Value of a broken umbrella: abandoned nest sites of the black stork (Ciconia nigra) host rich biodiversity

Protecting habitats for charismatic vertebrates can provide an ‘umbrella’ for less conspicuous organisms, especially when these are threatened by the same processes. However, such a conservation scheme is vulnerable to the extirpation of the focal species. We studied wider biodiversity values in long protected black stork (Ciconia nigra) nest sites, which were abandoned by the bird and thus legally subject to de-listing. In 20 abandoned nest sites in Estonia, we (i) mapped breeding birds within 600 m from the stork nest, and (ii) carried out time-limited surveys of lichens, polypore fungi, vascular plants and bryophytes in 2-ha plots. The breeding bird assemblages (64 species recorded) included 19 red-listed species, and showed no clear aggregation to the immediate surroundings of the stork nest. We recorded 740 plant and fungal species, of which 134 (18%) were of conservation concern (nationally protected, red-listed or extremely rare). Across the 2-ha plots, the numbers of the species of conservation concern varied more than three-fold (maximum 42 species), being affected notably by dead wood accumulation over time and presence of nemoral broad-leaved trees. The results demonstrate that many abandoned nest sites of the black stork have broader biodiversity significance, both due to the bird’s habitat requirements and the natural development during the protection. Expanding the umbrella function to sites abandoned by a focal species, but intact from anthropogenic degradation, can thus be a cost-effective conservation approach due to its low additional administrative burden. In most jurisdictions, the assessment procedure for such situations should be formalized, however.

     

Long-Term Impacts of Forest Ditching on Non-Aquatic Biodiversity: Conservation Perspectives for a Novel Ecosystem

Artificial drainage (ditching) is widely used to increase timber yield in northern forests. When the drainage systems are maintained, their environmental impacts are likely to accumulate over time and along accompanying management, notably after logging when new forest develops on decayed peat. Our study provides the first comprehensive documentation of long-term ditching impacts on terrestrial and arboreal biodiversity by comparing natural alder swamps and second-generation drained forests that have evolved from such swamps in Estonia. We explored species composition of four potentially drainage-sensitive taxonomic groups (vascular plants, bryophytes, lichens, and snails), abundance of species of conservation concern, and their relationships with stand structure in two-ha plots representing four management types (ranging from old growth to clearcut). We found that drainage affected plot-scale species richness only weakly but it profoundly changed assemblage composition. Bryophytes and lichens were the taxonomic groups that were most sensitive both to drainage and timber-harvesting; in closed stands they responded to changed microhabitat structure, notably impoverished tree diversity and dead-wood supply. As a result, natural old-growth plots were the most species-rich and hosted several specific species of conservation concern. Because the most influential structural changes are slow, drainage impacts may be long hidden. The results also indicated that even very old drained stands do not provide quality habitats for old-growth species of drier forest types. However, drained forests hosted many threatened species that were less site type specific, including early-successional vascular plants and snails on clearcuts and retention cuts, and bryophytes and lichens of successional and old forests. We conclude that three types of specific science-based management tools are needed to mitigate ditching effects on forest biodiversity: (i) silvicultural techniques to maintain stand structural complexity; (ii) context-dependent spatial analysis and planning of drained landscapes; and (iii) lists of focal species to monitor and guide ditching practices.     

Correlations between forest stand diversity and landscape pattern in Otepää Nature Park, Estonia

Rank correlations between tree species diversity in forest stands and parameters of landscape pattern were calculated using data from 4933 locations in Otepää Nature Park. Stand diversity was characterised by the number of tree species in the stand formula and by the index of dominance of tree species’ coverage. Landscape diversity was characterised by locally calculated pattern parameters from three categorical map layers (1:10 000 base map, 1:10 000 soil map, combination of these maps) and from six numerical variables (elevation, slope angle, four channels of a Landsat 7 ETM image).A weak trend appeared for more diverse forest stands to be located in more diverse landscapes according to the base map. Forest stand diversity is also higher on steeper slopes and in places surrounded by slopes of varying steepness. The correlation between landscape diversity and biodiversity depends on the radius of the kernel in which landscape characteristics are calculated. Evidence of an indicative neighbourhood could be seen in many spatial relationships. The spatial correlation between stand diversity and indices calculated from the base map was most visible at distances ranging from 400 to 500 m; surface elevation and its variation correlates with stand diversity at distances of 100–200 m. Some relationships between forest diversity and landscape diversity that had a different sign of correlation in proximate and distant kernels can be interpreted as a need to standardise local landscape indices with the index values in a wider neighbourhood as a reference.     

Correspondence of vegetation boundaries to redox barriers in a Northern European moraine plain

Little attention has been devoted to the investigation of the formation and functioning of ecotones at the interfaces between the upland and riparian zones. The margins of riparian mires act as redox geochemical barriers. Such biogeochemical hot spots retain elements that have leached from upland soils, favouring the growth of mesomorphic plants in hydromorphic soils. This paper aims to clarify the correspondence of vegetation borders to horizontal redox barriers of a Northern European moraine plain in Estonia.24 random transects were surveyed on the moraine plain, sampled across sharp soil moisture boundaries as proxies of redox barriers. The shifts in vegetation perpendicular to the boundaries were investigated. Curves of Euclidean distance were computed by moving a 20 m split-window along transects. The curves showed peaks of high dissimilarity a few metres below the redox barriers in the sites of natural soil moisture. In artificially drained sites, the relict redox barriers poorly corresponded to the vegetation borders. We conclude that in the studied moraine plain, the vegetation boundaries between riparian mires and uplands correspond to the redox barriers. The same can be set as a hypothesis for Northern European moraine plains. Related ecotones can be observed on the footslopes, revealing redox barrier in the landscape and related hot spots in cultural landscapes. In field margins, the redox barriers and corresponding ecotones occur below cultivation terraces. The ecotones may represent functional boundaries for delineating wetlands. Man-made drainage removes soil redox barriers and corresponding vegetation boundaries, making the landscape uniform and therefore vulnerable to disturbances. As a management implication, footslope ecotones should be preserved in their natural condition.     

Wolf population genetics in Europe: a systematic review,meta‐analysis and suggestions for conservation and management

The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human–carnivore conflict, which has led to long‐term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the ‘pre‐genomic era’ and the first insights of the ‘genomics era’. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large‐scale trends and patterns of genetic variation in European wolf populations, we conducted a meta‐analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south‐west (lowest genetic diversity) to north‐east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650?850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science‐based wolf conservation and management at regional and Europe‐wide scales.     

Enhancements and modifications of primer design program Primer3

The determination of annealing temperature is a critical step in PCR design. This parameter is typically derived from the melting temperature of the PCR primers, so for successful PCR work it is important to determine the melting temperature of primer accurately. We introduced several enhancements in the widely used primer design program Primer3. The improvements include a formula for calculating melting temperature and a salt correction formula. Also, the new version can take into account the effects of divalent cations, which are included in most PCR buffers. Another modification enables using lowercase masked template sequences for primer design. Availability: Features described in this article have been implemented into the development code of Primer3 and will be available in future versions (version 1.1 and newer) of Primer3. Also, a modified version is compiled under the name of mPrimer3 which is distributed independently. The web-based version of mPrimer3 is available at http://bioinfo.ebc.ee/mprimer3/ and the binary code is freely downloadable from the URL http://bioinfo.ebc.ee/download/.     

Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides

Background  

The hybridization of synthetic Streptococcus pneumoniae tmRNA on a detection microarray is slow at 34°C resulting in low signal intensities.     

MultiPLX: automatic grouping and evaluation of PCR primers

SUMMARY: MultiPLX is a new program for automatic grouping of PCR primers. It can use many different parameters to estimate the compatibility of primers, such as primer-primer interactions, primer-product interactions, difference in melting temperatures, difference in product length and the risk of generating alternative products from the template. A unique feature of the MultiPLX is the ability to perform automatic grouping of large number (thousands) of primer pairs. AVAILABILITY: Binaries for Windows, Linux and Solaris are available from http://bioinfo.ebc.ee/download/. A graphical version with limited capabilities can be used through a web interface at http://bioinfo.ebc.ee/multiplx/. The source code of the program is available on request for academic users. CONTACT: maido.remm@ut.ee.