SABSPV - A Monte Carlo Integrator for Small-Angle Bhabha Scattering

SABSPV is a code designed to perform a theoretical evaluation of small-angle Bhabha scattering cross sections by suitably matching fixed-order perturbative calculations and structure-function techniques. The implementation of realistic experimental triggering conditions is achieved by using Monte Carlo integration.Comment: 12 pages, LaTeX, no figures, no macro

Molecular typing of bacteria of the genus Asaia in malaria vector Anopheles arabiensis Patton, 1905

The acetic acid bacterium Asaia spp. was successfully detected in Anopheles arabiensis Patton, 1905, one of the major vector of human malaria in Sub-Saharan Africa. A collection of 45 Asaia isolates in cellfree media was established from 20 individuals collected from the field in Burkina Faso. 16S rRNA universal polymerase chain reaction (PCR) and specific qPCR, for the detection of Asaia spp. were performed in order to reveal the presence of different bacterial taxa associated with this insect. The isolates were typed by internal transcribed spacer-PCR, BOX-PCR, and randomly amplified polymorphic DNA-PCR, proved the presence of different Asaia in A. arabiensis

Endemism in recently diverged angiosperms is associated with polyploidy

Endemic (range restricted or precinctive) plant species are frequently observed to exhibit polyploidy (chromosome set duplication), which can drive shifts in ecology for angiosperms, but whether endemism is generally associated with polyploidy throughout the flowering plants has not been determined. We tested the hypothesis that polyploidy is more frequent and more pronounced (higher evident ploidy levels) for recently evolved endemic angiosperms. Chromosome count data, molecular dating and distribution for 4210 species (representing all major clades of angiosperms and including the largest families) were mined from literature-based databases. Upper boundary regression was used to investigate the relationship between the maximum number of chromosomes and time since taxon divergence, across clades and separately for families, comparing endemic with non-endemic species. A significant negative exponential relationship between maximum number of chromosomes and taxon age was evident across angiosperms (R2adj = 0.48 for all species, R2adj = 0.49 for endemics; R2adj = 0.44 for non-endemics; p always < 0.0001), recent endemics demonstrating greater maximum chromosome numbers (y intercept = 164 cf. 111) declining more rapidly with taxon age (decay constant = 0.12, cf. 0.04) with respect to non-endemics. The majority of families exhibited this relationship, with a steeper regression slope for endemic Campanulaceae, Asteraceae, Fabaceae, Poaceae, Caryophyllaceae and Rosaceae, cf. non-endemics. Chromosome set duplication is more frequent and extensive in recent angiosperms, particularly young endemics, supporting the hypothesis of recent polyploidy as a key explanation of range restriction. However, as young endemics may also be diploid, polyploidy is not an exclusive driver of endemism

http://zoobank.org/urn:lsid:zoobank.org:pub:3BEA5254-C4C0-47D9-9C5E-DA0448C3259E

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Rediscovery of a lost semi-aquatic Leaf Beetle in the Hula Valley, Israel (Coleoptera, Chrysomelidae, Donaciinae)

: Between 1951-1958, most of the Hula Lake and its surrounding swamps in the Upper Jordan River (Rift) Valley of Israel were drained with the supposed purposes to eliminate malaria and to reclaim land for agriculture; both reasons later proved to be unnecessary decisions. With the paucity of biological knowledge of the Hula region, especially its aquatic invertebrates, accurate assessment of the environmental damage from this drainage is still being realized. Based on natural history museum collection specimen records, the pre-drainage presence of some aquatic insect species has been verified. Among these was Donaciabicolora, a member of a semi-aquatic subfamily (Donaciinae) of Leaf Beetles (Chrysomelidae) and whose Israeli populations were thought to have gone extinct because of the drainage of the Hula and other locations. Recently this species was rediscovered in two populations. However, the molecular identification of two of these recently collected specimens from one population revealed that the identity of this species is actually Donaciasimplex. In this work, the re-discovery of this species is detailed, and its conservation importance discussed

Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins

DNA metabarcoding is a widespread approach for the molecular identification of organisms. While the associated wet-lab and data processing procedures are well established and highly efficient, the reference databases for taxonomic assignment can be implemented to improve the accuracy of identifications. Insects are among the organisms for which DNA-based identification is most commonly used; yet, a DNA-metabarcoding reference database specifically curated for their species identification using software requiring local databases is lacking. Here, we present COins, a database of 5' region cytochrome c oxidase subunit I sequences (COI-5P) of insects that includes over 532 000 representative sequences of >106 000 species specifically formatted for the QIIME2 software platform. Through a combination of automated and manually curated steps, we developed this database starting from all COI sequences available in the Barcode of Life Data System for insects, focusing on sequences that comply with several standards, including a species-level identification. COins was validated on previously published DNA-metabarcoding sequences data (bulk samples from Malaise traps) and its efficiency compared with other publicly available reference databases (not specific for insects). COins can allow an increase of up to 30% of species-level identifications and thus can represent a valuable resource for the taxonomic assignment of insects' DNA-metabarcoding data, especially when species-level identification is needed https://doi.org/10.6084/m9.figshare.19130465.v1

Corrections and Additions to Descriptions of Some Species of the Subgenus Orthocladius s. str. (Diptera, Chironomidae, Orthocladiinae)

The larvae of some species of the subgenus Orthocladius s. str. (Diptera, Chironomidae) are here described for the first time with corrections and additions to the descriptions of adult males and pupal exuviae. The identification of larvae is generally not possible without association with pupal exuviae and/or adult males, so the descriptions here are based only on reared material or on pupae with the associated larval exuviae. Usually, Chironomidae larvae can be separated on the basis of morphometric characters, the most discriminant ones are: (1) the ratio between the width of median tooth of mentum (Dm) and the width of the first lateral tooth (Dl) = mental ratio (DmDl), (2) the ratio between the length of the first antennal segment (A1) and the combined length of segments 2-5 (A2-5) = antennal ratio (AR). The shape of mandible, maxilla, and other body parts are almost identical in all the species considered in this study. The larva of Orthocladius (Symposiocladius) lignicola is very characteristic and can be separated by the shape of mentum and the larvae of all the known species of Symposiocladius are characterized by the presence of large Lauterborn organs on antennae and of tufts of setae on abdominal segments. The larvae of Orthocladius (Orthocladius) oblidens and Orthocladius (Orthocladius) rhyacobius can be distinguished from other species basing on their large Dm and to each other by AR. A principal component analysis was carried out using 5 characters: (1) Dm, (2) Dl, (3) length of A1, (4) width of A1 (A1W), (5) combined length of segments 2-5 (A2-5). The most discriminant characters were Dm and A1, confirming that DmDl and AR can be used to separate species at larval stage, but the large superposition of morphometric characters in different species confirms that association with pupal exuviae is in any case needed to identify larvae. In future perspective, the development of reference DNA barcodes from specimens identified by specialists is recommended since possibly the best tool for larvae identification, but association of barcodes with morphotypes is in any case fundamental

Factors Controlling Morphotaxa Distributions of Diptera Chironomidae in Freshwaters

Many hydrobiological studies have dealt with the autecology of species within the family Chironomidae and discussed factors affecting species distribution. The aim of the present research is to consider the most important factors affecting chironomid species distribution. Habitat type (lentic, lotic, krenal, rhithral, etc.), water temperature, conductivity, and trophic status are confirmed key factors controlling their assemblage structure. Here, we introduce the term “morphotaxon” as the taxonomic level, intermediate between genus and species, more suitable to describe the ecological responses of Chironomidae. The present uncertainty related to species identification is at the base of the proposal, with the assumption that species belonging to the same morphotaxon have similar ecological needs. In this study, this hypothesis was found to be valid, with few exceptions represented by species-rich genera (e.g., Tanytarsus, Paratanytarsus). The morphotaxon can be viewed as an interim measure waiting for the implementation of new complementary approaches, such as species identification with molecular methods

Factors affecting soil invertebrate biodiversity in agroecosystems of the Po Plain area (Italy)

Soil is a fundamental component of the biosphere, whose properties and quality are affected by human activities, such as agriculture. Soil health is fundamental for different ecosystem services and soil biota has a crucial role in maintaining it. Elucidating how different crops and agricultural practices affect soil invertebrates communities is of relevance. In the present study, a DNA metabarcoding approach was adopted to evaluate the effects of different biotic and abiotic factors, including agricultural practices, on the composition and diversity of soil invertebrate communities of different agro-ecosystems (Po Plain-Italy). At this aim, the DNA markers and the more effective primers in retrieving soil metazoan communities were established. Bulk soil samples from different agro-ecosystems (i.e., cornfield, alfalfa, paddy fields, vineyard, stable meadow, woodland) were collected and, processed for obtaining 18S rRNA and coi sequences (raw reads analyzed using QIIME2 and R). Soil physical and chemical parameters were measured for each soil sample (e.g., pH, carbon-nitrogen ratio, texture, porosity) and metadata on farms management were retrieved. The most efficient primer pairs in recovering soil metazoans were M620F/M1260R for 18S rRNA, and mlCOIintF/jgHCO2198R for coi gene. Soil communities resulted dominated by Nematoda, Arthropoda, Annelida, Rotifera and Tardigrada. The most diverse invertebrate communities have been found in the soil of stable meadows and woodlands, while cornfields showed the lowest level of diversity. The diversity of soil invertebrate communities (Hill numbers) was positively correlated with the level of porosity and carbon-nitrogen ratio, while it was negatively correlated with the phosphate abundance. This pattern probably reflects the negative effect of excessive fertilization with phosphates on soil fauna, while the abundance of organic matter and microhabitats were found to enhance the presence of more complex communities. Other soil properties were correlated only with specific taxa (e.g., pH was negatively correlated with the diversity of Annelida and Rotifera)