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The growing awareness of biodiversity by forest managers has fueled the demand for information on abiotic and biotic factors that determine spatial biodiversity patterns. Detailed and area-wide environmental data on potential predictors and site-specific habitat characteristics, however, are usually not available across large spatial extents. Recent developments in environmental data acquisition such as the advent of Light Detection And Ranging (LiDAR) remote sensing provide opportunities to characterize site-specific habitat conditions at a high level of detail and across large areas. Here, we used a dataset of regularly distributed local-scale records of vascular plant, bryophyte and snail (Gastropoda) species to model richness patterns in forests across an environmentally heterogeneous region in Central Europe (Switzerland). We spatially predicted species richness based on a set of area-wide environmental factors representing climate, topography, soil pH and remotely sensed vegetation structure. Additionally, we investigated the relationship between species richness and field measures of forest stand structure and composition obtained from National Forest Inventory (NFI) data to identify potential target variables for habitat management. The predictions for species richness were most accurate for snails, followed by bryophyte and vascular plants, with R² values ranging from 0.37 to 0.07. Besides climate, site-specific factors such as soil pH, indices of topographic position and wetness as well as canopy structure were important for predicting species richness of all three target groups. Several NFI variables were identified as potential target variables for managing snail species richness. Stands with tree species from the genera Fraxinus, Tilia, Ulmus and Acer, for example, showed a positive relationship with snail species richness, as did an increasing overstory cover or higher volumes of deadwood. However, only weak relationships were found between NFI variables and species richness of vascular plants, and none for bryophytes. Our findings support the assumption that besides climate, site-specific habitat factors are important determinants of spatial variation of species richness at the local scale. The strength and direction of the determinants vary with taxa, thus indicating a functional relationship between site conditions and the respective species community.

Zellweger, F., Braunisch, V., Morsdorf, F., Baltensweiler, A., Abegg, M., Roth, T., Bugmann, H., & Bollmann, K. (2015). Disentangling the effects of climate, topography, soil and vegetation on stand-scale species richness in temperate forests. Forest Ecology and Management, 349, 36–44. https://doi.org/10.1016/j.foreco.2015.04.008

The hypotheses that beta diversity should increase with decreasing latitude and increase with spatial extent of a region have rarely been tested based on a comparative analysis of multiple datasets, and no such study has focused on stream insects. We first assessed how well variability in beta diversity of stream insect metacommunities is predicted by insect group, latitude, spatial extent, altitudinal range, and dataset properties across multiple drainage basins throughout the world. Second, we assessed the relative roles of environmental and spatial factors in driving variation in assemblage composition within each drainage basin. Our analyses were based on a dataset of 95 stream insect metacommunities from 31 drainage basins distributed around the world. We used dissimilarity-based indices to quantify beta diversity for each metacommunity and, subsequently, regressed beta diversity on insect group, latitude, spatial extent, altitudinal range, and dataset properties (e.g., number of sites and percentage of presences). Within each metacommunity, we used a combination of spatial eigenfunction analyses and partial redundancy analysis to partition variation in assemblage structure into environmental, shared, spatial, and unexplained fractions. We found that dataset properties were more important predictors of beta diversity than ecological and geographical factors across multiple drainage basins. In the within-basin analyses, environmental and spatial variables were generally poor predictors of variation in assemblage composition. Our results revealed deviation from general biodiversity patterns because beta diversity did not show the expected decreasing trend with latitude. Our results also call for reconsideration of just how predictable stream assemblages are along ecological gradients, with implications for environmental assessment and conservation decisions. Our findings may also be applicable to other dynamic systems where predictability is low.

Heino, J., Melo, A. S., Bini, L. M., Altermatt, F., Al-Shami, S. A., Angeler, D. G., Bonada, N., Brand, C., Callisto, M., Cottenie, K., Dangles, O., Dudgeon, D., Encalada, A., Göthe, E., Grönroos, M., Hamada, N., Jacobsen, D., Landeiro, V. L., Ligeiro, R., … Townsend, C. R. (2015). A comparative analysis reveals weak relationships between ecological factors and beta diversity of stream insect metacommunities at two spatial levels. Ecology and Evolution, 5(6), 1235–1248. https://doi.org/10.1002/ece3.1439

Aquatic biodiversity in rivers and streams is threatened in many regions worldwide. As biodiversity loss has severe consequences on ecosystem functioning, it is important to understand the causes of decline and to predict biodiversity in space and time. In order to achieve this, the identification of the driving factors and the appropriate choice of indicator groups are needed. We developed a spatially explicit habitat distribution model for aquatic macroinvertebrates in Swiss watercourse networks using national biodiversity monitoring data from 410 randomly selected sampling sites. We specifically looked at two worldwide frequently used macroinvertebrate indicator groups. Using generalized linear models, we related firstly species richness of mayfly, stonefly and caddisfly (Ephemeroptera, Plecoptera, Trichoptera; EPT) and secondly richness of all macroinvertebrate families and higher-order taxa (macroinvertebrate family richness) to 38 nationwide available environmental variables. We then predicted richness of both indicator groups at the landscape scale, providing the first nationwide prediction of EPT species and macroinvertebrate family richness. Consistent with previous work, we found that variables describing land use and topology were most important for explaining richness at the landscape level. However, the two indicator groups showed opposing patterns of richness and a different sensitivity to land-use variables. This indicates that the sole use of one of these groups may be misleading with respect to water quality assessments and to the identification of overall diversity hotspots. We conclude that commonly used richness patterns derived from aggregated groups, such as family-level macroinvertebrate richness, may be less appropriate for conservation strategies.

Kaelin, K., & Altermatt, F. (2016). Landscape-level predictions of diversity in river networks reveal opposing patterns for different groups of macroinvertebrates. Aquatic Ecology, 50(2), 283–295. https://doi.org/10.1007/s10452-016-9576-1

Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development. Here, we propose an approach to deal with multiple primer-binding sites by purposefully positioning primers within the detected repetitive element. We developed a new protocol to determine the family type and the primer position in relation to MDFs using the software packages REPARK and REPEATMASKER together with an in-house R script. We re-evaluated newly developed nSSR markers for the lepidopteran Marbled White (Melanargia galathea) and explored the implications of our results with regard to published data sets of the butterfly Euphydryas aurinia, the grasshopper Stethophyma grossum, the conifer Pinus cembra and the crucifer Arabis alpina. For M. galathea, we show that it is not only possible to develop reliable nSSR markers for MDF loci, but even to benefit from their presence in some cases: We used one unlabelled primer, successfully binding within an MDF, for two different loci in a multiplex PCR, combining this family primer with uniquely binding and fluorescently labelled primers outside of MDFs, respectively. As MDFs are abundant in many taxa, we propose to consider these during nSSR marker development in taxa concerned. Our new approach might help in reducing the number of tested primers during nSSR marker development.

Schmid, M., Csencsics, D., & Gugerli, F. (2016). Repetitive flanking sequences challenge microsatellite marker development: A case study in the lepidopteran Melanargia galathea. Molecular Ecology Resources, 16(6), 1499–1507. https://doi.org/10.1111/1755-0998.12547