Search results for "taxonomic"

DNA traces the origin of honey by identifying plants, bacteria and fungi

2021

The regional origin of a food product commonly affects its value. To this, DNA-based identification of tissue remains could offer fine resolution. For honey, this would allow the usage of not only pollen but all plant tissue, and also that of microbes in the product, for discerning the origin. Here we examined how plant, bacterial and fungal taxa identified by DNA metabarcoding and metagenomics differentiate between honey samples from three neighbouring countries. To establish how the taxonomic contents of honey reflect the country of origin, we used joint species distribution modelling. At the lowest taxonomic level by metabarcoding, with operational taxonomic units, the country of origin …

Flawed Meta-Analysis of Biodiversity Effects of Forest Management

2010

It appears that the negative effect of forest managementon biodiversity has become an axiom. Whether the neg-ative effect, however, is a fact based on solid empiricalevidence is not self-evident. Most of the studies that ad-dress the issue suffer from a lack of geographic extentand taxonomic narrowness. Therefore, a synthesis draw-ing together results from the individual studies is direlyneeded. In their recent paper, Paillet et al. (2010) rise tothis challenge and present a formal pan-European meta-analysis of data from 49 papers representing 120 indi-vidual comparisons across 10 taxonomic groups. Theirsynthesis has the potential to be a landmark paper inecological research, but also to af…

OPTIMA Newsletter 42(1-2)

2015

OPTIMA Newsletter nº 42 continues the standard followed in the previous issues. The Newsletter is divided into two parts, the first with the News and the second with the Notices of Publications. The first section regarding news has became gradually thinner due to the fast and cheap channel represented by e-mail. The news here reported are only those that it makes sense to also produce as hard copy. Short news from OPTIMA Commissions are included, limited to those that reported activity in 2013, 2014 and beginning of 2015.

THE FINGERPRINT OF THE HUMAN GASTROINTESTINAL TRACT MICROBIOTA: A HYPOTHESIS OF MOLECULAR MAPPING

2017

The precise etiology of Inflammatory Bowel Disease (IDB) remains unclear and several factors are believed to play a role in its development and progression, including the composition of microbial communities resident in the gastrointestinal tract. Human intestinal microbiota are extensive with at least 15,000-36,000 bacterial species. However, thanks to the new development in sequencing and molecular taxonomic methodologies, our understanding of the microbiota population composition, dynamics, and ecology has greatly increased. Intestinal microbiota play a critical role in the maintenance of the host intestinal barrier homeostasis, while dysbiosis, which involves reduction in the microbiome…

Diatoms from thermal-sulphur waters of “Fiume Caldo” (North-western Sicily).

2007

The present study describes the taxonomic composition, richness and seasonal dynamics of the diatom community from thermal-sulphur waters of "Fiume Caldo" (Northwestern Sicily). The diatom flora of these waters consists of 64 taxa, showing similarities with thermal diatom communities from different geographical areas. Among the recorded taxa, Diadesmis confervacea Kütz. is a new record for Sicily. Seasonal changes in assemblage composition and richness have been recorded; the highest diversity values were observed during winter and spring, while during summer the diatom community consisted of a limited number of organisms whereas blue-green algae were quantitatively dominant. Inside the stu…

Comparing biological classifications of freshwater phytoplankton: a case study from South China

2012

The use of ecological classification systems is becoming more and more widely used when studying phytoplankton. Grouping phytoplankton species into ecologically coherent groups allow to reduce redundancy and in this way, to handle a minor number of biological variables when investigating the ecological status of aquatic ecosystems. Three ecological classifications are mostly used when freshwater phytoplankton is studied: functional groups or coda, morpho-functional groups (MFGs) and morphology-based functional groups (MBFGs). In this study, these three ecological classifications were comparatively used along with two taxonomic classifications based on species and genera to analyse phytoplan…

Characterizing a hybrid zone between a cryptic species pair of freshwater snails.

2015

Characterizing hybrid zones and their dynamics is a central goal in evolutionary biology, but this is particularly challenging for morphologically cryptic species. The lack of conspicuous divergence between parental types means intermediate hybrid forms often go undetected. We aimed to detect and characterize a suspected hybrid zone between a pair of morphologically cryptic lineages of the freshwater snail, Radix. We sampled Radix from across a contact zone between two mitochondrial lineages (Radix balthica and an undescribed lineage termed 'MOTU3') and detected admixture between two nuclear genotype clusters, which were significantly but not categorically associated with the mitochondrial …

Metagenomics reveals our incomplete knowledge of global diversity

2008

Metagenomic sequencing obtains huge amounts of sequences from environmental and clinical samples, thus providing a glimpse of the global prokaryotic diversity of both species and genes in these sources. The current trend in metagenomic analysis follows the so-called gene-centric approach, focused on describing the environments by the study of the functional roles of the proteins encoded in the sequenced genes. In this way, it is clear that metagenomic analysis relies heavily on the accurate knowledge of the universe of proteins stored in the databases. Nevertheless, it is known that some biases exist in the composition of databases (which are rich in sequences from common, cultivable and ea…

Overestimation of the strength of size-assortative pairing in taxa with cryptic diversity: a case of Simpson's paradox.

2015

5 pages; International audience; Size-assortative pairing is one of the most common pairing patterns observed in nature and it probably occurs in many taxa with cryptic diversity. Observed patterns of size-assortative pairing in natural populations may thus be influenced by the co-occurrence of noninterbreeding cryptic groups of individuals living in sympatry. To quantify this potential bias, we sampled amphipods from the Gammarus pulex/Gammarus fossarum crustacean species complex in rivers containing two sympatric and morphologically cryptic groups, i.e. molecular operational taxonomic units (MOTUs). Within each river, MOTUs did not interbreed and differed in mean body size. We measured th…

2014

Large prosomal scent glands constitute a major synapomorphic character of the arachnid order Opiliones. These glands produce a variety of chemicals very specific to opilionid taxa of different taxonomic levels, and thus represent a model system to investigate the evolutionary traits in exocrine secretion chemistry across a phylogenetically old group of animals. The chemically best-studied opilionid group is certainly Laniatores, and currently available chemical data allow first hypotheses linking the phylogeny of this group to the evolution of major chemical classes of secretion chemistry. Such hypotheses are essential to decide upon a best-fitting explanation of the distribution of scent-g…