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 diversity, genetic structure and diet of ancient and contemporary red deer (Cervus elaphus L.) from north-eastern France

In north-eastern France, red deer (Cervus elaphus L.) populations were rebuilt from a few hundred individuals, which have subsisted in remote valleys of the Vosges mountains, and to a lesser extent from individuals escaped from private enclosures; at present times, this species occupies large areas, mainly in the Vosges Mountains. In this study, we examined the population dynamics of red deer in the Vosges Mountains using ancient and contemporary mitochondrial DNA (mtDNA) from 140 samples (23 ancient + 117 modern) spanning the last 7'000 years. In addition, we reconstructed the feeding habits and the habitat of red deer since the beginning of agriculture applying isotopic analyses in order to establish a basis for current environmental management strategies. We show that past and present red deer in the Vosges Mountains belong to mtDNA haplogroup A, suggesting that they originated from the Iberian refugium after the last glacial maximum (LGM). Palaeogenetic analysis of ancient bone material revealed the presence of two distinct haplotypes with different temporal distributions. Individuals belonging to the two haplotype groups apparently occupied two different habitats over at least 7'000 years. AM6 correlates with an ecological type that feeds in densely forested mountain landscapes, while AM235 correlates with feeding in lowland landscapes, composed of a mixture of meadows and riverine, herb-rich woodlands. Our results suggest that red deer of north-eastern France was able to adapt, over the long term, to these different habitat types, possibly due to efficient ethological barriers. Modern haplotype patterns support the historical record that red deer has been exposed to strong anthropogenic influences as a major game species.

Genetic wealth, population health: Major histocompatibility complex variation in captive and wild ring-tailed lemurs (Lemur catta)

Across species, diversity at the major histocompatibility complex (MHC) is critical to individual disease resistance and, hence, to population health; however, MHC diversity can be reduced in small, fragmented, or isolated populations. Given the need for comparative studies of functional genetic diversity, we investigated whether MHC diversity differs between populations which are open, that is experiencing gene flow, versus populations which are closed, that is isolated from other populations. Using the endangered ring-tailed lemur (Lemur catta) as a model, we compared two populations under long-term study: a relatively "open," wild population (n = 180) derived from Bezà Mahafaly Special Reserve, Madagascar (2003-2013) and a "closed," captive population (n = 121) derived from the Duke Lemur Center (DLC, 1980-2013) and from the Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed MHC-DRB diversity and, across populations, we compared the number of unique MHC-DRB alleles and their distributions. Wild individuals possessed more MHC-DRB alleles than did captive individuals, and overall, the wild population had more unique MHC-DRB alleles that were more evenly distributed than did the captive population. Despite management efforts to maintain or increase genetic diversity in the DLC population, MHC diversity remained static from 1980 to 2010. Since 2010, however, captive-breeding efforts resulted in the MHC diversity of offspring increasing to a level commensurate with that found in wild individuals. Therefore, loss of genetic diversity in lemurs, owing to small founder populations or reduced gene flow, can be mitigated by managed breeding efforts. Quantifying MHC diversity within individuals and between populations is the necessary first step to identifying potential improvements to captive management and conservation plans.

Immunogenetic heterogeneity in a widespread ungulate: the European roe deer (Capreolus capreolus)

Understanding how immune genetic variation is shaped by selective and neutral processes in wild populations is of prime importance in both evolutionary biology and epidemiology. The European roe deer (Capreolus capreolus) has considerably expanded its distribution range these last decades, notably by colonizing agricultural landscapes. This range shift is likely to have led to bottlenecks and increased roe deer exposure to a new range of pathogens that until recently predominantly infected humans and domestic fauna. We therefore investigated the historical and contemporary forces that have shaped variability in a panel of genes involved in innate and acquired immunity in roe deer, including Mhc-Drb and genes encoding cytokines or toll-like receptors (TLRs). Together, our results suggest that genetic drift is the main contemporary evolutionary force shaping immunogenetic variation within populations. However, in contrast to the classical view, we found that some innate immune genes involved in micropathogen recognition (e.g. Tlrs) continue to evolve dynamically in roe deer in response to pathogen-mediated positive selection. Most studied Tlrs (Tlr2, Tlr4 and Tlr5) had similarly high levels of amino acid diversity in the three studied populations including one recently established in southwestern France that showed a clear signature of genetic bottleneck. Tlr2 implicated in the recognition of Gram-positive bacteria in domestic ungulates, showed strong evidence of balancing selection. The high immunogenetic variation revealed here implies that roe deer are able to cope with a wide spectrum of pathogens and to respond rapidly to emerging infectious diseases.

Major Histocompatibility Complex (MHC) markers in conservation biology

Human impacts through habitat destruction, introduction of invasive species and climate change are increasing the number of species threatened with extinction. Decreases in population size simultaneously lead to reductions in genetic diversity, ultimately reducing the ability of populations to adapt to a changing environment. In this way, loss of genetic polymorphism is linked with extinction risk. Recent advances in sequencing technologies mean that obtaining measures of genetic diversity at functionally important genes is within reach for conservation programs. A key region of the genome that should be targeted for population genetic studies is the Major Histocompatibility Complex (MHC). MHC genes, found in all jawed vertebrates, are the most polymorphic genes in vertebrate genomes. They play key roles in immune function via immune-recognition and -surveillance and host-parasite interaction. Therefore, measuring levels of polymorphism at these genes can provide indirect measures of the immunological fitness of populations. The MHC has also been linked with mate-choice and pregnancy outcomes and has application for improving mating success in captive breeding programs. The recent discovery that genetic diversity at MHC genes may protect against the spread of contagious cancers provides an added impetus for managing and protecting MHC diversity in wild populations. Here we review the field and focus on the successful applications of MHC-typing for conservation management. We emphasize the importance of using MHC markers when planning and executing wildlife rescue and conservation programs but stress that this should not be done to the detriment of genome-wide diversity.

Impact of major histocompatibility complex class II polymorphisms on Iberian red deer parasitism and life history traits

Host genetic diversity plays an important role in buffering populations against pathogens. We characterized the allelic diversity at the second exon of the b (DRB-2) chain of the major histocompatibility complex class II (MHC-II) locus in a population of Iberian red deer (Cervus elaphus hispanicus) and its impact on parasitism by macroparasites, on a microparasite causing tuberculosis, and on relevant life history traits (spleen size and body condition). No DRB-2 haplotype conferred general resistance or susceptibility against all parasites. However, specific significant correlations were found between some DRB-2 haplotypes and specific parasites. We also detected associations between DRB-2 haplotypes and body condition and spleen size after controlling for body size, sex and age. Our results evidenced a functional significance of MHC-II genes in the defence of Iberian red deer against parasites. These results also support a role of MHC-II as a fitness-enhancing genetic element which can be mediated by parasite effects on life traits with a genetic basis. We conclude that MHC immunogenetic studies may assess management decisions in Iberian red deer because (i) loss of genetic diversity may lead to increased disease occurrence, and (ii) MHC genes are ecologically relevant since they underlie host infection rates and life history traits.