The adaptive value of density-dependent habitat specialization and social network centrality.

Density dependence is a fundamental ecological process. In particular, animal habitat selection and social behavior often affect fitness in a density-dependent manner. The Ideal Free Distribution (IFD) and niche variation hypothesis (NVH) present distinct predictions associated with Optimal Foraging Theory about how the effect of habitat selection on fitness varies with population density. Using caribou (Rangifer tarandus) in Canada as a model system, we test competing hypotheses about how habitat specialization, social behavior, and annual reproductive success (co)vary across a population density gradient. Within a behavioral reaction norm framework, we estimate repeatability, behavioral plasticity, and covariance among social behavior and habitat selection to investigate the adaptive value of sociality and habitat selection. In support of NVH, but not the IFD, we find that at high density habitat specialists had higher annual reproductive success than generalists, but were also less social than generalists, suggesting the possibility that specialists were less social to avoid competition. Our study supports niche variation as a mechanism for density-dependent habitat specialization.

Robust Responses of Female Caribou to Changes in Food Supply.

AbstractUngulates can respond to changes in food supply by altering foraging behavior, digestive function, and metabolism. A multifaceted response to an environmental change is considered robust. Short seasons of plant growth make herbivores sensitive to changes in food supply because maintenance and production must be accomplished in less time with fewer options in a more fragile response. Caribou live at high latitudes where short summers constrain their response to changes in food supply. We measured the ability of female caribou to resist and tolerate changes in the quality and quantity of their food supply during winter and summer. Caribou resisted changes in food abundance and quality by changing food intake and physical activity with changes in daily temperature within each season. Peak food intake rose by 134% from winter pregnancy to summer lactation (98 vs. 229 g kg-0.75 d-1), as digestible requirements to maintain the body increased by 85% for energy (1,164 vs. 2,155 kJ kg-0.75 d-1) and by 266% for N (0.79 vs. 2.89 g N kg-0.75 d-1). Caribou required a diet with a digestible content of 12 kJ g-1 and 0.8% N in pregnancy, 18 kJ g-1 and 1.9% N in early lactation, and 11 kJ g-1 and 1.2% N in late lactation, which corresponds with the phenology of the wild diet. Female caribou tolerated restriction of ad lib. food intake to 58% of their energy requirement (680 vs. 1,164 kJ kg-0.75 d-1) during winter pregnancy and to 84% of their energy requirement (1,814 vs. 2,155 kJ kg-0.75 d-1) during summer lactation without a change in stress level, as indicated by fecal corticosterone concentration. Conversely, caribou can respond to increased availability of food with a spare capacity to process digestible energy and N at 123% (2,642 vs. 2,155 kJ kg-0.75 d-1) and 145% (4.20 vs. 2.89 g N kg-0.75 d-1) of those respective requirements during lactation. Robust responses to changes in food supply allow caribou to sustain reproduction, which would buffer demographic response. However, herds may decline when thresholds of behavioral resistance and physiological tolerance are frequently exceeded. Therefore, the challenge for managing declining populations of caribou and other robust species is to identify declines in robustness before their response becomes fragile.

A taste of space: Remote animal observations and discrete-choice models provide new insights into foraging and density dynamics for a large subarctic herbivore.

Competition for resources and space can drive forage selection of large herbivores from the bite through the landscape scale. Animal behaviour and foraging patterns are also influenced by abiotic and biotic factors. Fine-scale mechanisms of density-dependent foraging at the bite scale are likely consistent with density-dependent behavioural patterns observed at broader scales, but few studies have directly tested this assertion. Here, we tested if space use intensity, a proxy of spatiotemporal density, affects foraging mechanisms at fine spatial scales similarly to density-dependent effects observed at broader scales in caribou. We specifically assessed how behavioural choices are affected by space use intensity and environmental processes using behavioural state and forage selection data from caribou (Rangifer tarandus granti) observed from GPS video-camera collars using a multivariate discrete-choice modelling framework. We found that the probability of eating shrubs increased with increasing caribou space use intensity and cover of Salix spp. shrubs, whereas the probability of eating lichen decreased. Insects also affected fine-scale foraging behaviour by reducing the overall probability of eating. Strong eastward winds mitigated negative effects of insects and resulted in higher probabilities of eating lichen. At last, caribou exhibited foraging functional responses wherein their probability of selecting each food type increased as the availability (% cover) of that food increased. Space use intensity signals of fine-scale foraging were consistent with density-dependent responses observed at larger scales and with recent evidence suggesting declining reproductive rates in the same caribou population. Our results highlight potential risks of overgrazing on sensitive forage species such as lichen. Remote investigation of the functional responses of foraging behaviours provides exciting future applications where spatial models can identify high-quality habitats for conservation.

Effectiveness of population-based recovery actions for threatened southern mountain caribou.

Habitat loss is affecting many species, including the southern mountain caribou (Rangifer tarandus caribou) population in western North America. Over the last half century, this threatened caribou population's range and abundance have dramatically contracted. An integrated population model was used to analyze 51 years (1973-2023) of demographic data from 40 southern mountain caribou subpopulations to assess the effectiveness of population-based recovery actions at increasing population growth. Reducing potential limiting factors on threatened caribou populations offered a rare opportunity to identify the causes of decline and assess methods of recovery. Southern mountain caribou abundance declined by 51% between 1991 and 2023, and 37% of subpopulations were functionally extirpated. Wolf reduction was the only recovery action that consistently increased population growth when applied in isolation, and combinations of wolf reductions with maternal penning or supplemental feeding provided rapid growth but were applied to only four subpopulations. As of 2023, recovery actions have increased the abundance of southern mountain caribou by 52%, compared to a simulation with no interventions. When predation pressure was reduced, rapid population growth was observed, even under contemporary climate change and high levels of habitat loss. Unless predation is reduced, caribou subpopulations will continue to be extirpated well before habitat conservation and restoration can become effective.

Reindeer in the Arctic reduce sleep need during rumination.

Timing and quantity of sleep depend on a circadian (∼24-h) rhythm and a specific sleep requirement.1 Sleep curtailment results in a homeostatic rebound of more and deeper sleep, the latter reflected in increased electroencephalographic (EEG) slow-wave activity (SWA) during non-rapid eye movement (NREM) sleep.2 Circadian rhythms are synchronized by the light-dark cycle but persist under constant conditions.3,4,5 Strikingly, arctic reindeer behavior is arrhythmic during the solstices.6 Moreover, the Arctic's extreme seasonal environmental changes cause large variations in overall activity and food intake.7 We hypothesized that the maintenance of optimal functioning under these extremely fluctuating conditions would require adaptations not only in daily activity patterns but also in the homeostatic regulation of sleep. We studied sleep using non-invasive EEG in four Eurasian tundra reindeer (Rangifer tarandus tarandus) in Tromsø, Norway (69°N) during the fall equinox and both solstices. As expected, sleep-wake rhythms paralleled daily activity distribution, and sleep deprivation resulted in a homeostatic rebound in all seasons. Yet, these sleep rebounds were smaller in summer and fall than in winter. Surprisingly, SWA decreased not only during NREM sleep but also during rumination. Quantitative modeling revealed that sleep pressure decayed at similar rates during the two behavioral states. Finally, reindeer spent less time in NREM sleep the more they ruminated. These results suggest that they can sleep during rumination. The ability to reduce sleep need during rumination-undisturbed phases for both sleep recovery and digestion-might allow for near-constant feeding in the arctic summer.

Effects of vehicle traffic on space use and road crossings of caribou in the Arctic.

Assessing the effects of industrial development on wildlife is a key objective of managers and conservation practitioners. However, wildlife responses are often only investigated with respect to the footprint of infrastructure, even though human activity can strongly mediate development impacts. In Arctic Alaska, there is substantial interest in expanding energy development, raising concerns about the potential effects on barren-ground caribou (Rangifer tarandus granti). While caribou generally avoid industrial infrastructure, little is known about the role of human activity in moderating their responses, and whether managing activity levels could minimize development effects. To address this uncertainty, we examined the influence of traffic volume on caribou summer space use and road crossings in the Central Arctic Herd within the Kuparuk and Milne Point oil fields on the North Slope of Alaska. We first modeled spatiotemporal variation in hourly traffic volumes across the road system from traffic counter data using gradient-boosted regression trees. We then used generalized additive models to estimate nonlinear step selection functions and road-crossing probabilities from collared female caribou during the post-calving and insect harassment seasons, when they primarily interact with roads. Step selection analyses revealed that caribou selected areas further from roads (~1-3 km) during the post-calving and mosquito seasons and selected areas with lower traffic volumes during all seasons, with selection probabilities peaking when traffic was <5 vehicles/h. Using road-crossing models, we found that caribou were less likely to cross roads during the insect seasons as traffic increased, but that response dissipated as insect harassment became more severe. Past studies suggested that caribou exhibit behavioral responses when traffic exceeds 15 vehicles/h, but our results demonstrate behavioral responses at much lower traffic levels. Our results illustrate that vehicle activity mediates caribou responses to road infrastructure, information that can be used in future land-use planning to minimize the behavioral responses of caribou to industrial development in sensitive Arctic landscapes.

A Summer Heat Wave Reduced Activity, Heart Rate, and Autumn Body Mass in a Cold-Adapted Ungulate.

AbstractHeat waves are becoming more frequent across the globe and may impose severe thermoregulatory challenges for endotherms. Heat stress can induce both behavioral and physiological responses, which may result in energy deficits with potential fitness consequences. We studied the responses of reindeer (Rangifer tarandus tarandus), a cold-adapted ungulate, to a record-breaking heat wave in northern Finland. Activity, heart rate, subcutaneous body temperature, and body mass data were collected for 14 adult females. The post-heat wave autumn body masses were then analyzed against longitudinal body mass records for the herd from 1990 to 2021. With increasing air temperature during the day, reindeer became less active and had reduced heart rate and increased body temperature, reflecting both behavioral and physiological responses to heat stress. Although they increased activity in the late afternoon, they failed to compensate for lost foraging time on the hottest days (daily mean temperature ≥20°C), and total time active was reduced by 9%. After the heat wave, the mean September body mass of herd females (69.7±6.6 kg, n=52) was on average 16.4% ± 4.8% lower than predicted (83.4±6.0 kg). Among focal females, individuals with the lowest levels of activity during the heat wave had the greatest mass loss during summer. We show how heat waves impose a thermoregulatory challenge on endotherms, resulting in mass loss, potentially as a result of the loss of foraging time. While it is well known that environmental conditions affect large herbivore fitness indirectly through decreased forage quality and limited water supply, direct effects of heat may be increasingly common in a warming climate.

Large herbivore diversity slows sea ice-associated decline in arctic tundra diversity.

Biodiversity is declining globally in response to multiple human stressors, including climate forcing. Nonetheless, local diversity trends are inconsistent in some taxa, obscuring contributions of local processes to global patterns. Arctic tundra diversity, including plants, fungi, and lichens, declined during a 15-year experiment that combined warming with exclusion of large herbivores known to influence tundra vegetation composition. Tundra diversity declined regardless of experimental treatment, as background growing season temperatures rose with sea ice loss. However, diversity declined slower with large herbivores than without them. This difference was associated with an increase in effective diversity of large herbivores as formerly abundant caribou declined and muskoxen increased. Efforts that promote herbivore diversity, such as rewilding, may help mitigate impacts of warming on tundra diversity.

Plasticity and repeatability in spring migration and parturition dates with implications for annual reproductive success.

In seasonal environments, animals should be adapted to match important life-history traits to when environmental conditions are optimal. Most animal populations therefore reproduce when resource abundance is highest to increase annual reproductive success. When facing variable, and changing, environments animals can display behavioural plasticity to acclimate to changing conditions. Behaviours can further be repeatable. For example, timing of behaviours and life history traits such as timing of reproduction may indicate phenotypic variation. Such variation may buffer animal populations against the consequences of variation and change. Our goal was to quantify plasticity and repeatability in migration and parturition timing in response to timing of snowmelt and green-up in a migratory herbivore (caribou, Rangifer tarandus, n = 132 ID-years) and their effect on reproductive success. We used behavioural reaction norms to quantify repeatability in timing of migration and timing of parturition in caribou and their plasticity to timing of spring events, while also quantifying phenotypic covariance between behavioural and life-history traits. Timing of migration for individual caribou was positively correlated with timing of snowmelt. The timing of parturition for individual caribou varied as a function of inter-annual variation in timing of snowmelt and green-up. Repeatability for migration timing was moderate, but low for timing of parturition. Plasticity did not affect reproductive success. We also did not detect any evidence of phenotypic covariance among any traits examined-timing of migration was not correlated with timing of parturition, and neither was there a correlation in the plasticity of these traits. Repeatability in migration timing suggests the possibility that the timing of migration in migratory herbivores could evolve if the repeatability detected in this study has a genetic or otherwise heritable basis, but observed plasticity may obviate the need for an evolutionary response. Our results also suggest that observed shifts in caribou parturition timing are due to plasticity as opposed to an evolutionary response to changing conditions. While this provides some evidence that populations may be buffered from the consequences of climate change via plasticity, a lack of repeatability in parturition timing could impede adaptation as warming increases.

The Effect of Species and Sex on the Element Content of Muskox (Ovibos moschatus) and Caribou (Rangifer tarandus groenlandicus) Tissues.

Muskox (Ovibos moschatus) and caribou (Rangifer tarandus groenlandicus) are wild ruminants that inhabit the Greenland tundra. They are part of the diet of many Greenlanders, being important sources of protein and micronutrients such as iron. The objective of this study is to analyse the element profiles of three tissues from these species: skeletal muscle, liver and adipose tissue, and to determine if they are affected by species and sex (male vs. female). Samples were obtained from annual hunts in two different regions of West Greenland. Element profiles were analysed using inductively-coupled plasma-optical emission spectrometry. The interaction between species and sex was only detected in Na (sodium) in the muscle and adipose tissue, where male and female caribou had the highest concentrations, respectively. The effect of sex was not statistically significant in the liver samples and only occasionally in the other tissues. Species was the most relevant factor in element profiles found in this study. Caribou had higher concentrations of K (potassium) and S (sulphur) in the muscle and liver. Fewer differences were detected between species in the adipose tissue, compared to the other tissues. These differences may reflect the feeding behaviour and the geographical location of both species. This study contributes to evaluate the element composition of the edible tissue of these wild ungulate species, as well as evaluating the factors of sex and species that could differentiate their composition.

Evaluating the impact of caribou habitat restoration on predator and prey movement.

Fragmentation of the boreal forest by linear features, including seismic lines, has destabilized predator-prey dynamics, resulting in the decline of woodland caribou (Rangifer tarandus caribou) populations. Restoration of human-altered habitat has therefore been identified as a critical management tool for achieving self-sustaining woodland caribou populations. However, only recently has testing of the response of caribou and other wildlife to restoration activities been conducted. Early work has centered around assessing changes in wildlife use of restored seismic lines. We evaluated whether restoration reduces the movement rates of predators and their associated prey, which is expected to decrease predator hunting efficiency and ultimately reduce caribou mortality. We developed a new method for using cameras to measure fine-scale movement by measuring speed as animals traveled between cameras in an array. We used our method to quantify speed of caribou, moose (Alces alces), bears (Ursus americanus), and wolves (Canis lupus) on treated (restored) and untreated seismic lines. Restoration treatments reduced travel speeds along seismic lines of wolves by 1.38 km/h, bears by 0.55 km/h, and caribou by 1.57 km/h, but did not reduce moose travel speeds. Reduced predator and caribou speeds on treated seismic lines are predicted to decrease encounter rates between predators and caribou and thus lower caribou kill rates. However, further work is needed to determine whether reduced movement rates result in reduced encounter rates with prey, and ultimately reduced caribou mortality.

La fragmentación del bosque boreal causado por los accidentes lineales, incluyendo a las líneas sísmicas, ha desestabilizado las dinámicas depredador-presa, lo que resulta en la declinación de las poblaciones de caribú (Rangifer tarandus caribou). Por esto, la restauración del hábitat con alteraciones antropogénicas ha sido identificada como una herramienta fundamental de gestión para obtener poblaciones autosuficientes de esta especie. Sin embargo, no es hasta hace poco que se ha analizado la respuesta del caribú y otras especies a las actividades de restauración; los primeros trabajos se centraban en analizar los cambios en el uso que les daban las especies a las líneas sísmicas restauradas. Evaluamos si la restauración reduce las tasas de movimiento de los depredadores y sus presas asociadas, las cuales se esperan disminuyan la eficiencia de caza de los depredadores y por último reduzcan la mortalidad del caribú. Desarrollamos un nuevo método para usar las cámaras para medir el movimiento detallado mediante la medición de la velocidad con la que los animales se trasladan a lo largo de una serie de cámaras. Usamos nuestro método para cuantificar la velocidad del caribú, alces (Alces alces), osos (Ursus americanus) y lobos (Canis lupus) en líneas sísmicas tratadas (restauradas) y no tratadas. Los tratamientos de restauración redujeron la velocidad de movimiento de los lobos (reducción de 1.38 km/hora), osos (0.55 km/hora) y caribú (1.57 km/hora), pero no afectaron la velocidad de movimiento de los alces. Se pronostica que la reducción en la velocidad de movimiento sobre las líneas sísmicas disminuye la proporción de encuentros entre el caribú y sus depredadores y, por lo tanto, reduce la proporción de muertes del caribú. Sin embargo, se necesita un análisis más profundo para determinar si la tasa reducida de movimiento resulta en una tasa reducida de encuentros con depredadores y si, por último, esto reduce la mortalidad del caribú.

Svalbard reindeer winter diets: Long-term dietary shifts to graminoids in response to a changing climate.

Arctic ecosystems are changing dramatically with warmer and wetter conditions resulting in complex interactions between herbivores and their forage. We investigated how Svalbard reindeer (Rangifer tarandus platyrhynchus) modify their late winter diets in response to long-term trends and interannual variation in forage availability and accessibility. By reconstructing their diets and foraging niches over a 17-year period (1995-2012) using serum δ13 C and δ15 N values, we found strong support for a temporal increase in the proportions of graminoids in the diets with a concurrent decline in the contributions of mosses. This dietary shift corresponds with graminoid abundance increases in the region and was associated with increases in population density, warmer summer temperatures and more frequent rain-on-snow (ROS) in winter. In addition, the variance in isotopic niche positions, breadths, and overlaps also supported a temporal shift in the foraging niche and a dietary response to extreme ROS events. Our long-term study highlights the mechanisms by which winter and summer climate changes cascade through vegetation shifts and herbivore population dynamics to alter the foraging niche of Svalbard reindeer. Although it has been anticipated that climate changes in the Svalbard region of the Arctic would be detrimental to this unique ungulate, our study suggests that environmental change is in a phase where conditions are improving for this subspecies at the northernmost edge of the Rangifer distribution.

Demographic responses of nearly extirpated endangered mountain caribou to recovery actions in Central British Columbia.

Recovering endangered species is a difficult and often controversial task that challenges status quo land uses. Southern Mountain caribou are a threatened ecotype of caribou that historically ranged in southwestern Canada and northwestern USA and epitomize the tension between resource extraction, biodiversity conservation, and Indigenous Peoples' treaty rights. Human-induced habitat alteration is considered the ultimate cause of caribou population declines, whereby an increased abundance of primary prey-such as moose and deer-elevates predator populations and creates unsustainable caribou mortality. Here we focus on the Klinse-Za and Quintette subpopulations, part of the endangered Central Group of Southern Mountain caribou in British Columbia. These subpopulations were trending toward immediate extirpation until a collaborative group initiated recovery by implementing two short-term recovery actions. We test the effectiveness of these recovery actions-maternity penning of adult females and their calves, and the reduction of a primary predator, wolves-in increasing vital rates and population growth. Klinse-Za received both recovery actions, whereas Quintette only received wolf reductions, providing an opportunity to test efficacy between recovery actions. Between 1995 and 2021, we followed 162 collared female caribou for 414 animal-years to estimate survival and used aerial counts to estimate population abundance and calf recruitment. We combined these data in an integrated population model to estimate female population growth, total population abundance, and recovery action effectiveness. Results suggest that the subpopulations were declining rapidly (λ = 0.90-0.93) before interventions and would have been functionally extirpated (<10 animals) within 10-15 years. Wolf reduction increased population growth rates by ~0.12 for each subpopulation. Wolf reduction halted the decline of Quintette caribou and allowed them to increase (λ = 1.05), but alone would have only stabilized the Klinse-Za (λ = 1.02). However, maternity penning in the Klinse-Za increased population growth by a further ~0.06, which when combined with wolf reductions, allowed populations to grow (λ = 1.08). Taken together, the recovery actions in these subpopulations increased adult female survival, calf recruitment, and overall population growth, more than doubling abundance. Our results suggest that maternity penning and wolf reductions can be effective at increasing caribou numbers in the short term, while long-term commitments to habitat protection and restoration are made.

Indigenous-led conservation: Pathways to recovery for the nearly extirpated Klinse-Za mountain caribou.

Indigenous Peoples around the northern hemisphere have long relied on caribou for subsistence and for ceremonial and community purposes. Unfortunately, despite recovery efforts by federal and provincial agencies, caribou are currently in decline in many areas across Canada. In response to recent and dramatic declines of mountain caribou populations within their traditional territory, West Moberly First Nations and Saulteau First Nations (collectively, the "Nations") came together to create a new vision for caribou recovery on the lands they have long stewarded and shared. The Nations focused on the Klinse-Za subpopulation, which had once encompassed so many caribou that West Moberly Elders remarked that they were "like bugs on the landscape." The Klinse-Za caribou declined from ~250 in the 1990s to only 38 in 2013, rendering Indigenous harvest of caribou nonviable and infringing on treaty rights to a subsistence livelihood. In collaboration with many groups and governments, this Indigenous-led conservation initiative paired short-term population recovery actions, predator reduction and maternal penning, with long-term habitat protection in an effort to create a self-sustaining caribou population. Here, we review these recovery actions and the promising evidence that the abundance of Klinse-Za caribou has more than doubled from 38 animals in 2013 to 101 in 2021, representing rapid population growth in response to recovery actions. With looming extirpation averted, the Nations focused efforts on securing a landmark conservation agreement in 2020 that protects caribou habitat over a 7986-km2 area. The Agreement provides habitat protection for >85% of the Klinse-Za subpopulation (up from only 1.8% protected pre-conservation agreement) and affords moderate protection for neighboring caribou subpopulations (29%-47% of subpopulation areas, up from 0%-20%). This Indigenous-led conservation initiative has set both the Indigenous and Canadian governments on the path to recover the Klinse-Za subpopulation and reinstate a culturally meaningful caribou hunt. This effort highlights how Indigenous governance and leadership can be the catalyst needed to establish meaningful conservation actions, enhance endangered species recovery, and honor cultural connections to now imperiled wildlife.

Increasing fire frequency and severity will increase habitat loss for a boreal forest indicator species.

Climate change will lead to more frequent and more severe fires in some areas of boreal forests, affecting the distribution and availability of late-successional forest communities. These forest communities help to protect globally significant carbon reserves beneath permafrost layers and provide habitat for many animal species, including forest-dwelling caribou. Many caribou populations are declining, yet the mechanisms by which changing fire regimes could affect caribou declines are poorly understood. We analyzed resource selection of 686 GPS-collared female caribou from three ecotypes and 15 populations in a ~600,000 km2 region of northwest Canada and eastern Alaska. These populations span a wide gradient of fire frequency but experience low levels of human-caused habitat disturbance. We used a mixed-effects modeling framework to characterize caribou resource selection in response to burns at different seasons and spatiotemporal scales, and to test for functional responses in resource selection to burn availability. We also tested mechanisms driving observed selection patterns using burn severity and lichen cover data. Caribou avoided burns more strongly during winter relative to summer and at larger spatiotemporal scales relative to smaller scales. During the winter, caribou consistently avoided burns at both spatiotemporal scales as burn availability increased, indicating little evidence of a functional response. However, they decreased their avoidance of burns during summer as burn availability increased. Burn availability explained more variation in caribou selection for burns than ecotype. Within burns, caribou strongly avoided severely burned areas in winter, and this avoidance lasted nearly 30 years after a fire. Caribou within burns also selected higher cover of terrestrial lichen (an important caribou food source). We found a negative relationship between burn severity and lichen cover, confirming that caribou avoidance of burns was consistent with lower lichen abundance. Consistent winter avoidance of burns and severely burned areas suggests that caribou will experience increasing winter habitat loss as fire frequency and severity increase. Our results highlight the potential for climate-induced alteration of natural disturbance regimes to affect boreal biodiversity through habitat loss. We suggest that management strategies prioritizing protection of core winter range habitat with lower burn probabilities would provide important climate-change refugia for caribou.

CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly.

Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length > 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here.

Calf/female ratio and population dynamics of wild forest reindeer in relation to wolf and moose abundances in a managed European ecosystem.

BACKGROUND: The alternative prey hypothesis describes the mechanism for apparent competition whereby the mortality of the secondary prey species increases (and population size decreases decreases) by the increased predation by the shared predator if the population size of the primary prey decreases. Apparent competition is a process where the abundance of two co-existing prey species are negatively associated because they share a mutual predator, which negatively affects the abundance of both prey Here, we examined whether alternative prey and/or apparent competition hypothesis can explain the population dynamics and reproductive output of the secondary prey, wild forest reindeer (Rangifer tarandus fennicus) in Finland, in a predator-prey community in which moose (Alces alces) is the primary prey and the wolf (Canis lupus) is the generalist predator. METHODS: We examined a 22-year time series (1996-2017) to determine how the population size and the calf/female ratio of wild forest reindeer in Eastern Finland were related to the abundances of wolf and moose. Only moose population size was regulated by hunting. Summer predation of wolves on reindeer focuses on calves. We used least squares regression (GLS) models (for handling autocorrelated error structures and resulting pseudo-R2s) and generalized linear mixed (GLMs) models (for avoidance of negative predictions) to determine the relationships between abundances. We performed linear and general linear models for the calf/female ratio of reindeer. RESULTS AND SYNTHESIS: The trends in reindeer population size and moose abundance were almost identical: an increase during the first years and then a decrease until the last years of our study period. Wolf population size in turn did not show long-term trends. Change in reindeer population size between consecutive winters was related positively to the calf/female ratio. The calf/female ratio was negatively related to wolf population size, but the reindeer population size was related to the wolf population only when moose abundance was entered as another independent variable. The wolf population was not related to moose abundance even though it is likely to consist the majority of the prey biomass. Because reindeer and moose populations were positively associated, our results seemed to support the alternative prey hypothesis more than the apparent competition hypothesis. However, these two hypotheses are not mutually exclusive and the primary mechanism is difficult to distinguish as the system is heavily managed by moose hunting. The recovery of wild forest reindeer in eastern Finland probably requires ecosystem management involving both habitat restoration and control of species abundances.

Demographic responses of a threatened, low-density ungulate to annual variation in meteorological and phenological conditions.

As global climate change progresses, wildlife management will benefit from knowledge of demographic responses to climatic variation, particularly for species already endangered by other stressors. In Canada, climate change is expected to increasingly impact populations of threatened woodland caribou (Rangifer tarandus caribou) and much focus has been placed on how a warming climate has potentially facilitated the northward expansion of apparent competitors and novel predators. Climate change, however, may also exert more direct effects on caribou populations that are not mediated by predation. These effects include meteorological changes that influence resource availability and energy expenditure. Research on other ungulates suggests that climatic variation may have minimal impact on low-density populations such as woodland caribou because per-capita resources may remain sufficient even in "bad" years. We evaluated this prediction using demographic data from 21 populations in western Canada that were monitored for various intervals between 1994 and 2015. We specifically assessed whether juvenile recruitment and adult female survival were correlated with annual variation in meteorological metrics and plant phenology. Against expectations, we found that both vital rates appeared to be influenced by annual climatic variation. Juvenile recruitment was primarily correlated with variation in phenological conditions in the year prior to birth. Adult female survival was more strongly correlated with meteorological conditions and declined during colder, more variable winters. These responses may be influenced by the life history of woodland caribou, which reside in low-productivity refugia where small climatic changes may result in changes to resources that are sufficient to elicit strong demographic effects. Across all models, explained variation in vital rates was low, suggesting that other factors had greater influence on caribou demography. Nonetheless, given the declining trajectories of many woodland caribou populations, our results highlight the increased relevance of recovery actions when adverse climatic conditions are likely to negatively affect caribou demography.

Determinants of heart rate in Svalbard reindeer reveal mechanisms of seasonal energy management.

Seasonal energetic challenges may constrain an animal's ability to respond to changing individual and environmental conditions. Here, we investigated variation in heart rate, a well-established proxy for metabolic rate, in Svalbard reindeer (Rangifer tarandus platyrhynchus), a species with strong seasonal changes in foraging and metabolic activity. In 19 adult females, we recorded heart rate, subcutaneous temperature and activity using biologgers. Mean heart rate more than doubled from winter to summer. Typical drivers of energy expenditure, such as reproduction and activity, explained a relatively limited amount of variation (2-6% in winter and 16-24% in summer) compared to seasonality, which explained 75% of annual variation in heart rate. The relationship between heart rate and subcutaneous temperature depended on individual state via body mass, age and reproductive status, and the results suggested that peripheral heterothermy is an important pathway of energy management in both winter and summer. While the seasonal plasticity in energetics makes Svalbard reindeer well-adapted to their highly seasonal environment, intraseasonal constraints on modulation of their heart rate may limit their ability to respond to severe environmental change. This study emphasizes the importance of encompassing individual state and seasonal context when studying energetics in free-living animals. This article is part of the theme issue 'Measuring physiology in free-living animals (Part II)'.

Reproduction of male reindeer (Rangifer tarandus).

The present review provides a comprehensive assessment on the basic aspects of the reproduction of the Rangifer male with a special focus on pubertal development, and the seasonal dynamics of gametogenesis, androgenesis, antler cycle and other physiological and behavioural characteristics of the rutting male. A greater understanding of the reproductive physiology of the males is needed to improve existing management strategies of semi-domestic stocks in the changing climate and to develop species-specific assisted reproductive technologies for improving the in situ and ex situ conservation programs to preserve endangered subspecies as well as to facilitate the transfer of genetic resources between fragmented wild or semi-domestic populations.