Modelling Capercaillie (Tetrao urogallus) lek sites distribution and their limiting factors in a central Norwegian managed forest landscape

Forest management has substantially altered Fennoscandian forests through clear-cutting practices started during the 1950s. Impacts on the natural biodiversity in mature boreal forest have been inevitable. The Capercaillie (Tetrao urogallus) is often regarded as an indicator species for natural old growth forest, displaying on traditional lek sites during spring. In a heterogeneous forest landscape of two adjoining municipalities in central Norway we studied whether forest management or other environmental factors can have influenced the lek distribution. We identified 15 active leks and 12 recently abandoned leks. The maximum entropy distribution modelling (MaxEnt) was used to investigate factors associated with lek distribution at two different scales, where the scale reflecting the lek site areas gave the most adequate result. Active leks were predominantly associated with mature stands of forest. In 65% of the study area the habitat suitability for lekking was most influenced by forest management. Furthermore, the recently abandoned leks were found less frequently in low productive and mature forests than the still active ones, implying that previous leks in productive forest stands may have been lost through logging. Based on our data we have developed models for the predicted distribution and the current limiting factors, showing that altered forest management could improve lek site suitability in large parts of this boreal forest

The potential area of occupancy of non-native plants across a warming high-Arctic archipelago: Implications for strategic biosecurity management

The terrestrial high-Arctic has, so far, escaped the worst impacts of non-native plant establishment. However, increasing human activity and changing climate raise the risk of introductions and establishment, respectively. The lack of biosecurity in the terrestrial Arctic is thus of concern. To facilitate the development of biosecurity measures on the rapidly warming and highly trafficked archipelago of Svalbard, we generated ecological niche models to map the bioclimatic niche potential of 27 non-native established or door-knocker vascular plant species across Svalbard, identify species with a high risk of widespread occupancy, and locate hotspots of potential current and future invasions. Under the current climate the three species with the highest threat in terms of broad potential area of occupancy and known invasion potential were Deschampsia cespitosa, Ranunculus subborealis subsp. villosus and Saussurea alpina. However, under future climate, most of the considered species have potentially wide distributions across the archipelago. Remote eastern islands were a hotspot region for broader potential establishment of non-native species under the current climate. Our results suggest that many non-native plant species have a broader macroclimatic niche on Svalbard than they currently occupy, and that other factors probably limit both dispersal and establishment outside their current localised distributions. Environmental management on Svalbard has a limited window of opportunity to act early in containing and preventing the spread of non-native plant species beyond the few settlements where they currently exist. Moreover, preventing introductions and establishments on the remote and rarely visited islands of Edgeøya, Barentsøya and Bjørnøya could be also a priority action to safeguard sanctuaries of the archipelago’s natural ecosystems

Why don't all species overexploit?

Overexploitation of natural resources is often viewed as a problem characteristic of only the human species. However, any species could evolve a capacity to overexploit its essential resources through natural selection and competition, even to the point of resource collapse. Here, we describe the processes that potentially lead to overexploitation and synthesize what is known about overexploitation limiters in other species. We propose that there are five pathways that counteract the evolutionary drive towards overexploitation and/or mitigate its consequences: top-down trophic control, interference, cost-efficiency tradeoffs, resource trait evolution, and spatial heterogeneity. These mechanisms constrain the number of exploiters and/or lower the rate of the resource usage at the individual level. We hypothesize that in ecosystems with reasonable functional diversity, coevolution strengthens this limiter network, preventing overexploitation, and thus argue that diversity begets stability via evolution. Violent population cycles in species-poor northern ecosystems and eruptions of invading alien species are exceptions that confirm this rule, because these ecosystems either lack functional diversity or there has not been enough time for coevolution to play out its stabilizing role. We propose that the overexploitation by our own species could be prevented via a network of socio-economical limiters that act in an analogous way.</p

Will borealization of Arctic tundra herbivore communities be driven by climate warming or vegetation change?

Poleward shifts in species distributions are expected and frequently observed with a warming climate. In Arctic ecosystems, the strong warming trends are associated with increasing greenness and shrubification. Vertebrate herbivores have the potential to limit greening and shrub advance and expansion on the tundra, posing the question of whether changes in herbivore communities could partly mediate the impacts of climate warming on Arctic tundra. Therefore, future changes in the herbivore community in the Arctic tundra will depend on whether the community tracks the changing climates directly (i.e. occurs in response to temperature) or indirectly, in response to vegetation changes (which can be modified by trophic interactions). In this study, we used biogeographic and remotely sensed data to quantify spatial variation in vertebrate herbivore communities across the boreal forest and Arctic tundra biomes. We then tested whether present-day herbivore community structure is determined primarily by temperature or vegetation. We demonstrate that vertebrate herbivore communities are significantly more diverse in the boreal forest than in the Arctic tundra in terms of species richness, phylogenetic diversity and functional diversity. A clear shift in community structure was observed at the biome boundary, with stronger northward declines in diversity in the Arctic tundra. Interestingly, important functional traits characterizing the role of herbivores in limiting tundra vegetation change, such as body mass and woody plant feeding, did not show threshold changes across the biome boundary. Temperature was a more important determinant of herbivore community structure across these biomes than vegetation productivity or woody plant cover. Thus, our study does not support the premise that herbivore-driven limitation of Arctic tundra shrubification or greening would limit herbivore community change in the tundra. Instead, borealization of tundra herbivore communities is likely to result from the direct effect of climate warming

Combining population genomics and ecological niche modeling to assess taxon limits between Carex jemtlandica and C. lepidocarpa

Carex section Ceratocystis (Cyperaceae) is a group of recently evolved plant species, in which hybridization is frequent, introgression is documented, taxonomy is complex, and morphological boundaries are vague. Within this section, a unified taxonomic treatment of the Carex jemtlandica-Carex lepidocarpa species complex does not exist, and Norway may currently be the sole country accepting species rank for both. Carex jemtlandica is mainly confined to Fennoscandia and is thus a Fennoscandian conservation responsibility. This motivated us to test the principal hypothesis that both C. jemtlandica and C. lepidocarpa represent evolutionary significant units, and that both deserve their current recognition at species level. We investigated their evolutionary distinctiveness in Norway, using restriction site-associated DNA sequencing and ecological niche modeling. Our genomic results reveal two genetic clusters, largely corresponding to C. jemtlandica and C. lepidocarpa that also remain distinct in sympatry, despite clear indications of ongoing hybridization and introgression. The ecological niche modeling suggests that they occupy different environmental niches. Jointly, our results clearly show that C. jemtlandica and C. lepidocarpa represent separately evolving entities that should qualify recognition as evolutionary significant units. Given the high level of introgression compared to other hybridizing species pairs in Carex we recommend treating C. jemtlandica as a subspecies of C. lepidocarpa.Peer reviewe

What evidence exists for temporal variability in Arctic terrestrial and freshwater biodiversity throughout the Holocene? A systematic map protocol

Background: The Arctic tundra is subject to the greatest climate change-induced temperature rises of any biome. Both terrestrial and freshwater biota are responding to recent climate warming through variability in their distribution, abundance, and richness. However, uncertainty arises within models of future change when considering processes that operate over centennial timescales. A systematic evidence synthesis of centennial-scale variability in biodiversity does not currently exist for the Arctic biome. Here, we sought to address the primary research question: what evidence exists for temporal variability in Arctic terrestrial and freshwater biodiversity throughout the Holocene (11,650 years before present (yBP)-OyBP)? Methods: Consultation with stakeholders informed key definitions, scoping and the appropriateness of the research question. The research question was structured using a PECO framework-Arctic biota (P), a timestamped year in the Holocene (E), another year in the Holocene (C), and the dimensions of biodiversity that have been measured (O)-to inform the search strategy. Search strings were benchmarked against a test list of 100 known sources to ensure a specific and comprehensive return of literature. Searches will occur across 13 bibliographic databases. The eligibility criteria specify that sources must: (a) use 'proxy' methods to measure biodiversity; (b) fall within the spatial extent of the contemporary Arctic tundra biome; and (c) consist of a time-series that overlaps with 11,650yBP to OyBP (1950AD). Information coded from studies will include proxy-specific information to account for both temporal uncertainty (i.e., the characteristics of age-depth models and dating methods) and taxonomic uncertainty (i.e., the samples and processes used for taxonomic identification). We will assess temporal uncertainty within each source by determining the quality of dating methods and measures; this information will be used to harmonise dates onto the IntCa120 calibration curve and determine the available temporal resolution and extent of evidence through space. Key outputs of this systematic map will be: (1) a graph database containing the spatial-temporal properties of each study dataset with taxonomic harmonisation; and (2) a geographical map of the evidence base.Peer reviewe

Low Spatial Habitat Overlap of Herbivores in the High Arctic Tundra

Herbivores play a crucial role in shaping tundra ecosystems through their effects on vegetation, nutrient cycling, and soil abiotic factors. Understanding their habitat use, co-occurrence, and overlap is therefore essential for informing ecosystem-based management and conservation. In the High Arctic, only a marginal proportion of the land area is vegetated, and climate change is impacting herbivore population sizes and their habitats. In this study, we assessed the spatial habitat overlap of a vertebrate herbivore community based on: 1) regional predictive summer habitat suitability models for the resident Svalbard reindeer (Rangifer tarandus platyrhynchus), resident Svalbard rock ptarmigan (Lagopus muta hyperborea), and the migratory pink-footed goose (Anser brachyrhynchus), and 2) presence of fecal pellets, reflecting the annual habitat use of reindeer, ptarmigan, and geese, including the pink-footed goose and barnacle goose (Branta leucopsis). Our findings revealed that only small proportions of the available land cover (∼ 12,516 km2; all land area excluding glaciers and freshwater) are suitable for each of the species (habitat suitability [HS] \u3e 0.5): reindeer (22 %), ptarmigan (11 %), and pink-footed goose (4 %). Overlapping suitable habitat [HS \u3e 0.5] for reindeer and goose accounted for only 3 % of the total vegetated area (∼ 8848 km2) and was primarily found in heath and moist habitats dominated by mosses, graminoids, and herbaceous plants. The overlapping suitable habitat for reindeer and ptarmigan covered 8 % of the vegetated area, in higher elevation ridges with vegetation on drier substrates. The shared habitat for ptarmigan and goose, and all three species of herbivores, was less than 1 % of the vegetated area. Additionally, an assessment of fecal pellets suggested that the highest overlap in habitat use among reindeer and goose occurred in bird cliff moss tundra, followed by moss tundra and heath habitats. The small proportion of the vegetated area suitable for all three herbivores indicates a high degree of habitat differentiation. Therefore, different habitats need to be considered for the management and conservation of resident and migratory herbivore species in this High Arctic Archipelago. Moreover, our results underscore the importance of the small but productive parts of the landscape that were used by all herbivores

A method for identifying genetic heterogeneity within phenotypically defined disease subgroups.

Many common diseases show wide phenotypic variation. We present a statistical method for determining whether phenotypically defined subgroups of disease cases represent different genetic architectures, in which disease-associated variants have different effect sizes in two subgroups. Our method models the genome-wide distributions of genetic association statistics with mixture Gaussians. We apply a global test without requiring explicit identification of disease-associated variants, thus maximizing power in comparison to standard variant-by-variant subgroup analysis. Where evidence for genetic subgrouping is found, we present methods for post hoc identification of the contributing genetic variants. We demonstrate the method on a range of simulated and test data sets, for which expected results are already known. We investigate subgroups of individuals with type 1 diabetes (T1D) defined by autoantibody positivity, establishing evidence for differential genetic architecture with positivity for thyroid-peroxidase-specific antibody, driven generally by variants in known T1D-associated genomic regions.We acknowledge the help of the Diabetes and Inflammation Laboratory Data Service for access and quality control procedures on the data sets used in this study. The JDRF/Wellcome Trust Diabetes and Inflammation Laboratory is in receipt of a Wellcome Trust Strategic Award (107212; J.A.T.) and receives funding from the NIHR Cambridge Biomedical Research Centre. J.L. is funded by the NIHR Cambridge Biomedical Research Centre and is on the Wellcome Trust PhD program in Mathematical Genomics and Medicine at the University of Cambridge. C.W. is funded by the MRC (grant MC_UP_1302/5). We thank M. Simmonds, S. Gough, J. Franklyn, and O. Brand for sharing their AITD genetic association data set and all patients with AITD and control subjects for participating in this study. The AITD UK national collection was funded by the Wellcome Trust. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution