Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies.

Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the "EuroBeringian clade" formed by animals from Arctic Islands, Eurasia, and a few from North America and the "North American clade" formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future.

Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia.

Domestic reindeer (Rangifer tarandus) play a vital role in the culture and livelihoods of indigenous people across northern Eurasia. These animals are well adapted to harsh environmental conditions, such as extreme cold, limited feed availability and long migration distances. Therefore, understanding the genomics of reindeer is crucial for improving their management, conservation and utilisation. In this study, we have generated a new genome assembly for the Fennoscandian domestic reindeer with high contiguity, making it the most complete reference genome for reindeer to date. The new genome assembly was utilised to explore genetic diversity, population structure and selective sweeps in Eurasian Rangifer tarandus populations which was based on the largest population genomic dataset for reindeer, encompassing 58 individuals from diverse populations. Phylogenetic analyses revealed distinct genetic clusters, with the Finnish wild forest reindeer (Rangifer tarandus fennicus) standing out as a unique subspecies. Divergence time estimates suggested a separation of ~ 52 thousand years ago (Kya) between the northern European Rangifer tarandus fennicus and Rangifer tarandus tarandus. Our study identified four main genetic clusters: Fennoscandian, the eastern/northern Russian and Alaskan group, the Finnish forest reindeer, and the Svalbard reindeer. Furthermore, two independent reindeer domestication processes were inferred, suggesting separate origins for the domestic Fennoscandian and eastern/northern Russian reindeer. Notably, shared genes under selection, including retroviral genes, point towards molecular domestication processes that aided adaptation of this species to diverse environments.

High resilience in the Yamal-Nenets social-ecological system, West Siberian Arctic, Russia.

Tundra ecosystems are vulnerable to hydrocarbon development, in part because small-scale, low-intensity disturbances can affect vegetation, permafrost soils, and wildlife out of proportion to their spatial extent. Scaling up to include human residents, tightly integrated arctic social-ecological systems (SESs) are believed similarly susceptible to industrial impacts and climate change. In contrast to northern Alaska and Canada, most terrestrial and aquatic components of West Siberian oil and gas fields are seasonally exploited by migratory herders, hunters, fishers, and domesticated reindeer (Rangifer tarandus L.). Despite anthropogenic fragmentation and transformation of a large proportion of the environment, recent socioeconomic upheaval, and pronounced climate warming, we find the Yamal-Nenets SES highly resilient according to a few key measures. We detail the remarkable extent to which the system has successfully reorganized in response to recent shocks and evaluate the limits of the system's capacity to respond. Our analytical approach combines quantitative methods with participant observation to understand the overall effects of rapid land use and climate change at the level of the entire Yamal system, detect thresholds crossed using surrogates, and identify potential traps. Institutional constraints and drivers were as important as the documented ecological changes. Particularly crucial to success is the unfettered movement of people and animals in space and time, which allows them to alternately avoid or exploit a wide range of natural and anthropogenic habitats. However, expansion of infrastructure, concomitant terrestrial and freshwater ecosystem degradation, climate change, and a massive influx of workers underway present a looming threat to future resilience.

Adipose gene expression profiles reveal insights into the adaptation of northern Eurasian semi-domestic reindeer (Rangifer tarandus).

Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging conditions of northern Eurasia. Adipose tissues play a crucial role in northern animals by altering gene expression in their tissues to regulate energy homoeostasis and thermogenic activity. Here, we perform transcriptome profiling by RNA sequencing of adipose tissues from three different anatomical depots: metacarpal (bone marrow), perirenal, and prescapular fat in Finnish and Even reindeer (in Sakha) during spring and winter. A total of 16,212 genes are expressed in our data. Gene expression profiles in metacarpal tissue are distinct from perirenal and prescapular adipose tissues. Notably, metacarpal adipose tissue appears to have a significant role in the regulation of the energy metabolism of reindeer in spring when their nutritional condition is poor after winter. During spring, genes associated with the immune system are upregulated in the perirenal and prescapular adipose tissue. Blood and tissue parameters reflecting general physiological and metabolic status show less seasonal variation in Even reindeer than in Finnish reindeer. This study identifies candidate genes potentially involved in immune response, fat deposition, and energy metabolism and provides new information on the mechanisms by which reindeer adapt to harsh arctic conditions.

Detection of snow surface thawing and refreezing in the Eurasian Arctic with QuikSCAT: implications for reindeer herding.

Snow conditions play an important role for reindeer herding. In particular, the formation of ice crusts after rain-on-snow (ROS) events or general surface thawing with subsequent refreezing impedes foraging. Such events can be monitored using satellite data. A monitoring scheme has been developed for observation at the circumpolar scale based on data from the active microwave sensor SeaWinds on QuikSCAT (Ku-band), which is sensitive to changes on the snow surface. Ground observations on Yamal Peninsula were used for algorithm development. Snow refreezing patterns are presented for northern Eurasia above 60 degrees N from autumn 2001 to spring 2008. Western Siberia is more affected than Central and Eastern Siberia in accordance with climate data, and most events occur in November and April. Ice layers in late winter have an especially negative effect on reindeer as they are already weakened. Yamal Peninsula is located within a transition zone between high and low frequency of events. Refreezing was observed more than once a winter across the entire peninsula during recent years. The southern part experienced refreezing events on average four times each winter. Currently, herders can migrate laterally or north-south, depending on where and when a given event occurs. However, formation of ice crusts in the northern part of the peninsula may become as common as they are now in the southern part. Such a development would further constrain the possibility to migrate on the peninsula.

Long-Term Trends and Role of Climate in the Population Dynamics of Eurasian Reindeer.

Temperature is increasing in Arctic and sub-Arctic regions at a higher rate than anywhere else in the world. The frequency and nature of precipitation events are also predicted to change in the future. These changes in climate are expected, together with increasing human pressures, to have significant impacts on Arctic and sub-Arctic species and ecosystems. Due to the key role that reindeer play in those ecosystems, it is essential to understand how climate will affect the region's most important species. Our study assesses the role of climate on the dynamics of fourteen Eurasian reindeer (Rangifer tarandus) populations, using for the first time data on reindeer abundance collected over a 70-year period, including both wild and semi-domesticated reindeer, and covering more than half of the species' total range. We analyzed trends in population dynamics, investigated synchrony among population growth rates, and assessed the effects of climate on population growth rates. Trends in the population dynamics were remarkably heterogeneous. Synchrony was apparent only among some populations and was not correlated with distance among population ranges. Proxies of climate variability mostly failed to explain population growth rates and synchrony. For both wild and semi-domesticated populations, local weather, biotic pressures, loss of habitat and human disturbances appear to have been more important drivers of reindeer population dynamics than climate. In semi-domesticated populations, management strategies may have masked the effects of climate. Conservation efforts should aim to mitigate human disturbances, which could exacerbate the potentially negative effects of climate change on reindeer populations in the future. Special protection and support should be granted to those semi-domesticated populations that suffered the most because of the collapse of the Soviet Union, in order to protect the livelihood of indigenous peoples that depend on the species, and the multi-faceted role that reindeer exert in Arctic ecosystems.