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Abstract Background Since the 1950s, the Norwegian–Swedish Coldblooded trotter (NSCT) has been intensively selected for harness racing performance. As a result, the racing performance of the NSCT has improved remarkably; however, this improved racing performance has also been accompanied by a gradual increase in inbreeding level. Inbreeding in NSCT has historically been monitored by using traditional methods that are based on pedigree analysis, but with recent advancements in genomics, the NSCT industry has shown interest in adopting molecular approaches for the selection and maintenance of this breed. Consequently, the aims of the current study were to estimate genomic-based inbreeding coefficients, i.e. the proportion of runs of homozygosity (ROH), for a sample of NSCT individuals using high-density genotyping array data, and subsequently to compare the resulting rate of genomic-based F (FROH) to that of pedigree-based F (FPED) coefficients within the breed. Results A total of 566 raced NSCT were available for analyses. Average FROH ranged from 1.78 to 13.95%. Correlations between FROH and FPED were significant (P

In reindeer husbandry, animal breeding could offer tools for improving productivity by selection. The traits affecting meat production efficiency are primarily related to calf growth and survival, and to dam’s longevity and lifetime ability to raise heavy calves. Information on genetic (co)variation in these traits is scarce but needed in estimating the potential and effectiveness of selection as well as biological constraints. The objectives of the study were to estimate these genetic parameters from the data of an experimental reindeer herd at Kutuharju (Inari, Finland). Heritabilities (h2) and genetic correlations (rg) among the average daily gain of calves (ADG), dams’ age at maturity, individual fitness (λind) and the cumulative sum of her calves’ weaning weight over seven years (WW7) were studied with AS-Reml software using the dataset from the experimental herd. The pedigree included also sire information to allow the separation of the maternal effects. Direct and maternal heritabilities of ADG were moderate (0.24±0.09 and 0.18±0.05, respectively) and the direct-maternal correlation was highly negative (-0.73±0.17). Indeed, selection on growth necessitates information on both calf and dam. The genetic correlation of growth with birth date and birth weight could not be detected with the data. The age at maturity and λind had a small heritable component (0.07±0.12 and 0.10±0.06, respectively), whereas the heritability value of WW7 was 0.23±0.07. Reindeer herders’ empirical selection on calf’s autumn weight favours fast growth (rg between growth and autumn weight = 0.35±0.24). Dam’s weight in her first autumn was strongly correlated with her lifetime production expressed by her individual fitness (rg = 0.71±0.23) and the cumulative sum of her calves’ weaning weight (rg = 0.63±0.12). Hence, the early information on the dam (her weight in her first autumn or her first calf’s autumn weight) works as useful selection criteria for the traits related to lifetime production.

The factors causing variation in birth date and birth weight were analysed from the data from an experimental reindeer herd consisting of 1136 calves with parental information. The traits had coefficient of variation of 37 and 14%, respectively. The variation in both traits was affected by year and sex (male calves heavier) and by management factors, such as the age distribution of females and males. Early calving results from the use of older breeding males and is most apparent in prime age females. In both traits the heritability was moderate (0.23 and 0.24) with a high proportion of maternal genetic variation (0.23) in birth weight. The North Atlantic Oscillation (NAO) indices, summarizing the major weather conditions prior to rut, explained part of the annual variation in the traits. The amount of total genetic variation in relation to trait mean, or the evolvability, was 21% in birth date and 10% in birth weight indicating that selection could successfully be used to improve herd productivity and that the traits have substantial potential for adapting to possible changing environmental conditions. The results on genetic correlations imply that selection on calf’s birth weight leads on one hand to calves being born earlier and on the other hand to dams with later parturition.

In most mammals dispersal is male-biased and in many polygynous ungulates female philopatry and matrilineal grouping involve small-scale genetic structure. We have through sex-related differences in microsatellite allele distribution addressed sex-biased dispersal in a spatially expanding northern ungulate population. The Norwegian red deer population (Cervus elaphus atlanticus) has the last hundred years grown substantially and expanded spatially after a major decline from 300 to 100 years ago. Previous Bayesian analyses suggest a present division of genetic variation into five geographically separated subpopulations. Among these subpopulations the overall Fst values were 0.067 (SE=0.014) for males and 0.094 (SE=0.017) for females. Pairwise Fst values were significantly higher for females than males, demonstrating a stronger genetic structure among females, and that dispersal has been lower in females than males. Accordingly, a higher number of male than female first generation dispersers were identified among the five subpopulations using Bayesian assignment with prior population information, but significantly so only with relaxed stringency levels of assignment. The identified male-biased dispersal distances varied from 30 to 300 kilometers suggesting male biased dispersal on a large scale in red deer.

Displacement is the effect most often predicted when recreational activities in wild reindeer (Rangifer tarandus tarandus) areas are discussed. Wild reindeer in Blefjell (225 km2) are exposed to humans more frequently than in Hardangervidda (8200 km2), from which the Blefjell herd originate. We recorded fright and flight response distances of groups of reindeer in both herds to a person directly approaching them on foot or skis during winter, summer, and autumn post-hunting and rutting season in 2004-2006. The response distances sight, alert, flight initiation and escape were shorter in Blefjell than in Hardangervidda while the probability of assessing the observer before flight tended to be greater in Blefjell. To test whether these results could be due to habituation or genetic influence of semi-domestic reindeer previously released in the Blefjell region, we compared the genetic variation of the Blefjell reindeer with previously reported variation in semi-domestic reindeer and in the wild reindeer from Hardangervidda. Microsatellite analyses revealed closer genetic ancestry of the Blefjell reindeer to the wild Hardangervidda reindeer and not to the semi-domestic reindeer at both the herd and the individual level. We conclude that the decreased flight responses in Blefjell reindeer appear to be a habituation response to frequent human encounters rather than traits inherited from a semi-domestic origin.

Reindeer and caribou was probably the key species for the human immigration and colonization in the Arctic and sub-Arctic by the retreat of the ice in the last glacial period. The close connection between human and reindeer has contributed to great interest and variation in reindeer taxonomy and origin. Through the history several both species, subspecies and types of reindeer and caribou have been described. The early taxonomy of the species is marked by comparisons of individual specimen using traits as body size, skin colour or antler formations - characteristics known to be highly variable and subjected to environmental and nutritional level. During the mid 1900s the taxonomy was more based on variation of morphological traits among populations by analysing a large series of specimens representative of the various geographic populations and a consensus of classification of several subspecies, all belonging to the same species, evolved. During late 1900 the development of modern molecular techniques procured tools for revealing genetic structure of populations reflecting different origin and isolation rather than environmental influences. The genetic structure revealed a major genetic dichotomy between American woodland caribou on the one hand and all other types of reindeer and caribou on the other which gave evidence that the ancestors of present woodland caribou had survived and evolved in ice free refugium south to the glacier in North America and the ancestors of all other types of reindeer and caribou had evolved separated from these in refugium in Eurasia and Beringia. The ancestors of present reindeer in Scandinavia appear furthermore to have evolved from different populations separated during the last glaciation period and the colonization and origin of present wild and domestic reindeer will be discussed in this perspective. Taksonomi og opprinnelse til rein Abstract in Norwegian / Sammendrag: Rein og caribou har hatt stor betydning for det moderne menneskets utvikling og kolonisering av nordlige Eurasia og Amerika etter siste istid. Den nære sammenhengen mellom mennesker og rein har bidratt til stor interesse og variasjon i oppfatningen av reinens taksonomi og opprinnelse. Et utall av både arter, underarter og raser av rein er beskrevet opp gjennom historien. Tidlig taksonomi av rein bar preg av å være basert på enkeltobservasjoner og på morfologiske karakterer som kroppsstørrelse, pelsfarge og størrelse og form på gevir, karakterer som i stor grad påvirkes av miljø og næringsforhold. Først på midten av 1900 tallet ble taksonomien i større grad basert på ulike morfologiske trekk som viste variasjon mellom bestander av rein, og en fikk bl.a. en forståelse av at alle underarter og former av rein og caribou tilhørte samme art. Med utviklingen av den moderne molekylærbiologien på slutten av 1900-tallet fikk en tilgang til verktøy som avdekket genetiske strukturer som reflekterer ulik opprinnelse og utvikling mer enn miljømessig påvirkning. Den genetiske strukturen som ble avdekket, viste liten overensstemmelse med oppdelingen i underarter som var basert på morfologiske trekk. Molekylærgenetiske struktur viser et hovedskille mellom amerikansk woodland caribou på den ene siden og all annen rein og caribou på den andre siden, noe som reflekterer at forfedrene til woodland caribou levde og utviklet seg i isfrie områder sør for iskanten i Nord-Amerika, mens forfedrene til andre typer rein levde atskilt fra disse i isfrie områder i Eurasia og Beringia. Forfedrene til dagens rein i Fennoskandia syntes også å ha utviklet seg fra atskilte bestander av rein som kan føres tilbake til slutten av siste istid. Innvandring og opprinnelse til dagens vill- og tamrein i Fennoskandia vil bli belyst i dette perspektiv.

The classification and colonization of reindeer and caribou (Rangifer tarandus) was assessed from analysis of both proteins, nuclear DNA and mitochondrial DNA. I demonstrate that the current subspecies designations are not compatible with the differentiation at these markers, suggesting that the morphological differences among extant subspecies did not evolve in separate glacial refugia. Thus, morphological differences among extant subspecies probably evolved as adaptive responses to post-glacial environmental changes. An exception to this is the North American woodland caribou, where all three marker systems support a subspecies-specific refugium as the ancestral origin of these animals. Three major mtDNA haplogroups reported, represent three separate origins of the species during the last glaciation. The most influential origin has contributed to the gene pool of all extant subspecies, suggesting the existence of a large and continuous glacial population ranging across extensive areas of tundra in Eurasia and Beringia. The North American tundra forms (R.t. granti and groenlandicus) and the arctic forms (R.t platyrhynchus, R.t pearyi and R.t eogroenlandicus) almost exclusively comprise haplotypes of such an origin. Another small and isolated refugium seems to have arisen in western Eurasia in close connection to the extensive ice sheet that covered Fennoscandia. The two Eurasian subspecies R.t. tarandus and R.t. fennicus appear to have a diphyletic origin as both the putatively small and isolated Eurasian refugium and the large Beringia refugium have contributed to their gene pools. A third distinct and geographically well-defined refugial area was probably located south to the extensive North American continental ice sheet from where the ancestors of the present North American woodland caribou (R.t. caribou) likely originated. Abstract in Norwegian / Sammendrag: Systematisk inndeling og kolonisering av rein (Rangifer tarandus) ble bestemt ved å analysere for variasjon i genetiske markører som proteiner, kjerneDNA og mitokondrieDNA. Dagens oppdeling av rein i underarter viser liten overensstemmelse med variasjonsmønsteret i de undersøkte markørene, noe som viser at de morfologiske forskjellene som karakteriserer dagens underarter ikke har utviklet seg i atskilte refugier i løpet av siste istid. Unntak fra dette er nordamerikansk skogsrein (woodland caribou-R.t. caribou) hvor alle tre markørsystemene indikerer at denne har utviklet seg i et refugium forskjellig fra andre underarter. De tre registrerte hovedhaplogruppene i mitokondrie-DNA representerer tre atskilte opprinnelser av rein i løpet av siste istid. Den mest innflytelsesrike av disse bidro vesentlig til genbanken til alle dagens underarter av rein, noe som tyder på at det under siste istid eksisterte en stor reinpopulasjon med kontinuerlig utbredelse gjennom store deler av tundraen i Eurasia og Beringia. De nordamerikanske tundrareintypene (R.t. granti og R.t. groenlandicus), samt de arktiske typene (R.t. platyrhunchus, R.t. pearyi og R.t. eogroenlandicus) består nærmest utelukkende av haplotyper med denne opprinnelse. Et annet lite og isolert refugium syntes å ha oppstått i Vest-Europa i nærheten av den omfattende isbreen som dekket Fennoskandia. De to europeiske underarter, R.t. tarandus og R.t. fennicus, syntes å ha en todelt opprinnelse med genetisk påvirkning fra både det antatt lille og isolerte refugiet i Eurasia samt fra det store Beringia refugiet. Et tredje geografisk distinkt refugium var antagelig lokalisert sør for den omfattende isbreen i Nord Amerika hvorfra forfedrene til dagens nordamerikanske skogsrein (R.t. caribou) har sin mest sannsynlige opprinnelse.

Polycrylamide gel electrophoresis was used to analyse tranferrrin variation in caribou populations from Manitoba, Ontario, Québec/Labrador, and from Baffin Island, Northwest Territories in eastern Canada. The transferrin allele frequencies in these populations were compared with those previously reported for Canadian barren-ground caribou, Rangifer tarandus groenlandicus, Alaska caribou, R.t. grand, Peary caribou, R.t. pearyi, Svalbard reindeer, R.t. pla-tyrhynchus, and Eurasian tundra reindeer, R.t. tarandus. A total of twenty different alleles was detected in the analysed material, considerable genetic heterogeneity being detected among regions. Three alleles that were relatively common in caribou from Ontario, Manitoba and Québec/Labrador, were not present in R.t. grand, R.t. pearyi, R.t. tarandus or R.t. platyrhynchus, and present only at very low frequencies 'm R.t. groenlandicus. These findings, together with genetic identity analyses, suggest that the caribou in Manitoba, Ontario, and Québec/Labrador are mainly of the R.t. caribou type, and that little interbreeding has occurred with other subspecies. The large genetic distance in the transferrin locus between R.t. caribou and other subspecies of reindeer/caribou suggests that, during the Wisconsin glaciation the ancestral populations of R.t. caribou survived in a refugium different from that of the ancestral populations of the other subspecies. Significant genetic differences between Baffin Island caribou and all other populations were mainly due to the presence of one allele that was in high frequency in Baffin Island caribou, but that was absent, or present in very low frequencies, in all other reindeer/caribou populations. The genetic differences between Baffin Island caribou and the other subspecies were greater than the differences between several of the currently recognized subspecies.

Blood samples were obtained from 95 barren-ground caribou (Rangifer tarandus groenlandicus) of the Beverly herd in Northwest Territories, Canada. Polyacrylamid gel electrophoresis was used to score for genetic variation in the locus coding for transferrin. The pattern of allele frequency distribution are compared with previously reported values of Eurasian tundra reindeer (R.t. tarandus), Alaska caribou (R.t. granti), Peary caribou (R.t. pearyi), and Svalbard reindeer (R.t. platyrhynchus). In the Beverly herd a total of 21 different transferrin alleles were detected. The amount of genetic variation was higher in the Canadian barren-ground caribou than what has been detected in other subspecies of reindeer/caribou. Highly gene-tical differences in the allele frequencies were detected between the Canadian barren-ground caribou and the other subspecies. The genetic identity analyses indicates approximately the same amount of genetic differentiation when the Canadian barren-ground caribou are compared with Alaska caribou as with the Peary caribou. The allele frequency pattern could be explained by a possible origin of the Canadian barren-ground caribou from an ancestral population which was genetical influenced by animals surviving the We-ichselian glaciation in refugia both in high Arctic, in Beringia, and south of the ice sheet.

Polyacrylamide gel electrophoresis was used to analyse transferrin variation in wild caribou (Rangifer tarandus granti) and domestic reindeer (R.t. tarandus) from Alaska. Eighteen alleles were detected in caribou and ten alleles were detected in reindeer. The most common allele was Tf 1 with a frequency of 0.304 and 0.408 in caribou and reindeer, respectively. The allele frequency distributions were significantly different in reindeer and caribou. This finding, together with the absence in reindeer of nine alleles present in caribou, suggests that little genetic exchange has taken place between caribou and reindeer in Alaska. The allele frequency distribution in Alaska caribou and reindeer are compared with those for other populations of caribou and reindeer. This comparison indicates that Alaskan caribou as well as Eurasian reindeer have evolved from a common ancesteral population different from the ancesteral population of Peary cairbou (R.t. pearyi) and Svalbard reindeer (R.t. platyrhynchus).

Polyacrylamide gel electrophoresis was used to analyse transferrin variation in herds of semi-domestic reindeer from Scandinavia. The results are compared with previously reported values for other populations of both semi-domestic and wild reindeer using the same techniques as in the present study. In all populations the number of alleles was high, ranging from seven to eleven, and the heterozygosity was correspondingly high, with a mean of 0.749. This high genetic variation in all populations suggests that inbreeding is not widespread among Scandinavian reindeer. The pattern of allele frequency distribution indicates a high degree of genetic heterogeneity in the transferrin locus, both between the different semi-domestic herds and between the different wild populations. The mean value of genetic distance was 0.069 between semi-domestic herds and 0.091 between wild populations. Between semi-domestic and wild populations the genetic distance was particularly high, with a mean of 0.188. This high value was mainly due to a different pattern in the distribution of the two most common transferrin alleles: Tfu was most common among semi-domestic herds, while TfEI was most common among wild populations. These differences in transferrin allele distribution are discussed in relation to possible different origins of semi-domestic and wild reindeer in Scandinavia, or alternatively, to different selection forces acting on transferrin genotypes in semi-domestic and wild populations. Transferrin-variasjon og genetisk struktur hos rein i Skandinavia. Abstact in Norwegian / Sammendrag: Transferrin-variasjon i tamreinflokker ble analysert ved hjelp av polyacrylamid gel elektroforese. Resultatene er sammenlignet med verdier som tidligere er beskrevet for både tamrein og villrein hvor det ble benyttet samme metode som i denne undersøkelsen. I alle populasjonene ble det registrert et høyt antall alleler (7-11) og heterozygositeten var tilsvarende høy med en middelverdi på 0.749. Denne høye graden av genetisk variasjon i alle undersøkte populasjoner indikerer at det ikke foregår mye innavl blant rein i Skandinavia. Utbredelsen av de enkelte allelene viste høy grad av genetisk oppdeling i transferrin-locuset mellom flokker av både tamrein og villrein. Middelverdien for genetisk avstand var 0.069 mellom tamreinflokker og 0.091 mellom villreinflokker. Særlig stor genetisk avstand (middelverdi 0.188) ble funnet mellom tamrein og villrein. Denne store forskjellen skyldes i stor grad forskjellig mønster i utbredelsen av de to vanligste allelene: Tf' var mest vanlig blant tamrein og Tf1' var mest vanlig blant villrein. Denne forskjellen er diskutert i relasjon til forskjellig opprinnelse av tamrein og villrein og alternativt, i relasjon til forskjellig seleksjonskrefter som virker på transferrin genotyper i tamrein og villrein.