Mitochondrial DNA and microsatellite DNA variation in domestic reindeer (Rangifer tarandus tarandus) and relationships with wild caribou (Rangifer tarandus granti, Rangifer tarandus groenlandicus, and Rangifer tarandus caribou)

Reindeer (Rangifer tarandus tarandus) in Alaska are semidomestic livestock descended from 1280 animals introduced from Siberia, Russia, approximately 100 years ago. Genetic variation at 18 microsatellite DNA loci and the cytochrome b gene of mitochondrial DNA (mtDNA) was quantified in reindeer from Alaska, Siberia (Russia), and Scandinavia and compared with wild North American caribou. Mean sequence divergence among 15 mtDNA haplotypes in reindeer was 0.007 substitutions per nucleotide site, and reindeer mtDNA is polyphyletic with caribou mtDNA. Microsatellite allele and mtDNA haplotype frequencies are similar between Alaskan and Russian reindeer and differentiated between these and Scandinavian reindeer. The frequencies of microsatellite alleles and mtDNA haplotypes are different in reindeer and wild caribou (Rangifer tarandus granti, Rangifer tarandus groenlandicus, and Rangifer tarandus caribou). Alaskan reindeer have maintained a genetic variation comparable to that in Russia and differentiated from that of wild caribou, >100 years after their introduction to Alaska.     

Genetic variation in domestic reindeer and wild caribou in Alaska

Reindeer ( Rangifer tarandus tarandus ) were introduced into Alaska 100 years ago and have been maintained as semidomestic livestock. They have had contact with wild caribou ( R. t. granti ) herds, including deliberate crossbreeding and mixing in the wild. Reindeer have considerable potential as a domestic animal for meat or velvet antler production, and wild caribou are important to subsistence and sport hunters. Our objective was to quantify the genetic relationships of reindeer and caribou in Alaska. We identified allelic variation among five herds of wild caribou and three herds of reindeer with DNA sequencing and restriction enzymes for three loci: a DQA locus of the major histocompatibility complex ( Rata-DQA1 ), K-casein and the D-loop of mitochondrial DNA. These loci are of interest because of their potential influence on domestic animal performance and the fitness of wild populations. There is considerable genetic variation in reindeer and caribou for all three loci, including five, three and six alleles for DQA , K-casein and D-loop respectively. Most alleles occur in both reindeer and caribou, which may be the result of recent common ancestry or genetic introgression in either direction. However, allele frequencies differ considerably between reindeer and caribou, which suggests that gene flow has been limited.     

Evidence of alphaherpesvirus infections in Alaskan caribou and reindeer

Background  

The reindeer (Rangifer tarandus tarandus) industry in Alaska began with animals imported from Siberia (Russia) in the 1890's. Cervid herpes virus 2 (CvHV2) is endemic in reindeer in Scandinavia. We sought to determine if the same virus, or similar herpesviruses, were circulating in Alaskan reindeer and caribou (Rangifer tarandus granti). Serum samples from 292 reindeer were collected during annual reindeer handlings (1988-2005) near Nome, Alaska. In 2005, swab samples were collected from 40 calves from this herd, near Nome, Alaska. In 2007, ocular and nasal swab samples were collected from 30 apparently healthy reindeer calves near Wales, Alaska. Samples of plasma and white blood cells were collected from three Alaskan caribou herds, Mulchatna (n = 24), Teshekpuk (n = 34) and the Western Arctic (n = 87) in 2009.     

Genetic polymorphism of the serum transferrins of the northern reindeer (Rangifer tarandus L.) of northwestern Siberia]

On the basis of the examination of random samples of seven populations of reindeer inhabiting the Montane-Taiga Zone and of nine population inhabiting the Tundra Zone of the Magadan Region 8 alleles of transferrin locus described earlier (TfA, TfC, TfE, TfG, TfH, TfJ, TfK and TfM) were identified and the ninth hitherto unknown allele (TfN) was discovered. Gene concentrations of all these alleles in populations studies were determined. The reindeer of the North-East of Siberia differ in frequencies of Tf alleles from those of Norway and, apparently, also from the reindeer inhabiting the northern regions of the European part of the USSR and from the American caribou. The allele TfK is possibly associated with the resistance of reindeer to necrobacteriosis.     

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

Defining genetic populations and detecting hybridization with introduced or domestic taxa are two major concerns for the conservation of population-level diversity. We studied the genetic population structure of large, migratory caribou herds (Rangifer tarandus granti) on Alaska’s North Slope and their potential hybridization with introduced domestic reindeer (R. t. tarandus). Using a population genetics approach, we determined: (1) whether the four caribou herds could be differentiated; (2) how distance and population size appear to drive genetic population structure; and (3) how contact with reindeer has affected the genetic identity of herds. Samples from four caribou herds (n = 245) and reindeer (n = 67) were analyzed at 19 microsatellite loci. We found that North Slope caribou are isolated by distance, with no differentiation among herd pairs except for the most geographically distant herds (F _st  = 0.003, Jost’s D = 0.023; P-values < 0.001). We detected reindeer-caribou admixture in all populations except Kodiak Island, including 8 % of individuals in caribou herds and 14 % of individuals in Seward Peninsula reindeer herds. However, considering the stable or increasing trend in North Slope herds, reindeer introgression has had no apparent deleterious effect on herd demographics. Our findings indicate long-term genetic exchange among North Slope caribou herds when their ranges overlap, and suggest that herd size may influence susceptibility to reindeer introgression. As North Slope herd ranges are increasingly altered by industrial development, this study can provide a baseline for detecting potential future impacts to what are currently large, diverse, and naturally evolving herds.     

Linkages between large‐scale climate patterns and the dynamics of Arctic caribou populations

Recent research has linked climate warming to global declines in caribou and reindeer (both Rangifer tarandus) populations. We hypothesize large‐scale climate patterns are a contributing factor explaining why these declines are not universal. To test our hypothesis for such relationships among Alaska caribou herds, we calculated the population growth rate and percent change of four arctic herds using existing population estimates, and explored associations with indices of the Arctic Oscillation (AO) and the Pacific Decadal Oscillation (PDO). The AO, which more strongly affects eastern Alaska, was negatively associated with the population trends of the Porcupine Caribou Herd and Central Arctic Herd, the easternmost of the herds. We hypothesize that either increased snowfall or suboptimal growing conditions for summer forage plants could explain this negative relationship. Intensity of the PDO, which has greatest effects in western Alaska, was negatively associated with the growth rate of the Teshekpuk Caribou Herd in northwestern Alaska, but the Western Arctic Herd in western Alaska displayed the opposite trend. We suggest that the contrasting patterns of association relate to the spatial variability of the effects of the PDO on western and northwestern Alaska. Although predation and winter range quality have often been considered the primary causes of population variation, our results show that large‐scale climate patterns may play an important role in caribou population dynamics in arctic Alaska. Our findings reveal that climate warming has not acted uniformly to reduce caribou populations globally. Further research should focus on the relative importance of mechanisms by which climate indices influence caribou population dynamics.     

Microsatellite DNA evidence for genetic drift and philopatry in Svalbard reindeer

Mainland populations of Arctic reindeer and caribou Rangifer tarandus often undergo extensive movements, whereas populations on islands tend to be isolated and sedentary. To characterize the genetic consequences of this difference, levels of genetic diversity and subdivision of Svalbard reindeer (R. t. platyrhynchus) from two adjacent areas on Nordenskjiöldland, Spitsbergen were estimated using data from up to 14 microsatellites. The mean number of alleles per locus in Svalbard reindeer was 2.4 and mean expected heterozygosity per locus was 0.36. The latter value was significantly lower than in Canadian caribou and Norwegian reindeer but higher than in some other cervid species. Large samples of females (n = 743) and small samples of males (n = 38) from two sites ≈ 45 km apart showed genetic subdivision, which could be due to local population fluctuations or limited gene flow. To our knowledge, this is the first study to report significant differentiation at microsatellite loci in Rangifer at such short geographical distances. Neither population showed genetic evidence for recent population bottlenecks when loci unbiased with respect to heterozygosity were analysed. In contrast, false signals of a recent bottleneck were detected when loci upwardly biased with respect to heterozygosity were analysed. Thus, Svalbard reindeer appeared to conform to the paradigm of island populations made genetically depauperate by genetic drift.     

Population genetics of the native caribou (Rangifer tarandus groenlandicus) and the semi-domestic reindeer (Rangifer tarandus tarandus) in Southwestern Greenland: Evidence of introgression

Over the past centuries the native caribou ofWest Greenland has gone through extensive population size fluctuations, with reductionsas great as 90% in less than 20 years.Norwegian semi-domestic reindeer wereintroduced to the Nuuk area in 1952 because ofthe small number of caribou in Greenland.Although the reindeer and caribou wereinitially kept separated, mixing has occurredsince the 1970's. We investigated the genotypicstructure of caribou and reindeer in South-westGreenland, using five polymorphicmicrosatellite markers isolated from cattle,sheep, goat and red deer. A total of ninetysamples were collected, which included samplesfrom caribou of four different regions andsamples from two different reindeer herds.Based on the genetic variation of the fivemarkers, our results shows that the caribou andthe reindeer populations in the six regionssampled are genetically differentiated withineach group and the two subspecies aredifferentiated from each other. A likelyexplanation for the genetic isolation of thepopulations investigated is that naturalbarriers (glaciers and wide fjords) exists inthe area. Furthermore we found that introducedNorwegian domestic reindeer hybridized with thenative Greenlandic caribou in two areasneighbouring Nuuk.     

Temporal and structural genetic variation in reindeer (Rangifer tarandus) associated with the pastoral transition in Northwestern Siberia

Just as the domestication of livestock is often cited as a key element in the Neolithic transition to settled, the emergence of large‐scaled reindeer husbandry was a fundamental social transformation for the indigenous peoples of Arctic Eurasia. To better understand the history of reindeer domestication, and the genetic processes associated with the pastoral transition in the Eurasian Arctic, we analyzed archaeological and contemporary reindeer samples from Northwestern Siberia. The material represents Rangifer genealogies spanning from 15,000 years ago to the 18th century, as well as modern samples from the wild Ta?myr population and from domestic herds managed by Nenetses. The wild and the domestic population are the largest populations of their kind in Northern Eurasia, and some Nenetses hold their domestic reindeer beside their wild cousins. Our analyses of 197 modern and 223 ancient mitochondrial DNA sequences revealed two genetic clusters, which are interpreted as representing the gene pools of contemporary domestic and past wild reindeer. Among a total of 137 different mitochondrial haplotypes identified in both the modern and archaeological samples, only 21 were detected in the modern domestic gene pool, while 11 of these were absent from the wild gene pool. The significant temporal genetic shift that we associate with the pastoral transition suggests that the emergence and spread of reindeer pastoralism in Northwestern Siberia originated with the translocation and subsequent selective breeding of a special type of animal from outside the region. The distinct and persistent domestic characteristics of the haplotype structure since the 18th century suggests little genetic exchange since then. The absence of the typical domestic clade in modern nearby wild populations suggests that the contemporary Nenets domestic breed feature an ancestry from outside its present main distribution, possibly from further South.     

Genetic consequences of a demographic bottleneck in the Scandinavian arctic fox

Demographic bottlenecks can result in a loss of genetic variation due to the bottleneck effect and subsequent genetic drift. The arctic fox population in Scandinavia went through a severe demographic bottleneck in the early 20th century, and is today classified as critically endangered. In this study, we investigated the pre-bottleneck genetic variation in Scandinavia and compared it to modern samples from Scandinavia and North Russia. Variation in the mtDNA control region and five microsatellite loci was examined through ancient DNA analysis on museum specimens. The microsatellite data from the museum specimens was further used to simulate the expected effect of the bottleneck. The arctic foxes in Scandinavia have lost approximately 25% of the microsatellite alleles and four out of seven mtDNA haplotypes. The results also suggest that the genetic differentiation between North Russia and Scandinavia has doubled over the last 100 years. However, the level of heterozygosity was significantly higher than expected from the simulations. This highlights both the advantage of using museum specimens and the importance of generating specific predictions in conservation genetics.     

Polymorphism of trinucleotide repeats at loci FRAXA and FRAXE in the population of Tomsk

Polymorphism of CGG and GCC trinucleotide repeats, whose expansions at the FRAXA and FRAXE loci have been identified as causative mutations in two forms of mental retardation, was studied in Slavic population of Tomsk. At the FRAXA locus a total of 31 allelic variants ranging from 8 to 56 copies of CGG repeat with two modal classes of 28-29 and 18-20 repeat units (with the frequencies of 24.6 and 11.5% respectively) were revealed. Compared to other populations, this locus was characterized by unusually high frequency of intermediate alleles with the sizes of more than 40 CGG repeat units (12.4%). Since intermediate repeats of the FRAXA locus were more prone to instability than normal alleles, it was suggested that Slavic population of Siberia had higher risk of the development of FMR1 dynamic mutations, giving rise to the Martin-Bell syndrome. The FRAXE allele frequency distribution was demonstrated to be normal with 18 allelic variants ranging from 9 to 27 GCC repeat units. In the population of Tomsk this locus had higher than in other populations frequency (26.7%) of short (less than 15 repeat units in size) alleles. In addition, in the Tomsk population both loci were characterized by high level of heterozygosity and low frequencies of modal allele classes. These results can be explained by the high level of outbreeding typical of the population of Siberia.     

Prion protein genes in caribou from Alaska

Prion protein genes were sequenced in free-ranging Alaska caribou (Rangifer tarandus grantii). Caribou prion alleles are identical or nearly so to those of wapiti, white-tailed deer, and mule deer. Five single-nucleotide polymorphisms were detected with substitutions at residues 2 (V-->M), 129 (G-->S), 138 (S-->N), 146 (N-->N), and 169 (V-->M). The 138N codon had been previously reported only in prion pseudogenes of other cervids. In caribou, the 138S and 138N alleles are present at frequencies of approximately 0.7 and 0.3, respectively, and they are seen in both homozygotes and heterozygotes of three geographically separated herds, each a component of the continental metapopulation. Genetics seems to permit the spread of chronic wasting disease from middle-latitude deer to high-latitude caribou in North America.     

Population structure over a broad spatial scale driven by nonanthropogenic factors in a wide‐ranging migratory mammal,Alaskan caribou

Wide‐ranging mammals face significant conservation threats, and knowledge of the spatial scale of population structure and its drivers is needed to understand processes that maintain diversity in these species. We analysed DNA from 655 Alaskan caribou (Rangifer tarandus granti) from 20 herds that vary in population size, used 19 microsatellite loci to document genetic diversity and differentiation in Alaskan caribou, and examined the extent to which genetic differentiation was associated with hypothesized drivers of population subdivision including landscape features, population size and ecotype. We found that Alaskan caribou are subdivided into two hierarchically structured clusters: one group on the Alaska Peninsula containing discrete herds and one large group on the Mainland lacking differentiation between many herds. Population size, geographic distance, migratory ecotype and the Kvichak River at the nexus of the Alaska Peninsula were associated with genetic differentiation. Contrary to previous hypotheses, small Mainland herds were often differentiated genetically from large interconnected herds nearby, and genetic drift coupled with reduced gene flow may explain this pattern. Our results raise the possibility that behaviour helps to maintain genetic differentiation between some herds of different ecotypes. Alaskan caribou show remarkably high diversity and low differentiation over a broad geographic scale. These results increase information for the conservation of caribou and other migratory mammals threatened by population reductions and landscape barriers and may be broadly applicable to understanding the spatial scale and ecological drivers of population structure in widespread species.     

Genetic analyses reveal independent domestication origins of Eurasian reindeer

Although there is little doubt that the domestication of mammals was instrumental for the modernization of human societies, even basic features of the path towards domestication remain largely unresolved for many species. Reindeer are considered to be in the early phase of domestication with wild and domestic herds still coexisting widely across Eurasia. This provides a unique model system for understanding how the early domestication process may have taken place. We analysed mitochondrial sequences and nuclear microsatellites in domestic and wild herds throughout Eurasia to address the origin of reindeer herding and domestication history. Our data demonstrate independent origins of domestic reindeer in Russia and Fennoscandia. This implies that the Saami people of Fennoscandia domesticated their own reindeer independently of the indigenous cultures in western Russia. We also found that augmentation of local reindeer herds by crossing with wild animals has been common. However, some wild reindeer populations have not contributed to the domestic gene pool, suggesting variation in domestication potential among populations. These differences may explain why geographically isolated indigenous groups have been able to make the technological shift from mobile hunting to large-scale reindeer pastoralism independently.     

Global declines of caribou and reindeer

Caribou and reindeer herds are declining across their circumpolar range, coincident with increasing arctic temperatures and precipitation, and anthropogenic landscape change. Here, we examine the mechanisms by which climate warming and anthropogenic landscape change influence caribou and reindeer population dynamics, namely changes in phenology, spatiotemporal changes in species overlap, and increased frequency of extreme weather events, and demonstrate that many caribou and reindeer herds show demographic signals consistent with these changes. While many caribou and reindeer populations historically fluctuated, the current, synchronous population declines emphasize the species' vulnerability to global change. Loss of caribou and reindeer will have significant, negative socioeconomic consequences for northern indigenous cultures.     

Arctic fisheries catches in Russia, USA, and Canada: baselines for neglected ecosystems

The Amerasian Arctic, covering northern Siberia (Russia), Arctic Alaska (USA), and the Canadian Arctic, extends over seven coastal Large Marine Ecosystems and makes up the seasonally ice-free part of FAO Statistical Area 18 (Arctic Sea). Historically, the harsh climate has limited marine fisheries (here excluding marine mammal hunting) to small-scale operations conducted mainly in estuaries and river deltas. Most of the catches have traditionally not been reported to FAO, with the result that total catch estimated here from 1950 to 2006 is 75 times higher than the sum of the catches reported for FAO 18 (Arctic). Catches were reconstructed from data on fishing communities in Canada and Alaska, and from various government and non-government sources for Siberia. Based on national data supplied to FAO since 1950, catches have been reported as 12,700 t in toto (reported on behalf of the former Soviet Union). This compares with our reconstructed catches of over 950,000 t, i.e., 770,000, 89,000, and 94,000 t by Russia, USA, and Canada, respectively for the same time period. The reconstructed catch (mainly whitefishes in Siberia, various salmonids in Alaska, and Arctic char in Canada) was 24,100 t year⁻¹ in 1950, but declined to 10,200 t year⁻¹ by the mid-2000s. Reasons for these trends are discussed by country, along with sources of uncertainty (particularly large for Siberia). Catches were allocated to Large Marine Ecosystems to present ecosystem-relevant baselines for the impact of fisheries on the Arctic, which can be expected to increase, as industrial fisheries move into a warming Arctic following the invasion of boreal species, unless countries apply precautionary ecosystem-based management approaches.     

Variation of short tandem repeats within and between species belonging to the Canidae family

Frequency distribution and allele size in 20 canine microsatellite loci were analyzed in 33 flat-coated retrievers, 32 dachshunds, 10 red foxes, and 10 Arctic foxes. Overall, the major difference between the two dog breeds was the relative allele frequencies rather than the size ranges of alleles at the individual locus. The average heterozygosity within the two dog breeds was not significantly different. Since the average heterozygosity at several polymorphic loci is a relative measure of heterogeneity within the population, analysis of heterozygosity within microsatellite loci is suggested as a measure for the diversity of populations. Eighty percent (16 of 20) of the canine microsatellite primer pairs amplified corresponding loci in the two fox species. This reflects a very high sequence conservation within the Canidae family relative to findings in, for instance, the Muridae family. This indicates that it will be possible to utilize the well-characterized fox karyotype instead of the dog karyotype as a step towards physical mapping of the dog genome. Analysis of exclusion power and probabilities of genetic identity between unrelated animals by use of the seven most informative loci demonstrated that it will be possible to assemble a panel of microsatellite loci that is effective for parentage analysis in all breeds.     

The genetic structure of populations of Chuckotka Peninsula Eskimos and Chuckchi based on study of 13 loci of serum and erythrocyte proteins and enzymes

The Eskimos and Chuckchi of the Chuckotka Peninsula were studied at 13 loci of serum and erythrocyte proteins and enzymes by electrophoresis. Six loci-including albumin, transferrin, carbonic anhydrase I and II, monoamine oxidase, and superoxide dismutase-were monomorphic in the studied populations. The mean frequencies of alleles in nine polymorphic loci of Chuckotka Eskimos and Chuckchi, Eskimos of Alaska, Canada, and Greenland, some Mongoloid populations of Siberia, American Indians, and Lapps of circumpolar areas of Western Europe were obtained. The genetic distances between these populations were calculated. The Eskimos of Chuckotka were closest to the Alaskan Eskimos. The relative heterozygosity of Chuckotka Eskimos was calculated and was the highest in Chuckchi. The average heterozygosity in Eskimo populations increased in the following order, from least to greatest: Chuckotka Eskimos, St. Lawrence Island Eskimos, Alaskan Eskimos, Greenland Eskimos, and Canadian Eskimos. The average heterozygosity of the Chuckchi was similar to that of Western Hemisphere Eskimos.     

Strong founder effect in Drosophila pseudoobscura colonizing New Zealand from North America

The North American native species Drosophila pseudoobscura was first identified in New Zealand in the last few decades. Here, we have studied the genetic consequences of its spread across the Pacific Ocean. Using 10 microsatellites that are highly variable in North American populations, we found that the New Zealand population has substantially fewer alleles, a much lower average heterozygosity, and significantly different allele frequencies at these loci. We have discussed the relative sensitivity of these parameters for detecting the founding event. X-linked loci were more strongly differentiated between continents than autosomal loci, as reflected by larger changes in allele frequencies and greater reductions in numbers of alleles and average heterozygosity. The severity of the genetic diversity loss supports a scenario of a few D. pseudoobscura females being introduced to New Zealand from North America.