Genetic variation and structure in Scandinavian red deer (Cervus elaphus): influence of ancestry, past hunting, and restoration management

Comparative Analysis of Microsatellite and SNP Markers for Genetic Management of Red Deer

The analysis of population genetic structure and individual multilocus heterozygosity are crucial for wildlife management and conservation. Microsatellite markers have traditionally been used to assess these genetic parameters. However, single-nucleotide polymorphisms (SNPs) are becoming increasingly popular. Our goal here was to determine to what extent SNPs can provide better insights than microsatellites into the overall genetic status and population genetic processes in the species. To this end, we genotyped 210 red deer (Cervus elaphus) in the Spanish wild population with both 11 microsatellites and 31,712 SNPs. We compared parameters related to population genetic structure and individual multilocus heterozygosity obtained with both types of markers. Our results showed correlations between parameters measured using both microsatellites and SNPs, particularly those related to the level of genetic diversity and genetic differentiation. However, we found notably lower precision of microsatellites in measuring the distribution of genetic diversity among individuals. We conclude that microsatellites can be used to monitor the overall genetic status and detect broad patterns in red deer populations. Nevertheless, the greater precision of SNPs in inferring genetic structure and multilocus heterozygosity leads us to encourage scientists and wildlife managers to prioritize their use whenever possible.

Human-driven genetic differentiation in a managed red deer population

Nineteen red deer areas in a densely populated region with a huge network of fenced motorways and the division into administrative management units (AMUs) with restricted ecological connectivity were investigated. In the season 2018/2019, a total of 1291 red deer samples (on average 68 per area) were collected and genotyped using 16 microsatellite markers. The results show a clear genetic differentiation between most of the AMUs. Fourteen AMUs may be combined into four regions with a considerable internal genetic exchange. Five areas were largely isolated or showed only a limited gene flow with neighbouring areas. Ten of the 19 AMUs had an effective population size below 100. Effective population sizes greater than 500–1000, required to maintain the evolutionary potential and a long-term adaptation potential, were not achieved by any of the studied AMUs, even when AMUs with an appreciable genetic exchange were aggregated. Substantial genetic differentiation between areas can be associated with the presence of landscape barriers hindering gene flow, but also with the maintenance of ‘red deer–free’ areas. Efforts to sustainably preserve the genetic diversity of the entire region should therefore focus on measures ensuring genetic connectivity. Opportunities for this goal arise from the establishment of game bridges over motorways and from the protection of young male stags migrating through the statutory ‘red deer–free’ areas.

Ethical Considerations for Wildlife Reintroductions and Rewilding

The recovery of many populations of large carnivores and herbivores in major parts of Europe and North America offers ecosystem services and opportunities for sustainable utilization of wildlife. Examples of services are hunting, meat, and skin, along with less invasive utilization such as ecotourism and wildlife spotting. An increasing number of studies also point out the ecosystem function, landscape engineering, and cascading effects of wildlife as values for human existence, biodiversity conservation, and ecosystem resilience. Within this framework, the concept of rewilding has emerged as a means to add to the wilderness through either supplementary release of wildlife species already present or reintroduction of species formerly present in a certain area. The latter involves translocation of species from other geographical areas, releases from captivity, feralization, retro-breeding, or de-domestication of breeds for which the wild ancestor is extinct. While all these initiatives aim to reverse some of the negative human impacts on life on earth, some pose challenges such as conflicts of interest between humans and wildlife in, for example, forestry, agriculture, traffic, or disease dynamics (e.g., zoonosis). There are also welfare aspects when managing wildlife populations with the purpose to serve humans or act as tools in landscape engineering. These welfare aspects are particularly apparent when it comes to releases of animals handled by humans, either from captivity or translocated from other geographical areas. An ethical values clash is that translocation can involve suffering of the actual individual, while also contributing to reintroduction of species and reestablishment of ecological functions. This paper describes wildlife recovery in Europe and North America and elaborates on ethical considerations raised by the use of wildlife for different purposes, in order to find ways forward that are acceptable to both the animals and humans involved. The reintroduction ethics aspects raised are finally formulated in 10 guidelines suggested for management efforts aimed at translocating wildlife or reestablishing wilderness areas.

Intensive Management and Natural Genetic Variation in Red Deer (Cervus elaphus)

The current magnitude of big-game hunting has outpaced the natural growth of populations, making artificial breeding necessary to rapidly boost hunted populations. In this study, we evaluated if the rapid increase of red deer (Cervus elaphus) abundance, caused by the growing popularity of big-game hunting, has impacted the natural genetic diversity of the species. We compared several genetic diversity metrics between 37 fenced populations subject to intensive management and 21 wild free-ranging populations. We also included a historically protected population from a national park as a baseline for comparisons. Contrary to expectations, our results showed no significant differences in genetic diversity between wild and fenced populations. Relatively lower genetic diversity was observed in the protected population, although differences were not significant in most cases. Bottlenecks were detected in both wild and fenced populations, as well as in the protected population. Assignment tests identified individuals that did not belong to their population of origin, indicating anthropogenic movement. We discuss the most likely processes, which could have led to the observed high levels of genetic variability and lack of differentiation between wild and fenced populations and suggest cautionary points for future conservation. We illustrate our comparative approach in red deer. However, our results and interpretations can be largely applicable to most ungulates subject to big-game hunting as most of them share a common exploitation-recovery history as well as many ecological traits.

Temporal variations in activity patterns during rut – implications for survey techniques of red deer, Cervus elaphus

Context Intraspecific differences in behaviour can affect censuses and bias population estimates, suggesting that choice and implementation of census methods are fundamental, and need to be adapted to behavioural variations. Aims We investigated temporal variations in activity patterns during the rut among red deer (Cervus elaphus) categories and the implications for two different census methods. Methods We used a long-term dataset collected during 17 consecutive red deer rutting seasons in southernmost Sweden. The two census methods were: (1) a collection of observation ratios; and (2) a count of individuals including identification of males. Both methods are commonly used in ungulate management. Key results There was a difference in activity among age and sex categories, with a temporal variation in activity and/or presence at rutting grounds of adult (≥6 years) and subadult (2–5 years) males. Observation ratios of adult and subadult males increased from low at the start of the rut to a top level during peak rut, with subadults lagging behind adults. Before and during peak rut, the proportion of adult males was higher than that of subadults. After peak rut, the proportion of adult males decreased, whereas subadult males remained high, resulting in a higher number of subadults than of adults. The comparison of the two census methods revealed a strong correlation regarding the trends of population size and for the age and sex categories. There was also a strong consistency concerning the calf/female ratio. The male proportion was, however, consistently lower in the collected observations than in the counts. Conclusions The lower proportion of males in observations compared with counts may be explained by behavioural differences among male age classes, i.e. by temporal variations in presence and activity. That females, calves and yearling males are stationary during the rut, but adult and subadult males arrive and depart the rutting grounds at varying points of time, can lead to an underestimated male proportion in continuously collected observation data. Implications The results suggest that census should be conducted during peak rut, and that incorporating identification of individual males in the monitoring may be beneficiary.

Genetic Structure and Effective Population Sizes in European Red Deer (Cervus elaphus) at a Continental Scale: Insights from Microsatellite DNA

We analyzed more than 600 red deer (Cervus elaphus) from large parts of its European distribution range at 13 microsatellite loci, presenting the first continent-wide study of this species using nuclear markers. Populations were clearly differentiated (overall F ST = 0.166, Jost's D est = 0.385), and the BAPS clustering algorithm yielded mainly geographically limited and adjacent genetic units. When forced into only 3 genetic clusters our data set produced a very similar geographic pattern as previously found in mtDNA phylogeographic studies: a western group from Iberia to central and parts of Eastern Europe, an eastern group from the Balkans to Eastern Europe, and a third group including the threatened relict populations from Sardinia and Mesola in Italy. This result was also confirmed by a multivariate approach to analyzing our data set, a discriminant analysis of principal components. Calculations of genetic diversity and effective population sizes (linkage disequilibrium approach) yielded the lowest results for Italian (Sardinia, Mesola; N e between 2 and 8) and Scandinavian red deer, in line with known bottlenecks in these populations. Our study is the first to present comparative nuclear genetic data in red deer across Europe and may serve as a baseline for future analyses of genetic diversity and structuring in this widespread ungulate.

Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications

Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations.