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

The loss of genetic diversity is a challenge many species are facing, and genomics is a potential tool that can inform and prioritize decision making. Caribou populations have experienced significant recent declines throughout Québec, Canada, and some are considered threatened or endangered. We calculated the ancestral and contemporary patterns of genomic diversity of five caribou populations and applied a comparative framework to assess the interplay between demography and genomic diversity. We calculated a caribou specific mutation rate, μ, by extracting orthologous genes from related ungulates. Whole genome re-sequencing was completed on 67 caribou and genotype likelihoods were estimated. We calculated nucleotide diversity, θπ and estimated the coalescent or ancestral Ne, which ranged from 12,030 to 15,513. When compared to the census size, NC, the endangered Gaspésie Mountain caribou population had the highest Ne:NC ratio which is consistent with recent work suggesting high ancestral Ne:NC is of conservation concern. These ratios were highly correlated with genomic signatures (i.e. Tajima’s D) and explicit demographic model parameters. Values of contemporary Ne, estimated from linkage-disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary Ne:NC ratio. Importantly, conservation genetics theory would predict this population to be of less concern based on this ratio. Of note, F varied only slightly between populations, and runs of homozygosity were not abundant in the genome. Our study highlights how genomic patterns are nuanced and misleading if viewed only through a contemporary lens; a holistic view should integrate ancestral Ne and Tajima’s D into conservation decisions.

What do caribou eat? A review of the literature on caribou diet

Historically the study of diet caribou and reindeer (Rangifer tarandus (Gmelin, 1788)) has been specific to herds and few comprehensive circumpolar analyses of Rangifer diet exist. As a result, the importance of certain diet items may play an outsized role in the caribou diet zeitgeist, e.g., lichen. It is incumbent to challenge this notion and test the relevant importance of various diet items within the context of prevailing hypotheses. We provide a systematic overview of 30 caribou studies reporting caribou diet and test biologically relevant hypotheses about spatial and temporal dietary variation. Our results indicate that in the winter caribou primarily consume lichen, but in warmer seasons, and primary productivity is lower, caribou primarily consume graminoids and other vascular plants. In more productive environments, where caribou have more competitors and predators, consumption of lichen increased. Overall, our description of caribou diet reveals that caribou diet is highly variable, but in circumstances where they can consume vascular plants, they will. As climate change affects Boreal and Arctic ecosystems, the type and volume of food consumed by caribou has become an increasingly important focus for conservation and management of caribou.

Habitat Selection by Brown Bears with Varying Levels of Predation Rates on Ungulate Neonates

In northern Eurasia, large carnivores overlap with semi-domestic reindeer (Rangifer tarandus) and moose (Alces alces). In Scandinavia, previous studies have quantified brown bear (Ursus arctos) spring predation on neonates of reindeer (mostly in May) and moose (mostly in June). We explored if habitat selection by brown bears changed following resource pulses and whether these changes are more pronounced on those individuals characterised by higher predatory behaviour. Fifteen brown bears in northern Sweden (2010–2012) were fitted with GPS proximity collars, and 2585 female reindeers were collared with UHF transmitters. Clusters of bear positions were visited to investigate moose and reindeer predation. Bear kill rates and home ranges were calculated to examine bear movements and predatory behaviour. Bear habitat selection was modelled using resource selection functions over four periods (pre-calving, reindeer calving, moose calving, and post-calving). Coefficients of selection for areas closer to different land cover classes across periods were compared, examining the interactions between different degrees of predatory behaviour (i.e., high and low). Bear habitat selection differed throughout the periods and between low and high predatory bears. Differences among individuals’ predatory behaviour are reflected in the selection of habitat types, providing empirical evidence that different levels of specialization in foraging behaviour helps to explain individual variation in bear habitat selection.

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.

The age distribution in the Taimyr population wild northern deer (Rangifer Tarandus) in the first decades of 21 centuries

Objective: mathematical demography means to identify and evaluate the age distribution of male and female of Taimyr tundra reindeer in the first decade of the XXI century and future trends in demographic situation Taimyr population.Materials and methods. The base material for evaluating the current state of the population age structure Taimyr steel fishing representative sample of male and female wild deer (n = 10845 individuals) collected in the West, Central and Taimyr Putorana in 2001-2008., And the deer samples (n = 1569 individuals), the floor of which is unknown. Determination of individual animals from age and older (n = 9773 individuals) performed on histological sections of cutters according to the corresponding procedure. To repay the random deviations of sample data because of a lack of presence of immature animals (calves, yearlings, young 1-2 years) (selectivity of fishing is directed primarily at the production of individuals older than 3 years, why animals in different age groups in the samples is greater than there are in the population) applies a smoothing procedure. Then, positive deviation of the number of individuals in the same age group were leveled due to negative deviations in adjacent groups.Results. By smoothed age ranges of the field samples from 2001-2008 the current age distribution of Taimyr wild reindeer calculated and analyzed. The study showed that the theoretical current age distribution of males with realized breeding is 77.03, females - 80.56, in the combined groups of animals - 82.35%. The real population has 18-19 age generations of males and females. The reproductive core of males from 3 to 10 years old is 48.43%, individuals of age limit 11 years and older occupy 1.96% of this sex and age structure, calves and young animals for 1-2 years - 24.64%. For the reproductive part of females aged 3–15 years, the overall age distribution is 55.34%, and the proportion of juveniles and young animals, according to calculations, is determined in this part of the population at 25.16%. In the combined current age distribution, males, females: calves and young animals accounted for 27.72%, the sexually mature part with animals of older and age-specific ages - 54.63%.Conclusion. Demographic Taimir population modeling operation in the first decade of the XXI century long materials commercial samples collected at commercial points shown at current age distribution of the realized and reproduction conditions for existing commercial load males - 77.03 for females - 80.56 and for unified groups (males, females) - 82.4%. Meanwhile, the steady state and stable age distribution Taimyr tundra wild deer can reach a middle-level only when the fecundity of female reproductive generations with clean reproduction rate (R0) equal in population groupings 1.0