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.     

No evidence of inbreeding depression in fast declining herds of migratory caribou

Identifying inbreeding depression early in small and declining populations is essential for management and conservation decisions. Correlations between heterozygosity and fitness (HFCs) provide a way to identify inbreeding depression without prior knowledge of kinship among individuals. In Northern Quebec and Labrador, the size of two herds of migratory caribou (Rivière‐George, RG and Rivière‐aux‐Feuilles, RAF) has declined by one to two orders of magnitude in the last three decades. This raises the question of a possible increase in inbreeding depression originating from, and possibly contributing to, the demographic decline in those populations. Here, we tested for the association of genomic inbreeding indices (estimated with 22,073 SNPs) with body mass and survival in 400 caribou sampled in RG and RAF herds between 1996 and 2016. We found no association of individual heterozygosity or inbreeding coefficient with body mass or annual survival. Furthermore, those genomic inbreeding indices remained stable over the period monitored. These results suggest that the rapid and intense demographic decline of the herds did not cause inbreeding depression in those populations. Although we found no evidence for HFCs, if demographic decline continues, it is possible that such inbreeding depression would be triggered.     

Impacts of climate change on the seasonal distribution of migratory caribou

Arctic ecosystems are especially vulnerable to global climate change as temperature and precipitation regimes are altered. An ecologically and socially highly important northern terrestrial species that may be impacted by climate change is the caribou, Rangifer tarandus . We predicted the current and potential future occurrence of two migratory herds of caribou [Rivière George herd (RG) and Rivière-aux-Feuilles (RAF) herd] under a Canadian General Circulation Model climate change scenario, across all seasons in the Québec–Labrador peninsula, using climatic and habitat predictor variables. Argos satellite-tracking collars have been deployed on 213 caribou between 1988 and 2003 with locations recorded every 4–5 days. In addition, we assembled a database of climate (temperature, precipitation, snowfall, timing and length of growing season) and habitat data obtained from the SPOT VEGETATION satellite sensor. Logistic regression models indicated that both climatic and physical habitat variables were significant predictors of current migratory caribou occurrence. Migratory caribou appeared to prefer regions with higher snowfall and lichen availability in the fall and winter. In the summer, caribou preferred cooler areas likely corresponding to a lower prevalence of insects, and they avoided disturbed and recently burnt areas. Climate change projections using climate data predicted an increased range for the RAF herd and decreased range for the RG herd during 2040–2069, limiting the herds to northeastern regions of the Québec–Labrador peninsula. Direct and indirect consequences of climate change on these migratory caribou herds possibly include alteration in habitat use, migration patterns, foraging behaviour, and demography, in addition to social and economic stress to arctic and subarctic native human populations.     

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.     

Caribou movement as a correlated random walk

Movement is a primary mechanism coupling animals to their environment, yet there exists little empirical analysis to test our theoretical knowledge of this basic process. We used correlated random walk (CRW) models and satellite telemetry to investigate long-distance movements of caribou, the most vagile, non-volant terrestrial vertebrate in the world. Individual paths of migratory and sedentary female caribou were quantified using measures of mean move length and angle, and net squared displacements at each successive move were compared to predictions from the models. Movements were modelled at two temporal scales. For paths recorded through one annual cycle, the CRW model overpredicted net displacement of caribou through time. For paths recorded over shorter intervals delineated by seasonal behavioural changes of caribou, there was excellent correspondence between model predictions and observations for most periods for both migratory and sedentary caribou. On the smallest temporal scale, a CRW model significantly overpredicted displacements of migratory caribou during 3 months following calving; this was also the case for sedentary caribou in late summer, and in late winter. In all cases of overprediction there was significant positive autocorrelation in turn direction, indicating that movements were more tortuous than expected. In one case of underprediction, significant negative autocorrelation of sequential turn direction was evident, indicating that migratory caribou moved in straightened paths during spring migration to calving grounds. Results are discussed in light of known migration patterns and possible limiting factors for caribou, and indicate the applicability of CRW models to animal movement at vast spatial and temporal scales, thus assisting in future development of more sophisticated models of population spread and redistribution for vertebrates. Received: 14 July 1999 / Accepted: 15 November 1999     

Interchange and Overlap Among Four Adjacent Arctic Caribou Herds

Barren ground caribou (Rangifer tarandus granti) are distributed in herds that seasonally use specific geographic regions within an annual range, with varying levels of fidelity during different periods (e.g., calving, insect relief, wintering). As a result, caribou management is generally tailored to individual herds that often range across administrative boundaries. Herd ranges can shift over time, seasonal ranges of adjacent herds often overlap, herds merge, and there is often little genetic differentiation among adjacent herds. If substantial herd interchange occurs, it would have important management implications by influencing estimates of herd size, herd composition, and harvest rates. We compiled satellite telemetry data from 2003–2015 for 4 large arctic caribou herds to quantify herd interchange rates. We calculated a metric of herd interchange based on the relationship of caribou locations to typical weekly herd ranges (all yrs combined) and the distance to other radio-collared caribou from each of the 4 herds (yr specific). Although herd membership cannot always be clearly defined based on location, this metric provides an objective measure of the strength of evidence of herd membership that can be used to make comparisons among herds and time periods. We also calculated herd overlap and quantified how it varied throughout the year. Herd interchange was rare in the 2 larger herds, generally occurring when caribou overwintered with an adjacent herd, whereas herd interchange from the 2 smaller herds was more frequent and could last longer than a year. Although sample sizes were limited, there were no clear patterns in herd interchange with year or annual herd size. The 2 smaller herds had large seasonal overlap with adjacent herds, suggesting that herd interchange may be related to spatiotemporal herd overlap and relative herd size. Our results can help managers understand herd interchange and overlap to make management decisions, interpret research results, and develop more accurate population models. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society.     

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.     

Integrative use of spatial, genetic, and demographic analyses for investigating genetic connectivity between migratory, montane, and sedentary caribou herds

Genetic differentiation is generally assumed to be low in highly mobile species, but this simplistic view may obscure the complex conditions and mechanisms allowing genetic exchanges between specific populations. Here, we combined data from satellite-tracked migratory caribou (Rangifer tarandus), microsatellite markers, and demographic simulations to investigate gene flow mechanisms between seven caribou herds of eastern Canada. Our study included one montane, two migratory, and four sedentary herds. Satellite-tracking data indicated possibilities of high gene flow between migratory herds: overlap of their rutting ranges averaged 10% across years and 9.4% of females switched calving sites at least once in their lifetime. Some migratory individuals moved into the range of the sedentary herds, suggesting possibilities of gene flow between these herds. Genetic differentiation between herds was weak but significant (FST=0.015): migratory and montane herds were not significantly distinct (FST all9) than vice-versa (4Nm all<5), which suggests migratory herds had a demographic impact on sedentary herds. Demographic simulations showed that an effective immigration rate of 0.0005 was sufficient to obtain the empirical FST of 0.015, while a null immigration rate increased the simulated FST to >0.6. In conclusion, the weak genetic differentiation between herds cannot be obtained without some genetic exchanges among herds, as demonstrated by genetic and spatial data.     

Caribou Distribution and Movements in a Northern Alaska Oilfield

As industrial development increases in the range of barren-ground caribou (Rangifer tarandus granti) across the warming Arctic, the need to understand the responses of caribou to development and to assess the effectiveness of mitigation measures increase accordingly. The Central Arctic Herd (CAH) of caribou ranges across northern Alaska, USA, and the herd's summer range includes the Prudhoe Bay and Kuparuk oilfields, where the herd has been exposed to oil development for >4 decades. We used location data from global positioning system (GPS) radio-collars deployed on female CAH caribou for 106 collar-years, recording locations every 2 hours during 2008–2019, to examine caribou distribution and movements during 7 different seasons of the year in relation to infrastructure in the Kuparuk oilfield, which is characterized by more design improvements and mitigation measures than the older Prudhoe Bay oilfield. We examined movement metrics in terms of distance to gravel infrastructure (roads and pads) and time before and after movements across infrastructure (crossings). We also employed integrated step-selection analysis to compare caribou movements with random movements. Caribou distribution was influenced by insect activity, distance to coast, landcover, and terrain ruggedness, and we found large seasonal differences in caribou responses to infrastructure. Consistent with previous research findings, avoidance of areas near roads and pads was strongest during the calving season and some caribou used roads and pads as insect-relief habitat when oestrid flies (warble fly [Hypoderma tarandi] and nose bot fly [Cephenemyia trompe]) were active. Caribou moved through the Kuparuk oilfield repeatedly during summer, averaging >2 road or pad crossings a day when harassment by mosquitoes (Aedes [Ochlerotatus] spp.) and oestrid flies were the predominant factors influencing caribou movements. Caribou moved faster while crossing roads and pads but showed little pattern in speed or turn angle with distance to roads and pads. These results demonstrate that the effects of petroleum development on a caribou herd with long-term exposure to industrial activity vary widely by season. Maternal caribou avoid active roads and pads during calving, but the incorporation of appropriate mitigation measures in oilfield design allows caribou to move through the Kuparuk oilfield during other snow-free seasons. © 2020 The Wildlife Society.     

Growth and condition of three introduced reindeer herds on South Georgia: the effects of diet and density

The patterns of growth and seasonal changes in body weight and fat reserves of three herds of introduced reindeer on the sub-Antarctic island of South Georgia were investigated. Two of the herds, derived from the same stock, were at different densities but the higher density herd was on the better range. In this herd there was a significant growth advantage to the male reindeer, but not to females. The third herd, of a different stock, was also at a lower density on a range which had become overgrazed. The two lower-density herds showed the same annual changes in body weight and only slight differences in the fluctuation of their fat reserves. In addition, body weights in both these herds fluctuated to the same degree as those of a barren-ground caribou in the Northern Hemisphere but fluctuations in the fat reserves of South Georgia reindeer were considerably more severe. The results suggest that the South Georgia reindeer herds are limited by forage availability.     

Climate-Driven Effects of Fire on Winter Habitat for Caribou in the Alaskan-Yukon Arctic

Climatic warming has direct implications for fire-dominated disturbance patterns in northern ecosystems. A transforming wildfire regime is altering plant composition and successional patterns, thus affecting the distribution and potentially the abundance of large herbivores. Caribou (Rangifer tarandus) are an important subsistence resource for communities throughout the north and a species that depends on terrestrial lichen in late-successional forests and tundra systems. Projected increases in area burned and reductions in stand ages may reduce lichen availability within caribou winter ranges. Sufficient reductions in lichen abundance could alter the capacity of these areas to support caribou populations. To assess the potential role of a changing fire regime on winter habitat for caribou, we used a simulation modeling platform, two global circulation models (GCMs), and a moderate emissions scenario to project annual fire characteristics and the resulting abundance of lichen-producing vegetation types (i.e., spruce forests and tundra >60 years old) across a modeling domain that encompassed the winter ranges of the Central Arctic and Porcupine caribou herds in the Alaskan-Yukon Arctic. Fires were less numerous and smaller in tundra compared to spruce habitats throughout the 90-year projection for both GCMs. Given the more likely climate trajectory, we projected that the Porcupine caribou herd, which winters primarily in the boreal forest, could be expected to experience a greater reduction in lichen-producing winter habitats (−21%) than the Central Arctic herd that wintered primarily in the arctic tundra (−11%). Our results suggest that caribou herds wintering in boreal forest will undergo fire-driven reductions in lichen-producing habitats that will, at a minimum, alter their distribution. Range shifts of caribou resulting from fire-driven changes to winter habitat may diminish access to caribou for rural communities that reside in fire-prone areas.     

Behaviour of West Greenland caribou during a population decline

The major decline of the West Greenland caribou herd during the 1970s prompted a study in 1977–78 of caribou behaviour in relation to environmental factors associated with the decline. Quantification of caribou activity revealed behavioural responses to critically low standing crops of preferred winter forage. Caribou on poor winter range were mostly inactive with low feeding intensities and abnormal diurnal activity patterns. In addition, these animals exhibited very restricted movements, frequently occurred alone or in small groups, and were unable to maintain normal social bonds. In contrast, where fruticose lichen winter forage was available, caribou did not display these behavioural traits. After the initiation of new vegetative growth, feeding intensity increased and social tendency returned. Comparison with behavioural data from other Rangifer populations suggests that the observed responses to low forage quality are not restricted to Greenland but are a normal response of barren-ground caribou to winter ranges poor in lichen forage.     

Hand‐Rearing Wild Caribou Calves for Studies of Nutritional Ecology

Caribou (Rangifer tarandus) are considered difficult to hand‐rear in captivity because they are sensitive to the composition and volume of formulated milks. We used a strict feeding schedule and a commercial milk formula designed specifically for caribou to bottle‐feed neonates captured from five wild caribou herds in Alaska. Under a feeding protocol adjusted for age and mass, the growth rates and body mass of 26 hand‐reared caribou calves to weaning were similar to those of three maternally nursed caribou. This protocol allows caretakers to hand‐rear caribou that are as representative as possible of maternally raised neonates. Zoo Biol. 32:163–171, 2013. © 2012 Wiley Periodicals, Inc.     

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.     

Changing northern vegetation conditions are influencing barren ground caribou (Rangifer tarandus groenlandicus) post‐calving movement rates

Aim

To quantify changes in vegetation productivity over the past three decades across five barren ground caribou (Rangifer tarandus groenlandicus) herd ranges and assess how these changes are influencing caribou movement rates.

Location

Northwest Territories and Nunavut, Canada.

Methods

As an indicator of vegetation productivity, the enhanced vegetation index (EVI) was calculated on newly developed cloud‐free, gap‐free, Landsat surface reflectance image composites representing 1984–2012. Changes in EVI were assessed on a pixel basis using Theil‐Sen's nonparametric regression and compared across herd ranges and land cover types using generalized least squares regression. Animal movement velocity was calculated from caribou telemetry data and generalized additive mixed models were used to link movement rates with vegetation productivity during the post‐calving phase of the year (July and August).

Results

Vegetation productivity increased across the five caribou herd ranges examined. The largest productivity increase occurred over the ranges of the most western herds, with the largest observed changes in grassland or shrub habitats. Caribou tended to move more slowly through tundra habitats with elevated levels of productivity to a point, while grasslands movement rates decreased linearly with increasing productivity. Movement velocities peaked at intermediate productivity levels in shrub habitats.

Main conclusions

Over the three decades of collected data, barren ground caribou habitats have become more productive, which is consistent with other studies that have documented increases in Arctic vegetation productivity. The more western herds, whose ranges are also closest to the Arctic Ocean, experienced the largest increases in productivity. Finally, we demonstrate that barren ground caribou movement patterns will likely change as a result of changing vegetation productivity in complex manners depending on herd, habitat type and the magnitude of change in vegetation productivity.     

Reconstruction of caribou evolutionary history in Western North America and its implications for conservation

The role of Beringia as a refugium and route for trans-continental exchange of fauna during glacial cycles of the past 2million years are well documented; less apparent is its contribution as a significant reservoir of genetic diversity. Using mitochondrial DNA sequences and 14 microsatellite loci, we investigate the phylogeographic history of caribou (Rangifer tarandus) in western North America. Patterns of genetic diversity reveal two distinct groups of caribou. Caribou classified as a Northern group, of Beringian origin, exhibited greater number and variability in mtDNA haplotypes compared to a Southern group originating from refugia south of glacial ice. Results indicate that subspecies R. t. granti of Alaska and R. t. groenlandicus of northern Canada do not constitute distinguishable units at mtDNA or microsatellites, belying their current status as separate subspecies. Additionally, the Northern Mountain ecotype of woodland caribou (presently R. t. caribou) has closer kinship to caribou classified as granti or groenlandicus. Comparisons of mtDNA and microsatellite data suggest that behavioural and ecological specialization is a more recently derived life history characteristic. Notably, microsatellite differentiation among Southern herds is significantly greater, most likely as a result of human-induced landscape fragmentation and genetic drift due to smaller population sizes. These results not only provide important insight into the evolutionary history of northern species such as caribou, but also are important indicators for managers evaluating conservation measures for this threatened species.     

How landscape dynamics link individual‐ to population‐level movement patterns: a multispecies comparison of ungulate relocation data

Aim To demonstrate how the interrelations of individual movements form large‐scale population‐level movement patterns and how these patterns are associated with the underlying landscape dynamics by comparing ungulate movements across species. Locations Arctic tundra in Alaska and Canada, temperate forests in Massachusetts, Patagonian Steppes in Argentina, Eastern Steppes in Mongolia. Methods We used relocation data from four ungulate species (barren‐ground caribou, Mongolian gazelle, guanaco and moose) to examine individual movements and the interrelation of movements among individuals. We applied and developed a suite of spatial metrics that measure variation in movement among individuals as population dispersion, movement coordination and realized mobility. Taken together, these metrics allowed us to quantify and distinguish among different large‐scale population‐level movement patterns such as migration, range residency and nomadism. We then related the population‐level movement patterns to the underlying landscape vegetation dynamics via long‐term remote sensing measurements of the temporal variability, spatial variability and unpredictability of vegetation productivity. Results Moose, which remained in sedentary home ranges, and guanacos, which were partially migratory, exhibited relatively short annual movements associated with landscapes having very little broad‐scale variability in vegetation. Caribou and gazelle performed extreme long‐distance movements that were associated with broad‐scale variability in vegetation productivity during the peak of the growing season. Caribou exhibited regular seasonal migration in which individuals were clustered for most of the year and exhibited coordinated movements. In contrast, gazelle were nomadic, as individuals were independently distributed and moved in an uncoordinated manner that relates to the comparatively unpredictable (yet broad‐scale) vegetation dynamics of their landscape. Main conclusions We show how broad‐scale landscape unpredictability may lead to nomadism, an understudied type of long‐distance movement. In contrast to classical migration where landscapes may vary at broad scales but in a predictable manner, long‐distance movements of nomadic individuals are uncoordinated and independent from other such individuals. Landscapes with little broad‐scale variability in vegetation productivity feature smaller‐scale movements and allow for range residency. Nomadism requires distinct integrative conservation strategies that facilitate long‐distance movements across the entire landscape and are not limited to certain migration corridors.     

Implications of body condition on the unsustainable predation rates of endangered mountain caribou

Both top-down and bottom-up processes influence herbivore populations, and identifying dominant limiting factors is essential for applying effective conservation actions. Mountain caribou are an endangered ecotype of woodland caribou (Rangifer tarandus caribou) that have been declining, and unsustainable predation has been identified as the proximate cause. To investigate the role of poor nutrition, we examined the influence of sex, season, age class, and available suitable habitat (i.e., old-growth forest>140 years) per caribou on bone marrow fat content of caribou that died (n = 79). Sex was the only strong predictor of marrow fat. Males that died during and post rut had lower marrow fat than females or males at other times of year. Old-growth abundance per caribou, season, and age class did not predict marrow fat. Caribou killed by predators did not have less marrow fat than those that died in accidents, suggesting that nutritionally stressed caribou were not foraging in less secure habitats or that predators selected nutritionally stressed individuals. Marrow fat in endangered and declining populations of mountain caribou was similar to caribou in other, more viable populations. Our results support previous research suggesting that observed population declines of mountain caribou are due to excessive predation that is not linked to body condition.     

Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon

The long‐term persistence of forest‐dwelling caribou (Rangifer tarandus caribou) will probably be determined by management and conservation decisions. Understanding the evolutionary relationships between modern caribou herds, and how these relationships have changed through time will provide key information for the design of appropriate management strategies. To explore these relationships, we amplified microsatellite and mitochondrial markers from modern caribou from across the Southern Yukon, Canada, as well as mitochondrial DNA from Holocene specimens recovered from alpine ice patches in the same region. Our analyses identify a genetically distinct group of caribou composed of herds from the Southern Lakes region that may warrant special management consideration. We also identify a partial genetic replacement event occurring 1000 years before present, coincident with the deposition of the White River tephra and the Medieval Warm Period. These results suggest that, in the face of increasing anthropogenic pressures and climate variability, maintaining the ability of caribou herds to expand in numbers and range may be more important than protecting the survival of any individual, isolated sedentary forest‐dwelling herd.     

The role of introgression and ecotypic parallelism in delineating intraspecific conservation units

Parallel evolution can occur through selection on novel mutations, standing genetic variation or adaptive introgression. Uncovering parallelism and introgressed populations can complicate management of threatened species as parallelism may have influenced conservation unit designations and admixed populations are not generally considered under legislations. We examined high coverage whole‐genome sequences of 30 caribou (Rangifer tarandus) from across North America and Greenland, representing divergent intraspecific lineages, to investigate parallelism and levels of introgression contributing to the formation of ecotypes. Caribou are split into four subspecies and 11 extant conservation units, known as designatable units (DUs), in Canada. Using genomes from all four subspecies and six DUs, we undertake demographic reconstruction and confirm two previously inferred instances of parallel evolution in the woodland subspecies and uncover an additional instance of parallelism of the eastern migratory ecotype. Detailed investigations reveal introgression in the woodland subspecies, with introgressed regions found spread throughout the genomes encompassing both neutral and functional sites. Our investigations using whole genomes highlight the difficulties in unequivocally demonstrating parallelism through adaptive introgression in nonmodel species with complex demographic histories, with standing variation and introgression both potentially involved. Additionally, the impact of parallelism and introgression on conservation policy for management units needs to be considered in general, and the caribou designations will need amending in light of our results. Uncovering and decoupling parallelism and differential patterns of introgression will become prevalent with the availability of comprehensive genomic data from nonmodel species, and we highlight the need to incorporate this into conservation unit designations.