Supervised regionalization methods: A survey

This paper reviews almost four decades of contributions on the subject of supervised regionalization methods. These methods aggregate a set of areas into a predefined number of spatially contiguous regions while optimizing certain aggregation criteria. The authors present a taxonomic scheme that classifies a wide range of regionalization methods into eight groups, based on the strategy applied for satisfying the spatial contiguity constraint. The paper concludes by providing a qualitative comparison of these groups in terms of a set of certain characteristics, and by suggesting future lines of research for extending and improving these methods.

Clave para la determinación de exuvias pupales de los quironómidos (Diptera: Chironomidae) de ríos altoandinos tropicales

The Chironomidae is a cosmopolitan family of Nematoceran flies with more than 20 000 species described. However the diversity of genera and species of the family in the Andean region beyond the 2 000m.a.s.l are scarcely known. We conducted faunal surveys and biomonitoring research in different streams of Colombia, Ecuador and Peru from May 2005 to October 2011. Based on specimens collections, and a taxonomic key was developed to identify pupae and pupal exuviae of 46 genera of midges (Diptera, Chironomidae) collected from streams at high altitude areas on the Andean tropical mountains. We included illustrations and brief taxonomic descriptions for all genera, of which several ones have not yet been formally described; in this latter case we used the nomenclature of Roback & Coffman (1983). For two genera, Cricotopus and Genus 1, keys to the most common morphospecies were provided. Results showed that in this area the chironomid assemblages are dominated by the members of the subfamily Orthocladiinae (22 genera) followed by the Chironominae (13). Six genera of Tanypodinae were identified, while only three and two genera were present from subfamilies Podonominae and Diamesinae. This key may be very useful for both studies about drift in streams, and for biomonitoring purposes.

Supervised regionalization methods: A survey

This paper reviews almost four decades of contributions on the subject of supervised regionalization methods. These methods aggregate a set of areas into a predefined number of spatially contiguous regions while optimizing certain aggregation criteria. The authors present a taxonomic scheme that classifies a wide range of regionalization methods into eight groups, based on the strategy applied for satisfying the spatial contiguity constraint. The paper concludes by providing a qualitative comparison of these groups in terms of a set of certain characteristics, and by suggesting future lines of research for extending and improving these methods.

Crustacean and aquatic insect assemblages in the Mediterranean coastal ecosystems of Empord`a wetlands (NE Iberian peninsula)

Coastal wetlands are characterized by high biodiversity, which is one of the main criteria considered when establishing protection policies or when proposing adequate management actions. In this study, the crustacean and aquatic insect composition of the Empord`a wetlands is described. These two faunal groups contribute highly to the total biodiversity in these wetlands but are seldom considered when managing natural areas. A selection (84 sampling points) of all water body types present in the Empord`a wetlands were sampled monthly (surber and dip net with a 250 μm mesh). Sampling was carried out during 3 surveys (1991-92, 1996-97 and 1999-2000). A rich fauna of 125 crustacean and 295 aquatic insect taxa was identified. We characterized each water body type using the most abundant species and the relative species richness of the taxonomic groups. A classification of the water body types, according to similarity between inventories, groups the brackish and hyperhaline systems in one cluster and the various freshwater systems in another one. Among freshwater systems, lotic waters and freshwater wetlands have a high similarity, whereas rice fields and freshwater springs have a low similarity

The dynamics of biofilm bacterial communities is driven by flow wax and wane in a temporary stream

Biofilm communities are exposed to long periods of desiccation in temporary streams. We investigated how water flow intermittency affected the bacterial community structure colonizing three different streambed compartments in a Mediterranean stream. Massive parallel sequencing revealed different bacterial communities in biofilms from sand sediments and cobbles. Bacterial communities were similar (62% of shared operational taxonomic units) in the epipsammic and hyporheic biofilms, and more diverse than those in the epilithic biofilms. The non-flow phase caused a decrease of bacterial diversity in the biofilms, when communities included only bacterial taxa assumed to be adapted to water stress. The most sensitive bacterial communities to flow intermittency were in the epilithic, where the exposure to physical stress was the highest. In sand sediments a wide group of bacterial taxa was tolerant to desiccation. During non-flow the proliferation of opportunistic taxa in the superficial compartments evidenced the biological link with the terrestrial environment. Bacterial communities better tolerate rewetting than desiccation, since a major number of taxa tolerant to rewetting occurred in all biofilms. Overall, bacterial communities in sandy compartments showed higher resistance to flow intermittency than those in epilithic biofilms

Evolutionary analysis of mitogenomes from parasitic and free-living flatworms

Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.

Genotypic comparison of Pantoea agglomerans plant and clinical strains

Pantoea agglomerans strains are among the most promising biocontrol agents for avariety of bacterial and fungal plant diseases, particularly fire blight of apple and pear. However, commercial registration of P. agglomerans biocontrol products is hampered because this species is currently listed as a biosafety level 2 (BL2) organism due to clinical reports as an opportunistichuman pathogen. This study compares plant-origin and clinical strains in a search for discriminating genotypic/phenotypic markers using multi-locus phylogenetic analysis and fluorescent amplified fragment length polymorphisms (fAFLP) fingerprinting.Results: Majority of the clinical isolates from culture collections were found to be improperly designated as P. agglomerans after sequence analysis. The frequent taxonomic rearrangements underwent by the Enterobacter agglomerans/Erwinia herbicola complex may be a major problem in assessing clinical associations within P. agglomerans. In the P. agglomerans sensu stricto (in the stricter sense) group, there was no discrete clustering of clinical/biocontrol strains and no marker was identified that was uniquely associated to clinical strains. A putative biocontrol-specific fAFLP marker was identified only in biocontrol strains. The partial ORF located in this band corresponded to an ABC transporter that was found in all P. agglomerans strains. Conclusion: Taxonomic mischaracterization was identified as a major problem with P.agglomerans, and current techniques removed a majority of clinical strains from this species. Although clear discrimination between P. agglomerans plant and clinical strains was not obtained with phylogenetic analysis, a single marker characteristic of biocontrol strains was identified whichmay be of use in strain biosafety determinations. In addition, the lack of Koch's postulate fulfilment, rare retention of clinical strains for subsequent confirmation, and the polymicrobial nature of P. agglomerans clinical reports should be considered in biosafety assessment of beneficial strains in this species

Dinámica del heleoplancton en relación a las fluctuaciones hidrológicas en aiguamolls de l’Empordà (NE de la península Ibérica). Propuesta de un método sencillo de monitorización basado en la abundancia de grupos taxonómicos

Monitoring of the 'ecological water quality' in 'Aiguamolls de l’Empordà' Natural Park was carried out between September 1996 and August 1997 . The aim of this sampling programme was to design a simple method for rapid detect changes in water quality due to human activity. These include flow regulation by the Park management, nutrient entries from effluents of a nearby wastewater treatment plant or agricultural fertilising. The proposed method is based on the analysis of the abundance of characteristic taxonomic groups of aquatic invertebrates (heleoplankton). The simplicity of the method is ensured by the use of large taxa which are easier to recognise than species. The functioning of aquatic systems has been modelled by means of correspondence analysis between samples and taxa. Results can be summerized in five environmental conditions with a regular community structure. Dominated by one taxon: cladocerans, ostracods, calanoids, cyclopoids and harpacticoids. The dynamics of both freshwater and brackish lagoons can be modelled as displacements between these five groups of environmental conditions. Nevertheless, the “calanoids situation” and the “harpacticoids situation” occur mainly in brackish lagoons, whereas the “cladocerans situation” occurs mainly in freshwater. The four principal axes of data variation have been respectively identified as nutrient turnover rate, hypertrophy, degree of mineralization of the organic matter and eutrophy. The use of these taxa has been validated by comparison with a model obtained from the species. We conclude that in a highly fluctuating system such as the one here, only persistent situations of eutrophy or hypertrophy must be equated to low 'ecological water quality'

Deep-water macroalgal-dominated coastal detritic assemblages on the continental shelf off Mallorca and Menorca (Balearic Islands, Western Mediterranean)

We present a quantitative physiognomic characterization of major macroalgal-dominated assemblages on coastal detritic bottoms of the continental shelf off Mallorca and Menorca (Balearic Islands, Western Mediterranean). In late spring of 2007 and 2008, 29 samples were collected by bottom trawling at depths between -52 and -93 m. These samples were then sorted and identified to their lowest taxonomic level. Statistical analyses distinguished six different assemblage types: shallower water environments (-52 to -65 m in depth) were characterized by Osmundaria volubilis and Phyllophora crispa meadows and two types of Peyssonnelia beds; two assemblage types, Laminaria rodriguezii beds and maërl beds, were only present in deep-water environments (-77 to -81 m); and an assemblage dominated by P. crispa and Halopteris filicina was found in both shallow and deep waters (-57 to -93 m). We assess the distribution of these six assemblage types through the studied area.