High genetic load without purging in caribou, a diverse species at risk.

High intra-specific genetic diversity is associated with adaptive potential, which is key for resilience to global change. However, high variation may also support deleterious alleles through genetic load, thereby increasing the risk of inbreeding depression if population sizes decrease. Purging of deleterious variation has been demonstrated in some threatened species. However, less is known about the costs of declines and inbreeding in species with large population sizes and high genetic diversity even though this encompasses many species globally that are expected to undergo population declines. Caribou is a species of ecological and cultural significance in North America with a wide distribution supporting extensive phenotypic variation but with some populations undergoing significant declines resulting in their at-risk status in Canada. We assessed intra-specific genetic variation, adaptive divergence, inbreeding, and genetic load across populations with different demographic histories using an annotated chromosome-scale reference genome and 66 whole-genome sequences. We found high genetic diversity and nine phylogenomic lineages across the continent with adaptive diversification of genes, but also high genetic load among lineages. We found highly divergent levels of inbreeding across individuals, including the loss of alleles by drift but not increased purging in inbred individuals, which had more homozygous deleterious alleles. We also found comparable frequencies of homozygous deleterious alleles between lineages regardless of nucleotide diversity. Thus, further inbreeding may need to be mitigated through conservation efforts. Our results highlight the "double-edged sword" of genetic diversity that may be representative of other species atrisk affected by anthropogenic activities.

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.

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.

Population dynamics of caribou shaped by glacial cycles before the last glacial maximum.

Pleistocene glacial cycles influenced the diversification of high-latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger-scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20-30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre-LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high-latitude species.

Trophic consequences of terrestrial eutrophication for a threatened ungulate.

Changes in primary productivity have the potential to substantially alter food webs, with positive outcomes for some species and negative outcomes for others. Understanding the environmental context and species traits that give rise to these divergent outcomes is a major challenge to the generality of both theoretical and applied ecology. In aquatic systems, nutrient-mediated eutrophication has led to major declines in species diversity, motivating us to seek terrestrial analogues using a large-mammal system across 598 000 km2 of the Canadian boreal forest. These forests are undergoing some of the most rapid rates of land-use change on Earth and are home to declining caribou (Rangifer tarandus caribou) populations. Using satellite-derived estimates of primary productivity, coupled with estimates of moose (Alces alces) and wolf (Canis lupus) abundance, we used path analyses to discriminate among hypotheses explaining how habitat alteration can affect caribou population growth. Hypotheses included food limitation, resource dominance by moose over caribou, and apparent competition with predators shared between moose and caribou. Results support apparent competition and yield estimates of wolf densities (1.8 individuals 1000 km-2) above which caribou populations decline. Our multi-trophic analysis provides insight into the cascading effects of habitat alteration from forest cutting that destabilize terrestrial predator-prey dynamics. Finally, the path analysis highlights why conservation actions directed at the proximate cause of caribou decline have been more successful in the near term than those directed further along the trophic chain.

Hiding in plain sight: discovery and phylogeography of a cryptic species of Trichinella (Nematoda: Trichinellidae) in wolverine (Gulo gulo).

Understanding parasite diversity and distribution is essential in managing the potential impact of parasitic diseases in animals and people. Imperfect diagnostic methods, however, may conceal cryptic species. Here, we report the discovery and phylogeography of a previously unrecognized species of Trichinella in wolverine (Gulo gulo) from northwestern Canada that was indistinguishable from T. nativa using the standard multiplex PCR assay based on the expansion segment 5 (ESV) of ribosomal DNA. The novel genotype, designated as T13, was discovered when sequencing the mitochondrial genome. Phylogenetic analyses of the mitochondrial genome and of 15 concatenated single copy orthologs of nuclear DNA indicated a common ancestor for the encapsulated clade is shared by a subclade containing Trichinella spiralis and Trichinella nelsoni, and a subclade containing T13 and remaining taxa: T12 + (T2 + T6) + [(T5 + T9) + (T3 + T8)]. Of 95 individual hosts from 12 species of mammalian carnivores from northwestern Canada from which larvae were identified as T. nativa on multiplex PCR, only wolverines were infected with T13 (14 of 42 individuals). These infections were single or mixed with T. nativa and/or T6. Visual examination and motility testing confirmed that T13 is encapsulated and likely freeze-tolerant. We developed a new Polymerase Chain Reaction-Restriction Fragment Length Polymorphism which unequivocally distinguishes between T13 and T. nativa. We propose Trichinella chanchalensis n. sp. for T13, based on significant genetic divergence from other species of Trichinella and broad-based sampling of the Trichinella genome. Exploration of Alaskan and Siberian isolates may contribute to further resolution of a phylogeographically complex history for species of Trichinella across Beringia, including Trichinella chanchalensis n. sp. (T13).

Risk factors and prevalence of antibodies for Toxoplasma gondii in diaphragmatic fluid in wolverines (Gulo gulo) from the Northwest Territories, Canada.

Toxoplasma gondii, a zoonotic food borne parasite that can infect almost all warm-blooded animals including people, and ranks 4th among 24 most significant global foodborne parasites listed by the World Health Organization/United Nations Food and Agriculture Organization (FAO/WHO, 2014). Exposure to T. gondii has been reported in wildlife and people in the Canadian North, despite low densities of feline definitive hosts. The ecology of this host-parasite system could be affected by changing climate and landscape in boreal and sub-Arctic regions, and surveillance data are critically needed. Wolverines are an economically and culturally important species in northern Canada due to their valuable fur. Fluid obtained from diaphragmatic muscle of 127 wolverines (Gulo gulo) were tested for antibodies to T. gondii using an enzyme linked immunosorbent assay (ELISA). A seroprevalence of 62% (Confidence Interval (CI): 53-71%) was observed. This result indicates high levels of exposure, likely either through environmental contamination with T. gondii oocysts shed by infected wild felids, or consumption of carcasses/offal of other intermediate hosts containing tissue cysts with bradyzoites in tissues. We examined factors associated with seropositivity, including age, sex, harvest location, harvest location with respect to treeline, and body condition index. Adult (≥2 years) wolverines had 5.2 times higher odds of being sero-positive than juvenile (<1 years) wolverines. The highest seroprevalence was observed in wolverines from Sahtu and South Slave regions. Proportion of sero-positive wolverines harvested above and below the tree line was not significantly different (60% vs 65%). Age was the only significant predictor of T. gondii exposure in wolverines (using logistic regression analysis); further studies should target larger sample sizes. This study is an example of how fluid from diaphragmatic muscle can be used for screening for T. gondii antibodies in wolverines. The diaphragm, commonly collected for screening for another food borne parasite, Trichinella, in wildlife harvested for human consumption, can be used for screening of T. gondii exposure in wildlife. Due to their predatory and scavenging lifestyle and high trophic level, wolverines could serve as a sentinel species for T. gondii.

Trichinella Nativa Outbreak With Rare Thrombotic Complications Associated With Meat From a Black Bear Hunted in Northern Ontario.

BACKGROUND: Although trichinellosis is known to cause thrombotic disease, serious thrombotic events are rare and have not been previously associated with Trichinella nativa infection. METHODS: Patient interviews and medical chart reviews were conducted on 10 men who became ill following consumption of a common source of black bear meat. Trichinella serology on patient sera as well as polymerase chain reaction (PCR) and larval identification of the meat samples was conducted. RESULTS: All 10 exposed individuals developed an acute illness clinically compatible with trichinellosis, characterized by fever, abdominal pain, and diarrhea, along with eosinophilia ranging from 0.9 × 109/L to 6.1 × 109/L. Within 2 weeks of the diarrheal illness, systemic symptoms developed in all exposed individuals characterized by fever, myalgia, periorbital edema, and fatigue. ST-elevation myocardial infarction and sinus venous tract thrombosis occurred as a complication of trichinellosis in 2 patients. Acute serology was nonreactive in all patients, though convalescent serology was reactive in 6 of 8 (75%) patients for whom sera was available. Multiplex PCR identified T. nativa from the bear meat, and was corroborated by microscopic larval identification. CONCLUSIONS: We report a 100% attack rate of T. nativa from bear meat among those who were exposed, and demonstrate that this species can cause serious thrombotic complications of trichinellosis in humans. Education of hunters and the public regarding the importance of proper preparation of wild game prior to ingestion is warranted.

Trichinella Surveillance in Black Bears ( Ursus americanus ) from the Dehcho Region, Northwest Territories, Canada, 2002-15.

We used muscle digestion to test black bears ( Ursus americanus ) from the southwestern Northwest Territories, Canada, for Trichinella. Results showed a prevalence of 4.1%. Some bears had infection intensities of more than one larva per gram of muscle tissue; this level in meat is considered to pose a human consumption safety risk.

Subpopulation structure of caribou (Rangifer tarandus L.) in arctic and subarctic Canada.

Effective management and conservation of species, subspecies, or ecotypes require an understanding of how populations are structured in space. We used satellite-tracking locations and hierarchical and fuzzy clustering to quantify subpopulations within the behaviorally different barren-ground caribou (Rangifer tarandus groenlandicus), Dolphin and Union island caribou (R. t. groenlandicus x pearyi), and boreal (R. t. caribou) caribou ecotypes in the Northwest Territories and Nunavut, Canada. Using a novel approach, we verified that the previously recognized Cape Bathurst, Bluenose-West, Bluenose-East, Bathurst, Beverly, Qamanirjuaq, and Lorillard barren-ground subpopulations were robust and that the Queen Maude Gulf and Wager Bay barren-ground subpopulations were organized as individuals. Dolphin and Union island and boreal caribou formed one and two distinct subpopulation, respectively, and were organized as individuals. Robust subpopulations were structured by strong annual spatial affiliation among females; subpopulations organized as individuals were structured by migratory connectivity, barriers to movement, and/or habitat discontinuity. One barren-ground subpopulation used two calving grounds, and one calving ground was used by two barren-ground subpopulations, indicating that these caribou cannot be reliably assigned to subpopulations solely by calving-ground use. They should be classified by annual spatial affiliation among females. Annual-range size and path lengths varied significantly among ecotypes, including mountain woodland caribou (R. t. caribou), and reflected behavioral differences. An east-west cline in annual-range sizes and path lengths among migratory barren-ground subpopulations likely reflected differences in subpopulation size and habitat conditions and further supported the subpopulation structure identified.

Prevalence of Trichinella spp. in black bears, grizzly bears, and wolves in the Dehcho Region, Northwest Territories, Canada, including the first report of T. nativa in a grizzly bear from Canada.

Samples of muscle from 120 black bears (Ursus americanus), 11 grizzly bears (Ursus arctos), and 27 wolves (Canis lupus) collected in the Dehcho Region of the Northwest Territories from 2001 to 2010 were examined for the presence of Trichinella spp. larvae using a pepsin-HCl digestion assay. Trichinella spp. larvae were found in eight of 11 (73%) grizzly bears, 14 of 27 (52%) wolves, and seven of 120 (5.8%) black bears. The average age of positive grizzly bears, black bears, and wolves was 13.5, 9.9, and approximately 4 yr, respectively. Larvae from 11 wolves, six black bears, and seven grizzly bears were genotyped. Six wolves were infected with T. nativa and five with Trichinella T6, four black bears were infected with T. nativa and two with Trichinella T6, and all seven grizzly bears were infected with Trichinella T6 and one of them had a coinfection with T. nativa. This is the first report of T. nativa in a grizzly bear from Canada. Bears have been linked to trichinellosis outbreaks in humans in Canada, and black bears are a subsistence food source for residents of the Dehcho region. In order to assess food safety risk it is important to monitor the prevalence of Trichinella spp. in both species of bear and their cohabiting mammalian food sources.

Serum biochemistry, serology, and parasitology of boreal caribou (Rangifer tarandus caribou) in the Northwest Territories, Canada.

Boreal caribou (Rangifer tarandus caribou) are an ecologically and culturally important wildlife species and now range almost exclusively in the boreal forests of Canada, including the Northwest Territories, northern Alberta, and British Columbia. Boreal caribou are threatened throughout their Canadian range because of direct and indirect natural and anthropogenic factors. In the Northwest Territories, however, they have a continuous range that overall has not yet been subjected to the same degree of anthropogenic habitat fragmentation and degradation that has occurred elsewhere in Canada. To monitor the health of boreal caribou populations and individuals, we collected blood from 104 adult, female boreal caribou captured between March 2003 and February 2006 and measured serum biochemical parameters. Serum creatinine was higher in pregnant than in nonpregnant caribou. Several biochemical parameters differed among years, but they tended to be similar to those reported for reindeer. Serum antibodies were found to an alphaherpesvirus, Toxoplasma gondii, and to the Mycobacterium avium subspecies paratuberculosis in 37.5, 2.9, and 1.3% of boreal caribou, respectively. Fecal samples were collected from 149 boreal caribou, and Cryptosporidium sp. oocysts, Giardia sp. cysts, trichostrongyle ova, dorsal-spined nematode larvae, cestode ova, and Eimeria sp. were found. Trypanosoma sp. was detected in the blood of 72.1% of boreal caribou. Eimeria sp., Cryptosporidium sp., and Giardia sp. have not been previously reported in boreal caribou.

Amphibian chytrid fungus and ranaviruses in the Northwest Territories, Canada.

Pathogens can cause serious declines in host species, and knowing where pathogens associated with host declines occur facilitates understanding host-pathogen ecology. Suspected drivers of global amphibian declines include infectious diseases, with 2 pathogens in particular, Batrachochytrium dendrobatidis (Bd) and ranaviruses, causing concern. We explored the host range and geographic distribution of Bd and ranaviruses in the Taiga Plains ecoregion of the Northwest Territories, Canada, in 2007 and 2008. Both pathogens were detected, greatly extending their known geographic distributions. Ranaviruses were widespread geographically, but found only in wood frogs. In contrast, Bd was found at a single site, but was detected in all 3 species of amphibians in the survey area (wood frogs, boreal chorus frogs, western toads). The presence of Bd in the Northwest Territories is not congruent with predicted distributions based on niche models, even though findings from other studies at northern latitudes are consistent with those same models. Unexpectedly, we also found evidence that swabs routinely used to collect samples for Bd screening detected fewer infections than toe clips. Our use and handling of the swabs was consistent with other studies, and the cause of the apparent lack of integrity of swabs is unknown. The ranaviruses detected in our study were confirmed to be Frog Virus 3 by sequence analysis of a diagnostic 500 bp region of the major capsid protein gene. It is unknown whether Bd or ranaviruses are recent arrivals to the Canadian north. However, the genetic analyses required to answer that question can inform larger debates about the origin of Bd in North America as well as the potential effects of climate change and industrial development on the distributions of these important amphibian pathogens.