Spatiotemporal land use modelling to assess land availability for energy crops – illustrated for Mozambique

A method and tool have been developed to assess future developments in land availability for bioenergy crops in a spatially explicit way, while taking into account both the developments in other land use functions, such as land for food, livestock and material production, and the uncertainties in the key determinant factors of land use change (LUC). This spatiotemporal LUC model is demonstrated with a case study on the developments in the land availability for bioenergy crops in Mozambique in the timeframe 2005–2030. The developments in the main drivers for agricultural land use, demand for food, animal products and materials were assessed, based on the projected developments in population, diet, GDP and self‐sufficiency ratio. Two scenarios were developed: a business‐as‐usual (BAU) scenario and a progressive scenario. Land allocation was based on land use class‐specific sets of suitability factors. The LUC dynamics were mapped on a 1 km² grid level for each individual year up to 2030. In the BAU scenario, 7.7 Mha and in the progressive scenario 16.4 Mha could become available for bioenergy crop production in 2030. Based on the Monte Carlo analysis, a 95% confidence interval of the amount of land available and the spatially explicit probability of available land was found. The bottom‐up approach, the number of dynamic land uses, the diverse portfolio of LUC drivers and suitability factors, and the possibility to model uncertainty mean that this model is a step forward in modelling land availability for bioenergy potentials.     

Distribution and population structure of the anther smut Microbotryum silenes‐acaulis parasitizing an arctic–alpine plant

Cold‐adapted organisms with current arctic–alpine distributions have persisted during the last glaciation in multiple ice‐free refugia, leaving footprints in their population structure that contrast with temperate plants and animals. However, pathogens that live within hosts having arctic–alpine distributions have been little studied. Here, we therefore investigated the geographical range and population structure of a fungus parasitizing an arctic–alpine plant. A total of 1437 herbarium specimens of the plant Silene acaulis were examined, and the anther smut pathogen Microbotryum silenes‐acaulis was present throughout the host's geographical range. There was significantly greater incidence of anther smut disease in more northern latitudes and where the host locations were less dense, indicating a major influence of environmental factors and/or host demographic structure on the pathogen distribution. Genetic analyses with seven microsatellite markers on recent collections of 195 M. silenes‐acaulis individuals revealed three main genetic clusters, in North America, northern Europe and southern Europe, likely corresponding to differentiation in distinct refugia during the last glaciation. The lower genetic diversity in northern Europe indicates postglacial recolonization northwards from southern refugia. This study combining herbarium surveys and population genetics thus uniquely reveals the effects of climate and environmental factors on a plant pathogen species with an arctic–alpine distribution.     

Divergent selection and drift shape the genomes of two avian sister species spanning a saline–freshwater ecotone

The role of species divergence due to ecologically based divergent selection—or ecological speciation—in generating and maintaining biodiversity is a central question in evolutionary biology. Comparison of the genomes of phylogenetically related taxa spanning a selective habitat gradient enables discovery of divergent signatures of selection and thereby provides valuable insight into the role of divergent ecological selection in speciation. Tidal marsh ecosystems provide tractable opportunities for studying organisms' adaptations to selective pressures that underlie ecological divergence. Sharp environmental gradients across the saline–freshwater ecotone within tidal marshes present extreme adaptive challenges to terrestrial vertebrates. Here, we sequence 20 whole genomes of two avian sister species endemic to tidal marshes—the saltmarsh sparrow (Ammospiza caudacutus) and Nelson's sparrow (A. nelsoni)—to evaluate the influence of selective and demographic processes in shaping genome‐wide patterns of divergence. Genome‐wide divergence between these two recently diverged sister species was notably high (genome‐wide F_ST = 0.32). Against a background of high genome‐wide divergence, regions of elevated divergence were widespread throughout the genome, as opposed to focused within islands of differentiation. These patterns may be the result of genetic drift resulting from past tidal march colonization events in conjunction with divergent selection to different environments. We identified several candidate genes that exhibited elevated divergence between saltmarsh and Nelson's sparrows, including genes linked to osmotic regulation, circadian rhythm, and plumage melanism—all putative candidates linked to adaptation to tidal marsh environments. These findings provide new insights into the roles of divergent selection and genetic drift in generating and maintaining biodiversity.     

The difficulty of using species distribution modelling for the conservation of refugee species – the example of European bison

Refugee species have been confined to suboptimal habitat through historic anthropogenic factors. If this is unknown, management might actively conserve these species in suboptimal habitat assuming it represents optimal habitat. Similarly, species distribution modelling (SDM) might misguide conservation management of refugee species by only using presence data from suboptimal habitats. We illustrate this by commenting on a recent SDM for European bison that reconstructed the historic distribution of the species. We challenge the interpretation of this model by suggesting an alternative historic biogeography based on the refugee species concept. We argue that, in the case of refugee species, historic reconstructions using SDM cannot be used as a template for conservation management. Rather, experimental re‐introduction programmes should provide us with population performance and life history data from a range of suboptimal to optimal habitats. Such data could be used in mechanistic niche modelling to predict potential distribution of refugee species.     

Mapping the spatial distribution of the biomass and filter‐feeding effect of invasive dreissenid mussels on the winter‐spring phytoplankton bloom in Lake Michigan

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Regional vegetation mapping in Australia: a case study in the practical use of statistical modelling

Conservation evaluation of large areas ( > 10 000 km²) in Australia requires detailed mapping of vegetation types. Predicting the original vegetation cover of extensive cleared areas in an explicit, consistent and repeatable manner necessitates the use of statistical modelling. This paper describes an integrated approach to vegetation mapping in a region of New South Wales, Australia. The approach uses separate statistical models for each tree and shrub species to predict the vegetation composition in each grid cell in a geographic information system (GIS). Allocation of these grid cells to communities allows communities that no longer exist in the remaining remnants of woodland to be defined. Examples of use of this information for management are presented. This paper addresses the practical considerations which constrain the way statistical modelling can be used for vegetation mapping in an applied project. Constraints include: (1) data availability (use of sampling to fill gaps in existing data), (2) the effects of cover abundance values, (3) availability of GIS predictors, (4) data management, (5) current generalised additive model methods and (6) prediction methods. Careful attention to the practicality of all components of a vegetation mapping study is essential if modern methods are to be applied in regional studies which must provide functional products for land managers with limited resources, skills and finances at their disposal.     

Deer do not affect short‐term rates of vegetation recovery in overwash fans on Fire Island after Hurricane Sandy

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Upward elevation and northwest range shifts for alpine Meconopsis species in the Himalaya–Hengduan Mountains region

Climate change may impact the distribution of species by shifting their ranges to higher elevations or higher latitudes. The impacts on alpine plant species may be particularly profound due to a potential lack of availability of future suitable habitat. To identify how alpine species have responded to climate change during the past century as well as to predict how they may react to possible global climate change scenarios in the future, we investigate the climatic responses of seven species of Meconopsis, a representative genus endemic in the alpine meadow and subnival region of the Himalaya–Hengduan Mountains. We analyzed past elevational shifts, as well as projected shifts in longitude, latitude, elevation, and range size using historical specimen records and species distribution modeling under optimistic (RCP 4.5) and pessimistic (RCP 8.5) scenarios across three general circulation models for 2070. Our results indicate that across all seven species, there has been an upward shift in mean elevation of 302.3 m between the pre‐1970s (1922–1969) and the post‐1970s (1970–2016). The model predictions suggest that the future suitable climate space will continue to shift upwards in elevation (as well as northwards and westwards) by 2070. While for most of the analyzed species, the area of suitable climate space is predicted to expand under the optimistic emission scenario, the area contracts, or, at best, shows little change under the pessimistic scenario. Species such as M. punicea, which already occupy high latitudes, are consistently predicted to experience a contraction of suitable climate space across all the models by 2070 and may consequently deserve particular attention by conservation strategies. Collectively, our results suggest that the alpine high‐latitude species analyzed here have already been significantly impacted by climate change and that these trends may continue over the coming decades.     

Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range‐wide genetic diversity based on nuclear microsatellite data and detected four well‐differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modelled the ecological niche of Amborella based on the current climatic and environmental conditions. The predictive ability of the model was very good throughout the Central East mainland zone, but Amborella was predicted in the northern part of the island where this plant has not been reported. Furthermore, no significant barrier was detected based on habitat suitability that could explain the genetic differentiation across the area. Conversely, we found that the main genetic clusters could be related to the distribution of the suitable habitat at the last glacial maximum (LGM, c. 21 000 years BP), when Amborella experienced a dramatic 96.5% reduction in suitable area. At least two lineages survived in distinct putative refugia located in the Massif des Lèvres and in the vicinity of Mount Aoupinié. Our findings finally confirmed the importance of LGM rainforest refugia in shaping the current intra‐ and interspecific diversity in New Caledonian plants and revealed the possibility of an as yet unreported refugium. The combination of niche modelling and population genetics thereby offered novel insight into the biogeographical history of an emblematic taxon.     

Glacial refugia and postglacial expansion of the alpine–prealpine plant species Polygala chamaebuxus

The shrubby milkwort (Polygala chamaebuxus L.) is widely distributed in the Alps, but occurs also in the lower mountain ranges of Central Europe such as the Franconian Jura or the Bohemian uplands. Populations in these regions may either originate from glacial survival or from postglacial recolonization. In this study, we analyzed 30 populations of P. chamaebuxus from the whole distribution range using AFLP (Amplified Fragment Length Polymorphism) analysis to identify glacial refugia and to illuminate the origin of P. chamaebuxus in the lower mountain ranges of Central Europe. Genetic variation and the number of rare fragments within populations were highest in populations from the central part of the distribution range, especially in the Southern Alps (from the Tessin Alps and the Prealps of Lugano to the Triglav Massiv) and in the middle part of the northern Alps. These regions may have served, in accordance with previous studies, as long‐term refugia for the glacial survival of the species. The geographic pattern of genetic variation, as revealed by analysis of molecular variance, Bayesian cluster analysis and a PopGraph genetic network was, however, only weak. Instead of postglacial recolonization from only few long‐term refugia, which would have resulted in deeper genetic splits within the data set, broad waves of postglacial expansion from several short‐term isolated populations in the center to the actual periphery of the distribution range seem to be the scenario explaining the observed pattern of genetic variation most likely. The populations from the lower mountain ranges in Central Europe were more closely related to the populations from the southwestern and northern than from the nearby eastern Alps. Although glacial survival in the Bohemian uplands cannot fully be excluded, P. chamaebuxus seems to have immigrated postglacially from the southwestern or central‐northern parts of the Alps into these regions during the expansion of the pine forests in the early Holocene.     

Host–parasite genotypic interactions in the honey bee: the dynamics of diversity

Parasites are thought to be a major driving force shaping genetic variation in their host, and are suggested to be a significant reason for the maintenance of sexual reproduction. A leading hypothesis for the occurrence of multiple mating (polyandry) in social insects is that the genetic diversity generated within‐colonies through this behavior promotes disease resistance. This benefit is likely to be particularly significant when colonies are exposed to multiple species and strains of parasites, but host–parasite genotypic interactions in social insects are little known. We investigated this using honey bees, which are naturally polyandrous and consequently produce genetically diverse colonies containing multiple genotypes (patrilines), and which are also known to host multiple strains of various parasite species. We found that host genotypes differed significantly in their resistance to different strains of the obligate fungal parasite that causes chalkbrood disease, while genotypic variation in resistance to the facultative fungal parasite that causes stonebrood disease was less pronounced. Our results show that genetic variation in disease resistance depends in part on the parasite genotype, as well as species, with the latter most likely relating to differences in parasite life history and host–parasite coevolution. Our results suggest that the selection pressure from genetically diverse parasites might be an important driving force in the evolution of polyandry, a mechanism that generates significant genetic diversity in social insects.