Molecular phylogenetics and mitochondrial evolution

The myth of a "typical" mitochondrial genome (mtDNA) is a rock-hard belief in the field of genetics, at least for the animal kingdo

Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera

The class Branchiopoda, whose origin dates back to Cambrian, includes ~ 1200 species which mainly occupy freshwater habitats. The phylogeny and systematics of the class have been debated for long time, until recent phylogenomic analyses allowed to better clarify the relationships among major clades. Based on these data, the clade Anostraca (fairy and brine shrimps) is sister to all other branchiopods, and the Notostraca (tadpole shrimps) results as sister group to Diplostraca, which includes Laevicaudata + Spinicaudata (clam shrimps) and Cladoceromorpha (water fleas + Cyclestherida). In the present analysis, thanks to an increased taxon sampling, a complex picture emerges. Most of the analyzed mitogenomes show the Pancrustacea gene order while in several other taxa they are found rearranged. These rearrangements, though, occur unevenly among taxa, most of them being found in Cladocera, and their taxonomic distribution does not agree with the phylogeny. Our data also seems to suggest the possibility of potentially homoplastic, alternative gene order within Daphniidae

Molecular systematics and phylogenetics of the spider genus Mastigusa Menge, 1854 (Araneae, Cybaeidae)

The palearctic spider genus Mastigusa Menge, 1854 is characterized by a remarkable morphology and wide ecological variability, with free-living, cave dwelling and myrmecophile populations known. This genus has a long and tangled taxonomic history and was placed in different families in the past, all belonging to the “marronoid clade”, an informal grouping of families characterized by the lack of strong synapomorphies. Three species are currently recognized, but their identity and circumscription has been long debated. A molecular approach was never applied for trying to solve these uncertainties, and doubts still remain both about its phylogenetic placement and about the taxonomic status of the described species. For the first time the genus Mastigusa is included in a molecular phylogenetic analysis and strong support is found for its placement within the family Cybaeidae, in sister relationship with the genus Cryphoeca Thorell, 1870. An analysis of Mastigusa populations spanning across the distribution range of the genus identifies a high and previously overlooked genetic diversity, with six distinct genetic lineages showing a strong geographic pattern. Divergence times between Mastigusa and its sister genus and between the distinct Mastigusa lineages are estimated, and the groundwork is laid for a taxonomic revision of the species belonging to the genus

New association between red wood ant species (Formica rufa group) and the myrmecophilic spiders Mastigusa arietina and Thyreosthenius biovatus

Ants belonging to the Formica rufa species group, counting 10 representatives in Europe, are often referred to as red wood ants (RWAs). These dominant, mound building species are known to host in their nests an extremely diverse fauna of associated myrmecophilic arthropods, among which are the two W-Palaearctic spider species Mastigusa arietina (Thorell 1871) and Thyreosthenius biovatus (O. Pickard-Cambridge 1875). The actual host range of these spiders within the Formica rufa group is little known, due to the taxonomic uncertainties that have characterized RWAs in the past. We conducted a large-scale survey for assessing the occurrence of both spider species in association with different RWAs, with a focus on an accurate identification of the ant species. We recorded co-occurrence data for 5 European representatives of the Formica rufa group, and we reported for the first time on the co-occurrence of M. arietina with Formica aquilonia Yarrow 1955, Formica lugubris Zetterstedt 1838 and Formica paralugubris Seifert 1996, and of T. biovatus with F. aquilonia. We found no association between the rate of presence/absence of the two spiders and host ant species or sampling localities, which suggests a non-selective exploitation of RWA hosts by the two myrmecophilic spiders

First record of the genus Thyreosthenius (Araneae: Linyphiidae) from the Iberian Peninsula with notes on the host preference of the myrmecophilic T. biovatus

The presence of the spider genus Thyreosthenius Simon, 1884 (Linyphiidae) is for the first time confirmed in the Iberian Peninsula with an observation of the myrmecophile species T. biovatus (O. Pickard Cambridge, 1875). Four adult females and two sub-adult male specimens were collected inside mound nests belonging to the red wood ant species Formica lugubris Zetterstedt, 1838 in the Aragon and Catalonia regions of Spain. This represents the second known record of an occurrence of T. biovatus in association with F. lugubris, and the first for Continental Europe. In addition, the existing information on the host preference of this species is reviewed and discussed in relation to the new data from the Spanish Pyrenees

Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

Background Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics.Results We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived similar to 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads.Conclusions We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a "stealth drivers" model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes

Endothelial cells, endoplasmic reticulum stress and oxysterols

Oxysterols are bioactive lipids that act as regulators of lipid metabolism, inflammation, cell viability and are involved in several diseases, including atherosclerosis. Mounting evidence linked the atherosclerosis to endothelium dysfunction; in fact, the endothelium regulates the vascular system with roles in processes such as hemostasis, cell cholesterol, hormone trafficking, signal transduction and inflammation. Several papers shed light the ability of oxysterols to induce apoptosis in different cell lines including endothelial cells. Apoptotic endothelial cell and endothelial denudation may constitute a critical step in the transition to plaque erosion and vessel thrombosis, so preventing the endothelial damaged has garnered considerable attention as a novel means of treating atherosclerosis. Endoplasmic reticulum (ER) is the site where the proteins are synthetized and folded and is necessary for most cellular activity; perturbations of ER homeostasis leads to a condition known as endoplasmic reticulum stress. This condition evokes the unfolded protein response (UPR) an adaptive pathway that aims to restore ER homeostasis. Mounting evidence suggests that chronic activation of UPR leads to cell dysfunction and death and recently has been implicated in pathogenesis of endothelial dysfunction. Autophagy is an essential catabolic mechanism that delivers misfolded proteins and damaged organelles to the lysosome for degradation, maintaining basal levels of autophagic activity it is critical for cell survival. Several evidence suggests that persistent ER stress often results in stimulation of autophagic activities, likely as a compensatory mechanism to relieve ER stress and consequently cell death. In this review, we summarize evidence for the effect of oxysterols on endothelial cells, especially focusing on oxysterols-mediated induction of endoplasmic reticulum stress

Comparative genomics of Hox and ParaHox genes among major lineages of Branchiopoda with emphasis on tadpole shrimps

Hox and ParaHox genes (HPHGs) are key developmental genes that pattern regional identity along the anterior–posterior body axis of most animals. Here, we identified HPHGs in tadpole shrimps (Pancrustacea, Branchiopoda, Notostraca), an iconic example of the so-called “living fossils” and performed a comparative genomics analysis of HPHGs and the Hox cluster among major branchiopod lineages. Notostraca possess the entire Hox complement, and the Hox cluster seems to be split into two different subclusters, although we were not able to support this finding with chromosome-level assemblies. However, the genomic structure of Hox genes in Notostraca appears more derived than that of Daphnia spp., which instead retains the plesiomorphic condition of a single compact cluster. Spinicaudata and Artemia franciscana show instead a Hox cluster subdivided across two or more genomic scaffolds with some orthologs either duplicated or missing. Yet, branchiopod HPHGs are similar among the various clades in terms of both intron length and number, as well as in their pattern of molecular evolution. Sequence substitution rates are in fact generally similar for most of the branchiopod Hox genes and the few differences we found cannot be traced back to natural selection, as they are not associated with any signals of diversifying selection or substantial switches in selective modes. Altogether, these findings do not support a significant stasis in the Notostraca Hox cluster and further confirm how morphological evolution is not tightly associated with genome dynamics

Body measurement estimations using 3D scanner for individuals with severe motor impairments

In biomechanics, a still unresolved question is how to estimate with enough accuracy the volume and mass of each body segment of a subject. This is important for several applications ranging from the rehabilitation of injured subjects to the study of athletic performances via the analysis of the dynamic inertia of each body segment. However, traditionally this evaluation is done by referring to anthropometric tables or by approximating the volumes using manual measurements. We propose a novel method based on the 3D reconstruction of the subject’s body using the commercial low-cost camera Kinect v2. The software developed performs body segment separation in a few minutes leveraging alpha shape approximation of 3D polyhedrons to quickly compute a Montecarlo volume estimation. The procedure was evaluated on a total of 30 healthy subjects and the resulting segments’ lengths and masses were compared with the literature