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Robin V.,University of Kiel | Talon B.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Nelle O.,University of Kiel
Quaternary International | Year: 2013

The notion of naturalness is an important concept of forest sustainable management, biological conservation, or as a base for restoration projects. The naturalness degree of a forest system is commonly evaluated based on forest ecology indicators, primarily with a relative short time resolution (e.g. dendroecological indication). However, the current state of ecological systems is the result of processes occurring in interaction at different and hierarchically connected spatial and temporal scales, including long term resolution (e.g. Holocene scale). Consequently, to assess the naturalness degree of ecological systems it is important to deal with their various temporal and spatial scales. In order to do that, palaeoecological approaches are needed, but hitherto have rarely been applied in naturalness investigations. The difficulties of interpretation in terms of spatial resolution of the main used palaeoecological approaches (e.g. palynology) and the presence of archive sites favourable to provide palaeoecological proxies seem to be limiting factors. Pedoanthracology allows the investigation of forest dynamics at the local spatial scale potentially everywhere, and for a longer time resolution. This paper illustrates this by using pedoanthracology to contribute to the naturalness assessment of three study cases in various biomes in Europe, in the south French Alps, in Central Germany and in Northern Germany. The charcoal richness of soil samples was quantified, and fragments were analysed taxonomically. Radiocarbon dating of single charcoals, combined with soil description, allows interpretation of the data within a temporal and spatial framework.At the site in Northern Germany, the ancient occurrence of fire was identified, burning early Holocene pioneer forest vegetation, while during more recent times, the burning of Fagus forest happened, Fagus sylvatica being today's dominant forest tree. At the site south of the Harz Mountains, in Central Germany, the established reference system is a Quercus dominated forest, which has persisted for thousands of years until today, possibly due to human woodland management. At the third site, in the French Southern Alps, the local forest system has never been more mature than in the current state, because it was regularly renewed by fire disturbances. © 2012 Elsevier Ltd and INQUA.

Robin V.,University of Kiel | Nelle O.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental
Vegetation History and Archaeobotany | Year: 2014

Fire caused by humans played an important role in prehistoric clearance of woodland, which was a prerequisite for the rise of agriculture since at least the Neolithic revolution. Therefore, reconstructed fire history provides insights into the spread of agriculture. However, for central Europe, the past fire regime is still poorly known. Thus, to help to fill this gap, fire history has been investigated using data relevant at a local scale, which is the scale of woodland clearance processes according to local human practices. For this purpose, soil/soil sediment charcoal analysis has been conducted at four sites in northern Germany and five in central Germany. At each site, four to nine sequences of soil/soil sediment were excavated, described in the field and sampled. The sampled material has been differentiated by soil horizons formed in situ and colluvial sediments. The charcoal content of both types of sampled material was quantified and some of it was taxonomically analysed. Chronological information was obtained by radiocarbon dating 73 single charcoal pieces that had previously been identified taxonomically. Such data sets have permitted us to identify a minimum number of fire events for every site, which had burnt various types of woodlands and at different chronological phases. Based on the local scale data, regional trends were identified. Charcoals from the late Pleistocene and early Holocene derived from conifers only, and these most probably indicate wildfire events in flammable woodlands. Charcoals dated to the mid and late Holocene derived predominantly from broad-leaved trees probably resulting from human-ignited fires in weakly flammable woodlands. The calculated minimum fire frequency indicates an increase in fire occurrences during the Holocene following the phases of cultural human development. This supports the importance of human-made fire in northern central Europe during the Holocene. Such minimum fire frequency appears much higher during the iron age and the middle ages, but not before. This fits with the general statement of regional woodland loss and landscape opening relatively recently, during the late Holocene. © 2014 Springer-Verlag Berlin Heidelberg.

Laureti L.,University of Paris Descartes | Selva M.,University of Paris Descartes | Selva M.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Dairou J.,University Paris Diderot | Matic I.,University of Paris Descartes
DNA Repair | Year: 2013

ATP is the most important energy source for the maintenance and growth of living cells. Here we report that the impairment of the aerobic respiratory chain by inactivation of the ndh gene, or the inhibition of glycolysis with arsenate, both of which reduce intracellular ATP, result in a significant decrease in spontaneous mutagenesis in Escherichia coli. The genetic analyses and mutation spectra in the ndh strain revealed that the decrease in spontaneous mutagenesis resulted from an enhanced accuracy of the replicative DNA polymerase. Quantification of the dNTP content in the ndh mutant cells and in the arsenate-treated cells showed reduction of the dNTP pool, which could explain the observed broad antimutator effects. In conclusion, our work indicates that the cellular energy supply could affect spontaneous mutation rates and that a reduction of the dNTP levels can be antimutagenic. © 2013 Elsevier B.V.

Weber A.A.T.,University of Geneva | Weber A.A.T.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Pawlowski J.,University of Geneva
Protist | Year: 2014

Ribosomal DNA is commonly used as a marker for protist phylogeny and taxonomy because of its ubiquity and its expected species specificity thanks to the mechanism of concerted evolution. However, numerous studies reported the occurrence of intragenomic (intra-individual) polymorphism in various protists and particularly in Foraminifera. To infer to what extent the SSU rDNA intragenomic variability occurs in Foraminifera, we studied 16 foraminiferal species belonging to single-chambered monothalamids and multi-chambered Globothalamea, with one to six individuals per species. We performed single-cell DNA extractions and PCRs of a 600. bp fragment of SSU rDNA, and sequenced 9 to 23 clones per individual for a total of 818 sequences. We found intragenomic variability in almost all species, even after excluding singleton mutations. Intra-individual sequence divergence ranged from 0 to 5.15% and was higher than 1% in 11 species. Variability was usually located at the end of stem-loop structures and included compensatory single nucleotide polymorphisms and expansion segments polymorphisms. However, the polymorphisms did not change the secondary structure of the rRNA. Our results suggest a non-concerted evolution of rRNA genes in Foraminifera. The origin of this variability and its implications for species identification in environmental DNA studies are discussed. © 2014 Elsevier GmbH.

Lavrov D.V.,Iowa State University | Adamski M.,University of Bergen | Chevaldonne P.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Adamska M.,University of Bergen
Current Biology | Year: 2016

Summary One of the unusual features of DNA-containing organelles in general and mitochondria in particular is the frequent occurrence of RNA editing [1]. The term "RNA editing" refers to a variety of mechanistically unrelated biochemical processes that alter RNA sequence during or after transcription [2]. The editing can be insertional, deletional, or substitutional and has been found in all major types of RNAs [3, 4]. Although mitochondrial mRNA editing is widespread in some eukaryotic lineages [5-7], it is rare in animals, with reported cases limited both in their scope and in phylogenetic distribution [8-11] (see also [12]). While analyzing genomic data from calcaronean sponges Sycon ciliatum and Leucosolenia complicata, we were perplexed by the lack of recognizable mitochondrial coding sequences. Comparison of genomic and transcriptomic data from these species revealed the presence of mitochondrial cryptogenes whose transcripts undergo extensive editing. This editing consisted of single or double uridylate (U) insertions in pre-existing short poly(U) tracts. Subsequent analysis revealed the presence of similar editing in Sycon coactum and the loss of editing in Petrobiona massiliana, a hypercalcified calcaronean sponge. In addition, mitochondrial genomes of at least some calcaronean sponges were found to have a highly unusual architecture, with nearly all genes located on individual and likely linear chromosomes. Phylogenetic analysis of mitochondrial coding sequences revealed accelerated rates of sequence evolution in this group. The latter observation presents a challenge for the mutational-hazard hypothesis [13], which posits that mRNA editing should not occur in lineages with an elevated mutation rate. © 2016 Elsevier Ltd.

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