Using genetic tools to estimate the prevalence of non-native red deer (Cervus elaphus) in a Western European population

Spread of the Zoonotic Nematode Baylisascaris procyonis into a Naive Raccoon Population

The raccoon roundworm (Baylisascaris procyonis), a gastrointestinal nematode of the raccoon (Procyon lotor), may cause a severe form of larva migrans in humans, which can lead to death or permanent neurological damage. Although roundworms were inadvertently introduced to Europe alongside their raccoon hosts, the parasite is not present in every raccoon population. It is important to understand the geographic distribution of B. procyonis, as early and rapid treatment can prevent severe pathologies in humans. We present evidence for the roundworm spreading into a naive raccoon population through natural dispersal of infected raccoons. We sampled 181 raccoons from Saxony-Anhalt, a German federal state containing contact zones of different raccoon populations, two of which were previously free of the parasite. We screened the raccoons for roundworms and used microsatellite-based assignment tests to determine the genetic origin of the raccoons and their parasites. We detected roundworms in 16 of 45 raccoons sampled in a previously roundworm-free area in the northern part of the state. The largest proportion of the genetic ancestry (≥ 0.5) of the 16 raccoon hosts was assigned to the previously naive raccoon population. Conversely, the genetic ancestry of almost all the roundworms was assigned to the nearest roundworm population in the southern part of the state. Infected raccoons have, therefore, spread to the north of the state, where they interbred with and infected local raccoons. It seems likely that the roundworms will continue to spread. Health authorities should consider continuous surveillance programmes of naive populations and raise public awareness.

Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations

In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups. The gene flow intensity, relationship and admixture among populations were tested by the Bayesian approach and discriminant analysis of principal components (DAPC). The highest gene diversity (He = 0.19) and the lowest genomic inbreeding (FHOM = 0.04) found in Slovak wild population confirmed our hypothesis that artificial selection accompanied by bottlenecks has led to the increase in overall genomic homozygosity. The Bayesian approach and DAPC consistently identified three separate genetic groups. As expected, the farmed populations were clustered together, while the Slovak and Spanish populations formed two separate clusters. Identified traces of genetic admixture in the gene pool of farmed populations reflected a strong contemporary migration rate between them. This study suggests that even if the history of deer farming has been shorter than traditional livestock species, it may leave significant traces in the genome structure.

Genetic traces of dispersal and admixture in red deer (Cervus elaphus) populations from the Carpathian Basin

After the last glacial, the Carpathian Basin was repopulated from either eastward or northward colonisation routes for various species; one of these was the emblematic member of the European megafauna, the red deer, Cervus elaphus. We analysed 303 red deer individuals from the middle of the region, in seven Hungarian game reserves, at ten microsatellite loci (C01, C229, T26, T108, T123, T156, T172, T193, T501, T507), to investigate the genetic diversity of these subpopulations. We discovered high levels of genetic diversity of red deer subpopulations; allelic richness values ranging 4.99–7.01, observed heterozygosity 0.729–0.800, polymorphic information content 0.722–0.806, and Shannon’s information index 1.668–2.064. Multi-locus analyses indicated population admixtures of various degrees that corresponded to geographical location, and complex genetic structures were shown by clustering. Populations in the south-western and the north-eastern parts of the region formed two highly separated groups, and the red deer from populations in between them were highly admixed (in western Pannonia/Transdanubia, where the Danube flows into the Carpathian Basin). This pattern corresponds to the distribution of mitochondrial as well as Y-chromosome lineages. Assignment tests showed that a large fraction of individuals (29.4%) are found outside of their population of origin, indicating that the dispersal of red deer is rather common, which could be expected considering the life course of the species.

European-native vocalizing: sex and age-class acoustic variation in the Central European red deer (Cervus elaphus)

Within-population acoustic variation of European red deer Cervus elaphus follows two empirically established common rules: Rule 1: suggesting similar-pitched stag and hind calls because of potential prevalence of natural over sexual selection on call pitch; and Rule 2: predicting lower-pitched calls in adults, because larger vocal folds normally produce lower-pitched calls in mammals. We found that both rules were supported for native Pannonian red deer from Central Europe. All fundamental frequency () parameter values of hind contact calls (for the exclusion of the beginning ) were indistinguishable from those of stag rutting roars. These results agree with published data on vocalization of male and female American and Asian wapiti Cervus canadensis. Calls of adults of either sex were lower in frequency than calf calls. These results disagree with data collected from adult and young American wapiti producing same-frequency calls, probably because of a distinctive mechanism of sound production (whistling).

Genetic insights into an Apennine population of the Italian red deer

The red deer Cervus elephus has been a common species in Italy until the Middle Ages and the Renaissance, when its distribution range started to considerably decrease, due to gradual deforestation and hunting pressure. Afterwards, the red deer has been reintroduced to many regions of the world, including Italy. In the Italian Apennines, the Acquerino-Cantagallo Natural Reserve (ACQUERINO) hosts one of the largest peninsular red deer populations, originated from a series of successful reintroductions. In this study, we meant to detect the level of genetic variability of Acquerino-Cantagallo Natural Reserve deer population and to investigate the genetic relationships with the other Italian and European populations. We identified five mitochondrial DNA control region (D-loop) haplotypes, four falling in lineage A and one falling in lineage C, derived from at least two maternal lineages, confirming that ACQUERINO population should be the result of multiple reintroductions. Haplotype diversity (H = 0.50) and nucleotide (π = 0.004) diversity were low, but included into the deer range values. ACQUERINO population showed low levels of genetic diversity when compared to other European and Mediterranean populations, confirming that this expanding population may have been generated from a low number of founders.

Vocal phenotype of male rutting roars and genetic markers delineate East European red deer (Cervus elaphus) from Central and West European populations

This study investigates a population of red deer Cervus elaphus, founded by 10 individuals introduced in the nineteenth century from Germany to the Voronezh region of the European part of Southern Russia and then developed without further introductions. We characterize for the first time the vocal phenotype of the Voronezh red deer male rutting calls in comparison with similar data on the Pannonian (native Central European) and Iberian (native West European) red deer obtained by the authors during preceding studies. In addition, we provide for the first time the genetic data on Pannonian red deer. In Voronezh stags, the number of roars per bout (2.85 ± 1.79) was lower than in Pannonian (3.18 ± 2.17) but higher than in Iberian (2.11 ± 1.71) stags. In Voronezh stags, the duration of main (the longest within bouts) roars was longer (2.46 ± 1.14 s) than in Pannonian (1.13 ± 0.50 s) or Iberian (1.90 ± 0.50 s) stags. The maximum fundamental frequency of main roars was similar between Voronezh (175 ± 60 Hz) and Pannonian (168 ± 61 Hz) but higher in Iberian stags (223 ± 35 Hz). Mitochondrial cytochrome b gene analysis of red deer from the three study populations partially supports the bioacoustical data, of closer similarity between Voronezh and Pannonian populations. In contrast, microsatellite DNA analysis delineates Voronezh red deer from either Pannonian or Iberian red deer. We discuss that population bottlenecking might affect the acoustics of the rutting roars, in addition to genotype.

Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis

Host genetic diversity tends to limit disease spread in nature and buffers populations against epidemics. Genetic diversity in wildlife is expected to receive increasing attention in contexts related to disease transmission and human health. Ungulates such as wild boar (Sus scrofa) and red deer (Cervus elaphus) are important zoonotic hosts that can be precursors to disease emergence and spread in humans. Tuberculosis is a zoonotic disease with relevant consequences and can present high prevalence in wild boar and red deer populations. Here, we review studies on the genetic diversity of ungulates and determine to what extent these studies consider its importance on the spread of disease. This assessment also focused on wild boar, red deer, and tuberculosis. We found a disconnection between studies treating genetic diversity and those dealing with infectious diseases. Contrarily, genetic diversity studies in ungulates are mainly concerned with conservation. Despite the existing disconnection between studies on genetic diversity and studies on disease emergence and spread, the knowledge gathered in each discipline can be applied to the other. The bidirectional applications are illustrated in wild boar and red deer populations from Spain, where TB is an important threat for wildlife, livestock, and humans.

Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape

Red deer (Cervus elaphus) throughout central Europe are influenced by different anthropogenic activities including habitat fragmentation, selective hunting and translocations. This has substantial impacts on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, anthropogenic infrastructures) potentially has led to low levels of genetic diversity. Mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. Based on these findings, we suggest that connectivity among existing management units should be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.

Microsatellite based assignment reveals history of extirpated mountain ungulate

During the early 1900s, Northern chamois (Rupicapra rupicapra) populations in the northern Dinaric Mountains were extirpated. During the 1960s and 1970s there were several reintroductions of individuals from two Northern chamois subspecies (Alpine chamois, R. r. rupicapra and Balkan chamois, R. r. balcanica) from neighbouring areas in the attempt to re-establish the population. Accurate taxonomic classification, at subspecies level, of the autochthonous extirpated population was not known. To clarify which subspecies was present before reintroduction, we genotyped four male chamois skulls originating from Velebit Mountain, collected around 25 years before the population local extinction. DNA was successfully extracted from middle layer and outer sheath of horns. Assignment based on microsatellite loci, using both Bayesian clustering in STRUCTURE (with q values between 0.55 and 0.73) and DAPC (with individual membership probabilities of 0.99 and 1.00) indicated higher assessed likelihood for the Alpine subspecies.

Landscape genetic analyses of Cervus elaphus and Sus scrofa: comparative study and analytical developments

Red deer and wild boar are two major game species whose populations are managed and live in areas impacted by human activities. Measuring and understanding the impact of landscape features on individual movements and spatial patterns of genetic variability in these species is thus of importance for managers. A large number of individuals sampled across Wallonia (Belgium) for both species have been genotyped using microsatellite markers (respectively > 1700 and > 1200 genotyped individuals) and some individuals have also been followed using a capture-mark-recapture (CMR) protocol. The combined data set represents an unprecedented opportunity to study and compare the environmental factors impacting the interconnectivity of these large mammals. The present study describes and uses a landscape genetic workflow to compare spatial patterns of genetic variability and the impact of environmental factors on genetic differentiation. For the latter analyses, we investigate the correlation between genetic and environmental distances (pairwise approach) and also between local genetic dissimilarity and environmental conditions (point approach). Preliminary analyses of CMR data confirm that motorways act as significant barriers to dispersal. However, analyses performed with the pairwise approach do not highlight any evidence of an impact of motorways on genetic differentiation, which is presumably due to their recent establishment. Complementary analyses performed with the point approach reveal that low altitude tends to be associated with higher genetic dissimilarity. From a methodological point of view, the present workflow illustrates the complementary application of both pairwise and point approaches, as well as univariate and multivariate analyses.

Connections and containers: Using genetic data to understand how watershed evolution and human activities influence cutthroat trout biogeography

Species with large geographic distributions often exhibit complex patterns of diversity that can be further complicated by human activities. Cutthroat trout (Oncorhynchus clarkii) are one of the most widely distributed freshwater fish species in western North America exhibiting substantial phenotypic and genetic variability; however, fish stocking practices have translocated populations outside of their native range and may have obscured intraspecific boundaries. This study focuses on cutthroat trout populations representing three distinct evolutionary clades that are found intermixed within a contact zone between the Bonneville and upper Snake River watersheds in the western United States. We used mitochondrial and microsatellite genetic data, as well as historical stocking records, to evaluate whether populations of cutthroat trout in the contact zone are native or are introduced. We found significant genetic differentiation and fine-scale genetic population structure that was organized primarily by watershed boundaries. While we detected increased genetic diversity in some areas in close proximity to the greatest number of stocking events, the highly organized population structure both within and between areas of the contact zone indicates that the populations are native to the watersheds. Intermixing of distinct evolutionary lineages of cutthroat trout appears to be the result of historical connections between paleodrainages. Our analyses provide a context for understanding how genetic data can be used to assess the status of populations as native or introduced.

Using genetic tools to estimate the prevalence of non-native red deer (Cervus elaphus) in a Western European population

Game species like the red deer have been subjected to anthropogenic impacts for centuries. Translocations are often carried out—sometimes illegally—not only for sporting purposes, but also to increase trophy quality, reduce inbreeding, or mitigate bottlenecks after excessive persecution. Apart from the blurring of large‐scale genetic structure, translocations without adequate quarantine measure risk introducing pathogens into potentially immunologically naïve populations. It is therefore important to understand the frequency of clandestine translocations. Identification of non‐autochthonous animals and their potential origin is often difficult and, in red deer, has been hampered by the lack of large‐scale genotypic datasets for comparison. In the present study, we make use of a recently published European‐wide microsatellite dataset to detect and quantify the presence of non‐autochthonous red deer in a large population sample (n = 1,780) from Central Europe (Belgium). Using factorial correspondence analysis, assignment tests and Bayesian clustering algorithms we arrive at an estimate of 3.7% non‐autochthonous animals (or their descendants). Some of these animals were assigned to a nearby French population and may have immigrated into Belgium naturally, but the large majority must have been introduced by humans. Our analysis pointed to the British Isles and Germany/Poland as the potential origin of many introduced deer, regions known to have been source populations for translocations in Europe and beyond. We found evidence for recreational hunters using carcasses from farmed deer to fulfill mandatory hunting quotas. Our study is the first to quantify the extent of human‐mediated introductions in a European game species at such a large scale with large and representative sample sizes.