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Bonenfant, C.

Publications and source records attributed to Bonenfant, C..

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Evolutionary and ecological determinants of the phenology of births in wild large herbivores, a systematic review

1. IntroductionTiming of birth is a major determinant of individuals reproductive success and phenotypic performances, driven by multiple factors. However, there is currently no quantitative assessment of the support received by the drivers of the phenology of births in mammals. 2. Aimsour objective was to identify the drivers tested for their effect on the phenology of births in large herbivores and how much empirical support they received, as well as determine thematic, taxonomic and spatial gaps in the literature. 3. MethodsWe conducted a systematic review focusing on the drivers of the phenology of births in large herbivores. We extracted the outcomes of 124 articles and assessed the reliability of their findings using a general index based on the quality of the data and methods used. 4. Results and DiscussionWe identified a major research gap in Asian and South and Central American species. The effect of population and individual characteristics remained marginally accounted for, even though there was evidence of their importance in the determination of the phenology of births. The two dominant hypotheses (seasonality and predation) received good to moderate empirical support regarding their effect on birth timing and synchrony, respectively. Given the strong geographic and methodological biases, these hypotheses should be considered as most consistently supported in the existing literature rather than definitively established across systems. 5. ConclusionsWe encourage research in these understudied domains, as well as large scale multi-species comparative analyses to fill in these gaps and improve our understanding of reproductive phenology. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/694258v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@4f1a9org.highwire.dtl.DTLVardef@95c5a6org.highwire.dtl.DTLVardef@e3324forg.highwire.dtl.DTLVardef@1fc1a6f_HPS_FORMAT_FIGEXP M_FIG C_FIG This semi-systematic review supports the two dominant drivers of birth phenology, the seasonality and predation hypotheses. Even though there is evidence of their importance, the effects of female, offspring and population characteristics remain marginally accounted for. Asian and South and Central American species are currently understudied.

ecology↗

Alpine marmot (Marmota marmota) pups emerge increasingly earlier with the ongoing climate change

Advance in the phenology of plants and animals is a widely observed response to climate change. The magnitude of the observed changes is, however, very variable across species. Several biological factors could influence the strength of the phenological advances, including lifestyle. Hibernation has evolved in response to harsh environmental conditions and could, hence, potentially buffer organisms against changing climatic conditions. In the Alps, the alpine marmot hibernates for almost 6 months. During that time individuals are sheltered from cold and lack of food, so we could expect alpine marmots to be less responsive to earlier springs than non-hibernating mountain-dwelling species. Here we investigate temporal variation in the date at which pups emerge from their natal burrow for the first time. Using quantile regressions, we provide clear evidence of an earlier pup emergence between 1990 and 2023. Over the study period, the predicted change is of about 4.7 days. In particular, late emergence dates are becoming especially rare over time. Our findings are in line with previous work on other mountain species, which suggests a general advance in reproductive phenology among the organisms living in Alps. The rate of change of pup emergence dates over years is, however, weaker in the alpine marmot than in most other mammalian species studied so far.

ecology↗

Influence of traffic and weather on carcass persistence time of small wildlife on roads

The rapidly expanding road network threatens the persistence of many terrestrial species through habitat loss, fragmentation, chemical, light and noise pollution and mortality associated with wildlife-vehicle collisions. Roadkill monitoring under-estimate actual collision numbers as the time during which roadkill carcasses remain visible on the road is often shorter than the frequency of road monitoring. By placing passerines (< 20 g) and amphibian carcasses on stretches of roads we surveyed every 2 hours, we fine-tuned existing persistence estimates for these species. We found median disappearance times (time for half of the carcasses to disappear) of less than 30 minutes for birds and 1-18 hours for amphibians depending on the volume of traffic, which is much shorter than previous estimates. Rainfall did not impact carcass persistence. We show the implications of these results by (1) correcting the results of roadkill surveys performed on common toads in reproductive migration for the number of removed carcasses and (2) estimating the number of passerine-vehicle collisions in the Auvergne-Rhone-Alpes (AuRA) region of France using the citizen-science database Faune-AuRA. We estimate that a road survey conducted 3 hours after amphibian road crossing under-estimates the number of roadkill by half, and that about 6800 passerine collisions were missed in 2022 by contributors because of short carcass persistence on the road. Small-bodied carcasses are hard to detect for drivers, and for a collision-report rate of 1%, total collision numbers for passerines could be as high as 700 000 individuals from 21 reported passerine species in 2022 in AuRA.

ecology↗

A biologically realistic model to predict wildlife-vehicle collision risks

Road networks have major ecological impacts on living organisms consequent to habitat loss and fragmentation, chemical and acoustic pollution, and direct mortality when wildlife-vehicle collisions are involved (WVC). The many past empirical studies revealed biological traits shared by species most vulnerable to roadkills (e.g. population density). Similarly, spatial locations of WVC hot-spots are associated to landscape features at large spatial scales, and to road characteristics at small spatial scale. We currently lack a comprehensive theoretical framework for WVC. Animal movement in relation to habitats is an essential driver of encounters with roads, but this remains largely ignored in studies, even when movement ecology provides the necessary tools to investigate the impact of animal movement on WVC. We built a general individual-based model incorporating recent knowledge in movement ecology (movement typology: roaming, migratory route crossing a road, active attraction and active repulsion of roads) to estimate WVC risks. We explored the relative effects of animal and vehicle movement parameters (speed, abundance, road sinuosity and animal movement pattern) on collision probability. We show that animal behaviour toward roads has major impacts on the number and risks of WVC, but also modulate the effects of other factors (animal traveling speed, species local abundance, road traffic volume) on WVC. Sensitivity analyses show that the movement and behaviour of the animal has more influence on WVC risks than any of the characteristics of roads and vehicles we tested. Our results suggest that (1) effective roadkill mitigation should be species-specific and could vary in efficiency depending on the targets movement pattern (mating and migratory seasons, foraging habits...) and (2) empirical studies of WVC should incorporate knowledge about the behavioural habits of the focal species in relation to roads.

ecology↗

Population density and plant availability interplay to shape browsing intensity by roe deer in a deciduous forest

Browsing damage in forests relies on a complex interaction between herbivore density and both forest understory composition and relative availability. Although variation in the amount of browsed twigs is sometimes used to assess abundance of large herbivores, the potential confounding effect of resource availability on this relationship has not yet been investigated. To fill the gap, we measured how browsing intensity of the woody plants varied in response to changes in both roe deer (Capreolus capreolus) abundance and vegetation availability from an intensive long-term monitoring. We estimated plant availability and consumption by roe deer from a modified Aldous method throughout a 14 yearlong period during which we experimentally manipulated population density. The functional response was strongly non-linear and density-dependent. When plant availability was low (< 12.5%), browsing intensity strongly increased with plant availability with an increasing rate with roe deer density, whereas beyond this threshold, browsing intensity slightly increased with both plant availability and population density in an additive way. Thus, forest susceptibility to browsing increases with increasing competition for food, especially when plant availability is low. Moreover, the interplay between browsing intensity and population density at low plant availability prevents the use of browsing intensity to monitor roe deer abundance when plant availability is low. Our findings provide clear evidence that relying on key ecological concepts such as functional responses improves the accuracy of management tools when monitoring changes of the herbivore-plant system over time.

ecology↗

Does timing of birth affect juvenile and mare survival in wild plains zebra?

In large herbivores, the timing of births often coincides with the seasonal peak of food resources availability, likely to improve juvenile survival and reduce reproduction costs. Some species however, breed year-round, even in seasonal environments. Demographic processes, such as to what extent being born during the lean season reduces survival of juveniles and reproductive females, remain understudied in large mammals inhabiting tropical ecosystems. We investigated survival rates in plains zebras (Equus quagga) in Hwange National Park (Zimbabwe), a highly seasonal savanna ecosystem. We used capture-recapture models to analyse long-term demographic data (2008-2019). We investigated the effect of seasonality as a categorical (wet versus dry season) and continuous (duration of the dry season) variable on survival. We found little variability in early juvenile survival ({varphi} = 0.458 {+/-} 0.044 SE, < 6 m.o.), whereas late juvenile and yearling survival was higher and decreased with increasing length of the dry season (from 0.850 {+/-} 0.095 SE to 0.480 {+/-} 0.120 SE). Female survival was high (> 0.703 {+/-} 0.057 SE and up to 0.995 {+/-} 0.006 SE) but decreased with increasing exposure to the dry season in non-reproductive females. The probability of females becoming reproductive in the following year was not affected by the length of the dry season (0.423 and 0.420 for reproductive and non-reproductive females respectively). Our results highlight the importance of individual quality in reproductive performance, as reproductive females seem to buffer the effect of environmental variability on their own survival and that of their foal.

ecology↗

How many giraffes are there? A comparison of abundance estimators at Ongava Game Reserve, Namibia

Camera-traps are a versatile and widely adopted tool for collecting biological data for wildlife conservation and management. While estimating population abundance from camera-trap data is the primarily goal of many projects, the question of which population estimator is suitable for analysing these data needs to be investigated. We took advantage of a 21 day camera-trap monitoring period of giraffes (Giraffa camelopardalis angolensis) on the Ongava Game Reserve (Namibia) to compare capture-recapture (CR), rarefaction curves and N-mixture estimators of population abundance. A marked variation in detection probability of giraffes was observed both in time and between individuals. Giraffes were also less likely to be detected after they were seen at a waterhole (mean daily visit frequency of f = 0.25). We estimated the population size to be 119 giraffes (Cv = 0.10) using the most robust reference estimator (CR). All other estimators deviated from the CR population size by ca. -20 to > +80%. This was due the fact that these models did not account for the temporal and individual variations in detection probability. We found that modelling choice was much less forgiving for N-mixture models than CR estimators because it leads to very variable and inconsistent estimations of abundance. Double counts were problematic for N-mixture models, challenging the use of raw counts (i.e. when individuals are not identified) at waterholes, to monitor the abundance of giraffe or of other species without idiosyncratic coat patterns.

ecology↗

How to describe and measure phenology? An investigation on the diversity of metrics using phenology of births in large herbivores

Proposed in 1849 by Charles Morren to depict periodical phenomena governed by seasons, the term "phenology" has spread in many fields of biology. With the wide adoption of the concept of phenology flourished a large number of metrics with different meaning and interpretation. Here, we first a priori classified 52 previously published metrics used to characterise the phenology of births in large herbivores according to four biological characteristics of interest: timing, synchrony, rhythmicity and regularity of births. We then applied each metric retrieved on simulation data, considering normal and non-normal distributions of births, and varying distributions of births in time. We then evaluated the ability of each metric to capture the variation of the four phenology characteristics via a sensitivity analysis. Finally, we scored each metric according to eight criteria we considered important to describe phenology correctly. The high correlation we found among the many metrics we retrieved suggests that such diversity of metrics is unnecessary. We further show that the best metrics are not the most commonly used, and that simpler is often better. Circular statistics with the mean vector orientation and mean vector length seems, respectively, particularly suitable to describe the timing and synchrony of births in a wide range of phenology patterns. Tests designed to compare statistical distributions, like Mood and Kolmogorov-Smirnov tests, allow a first and easy quantification of rhythmicity and regularity of birth phenology respectively. By identifying the most relevant metrics our study should facilitate comparative studies of phenology of births or of any other life-history event. For instance, comparative studies of the phenology of mating or migration dates are particularly important in the context of climate change.

ecology↗

Can citizen science analysis of camera trap data be used to study reproduction? Lessons from Snapshot Serengeti program

Ecologists increasingly rely on camera-trap data to estimate biological parameters such as population abundance. Because of the huge amount of data, the assistance of non-scientists is often sought after, but an assessment of the data quality is necessary. We tested whether volunteers data from one of the largest citizen science projects - Snapshot Serengeti - could be used to study breeding phenology. We tested whether the presence of juveniles (less than one or 12 months old) of species in the Serengeti: topi, kongoni, Grants gazelle, could be reliably detected by the "naive" volunteers vs. trained observers. We expected a positive correlation between the proportion of volunteers identifying juveniles and their effective presence within photographs, assessed by the trained observers. The agreement between the trained observers was good (Fleiss {kappa} > 0.61 for juveniles of less than one and 12 month(s) old), suggesting that morphological criteria can be used to determine age. The relationship between the proportion of volunteers detecting juveniles less than a month old and their actual presence plateaued at 0.45 for Grants gazelle, reached 0.70 for topi and 0.56 for kongoni. The same relationships were much stronger for juveniles younger than 12 months, reaching 1 for topi and kongoni. The absence of individuals < one month and the presence of juveniles < 12 months could be reliably assumed, respectively, when no volunteer and when all volunteers reported a presence of a young. In contrast, the presence of very young individuals and the absence of juveniles appeared more difficult to ascertain from volunteers classification, given how the classification task was presented to them. Volunteers classification allows a moderately accurate but quick sorting of photograph with/without juveniles. We discuss the limitations of using citizen science camera-traps data to study breeding phenology, and the options to improve the detection of juveniles.

ecology↗

Cast away on Mindoro island: population dynamics of the critically endangered tamaraw (Bubalus mindorensis) at Mounts Iglit-Baco Natural Park

Endangered species, despite often living at low population densities, may undergo unexpected density-dependent feedbacks in the case of successful recovery or marked reduction in range. Because density-dependence dynamics can increase risk of extinction, these effects can hamper conservation efforts. In this study, we analyse the dynamics of the largest population of the tamaraw (Bubalus mindorensis), a critically endangered ungulate species endemic to Mindoro island, Philippines. The population is located within a < 3,000 ha area in Mounts Iglit-Baco Natural Park, with limited expansion possibilities. We took advantage of a 21 year time series of tamaraw counts to estimate annual population growth rate and possible density-dependence, accounting for sampling errors in the counts. The tamaraw population has been increasing at an average rate of +5% per year, as would be expected given its protected status by law. Population growth showed strong spatial structuring, with a population growth close to +10% in the core area of protection, and a reduction of abundance of -5% at the periphery of its range, inside the protected area. This range constriction is concerning because our best population dynamics model suggests significant negative density-dependence (Bayes factor = 0.9). The contraction of tamaraw range is likely caused by anthropogenic pressures forcing the species to live at relatively high densities in the core zone where protection is most effective, creating source-sink dynamics. Our study highlights the fact that, despite the continuous population growth over the last two decades, the long-term viability of the Mounts Iglit-Baco Natural Park tamaraw population remains uncertain.

ecology↗

Habitat selection by the Ringed Kingfisher (Megaceryle torquata stictipennis) in Basse-Terre, Guadeloupe: Possible negative association with chlordecone pollution

In the Lesser Antilles the Ringed Kingfisher Megaceryle torquata stictipennis is found on Martinique, Dominica and Guadeloupe. On Martinique and Guadeloupe, farmers growing bananas have made massive use of chlordecone from 1973 until 1993. Chlordecone is a remnant organochlorine insecticide which bioaccumulates in organisms easily. We carried out a survey of the Ringed Kingfisher in 2009 on Basse-Terre, Guadeloupe, traveling 270 km on 44 rivers to assess the effects of chlordecone on its habitat selection behaviour. We recorded 47 encounters of Ringed Kingfishers over the survey. A habitat selection analysis revealed that the Ringed Kingfishers were located mainly in sections of rivers flowing through the ombrophilous forest, but absent on the ocean shoreline or in the lower parts of rivers. The Ringed Kingfishers distribution on Guadeloupe could be negatively associated with areas heavily polluted by the chlordecone. We propose that the widespread use of chlordecone in banana plantations on Guadeloupe between 1973 and 1993 has adverse ecological consequences, and may be responsible for the absence of Ringed Kingfishers in lowland habitat on the island. ResumeDans les Petites Antilles, le Martin-pecheur a ventre roux Megaceryle torquata stictipennis ne vit que sur trois iles: Martinique, Dominique et Guadeloupe. En 2009, nous avons effectue un recensement en Guadeloupe, sur 270 km parcourus dans 44 rivieres. Douze territoires de Martin-pecheur a ventre roux ont ete trouves, et la taille totale de la population est estimee a 54-64 individus. Une analyse de la selection de lhabitat montre que le Martin-pecheur a ventre roux se trouvait principalement sur les rivieres dans la foret ombrophile et non pas sur le bord de locean ni dans la partie basse des rivieres. En Guadeloupe, le Martin -pecheur a ventre roux est negativement associe avec les surfaces hautement polluees par un insecticide organochlore, la chlordecone. Nous suggerons que lepandage massif de la chlordecone de 1973 a 1993, dans les bananeraies de Guadeloupe, doit etre grandement responsable de labsence du Martin-pecheur a ventre roux dans les habitats de basses altitudes de lile. ResumenEn las Antillas Menores, el Martin Gijante Neotropical Megaceryle torquata stictipennis solo vive en tres islas: Martinica, Santo Domingo y Guadalupe. En 2001, realizamos un censo en Guadalupe sobre 270 km recorridos en 44 rios. Doce territorios de Martin Gijante Neotropical han sido registrados, y el volumen total de la poblacion se estima a 54-64 individuales. Un analisis de la seleccion del habitat muestra que el Martin Gijante Neotropical se encontraba principalmente en los rios en el bosque lluvioso y no a la orilla del mar tampoco en la parte baja de los rios. En Guadalupe, el Martin Gijante Neotropical esta negativamente asociado con las superficies muy poluadas por un insecticida organicloro, la chlordecona. Sugeremos que la difusion masiva de la chlordecona entre 1973 y 1993, en las plantaciones de platanos de Guadalupe, debe de ser altamente responsable de la aucencia del Martin Gijante Neotropical en los habitats de baja altitud en la isla.

ecology↗

Revisiting giraffe photo-identification using deep learning and network analysis

An increasing number of ecological monitoring programs rely on photographic capture-recapture of individuals to study distribution, demography and abundance of species. Photo-identification of individuals can sometimes be done using idiosyncratic coat or skin patterns, instead of using tags or loggers. However, when performed manually, the task of going through photographs is tedious and rapidly becomes too time consuming as the number of pictures grows. Computer vision techniques are an appealing and unavoidable help to tackle this apparently simple task in the big-data era. In this context, we propose to revisit animal re-identification using image similarity networks and metric learning with convolutional neural networks (CNNs), taking the giraffe as a working example. We first developed an end-to-end pipeline to retrieve a comprehensive set of re-identified giraffes from about 4, 000 raw photographs. To do so, we combined CNN-based object detection, SIFT pattern matching, and image similarity networks. We then quantified the performance of deep metric learning to retrieve the identity of known individuals and detect unknown individuals never seen in the previous years of monitoring. After a data augmentation procedure, the re-identification performance of the CNN reached a Top-1 accuracy of about 90%, despite the very small number of images per individual in the training data set. While the complete pipeline succeeded in re-identifying known individuals, it slightly under-performed with unknown individuals. Fully based on open-source software packages, our work paves the way for further attempts to build automatic pipelines for re-identification of individual animals, not only in giraffes but also in other species.

ecology↗

Distribution and density of oxpeckers on giraffes in Hwange National Park, Zimbabwe

Oxpeckers (Buphagus sp.) are two bird species closely associated to large mammals, including giraffes (Giraffa camelopardalis). We tested whether oxpeckers distributed themselves at random across individuals or aggregated on individual giraffes, and if birds select the hosts body parts with the expected greatest amount of ticks. By counting oxpeckers on giraffes body from photographs, we quantified the distribution of birds per hosts and over predefined zones on the giraffe body. Oxpeckers displayed a strong aggregation behaviour with few hosts carrying many birds while many carried a limited number or no birds, a pattern that was most exaggerated for males. Oxpeckers were disproportionately found on the mane and back, where the density of ticks is presumably the highest. This high aggregation level of birds is typical of parasitic species and could suggest that oxpecker distribution may mirror the distribution of ticks, their primary food resource, on giraffes. Abundance of ticks appears as a major driver of the oxpecker foraging behaviour, and the oxpecker-large herbivores system proves to be highly relevant for the study of host-parasite dynamics.

ecology↗

Population responses of naive roe deer to the recolonization of the French Vercors by wolves

In a context of rapidly changing carnivore populations worldwide, it is crucial to understand the consequences of these changes for prey populations. The recolonization by wolves of the French Vercors mountain range and the long-term monitoring (2001-2017) of roe deer populations provided us a unique opportunity to assess both lethal and non-lethal effects of wolves on these populations. We compared roe deer population abundance and growth, fawn body mass, and browsing intensity in two contrasted areas: a central area (core of a wolf pack territory characterized by an intense use by wolves) and a peripheral area (used more occasionally). Both populations of roe deer strongly dropped after an extremely severe winter but the population of the central area facing with wolves was slower to recover (due to a much lower growth rate the following year) and remained at lower abundance levels for 5 years. Fawn body mass was lower in the central area during that period and was not influenced by weather conditions or population abundance. The browsing index in the forests in presence of wolves decreased for a longer period, suggesting that possible habitat shifts have occurred. Altogether, the effects of wolves on the roe deer population in the central area occurred mainly during a 5-year period following the establishment of wolves, with effects at the population level in the first years only through the interplay between wolf predation (before wolves started preying on red deer), harsh winter conditions and naivete of prey to this recolonizing predator.

ecology↗

Estimating the abundance of duiker (Cephalophus spp.) populations in African rainforests: an overview of relevant methods

Duikers are among the most sought after antelope species for bush meat in central Africa. Estimates of population abundance of duikers based on reliable methods is therefore of prime importance for their sustainable management. Here we retrieved 31 studies from the literature and compared methods used to estimate the abundance of duiker populations in African rainforests. Implemented methods all derived from seven main combinations of sampling designs and population abundance estimators. We then evaluated the relevance of those seven methods by scoring them based on eight criteria selected according to their pros and cons reported in the litterature for large-scale population management of wildlife. For management purposes, methods derived from distance sampling offer the best compromise between the implementation costs and the biological information collected. In particular, both diurnal and nocturnal distance sampling can be recommended. Hunter calls and drive-netting are less reliable, but can be used in association with other measurements in the framework of indicators of ecological changes, a monitoring approach that has been successfully used in temperate ecosystems for managing large herbivores. Funding informationMinistere de lEnvironnement et du Developpement Durable de la Republique Democratique du Congo, Campus France and Centre National de la Recherche Scientifique (CNRS). ResumeLes cephalophes sont parmi les especes dantilopes les plus recherchees pour la viande de brousse en Afrique centrale. Lestimation de labondance des populations de cephalophes revet donc une importance primordiale pour leur gestion durable et adaptative. Nous avons extrait 31 etudes de la litterature et compare les methodes utilisees pour estimer labondance des populations de cephalophes dans les forets tropicales africaines. Les methodes employees derivent de sept combinaisons principales de plans dechantillonnage et destimateurs dabondance. Nous avons evalue la pertinence de ces sept methodes sur la base de criteres selectionnes en fonction de leurs avantages et inconvenients pour une gestion a grande echelle de la population. Les methodes derivees de lechantillonnage par distance offrent le meilleur compromis entre les couts de mise en uvre et les informations biologiques collectees. Les methodes dechantillonnage diurne et nocturne se sont montrees les plus satisfaisantes. Les methodes dappel par les chasseurs et de battue au filet sont moins fiables, mais peuvent etre utilisees en association avec dautres mesures biologiques comme indicateurs de changements ecologiques, une approche qui a ete utilisee avec succes dans les ecosystemes temperes pour la gestion des grands herbivores. Mots-clesgestion durable, grands herbivores, indicateurs de changement ecologique, methode de recensement, viande de brousse

ecology↗

Comparison of ecological, biological and anthropogenic causes of vehicle-wildlife collisions among three large herbivore species

Wildlife-vehicle collisions are of increasing concern with regards to the continuous and accelerating anthropogenic development. Preventing and mitigating collisions with wildlife will require a better understanding of the environmental and biological drivers of collision risks. Because species of large mammals differ in terms of food requirements, habitat selection and movement behaviours we tested at the management unit level if the density of collisions with red deer, roe deer and wild boar differed in terms of spatial distribution and explanatory factors. From 20,275 documented collisions in France between years 1990 and 2006, we found marked differences in the most influential environmental factors accounting for the density of collisions among the three species. The effect of road density was higher for the red deer than for the two other species and did not level off at our spatial-scale of observation. As expected, the annual hunting harvest - interpreted as a proxy of population abundance - was positively associated with the density of collisions for all species, being the strongest for red deer. While the collision density decreased with the proportion of forest in a management unit for wild boar, it increased with the fragmentation of forests for red deer that commute among forest patches between day and night. To reduce the number of wildlife- vehicle collisions, our results suggest to generalise road fencing and/or a control of abundance of large herbivore populations. Mitigation measures should target units where the collision risk is the highest for the most problematic species.

ecology↗