was observed in monsoon and winter, when ICP emerged earlier, significantly correlating with the sunset timings. The daily activity records of adult ICP outside burrow significantly peaked in January–February when they prepare the burrows for the gestation period of 90–112 days, followed by rearing of the offspring. The temporal activity significantly reduced in the full moon nights, perhaps to avoid predators. The study affirms that environmental determinants including the timings of sunrise, sunset and lunar phase significantly affect the variations in temporal activity and burrow use patterns of ICP.

Climate change impacts on the conservation outlook of populations on the poleward periphery of species ranges: A case study of Canadian black-tailed prairie dogs (Cynomys ludovicianus)

Given climate change, species' climatically suitable habitats are increasingly expected to shift poleward. Some imperilled populations towards the poleward edge of their species' range might therefore conceivably benefit from climate change. Interactions between climate and population dynamics may be complex, however, with climate exerting effects both indirectly via influence over food availability and more directly, via effects on physiology and its implications for survival and reproduction. A thorough understanding of these interactions is critical for effective conservation management. We therefore examine the relationship between climate, survival and reproduction in Canadian black-tailed prairie dogs, a threatened keystone species in an imperilled ecosystem at the northern edge of the species' range. Our analyses considered 8 years of annual mark-recapture data (2007-2014) in relation to growing degree days, precipitation, drought status and winter severity, as well as year, sex, age and body mass. Survival was strongly influenced by the interaction of drought and body mass class, and winter temperature severity. Female reproductive status was associated with the interaction of growing degree days and growing season precipitation, with spring precipitation and with winter temperature severity. Results related to body mass suggested that climatic variables exerted their effects via regulation of food availability with potential linked effects of food quality, immunological and behavioural implications, and predation risk. Predictions of future increases in drought conditions in North America's grassland ecosystems have raised concerns for the outlook of Canadian black-tailed prairie dogs. Insights gained from the analyses, however, point to mitigating species management options targeted at decoupling the mechanisms by which climate exerts its negative influence. Our approach highlights the importance of understanding the interaction between climate and population dynamics in peripheral populations whose viability might ultimately determine their species' ability to track climatically suitable space.