Birth date determines early calf survival in migratory caribou.

The decline of most caribou (Rangifer tarandus) populations underlines the need to understand the determinants of key demographic parameters. In migratory caribou, we have limited information on rates and drivers of pre-weaning mortality. We fitted 60 pregnant females of the Rivière-aux-Feuilles caribou herd with GPS camera collars to track the survival of calves from birth to weaning in 2016-2018. Over the three years, calf survival rate before weaning, i.e. to 01-Sep, approximately three months of age, was 0.63 (CI 0.50-0.77). Summer mortality risk was mainly influenced by calf birth date, with calves born earlier in the calving season having a lower mortality risk than those born later. Mortality also increased when calves experienced low or high temperature during calving. This study provides the first estimates of pre-weaning survival of migratory caribou calves in this herd, illustrating the value of new technologies to collect data otherwise difficult to obtain in widely distributed migratory populations. This approach can easily be extended to other large herbivores and predators. Our study brings new insights on how climate change may affect summer juvenile survival given the increased temperatures and faster changes in plant phenology expected in the future.

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights.

BACKGROUND: Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining. RESULTS: We have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recent R. tarandus genome assembly. Combining physical mapping and comparative genomics, it was possible to document chromosomal evolution among Cervidae and closely related bovids. CONCLUSIONS: Our results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies of Rangifer tarandus.

Genomic health is dependent on long-term population demographic history.

Current genetic methods of population assessment in conservation biology have been challenged by genome-scale analyses due to their quantitatively novel insights. These analyses include assessments of runs-of-homozygosity (ROH), genomic evolutionary rate profiling (GERP), and mutational load. Here, we aim to elucidate the relationships between these measures using three divergent ungulates: white-tailed deer, caribou, and mountain goat. The white-tailed deer is currently expanding, while caribou are in the midst of a significant decline. Mountain goats remain stable, having suffered a large historical bottleneck. We assessed genome-wide signatures of inbreeding using the inbreeding coefficient F and %ROH (FROH ) and identified evolutionarily constrained regions with GERP. Mutational load was estimated by identifying mutations in highly constrained elements (CEs) and sorting intolerant from tolerant (SIFT) mutations. Our results showed that F and FROH are higher in mountain goats than in caribou and white-tailed deer. Given the extended bottleneck and low Ne of the mountain goat, this supports the idea that the genome-wide effects of demographic change take time to accrue. Similarly, we found that mountain goats possess more highly constrained CEs and the lowest dN/dS values, both of which are indicative of greater purifying selection; this is also reflected by fewer mutations in CEs and deleterious mutations identified by SIFT. In contrast, white-tailed deer presented the highest mutational load with both metrics, in addition to dN/dS, while caribou were intermediate. Our results demonstrate that extended bottlenecks may lead to reduced diversity and increased FROH in ungulates, but not necessarily an increase in mutational load, probably due to the purging of deleterious alleles in small populations.

Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec.

The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision-making. Most caribou (Rangifer tarandus) populations have experienced significant recent declines throughout Québec, Canada, and are considered of concern, threatened or endangered. Here, we calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. We first calculated a caribou specific mutation rate, µ, by extracting orthologous genes from related ungulates and estimating the rate of synonymous mutations. Whole genome re-sequencing was then completed on 67 caribou: from these data we calculated nucleotide diversity, θ π and estimated the coalescent or ancestral effective population size (N e), which ranged from 12,030 to 15,513. When compared to the census size, N C, the endangered Gaspésie Mountain caribou population had the highest ancestral N e:N C ratio which is consistent with recent work suggesting high ancestral N e:N C is of conservation concern. In contrast, values of contemporary N e, estimated from linkage-disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary N e:N C ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based on this ratio. Interestingly, F varied only slightly between populations, and despite evidence of bottlenecks across the province, runs of homozygosity were not abundant in the genome. Tajima's D estimates mirrored the demographic models and current conservation status. Our study highlights how genomic patterns are nuanced and potentially misleading if viewed only through a contemporary lens; we argue a holistic conservation genomics view should integrate ancestral N e and Tajima's D into management decisions.

Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus).

BACKGROUND: Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species. RESULTS: From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip. CONCLUSION: This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.

Association of Environmental Factors with Seasonal Intensity of Erysipelothrix rhusiopathiae Seropositivity among Arctic Caribou.

Several caribou (Rangifer tarandus) populations have been declining concurrently with increases in infectious diseases in the Arctic. Erysipelothrix rhusiopathiae, a zoonotic bacterium, was first described in 2015 as a notable cause of illness and death among several Arctic wildlife species. We investigated epidemiologic and environmental factors associated with the seroprevalence of E. rhusiopathiae in the Arctic and found that seropositivity was highest during warmer months, peaking in September, and was highest among adult males. Summer seroprevalence increases tracked with the oestrid index from the previous year, icing and snowing events, and precipitation from the same year but decreased with growing degree days in the same year. Seroprevalence of E. rhusiopathiae varied more during the later years of the study. Our findings provide key insights into the influence of environmental factors on disease prevalence that can be instrumental for anticipating and mitigating diseases associated with climate change among Arctic wildlife and human populations.

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.

Combining stable isotopes, morphological, and molecular analyses to reconstruct the diet of free-ranging consumers.

Accurate estimates of animal diet composition are essential to untangle complex interactions in food webs. Biomarkers and molecular tools are increasingly used to estimate diet, sometimes alongside traditional dietary tracing methods. Yet only a few empirical studies have compared the outcomes and potential gains of using a combination of these methods, especially using free-ranging animals with distinct foraging preferences.We used stable isotopes, morphological, and molecular analyses to investigate the diet of free-ranging consumers with two distinct diet types, that is, carnivore and omnivore. By combining the three analytical methods to assess the diet of consumers during the same period, we aimed to identify the limits of each method and to assess the potential benefits of their combined use to derive diet estimates.Our results showed that the different methods led to a consistent diet description for carnivores, which have a relatively simple diet mixture, but their outcomes somewhat differed for omnivore, which have a more complex diet. Still, the combined use of morphological and molecular analyses enhanced the diversity of food sources detected compared to the use of a single method independently of diet types. Precision of diet estimates derived from stable isotope analyses was improved by the addition of priors obtained from morphological and molecular diet analyses of the same population.Although we used free-ranging animals without a known diet, our empirical testing of three of the most widely used methods of diet determination highlights the limits of relying over a single approach, especially in systems with few or no a priori information about the foraging habits of consumers. The choice of an appropriate approach of diet description should be a key step when planning dietary studies of free-ranging populations. We recommend using more than one dietary determination methods especially for species with complex diet mixtures.

Nitrogen allocation to offspring and milk production in a capital breeder.

Nitrogen (N) is a limiting nutrient for many herbivores, especially when plant availability and N content are low during the period of maternal investment, which is common for arctic ungulates. We used natural abundance of N isotopes to quantify allocation of maternal nitrogen to neonatal calves and milk in wild migratory caribou (Rangifer tarandus). We contrasted female-calf pairs from two herds in northern Quebec/Labrador, Canada: Rivière-George herd (RG; low population size with heavy calves) and the Rivière-aux-Feuilles herd (RAF; high population size and small calves). We assessed whether females of both herds relied on body protein or dietary N to produce the neonatal calf and milk at calving and weaning. Female caribou of both herds relied mostly on body N for fetal development. RAF females allocated less body N to calves than did RG females (92% vs. 95% of calf N), which was consistent with the production of calves that were 8% smaller in RAF than in RG. Allocation of body N to milk was also high for both herds, similar at calving for RAF and RG females (88% vs. 91% of milk N, respectively), but lower in RAF than RG females (95% vs. 99% of milk N) at weaning, which was consistent with a small but significantly greater reliance on dietary N supplies to support milk production at weaning. Female caribou used body protein stores to ensure a constant supply of N for fetal growth and milk production that minimized the effects of trophic mismatches on reproduction. The combination of migration and capital investment may therefore allow females to produce calves and attenuate the effects of both temporal and spatial mismatches between vegetation green-up and calf growth, which ultimately would reduce trophic feedbacks on population growth. Our data suggest that small changes in maternal allocation of proteins over the long period of gestation produce significant changes in calf mass as females respond to changes in resources that accompany changes in the size and distribution of the population.

Variables associated with Besnoitia tarandi prevalence and cyst density in barren-ground caribou (Rangifer tarandus) populations.

Besnoitia tarandi has been documented in free-ranging reindeer and caribou (Rangifer tarandus spp.) since 1922 throughout their arctic and subarctic ranges; however, very little is known about its epidemiology. We evaluated variables associated with B. tarandi prevalence and cyst density with the use of barren-ground caribou (Rangifer tarandus) from two migratory herds in northern Quebec: the Rivière-aux-Feuilles and the Rivière-George herds. Diagnosis of infection was made upon the microscopic observation of characteristic cysts in a formalin-fixed section of skin from the anterior aspect of the metatarsus. The density of cysts (number of B. tarandi cysts/mm(2)) was calculated in a section of the dermis extending from the epidermis of the skin to the base of the hair follicles and adnexal structures. Statistically significant associations between B. tarandi prevalence and cyst density, sex, age, and time of harvest were observed. Male caribou had a slightly higher prevalence compared to females, whereas cyst densities were similar between sexes. We found a nonlinear increase in the odds of infection by B. tarandi by age combined with the opposite trend for intensity of infection. Higher B. tarandi prevalence was observed in caribou sampled in the fall compared to June of the same year, suggesting that transmission is increased during the summer. Higher densities of cysts observed during the fall compared to June of the following year may be the result of the elimination of B. tarandi cysts from the dermis during the winter, or lower winter survival of heavily infected caribou. Comparisons of B. tarandi prevalence and density across herds should take into account these different variables.

Detection of Mycobacterium avium subspecies paratuberculosis in several herds of Arctic Caribou (Rangifer tarandus ssp.).

Mycobacterium avium subspecies paratuberculosis (MAP) is a common pathogen in domestic ruminants that causes granulomatous inflammation of the small intestine leading to emaciation and wasting. Clinical disease (Johne's disease) is also reported for several wild ruminant species. Between 2007 and 2009 we collected 561 fecal samples from caribou (Rangifer tarandus ssp.) representing 10 herds of migratory caribou, two herds of caribou from Greenland, and three populations of boreal woodland caribou. Feces were tested for MAP by bacterial culture and PCR targeting the IS900 insertion sequence. In total, 31 samples from eight different populations representing all three ecotypes were found positive for MAP by PCR, with one sample from the Rivière-aux-Feuilles herd also being culture positive for the type II (cattle) strain. The proportion of positive animals was particularly high in the Akia-Maniitsoq herd in Greenland, and Rivière-aux-Feuilles and Riviè re-George herds in northeastern Canada (23.4, 11.5, and 10.0%, respectively). Our results indicate that MAP is present in several caribou herds of different ecotypes in northern Canada and Greenland and that MAP circulates within wildlife populations that do not have ongoing contact with domestic livestock. The epidemiology, pathogenicity, and effects on the health of caribou in northern ecosystems remain unknown.

Comparison of gross visual and microscopic assessment of four anatomic sites to monitor Besnoitia tarandi in barren-ground caribou (Rangifer tarandus).

The objective of this study was to establish a standardized protocol to monitor Besnoitia tarandi prevalence and intensity in barren-ground caribou (Rangifer tarandus) herds by: 1) calculating the relative sensitivity and specificity of the gross visual assessment of four anatomical sites compared with microscopic evaluation, and 2) determining which of four anatomical sampling sites was the most sensitive for detecting B. tarandi cysts by microscopy. Sampled tissues consisted of the conjunctiva of the left eye and skin sections from the rostrum, metatarsus, and thigh from 312 harvested caribou. Diagnosis of infection with B. tarandi was based on observation of at least one cyst by microscopic examination. For each tissue, the maximal density of cysts (number of B. tarandi cysts/mm(2) in the section examined) was calculated for a measured area consisting of the dermis extending from the epidermis of the skin to the base of the hair follicles and adnexal structures. For the conjunctiva, the entire submucosa was evaluated. Gross visual evaluation markedly underestimated B. tarandi prevalence in caribou with a relative sensitivity ranging from 0.29 in the conjunctiva to 0.13 in the skin section from the thigh, whereas relative specificities ranged from 0.98 to 1.00. The metatarsus and rostrum skin sections had the highest probabilities of cyst detection of all four anatomical sampling sites. The metatarsus harbored significantly higher densities of B. tarandi cysts than the rostrum, thigh, or conjunctiva. In conclusion, microscopic evaluation of a skin section from the anterior aspect of the mid-third portion of the metatarsal region could be used as a standardized comparative indicator of density of B. tarandi infection in Rangifer.