Green-up selection by red deer in heterogeneous, human-dominated landscapes of Central Europe.

The forage maturation hypothesis (FMH) assumes that herbivores cope with the trade-off between digestibility and biomass in forage by selecting vegetation at intermediate growth. The green wave hypothesis (GWH) extends the FMH to suggest how spatiotemporal heterogeneity in plant quality shapes migratory movements of herbivores. Growing empirical support for these hypotheses mainly comes from studies in vast landscapes with large-scale habitat heterogeneity. It is unclear, however, to what extent ungulates surf green waves in human-altered landscapes with small-scale heterogeneity in terms of land use and topography. We used plant phenological proxies derived from Sentinel 2 satellite data to analyze the habitat selection of 93 collared red deer (Cervus elaphus) in montane and alpine habitats. Using a step selection analysis, we investigated how plant phenology, that is, the instantaneous rate of green-up (IRG) and normalized difference vegetation index (NDVI), and a set of variables describing topography and human presence influenced red deer resource selection in open habitats. We learned that red deer selected areas with high biomass at green-up and avoided habitats with possible exposure to human activity. Additionally, landscape structure and topography strongly influenced spatial behavior of red deer. We further compared cumulative access to high-quality forage across migrant strategies and found migrants gained better access than residents. Many migratory individuals surfed the green wave, and their surfing behavior, however, became less pronounced with decreasing distance to settlements. Within the constraints of topography and human land use, red deer track spring green-up on a fine spatiotemporal scale and follow the green wave across landscapes in migration movements. Thus, they benefit from high-quality forage even in human-dominated landscapes with small-scale heterogeneity and vegetation emerging in a heterogenic, dynamic mosaic.

The evolutionary pathways for local adaptation in mountain hares.

Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole-genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. Demographic modelling suggested that the split of these mountain hares occurred around 20 thousand years ago, providing the opportunity to study adaptive evolution over a short timescale. Using genome-wide scans, we identified signatures of extreme differentiation among hares from distinct geographic areas that overlap with area-specific selective sweeps, suggesting targets for local adaptation. Several identified candidate genes are associated with traits related to the uniqueness of the different environments inhabited by the three groups of mountain hares, including coat colour, ability to live at high altitudes and variation in body size. In Irish mountain hares, a variant of ASIP, a gene previously implicated in introgression-driven winter coat colour variation in mountain and snowshoe hares (L. americanus), may underlie brown winter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptive seasonal colouration. Comparative genomic analyses across several hare species suggested that mountain hares' adaptive variants appear predominantly species-specific. However, using coalescent simulations, we also show instances where the candidate adaptive variants have been introduced via introgressive hybridization. Our study shows that standing adaptive variation, including that introgressed from other species, was a crucial component of the post-glacial dynamics of species.

Temperature increase and frost decrease driving upslope elevational range shifts in Alpine grouse and hares.

Global climate change has led to range shifts in plants and animals, thus threatening biodiversity. Latitudinal shifts have been shown to be more pronounced than elevational shifts, implying that northern range edge margins may be more capable to keeping pace with warming than upper elevational limits. Additionally, global climate change is expected to disadvantage habitat specialists. In the Alps, climatic variation along the elevation gradient allows the coexistence of habitat specialists and generalists. Alpine species are anticipated to adapt their elevational ranges to the change of various climate variables caused by global climate change. Regional differences might buffer elevational shifts. Furthermore, distinct climate variables might differently affect the shifts of habitat specialists and generalists. To study the effect of climate change on Alpine species, we analysed hunting bag, climate and biogeographical data of two grouse species (Tetrao tetrix and Lagopus muta) and two hare species (Lepus timidus varronis and L. europaeus) in Grisons, Switzerland, over a period of 30 years. Our results based on 84,630 harvested specimens were as follows: (1) only three out of seven climate variables changed significantly within the study period. (2) The grouse species significantly shifted towards higher elevations, whereas the hare species only shifted in their minimum/maximum elevations. (3) Hunting elevation of habitat generalists increased more than in habitat specialists. (4) The elevational shifts were mostly related to the number of frost days. (5) Hunting elevation increased especially in the southern biogeographical region. To conclude, all four taxa respond to climate change but habitat generalists more rapidly than habitat specialists. The range shift to higher elevations due to global climate change will lead to a reduction in habitat availability for snow-adapted species. Climate change is thus a serious threat to alpine biodiversity. Regions rich in alpine habitats will have an increased responsibility to conserve these species.

Stable body size of Alpine ungulates.

In many species, decreasing body size has been associated with increasing temperatures. Although climate-induced phenotypic shifts, and evolutionary impacts, can affect the structure and functioning of marine and terrestrial ecosystems through biological and metabolic rules, evidence for shrinking body size is often challenged by (i) relatively short intervals of observation, (ii) a limited number of individuals, and (iii) confinement to small and isolated populations. To overcome these issues and provide important multi-species, long-term information for conservation managers and scientists, we compiled and analysed 222 961 measurements of eviscerated body weight, 170 729 measurements of hind foot length and 145 980 measurements of lower jaw length, in the four most abundant Alpine ungulate species: ibex (Capra ibex), chamois (Rupicapra rupicapra), red deer (Cervus elaphus) and roe deer (Capreolus capreolus). Regardless of age, sex and phylogeny, the body mass and size of these sympatric animals, from the eastern Swiss Alps, remained stable between 1991 and 2013. Neither global warming nor local hunting influenced the fitness of the wild ungulates studied at a detectable level. However, we cannot rule out possible counteracting effects of enhanced nutritional resources associated with longer and warmer growing seasons, as well as the animals' ability to migrate along extensive elevational gradients in the highly diversified alpine landscape of this study.

Transcriptomic regulation of seasonal coat color change in hares.

Color molts from summer brown to winter white coats have evolved in several species to maintain camouflage year-round in environments with seasonal snow. Despite the eco-evolutionary relevance of this key phenological adaptation, its molecular regulation has only recently begun to be addressed. Here, we analyze skin transcription changes during the autumn molt of the mountain hare (Lepus timidus) and integrate the results with an established model of gene regulation across the spring molt of the closely related snowshoe hare (L. americanus). We quantified differences in gene expression among three stages of molt progression-"brown" (early molt), "intermediate," and "white" (late molt). We found 632 differentially expressed genes, with a major pulse of expression early in the molt, followed by a milder one in late molt. The functional makeup of differentially expressed genes anchored the sampled molt stages to the developmental timeline of the hair growth cycle, associating anagen to early molt and the transition to catagen to late molt. The progression of color change was characterized by differential expression of genes involved in pigmentation, circadian, and behavioral regulation. We found significant overlap between differentially expressed genes across the seasonal molts of mountain and snowshoe hares, particularly at molt onset, suggesting conservatism of gene regulation across species and seasons. However, some discrepancies suggest seasonal differences in melanocyte differentiation and the integration of nutritional cues. Our established regulatory model of seasonal coat color molt provides an important mechanistic context to study the functional architecture and evolution of this crucial seasonal adaptation.

Introgression drives repeated evolution of winter coat color polymorphism in hares.

Changing from summer-brown to winter-white pelage or plumage is a crucial adaptation to seasonal snow in more than 20 mammal and bird species. Many of these species maintain nonwhite winter morphs, locally adapted to less snowy conditions, which may have evolved independently. Mountain hares (Lepus timidus) from Fennoscandia were introduced into the Faroe Islands in 1855. While they were initially winter-white, within ∼65 y all Faroese hares became winter-gray, a morph that occurs in the source population at low frequency. The documented population history makes this a valuable model for understanding the genetic basis and evolution of the seasonal trait polymorphism. Through whole-genome scans of differentiation and single-nucleotide polymorphism (SNP) genotyping, we associated winter coat color polymorphism to the genomic region of the pigmentation gene Agouti, previously linked to introgression-driven winter coat color variation in the snowshoe hare (Lepus americanus). Lower Agouti expression in the skin of winter-gray individuals during the autumn molt suggests that regulatory changes may underlie the color polymorphism. Variation in the associated genomic region shows signatures of a selective sweep in the Faroese population, suggesting that positive selection drove the fixation of the variant after the introduction. Whole-genome analyses of several hare species revealed that the winter-gray variant originated through introgression from a noncolor changing species, in keeping with the history of ancient hybridization between the species. Our findings show the recurrent role of introgression in generating winter coat color variation by repeatedly recruiting the regulatory region of Agouti to modulate seasonal coat color change.

Acute and Chronic Lead Exposure in Four Avian Scavenger Species in Switzerland.

Despite irrefutable evidence of its negative impact on animal behaviour and physiology, lethal and sublethal lead poisoning of wildlife is still persistent and widespread. For scavenging birds, ingestion of ammunition, or fragments thereof, is the major exposure route. In this study, we examined the occurrence of lead in four avian scavengers of Switzerland and how it differs between species, regions, and age of the bird. We measured lead concentration in liver and bone of the two main alpine avian scavengers (golden eagle Aquila chrysaetos and bearded vulture Gypaetus barbatus) over the entire area of the Swiss Alps and two of the main avian scavengers occurring in the lowlands of Switzerland (red kite Milvus milvus and common raven Corvus corax). Of those four species, only the bearded vulture is an obligate scavenger. We found that lead burdens in the two alpine avian scavengers were higher than those found for the same species elsewhere in Europe or North America and reached levels compatible with acute poisoning, whereas lead burdens of the two lowland avian scavengers seemed to be lower. Several golden eagles, but only one red kite with abnormally high bone lead concentrations were found. In all four species, a substantial proportion of birds had elevated levels which presumably represent recent (liver lead levels) or past (bone lead levels) uptake of sublethal doses of lead.

Horn growth variation and hunting selection of the Alpine ibex.

Selective hunting can affect demographic characteristics and phenotypic traits of the targeted species. Hunting systems often involve harvesting quotas based on sex, age and/or size categories to avoid selective pressure. However, it is difficult to assess whether such regulations deter hunters from targeting larger "trophy" animals with longer horns that may have evolutionary consequences. Here, we compile 44,088 annually resolved and absolutely dated measurements of Alpine ibex (Capra ibex) horn growth increments from 8,355 males, harvested between 1978 and 2013, in the eastern Swiss Canton of Grisons. We aim to determine whether male ibex with longer horns were preferentially targeted, causing animals with early rapid horn growth to have shorter lives, and whether such hunting selection translated into long-term trends in horn size over the past four decades. Results show that medium- to longer-horned adult males had a higher probability of being harvested than shorter-horned individuals of the same age and that regulations do affect the hunters' behaviour. Nevertheless, phenotypic traits such as horn length, as well as body size and weight, remained stable over the study period. Although selective trophy hunting still occurs, it did not cause a measurable evolutionary response in Grisons' Alpine ibex populations; managed and surveyed since 1978. Nevertheless, further research is needed to understand whether phenotypic trait development is coinfluenced by other, potentially compensatory factors that may possibly mask the effects of selective, long-term hunting pressure.

Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares.

We report the first mountain hare (Lepus timidus) transcriptome, produced by de novo assembly of RNA-sequencing reads. Data were obtained from eight specimens sampled in two localities, Alps and Ireland. The mountain hare tends to be replaced by the invading European hare (Lepus europaeus) in their numerous contact zones where the species hybridize, which affects their gene pool to a yet unquantified degree. We characterize and annotate the mountain hare transcriptome, detect polymorphism in the two analysed populations and use previously published data on the European hare (three specimens, representing the European lineage of the species) to identify 4 672 putative diagnostic sites between the species. A subset of 85 random independent SNPs was successfully validated using PCR and Sanger sequencing. These valuable genomic resources can be used to design tools to assess population status and monitor hybridization between species.

European springtime temperature synchronises ibex horn growth across the eastern Swiss Alps.

Direct effects of climate change on animal physiology, and indirect impacts from disruption of seasonal synchrony and breakdown of trophic interactions are particularly severe in Arctic and Alpine ecosystems. Unravelling biotic from abiotic drivers, however, remains challenging because high-resolution animal population data are often limited in space and time. Here, we show that variation in annual horn growth (an indirect proxy for individual performance) of 8043 male Alpine ibex (Capra ibex) over the past four decades is well synchronised among eight disjunct colonies in the eastern Swiss Alps. Elevated March to May temperatures, causing premature melting of Alpine snowcover, earlier plant phenology and subsequent improvement of ibex food resources, fuelled annual horn growth. These results reveal dependency of local trophic interactions on large-scale climate dynamics, and provide evidence that declining herbivore performance is not a universal response to global warming even for high-altitude populations that are also harvested.

Mycoplasma conjunctivae infection is not maintained in alpine chamois in eastern Switzerland.

The occurrence of infectious keratoconjunctivitis (IKC) was assessed in alpine chamois (Rupicapra rupicapra rupicapra) in Grisons (Switzerland) from 1950 to 1999. The first IKC outbreaks were reported in the 1950's. Since then, the number of affected subpopulations constantly increased and, by 1999, IKC outbreaks were reported in 39 of 51 (77%) chamois sub-populations. From 1992-99, a total of 243 chamois which died of the consequences of IKC were recorded. The number of cases differed between years, and a distinct seasonal trend was observed. Infectious keratoconjunctivitis was more common during summer and autumn, with 48% of the cases recorded in August-October. Juveniles (< 4 yr of age) were mostly represented. To verify the presence of Mycoplasma conjunctivae in chamois we analyzed conjunctival swabs taken from animals affected with IKC. Among a sample of 28 affected chamois, M. conjunctivae was identified 14 times (50%). An indirect enzyme-linked immunosorbent assay (ELISA) was developed to detect specific M. conjunctivae antibodies in sera of alpine chamois with IKC. We performed a serologic investigation to assess whether M. conjunctivae infection is self-maintained in the chamois population in Grisons. In subpopulations with IKC oubreaks, seroprevalence was low (8%). Seroprevalence was even lower in subpopulations with recent IKC outbreaks (3%). We concluded that the M. conjunctivae infection is not self-maintained in alpine chamois in Grisons. The agent may originate in domestic sheep living in proximity to chamois during summer. Control of IKC in chamois should consider immunoprophylaxis in sheep or limiting interspecific transmission of M. conjunctivae.