Directional turnover towards larger-ranged plants over time and across habitats.

Species turnover is ubiquitous. However, it remains unknown whether certain types of species are consistently gained or lost across different habitats. Here, we analysed the trajectories of 1827 plant species over time intervals of up to 78 years at 141 sites across mountain summits, forests, and lowland grasslands in Europe. We found, albeit with relatively small effect sizes, displacements of smaller- by larger-ranged species across habitats. Communities shifted in parallel towards more nutrient-demanding species, with species from nutrient-rich habitats having larger ranges. Because these species are typically strong competitors, declines of smaller-ranged species could reflect not only abiotic drivers of global change, but also biotic pressure from increased competition. The ubiquitous component of turnover based on species range size we found here may partially reconcile findings of no net loss in local diversity with global species loss, and link community-scale turnover to macroecological processes such as biotic homogenisation.

Response to Comment on "Forest microclimate dynamics drive plant responses to warming".

Schall and Heinrichs question our interpretation that the climatic debt in understory plant communities is locally modulated by canopy buffering. However, our results clearly show that the discrepancy between microclimate warming rates and thermophilization rates is highest in forests where canopy cover was reduced, which suggests that the need for communities to respond to warming is highest in those forests.

Response to Comment on "Forest microclimate dynamics drive plant responses to warming".

Bertrand et al question our interpretation about warming effects on the thermophilization in forest plant communities and propose an alternative way to analyze climatic debt. We show that microclimate warming is a better predictor than macroclimate warming for studying forest plant community responses to warming. Their additional analyses do not affect or change our interpretations and conclusions.

Forest microclimate dynamics drive plant responses to warming.

Climate warming is causing a shift in biological communities in favor of warm-affinity species (i.e., thermophilization). Species responses often lag behind climate warming, but the reasons for such lags remain largely unknown. Here, we analyzed multidecadal understory microclimate dynamics in European forests and show that thermophilization and the climatic lag in forest plant communities are primarily controlled by microclimate. Increasing tree canopy cover reduces warming rates inside forests, but loss of canopy cover leads to increased local heat that exacerbates the disequilibrium between community responses and climate change. Reciprocal effects between plants and microclimates are key to understanding the response of forest biodiversity and functioning to climate and land-use changes.

Replacements of small- by large-ranged species scale up to diversity loss in Europe's temperate forest biome.

Biodiversity time series reveal global losses and accelerated redistributions of species, but no net loss in local species richness. To better understand how these patterns are linked, we quantify how individual species trajectories scale up to diversity changes using data from 68 vegetation resurvey studies of seminatural forests in Europe. Herb-layer species with small geographic ranges are being replaced by more widely distributed species, and our results suggest that this is due less to species abundances than to species nitrogen niches. Nitrogen deposition accelerates the extinctions of small-ranged, nitrogen-efficient plants and colonization by broadly distributed, nitrogen-demanding plants (including non-natives). Despite no net change in species richness at the spatial scale of a study site, the losses of small-ranged species reduce biome-scale (gamma) diversity. These results provide one mechanism to explain the directional replacement of small-ranged species within sites and thus explain patterns of biodiversity change across spatial scales.

DIRS retrotransposons amplify via linear, single-stranded cDNA intermediates.

The Dictyostelium Intermediate Repeat Sequence 1 (DIRS-1) is the name-giving member of the DIRS order of tyrosine recombinase retrotransposons. In Dictyostelium discoideum, DIRS-1 is highly amplified and enriched in heterochromatic centromers of the D. discoideum genome. We show here that DIRS-1 it tightly controlled by the D. discoideum RNA interference machinery and is only mobilized in mutants lacking either the RNA dependent RNA polymerase RrpC or the Argonaute protein AgnA. DIRS retrotransposons contain an internal complementary region (ICR) that is thought to be required to reconstitute a full-length element from incomplete RNA transcripts. Using different versions of D. discoideum DIRS-1 equipped with retrotransposition marker genes, we show experimentally that the ICR is in fact essential to complete retrotransposition. We further show that DIRS-1 produces a mixture of single-stranded, mostly linear extrachromosomal cDNA intermediates. If this cDNA is isolated and transformed into D. discoideum cells, it can be used by DIRS-1 proteins to complete productive retrotransposition. This work provides the first experimental evidence to propose a general retrotransposition mechanism of the class of DIRS like tyrosine recombinase retrotransposons.

Response of soil mites (Acari, Mesostigmata) to long-term Norway spruce plantation along a mountain stream.

During the nineteenth and twentieth centuries, coniferous monocultures were introduced, replacing natural broadleaved forests in Central Europe, mainly for economic benefits. In the mountains, Norway spruce [Picea abies (L.) H. Karst] was introduced in large areas previously covered with beech forests and also in natural riverside habitat corridors such as river valleys, despite its negative impact on the soil environment by e.g. organic matter accumulation, decrease of soil pH and changes in C/N ratio. We aimed to check how long-term Norway spruce plantations affect species richness and diversity of soil mites along a mountain river in former mixed and broadleaved forests. The study, based on 342 samples, was carried out in Stolowe Mountains National Park (SW Poland). Understory species biomass, soil pH and soil organic layer thickness significantly affected soil mite communities. Although coniferous forests did not differ from either broadleaved or mixed forests in mite density (number of individuals m-2) and species diversity (H'), they were characterized by low species richness and proportional abundance of Uropodina mites typical for broadleaved forests. In total, 4849 mites classified into 57 species were recorded from all forest types and no unique species were found in the sampled forests. Although the mite communities were dominated by the same common species (Veigaia nemorensis, Paragamasus runcatellus, Leptogamasus obesus and Trachytes aegrota), they still maintain the rare species of broadleaved forests and their high recovery potential may be used in forest conversion.

Natural forest remnants as refugia for bryophyte diversity in a transformed mountain river valley landscape.

Riparian forests are among the most threatened ecosystem types worldwide. Their exploitation and replacement by coniferous plantations affects species pools and contributes to loss of biodiversity. We aimed to investigate bryophyte species pools within different habitat types in a transformed mountain river valley. We especially focused on the contribution of habitat types (relative to their proportional cover) to the species pool of the whole area. The study was conducted along the Czerwona Woda river - a model stream in the Stolowe Mountains National Park (SW Poland, study area: 91.2 ha) - and an example of coniferous plantations replacing natural broadleaved forest vegetation. Our study revealed the presence of 147 bryophyte species. The most valuable habitats in terms of diversity of bryophyte assemblages were remnants of the natural vegetation - broadleaved forests and streams. These habitats, constituting <5% of the study area, hosted ca 40% of the total species pool (61 and 62 species, respectively), while the species pool of Picea abies forests (92 species) was proportional to cover of this habitat type (ca 60%). Remnants of natural vegetation were hotspots of bryophyte diversity within the heavily altered landscape, and may play a future role as sources of recolonization by forest specialists. Our study also confirmed the important role of riparian areas in maintaining bryophyte species diversity at the landscape scale. The river valley studied contributes >20-fold more to the bryophyte species pool of the whole national park than indicated by its size. Thus, river valleys require special treatment - conservation based on natural restoration, and should remain reserved from wood production, as areas providing a wide range of ecosystem services.

Retrotransposon Domestication and Control in Dictyostelium discoideum.

Transposable elements, identified in all eukaryotes, are mobile genetic units that can change their genomic position. Transposons usually employ an excision and reintegration mechanism, by which they change position, but not copy number. In contrast, retrotransposons amplify via RNA intermediates, increasing their genomic copy number. Hence, they represent a particular threat to the structural and informational integrity of the invaded genome. The social amoeba Dictyostelium discoideum, model organism of the evolutionary Amoebozoa supergroup, features a haploid, gene-dense genome that offers limited space for damage-free transposition. Several of its contemporary retrotransposons display intrinsic integration preferences, for example by inserting next to transfer RNA genes or other retroelements. Likely, any retrotransposons that invaded the genome of the amoeba in a non-directed manner were lost during evolution, as this would result in decreased fitness of the organism. Thus, the positional preference of the Dictyostelium retroelements might represent a domestication of the selfish elements. Likewise, the reduced danger of such domesticated transposable elements led to their accumulation, and they represent about 10% of the current genome of D. discoideum. To prevent the uncontrolled spreading of retrotransposons, the amoeba employs control mechanisms including RNA interference and heterochromatization. Here, we review TRE5-A, DIRS-1 and Skipper-1, as representatives of the three retrotransposon classes in D. discoideum, which make up 5.7% of the Dictyostelium genome. We compile open questions with respect to their mobility and cellular regulation, and suggest strategies, how these questions might be addressed experimentally.

Ellenberg's indicator values support prediction of suitable habitat for pre-diapause larvae of endangered butterfly Euphydryas aurinia.

In spite of the great popularity of Ellenberg's Indicator Values (EIVs) in plant ecology, animal ecologists seldom use EIVs to address ecological questions. In this study we used EIVs to test their potential usefulness for the prediction of suitable habitat for pre-diapause larvae of the endangered butterfly species Euphydryas aurinia. Nine transects crossing grasslands in SW Poland with abundant populations of E. aurinia were designed. We sampled 76 vegetation plots along the transects. In addition, the presence of the larval webs of E. aurinia in sampled plots was also recorded. We then calculated the mean community EIVs of light, nitrogen, soil reaction, moisture and temperature for each sample plots. Generalized linear mixed-effects models (GLMMs) were used to assess which factors determine the local occurrence of larval webs of E. aurinia. We found the larval webs only in 12 plots, while the host plant was present in 39 of the examined plots. The presence of the host plant was the most important predictor in both models including all plots or including only plots with host plants. The other significant predictor was the mean EIV of light, and its importance increased in models considering all plots. We attributed the importance of the EIV of light to the site openness and density of the vegetation layer. A positive relationship between this predictor and the presence of larval webs indicates that sites with looser vegetation, a lower contribution of shrubs and tall herbs and better penetration of photosynthetically active radiation to lower vegetation layers are preferred by E. aurinia for oviposition. Moreover, the significance of EIV of light may be linked with management practices. Many light-demanding species decline after cessation of mowing as a result of litter accumulation and the dominance of tall herbs. An absence of light-demanding species decreases the community's mean EIV of light and thus indicates the influence of meadow abandonment.

The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.

Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the function of centromeres, rendering tight retrotransposition control critical to maintaining chromosome integrity. We report that in deletion strains of the RNA-dependent RNA polymerase RrpC, full-length and shorter DIRS-1 messenger RNAs are strongly enriched. Shorter versions of a hitherto unknown long non-coding RNA in DIRS-1 antisense orientation are also enriched in rrpC- strains. Concurrent with the accumulation of long transcripts, the vast majority of small (21 mer) DIRS-1 RNAs vanish in rrpC- strains. RNASeq reveals an asymmetric distribution of the DIRS-1 small RNAs, both along DIRS-1 and with respect to sense and antisense orientation. We show that RrpC is required for post-transcriptional DIRS-1 silencing and also for spreading of RNA silencing signals. Finally, DIRS-1 mis-regulation in the absence of RrpC leads to retrotransposon mobilization. In summary, our data reveal RrpC as a key player in the silencing of centromeric retrotransposon DIRS-1. RrpC acts at the post-transcriptional level and is involved in spreading of RNA silencing signals, both in the 5' and 3' directions.