High genetic connectivity and introgression from domestic reindeer characterize northern Alaska caribou herds

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.

Pronounced Fidelity and Selection for Average Conditions of Calving Area Suggestive of Spatial Memory in a Highly Migratory Ungulate

A distinguishing characteristic of many migratory animals is their annual return to distinct calving (birthing) areas in the spring, yet the navigational mechanisms employed during migration that result in this pattern are poorly understood. Effective conservation of these species requires reliable delineation of such areas, quantifying the factors that influence their selection, and understanding the underlying mechanisms resulting in use of calving areas. We used barren-ground caribou (Rangifer tarandus granti) as a study species and identified calving sites of the Western Arctic Herd in Alaska using GPS collar data from 2010–2017. We assessed variability in calving areas by comparing spatial delineations across all combinations of years. To understand calving area selection at a landscape scale, we performed a resource selection analysis comparing calving sites to available locations across the herd’s range and incorporated time-varying, remotely sensed metrics of vegetation quality and quantity. We found that whereas calving areas varied from year to year, this annual variation was centered on an area of recurring attraction consistent with previous studies covering the last six decades. Calving sites were characterized by high-quality forage at the average time of calving, but not peak calving that year, and by a narrow range of distinct physiographic factors. Each year, calving sites were located on areas of above-average conditions based on our predictive model. Our findings indicate that the pattern of spring migration for pregnant females was to migrate to areas that consistently provide high-quality forage when averaged across years, and then upon arriving at this calving ground, refine selection using their perception of annually varying conditions that are driven by environmental stochasticity. We suggest that the well-documented and widespread pattern of fidelity to calving grounds by caribou is supportive of a navigational mechanism based on spatial memory at a broad scale to optimize foraging and energy acquisition at a critical life-history stage. The extent to which migrants depend on memory to reach their spring destinations has implications for the adaptability of populations to changing climate and human impacts.

Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1758): A novel approach using BovineHD BeadChip

Reindeer (Rangifer tarandus L. 1758) are an essential element of the Russian Far North, providing a significant source of nutrition for the representatives of 18 ethnicities. The species has wild and domestic forms, which are in constant interaction. The aim of our study was to characterize the genetic structure of domestic and wild reindeer populations, using a genome-wide bovine genotyping array (BovineHD BeadChip). The wild reindeer samples were obtained from the western Taymyr Peninsula population and from the taiga and tundra populations in the Sakha Republic (Yakutia). The domestic populations included the Evenk, Even, and Chukotka-Khargin breeds of Yakutia and the Nenets breed from the Nenets Autonomous district and Murmansk region. The level of genetic diversity was higher for the wild population. Analyzing Neighbor-Net tree, multidimensional scaling, and Structure results, we observed strong genetic population structure and clear differentiation between domestic and wild populations. All regional populations of domestic reindeer were clearly separated, while wild reindeer showed similar genetic backgrounds. Nevertheless, we found contrasting patterns in the genetic structure of the tundra and taiga reindeer, in accordance with their morphological and ecological differences. Thus, our study revealed a clear genetic differentiation between domestic and wild reindeer populations. It provides novel insights into the genetic diversity and structure of reindeer populations, to support resource utilization and aid in the development of genetic improvement strategies and conservation programs for this species.

Maintaining genetic integrity of coexisting wild and domestic populations: Genetic differentiation between wild and domestic Rangifer with long traditions of intentional interbreeding

This study investigates the genetic effect of an indigenous tradition of deliberate and controlled interbreeding between wild and domestic Rangifer. The results are interpreted in the context of conservation concerns and debates on the origin of domestic animals. The study is located in Northeastern Zabaĭkal'e, Russia at approximately 57 degrees North latitude. Blood and skin samples, collected from wild and domestic Rangifer, are analyzed for their mtDNA and microsatellite signatures. Local husbandry traditions are documented ethnographically. The genetic data are analyzed with special reference to indigenous understandings of the distinctions between local domestic types and wild Rangifer. The genetic results demonstrate a strong differentiation between wild and domestic populations. Notably low levels of mtDNA haplotype sharing between wild and domestic reindeer, suggest mainly male‐mediated gene flow between the two gene pools. The nuclear microsatellite results also point to distinct differences between regional domestic clusters. Our results indicate that the Evenki herders have an effective breeding technique which, while mixing pedigrees in the short term, guards against wholesale introgression between wild and domestic populations over the long term. They support a model of domestication where wild males and domestic females are selectively interbred, without hybridizing the two populations. Our conclusions inform a debate on the origins of domestication by documenting a situation where both wild and domestic types are in constant interaction. The study further informs a debate in conservation biology by demonstrating that certain types of controlled introgression between wild and domestic types need not reduce genetic diversity.

Reindeer introgression and the population genetics of caribou in southwestern Alaska

Alaska caribou (Rangifer tarandus granti) in southwestern Alaska are a poorly understood system, with differing descriptions of their regional population structure, population abundance that has varied greatly through time and instances of the release of domestic reindeer (R. t. tarandus) into their range. Here, we use 21 microsatellites and 297 individuals to investigate the genetic population structure of herds and examine for population bottlenecks. Then, using genetic characteristics of existing reindeer populations, we examine introgression into the wild caribou populations. Caribou of the area are genetically diverse (H E between 0.69 and 0.84), with diversity decreasing along the Alaska Peninsula (AP). Using G ST and Jost's D, we find extensive structuring among all herds; Migrate-n finds that AP herds share few effective migrants with other herds, with Southern AP and Unimak Island herds having the least. Bayesian clustering techniques are able to resolve all but Denali and Mulchatna caribou herds. Using a conservative assignment threshold of q reindeer ≥ 0.2, 3% of caribou show signs of domestic introgression. Denali herd has the most introgressed individuals (6.9%); those caribou herds that were historically adjacent to smaller reindeer herds, or were historically without adjacent herding, show no admixture. This domestic introgression persists despite the lack of managed reindeer in the region since the 1940s. Our results suggest that despite previous movement data indicating metapopulation-like dispersal in this region, there may be unknown barriers to reproduction by dispersing individuals. Finally, our results support findings that wild and domestic Rangifer can hybridize and show this introgression may persist dozens of generations after domestics are no longer present.