Genome-wide SNP assessment of contemporary European red deer genetic structure highlights the distinction of peripheral populations and the main admixture zones in Europe.

Genome-wide technologies open up new possibilities to clarify questions on genetic structure and phylogeographic history of taxa previously studied with microsatellite loci and mitochondrial sequences. Here, we used 736 individual red deer (Cervus elaphus) samples genotyped at 35,701 single nucleotide polymorphism loci (SNPs) to assess the population structure of the species throughout Europe. The results identified 28 populations, with higher degrees of genetic distinction in peripheral compared to mainland populations. Iberian red deer show high genetic differentiation, with lineages in Western and Central Iberia maintaining their distinctiveness, which supports separate refugial ranges within Iberia along with little recent connection between Iberian and the remaining Western European populations. The Norwegian population exhibited the lowest variability and the largest allele frequency differences from mainland European populations, compatible with a history of bottlenecks and drift during post-glacial colonization from southern refugia. Scottish populations showed high genetic distance from the mainland but high levels of diversity. Hybrid zones were found between Eastern and Western European lineages in Central Europe as well as in the Pyrenees, where red deer from France are in close contact with Iberian red deer. Anthropogenic restocking has promoted the Pyrenean contact zone, admixture events in populations on the Isle of Rum and in the Netherlands, and at least partly the admixture of the two main lineages in central-eastern Europe. Our analysis enabled detailed resolution of population structure of a large mammal widely distributed throughout Europe and contributes to resolving the evolutionary history, which can also inform conservation and management policies.

Is the Intrasexual Competition in Male Red Deer Reflected in the Ratio of Stable Isotopes of Carbon and Nitrogen in Faeces?

Isotopic analysis of carbon and nitrogen in faeces is a reliable methodology for studying ecology in wildlife. Here, we tested this technique to detect variations in carbon and nitrogen isotopic ratios (δ13C and δ15N) in two different intrasexual competition scenarios of male Iberian red deer (Cervus elaphus hispanicus) using faeces of individuals collected during hunting actions in South-eastern Spain. The carbon isotopic ratio (δ13C) was not found to be significant, likely due to similar diet composition in all individuals. However, the nitrogen isotopic ratio (δ15N) was found to be lower in populations where sexual competition between males during the rut was higher compared to low-competition populations. Therefore, this study suggests a different use of proteins by an individual male red deer depending on the sexually competitive context in which he lives. Although further research is needed, these results show the potential of isotopic analysis as a tool for studying individual and populational variations in the level of intrasexual competition, with implications in evolutionary ecology and population 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.

Exploring the potential links between gut microbiota composition and natural populations management in wild boar (Sus scrofa).

We surveyed wild boar (Sus scrofa) populations using 16S rRNA gene analysis of the gut microbiota in fresh faeces taken from 88 animals hunted in 16 hunting estates. The wild boar is a very convenient model system to explore how environmental factors including game management, food availability, disease prevalence, and behaviour may affect different biological components of wild individuals with potential implications in management and conservation. We tested the hypotheses that diet (according to stable carbon isotopes analyses), gender (i.e., animal behaviour studying males and females), and both health (analyses of serum samples to detect exposure to several diseases) and form statutes (i.e., thoracic circumference in adults) are reflected in changes in the intestinal microbiota. We focused on a gut functional biomarker index combining Oscillospiraceae and Ruminococcaceae vs. Enterobacteriaceae. We found that gender and the estate (population) were explanatory variables (c.a. 28% of the variance), albeit a high degree of overlapping among individuals was observed. The individuals with higher abundance of Enterobacteriaceae showed a gut microbiota with low diversity, mostly in males. Significant statistical differences for thoracic circumference were not found between males and females. Interestingly, the thoracic circumference was significantly and inversely related to the relative abundance of Enterobacteriaceae in males. Overall, we found that diet, gender, and form status were major factors that could be related to the composition and diversity of the gut microbiota. A high variability was observed in the biomarker index for populations with natural diet (rich in C3 plants). Although, we noticed a marginally significant negative trend between the index (higher abundance of Enterobacteriaceae) and the continuous feeding of C4 plants (i.e., supplementary maize) in the diet of males. This result suggests that continuous artificial feeding in hunting estates could be one of the factors negatively influencing the gut microbiota and the form status of wild boars that deserves further investigations.

Stable carbon and nitrogen isotope values in hair reveal management differences and hidden practices in wild boar populations.

The analysis of stable isotopes in different tissues has been widely used to obtain information on the ecology and nutritional patterns of wildlife. The isotope ratios of the stable isotopes of carbon and nitrogen (δ13C and δ15N) analysed in different tissues are directly related to the animal's diet and, to some extent, to the environment where the individual has growth. Specifically, this type of analysis in hair samples has become relevant as it provides information on the quality and long-term composition of the diet that produced the isotope accumulation during the tissue growth. We took samples of wild boar (Sus scrofa) hair from 7 different populations in the south-west of Spain (Mediterranean habitats), in the 2018/2019 hunting season. The main objectives of this study were (i) to investigate the use of hair stable isotopes to reveal differences in composition and quality of the diet of wild boar within the same population or between populations, and (ii) to use hair isotopes as a tool to uncover hidden management practices that may occur in hunting areas associated with the use of supplementary feeding or even captive breeding and release. Each animal had a hair (long 10 cm) analysed in duplicate, previously cut into parts of equal size (from the oldest part of the hair to the most recent part), that were analysed separately. We found differences in δ13C and δ 15N between hair parts and populations, which can be related to management actions at different times during the hair growth. Moreover, the use of corn, a type of plant not occurring naturally in the study area, can be documented with the isotope analysis to prove unauthorized supplementary feeding or captive origin of wild boar in hunting areas.

The dark-ventral-patch of male red deer, a sexual signal that conveys the degree of involvement in rutting behavior.

BACKGROUND: In polygynous mammals, signalling may play a decisive role in mating behavior, mediating the intensity of male fights and female mate choice. During the rutting season, male red deer may show a visible dark patch in their ventral fur. Recently, this patch has been suggested to act as a flexible sexual signal, due to its relationships with other variables such as age, body size, antler development, volatile compounds, or the competitive environment. The analysis of fur pigmentation at the ventral patch suggests that this might also visually indicate the male intrinsic predisposition to take part in mating competition. RESULTS: To assess the possible role of this trait as a communicative signal related to mate competition, we used red deer behavioral observations during the rut in Doñana National Park (Spain) to examine the link between the degree of expression of the dark ventral patch and the rutting activity (assessed from both intra-and-inter-sexual behaviors). Consistent with our predictions, we found in a field study that males with large dark patches showed a higher frequency of rutting behaviors (mainly roaring and flehmen), more interactions with females, and attained larger harem sizes. CONCLUSIONS: The dark ventral patch was a better predictor of male behavior than antler tines or territory holding, thus standing as a short-term indicator of male willingness to invest in mating competition.