Hashtags, testimonies, and measurements: Gender violence and its interpretation

In this article, I address gender violence through the act of witnessing and speaking out by the victims. Starting from a critical comment on some arguable points raised in the recent Hau Journal forum aimed at discussing forms and claims of the #MeToo movement, I let emerge the conundrums that anthropology faces in dealing with the issue. A focus on domestic abuse as a specific form of gender violence allows me to delve into the twine of intimacy, agency and consent in the experience of the victims. I detect the specific dynamics that characterize the issue of speaking/not speaking out against violence by abused women and that underpin analytical biases. Then, I illustrate how these complexities can be found in the general assessment and measurement of gender violence as a global phenomenon. I conclude with a reflection on violence and women’s voices as an opportunity for anthropological knowledge to deal with truth telling, intimacy, and the gendered act of speaking out.L’articolo affronta il tema della violenza di genere attraverso l’atto della testimonianza e della denuncia pubblica da parte delle vittime. Partendo da un commento critico su alcuni argomenti sollevati nel recente forum della rivista Hau dedicato a forme e rivendicazioni del movimento #MeToo, individuo le difficoltà che incontra l’antropologia nell’analizzare la violenza di genere. Il focus sulla violenza domestica come forma specifica di violenza di genere mi permette di affontare l’intreccio tra intimità, agency e consenso nell’esperienza della violenza. Sottolineo le specifiche dinamiche che caratterizzano la questione del denunciare/non denunciare la violenza da parte delle donne e che sono alla base di pregiudizi analitici. Quindi illustro come queste complessità si ritrovano nella valutazione e stima della violenza di genere come fenomeno globale. Concludo con una riflessione sulla violenza e la denuncia delle donne come una opportunità per il sapere antropologico nell’affrontare la dichiarazione di verità, l’intimità e l’aspetto sessuato della presa pubblica di parola

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

<p>Abstract</p> <p>Background</p> <p>The quality of multiple sequence alignments plays an important role in the accuracy of phylogenetic inference. It has been shown that removing ambiguously aligned regions, but also other sources of bias such as highly variable (saturated) characters, can improve the overall performance of many phylogenetic reconstruction methods. A current scientific trend is to build phylogenetic trees from a large number of sequence datasets (semi-)automatically extracted from numerous complete genomes. Because these approaches do not allow a precise manual curation of each dataset, there exists a real need for efficient bioinformatic tools dedicated to this alignment character trimming step.</p> <p>Results</p> <p>Here is presented a new software, named BMGE (Block Mapping and Gathering with Entropy), that is designed to select regions in a multiple sequence alignment that are suited for phylogenetic inference. For each character, BMGE computes a score closely related to an entropy value. Calculation of these entropy-like scores is weighted with BLOSUM or PAM similarity matrices in order to distinguish among biologically expected and unexpected variability for each aligned character. Sets of contiguous characters with a score above a given threshold are considered as not suited for phylogenetic inference and then removed. Simulation analyses show that the character trimming performed by BMGE produces datasets leading to accurate trees, especially with alignments including distantly-related sequences. BMGE also implements trimming and recoding methods aimed at minimizing phylogeny reconstruction artefacts due to compositional heterogeneity.</p> <p>Conclusions</p> <p>BMGE is able to perform biologically relevant trimming on a multiple alignment of DNA, codon or amino acid sequences. Java source code and executable are freely available at <url>ftp://ftp.pasteur.fr/pub/GenSoft/projects/BMGE/</url>.</p

Luca : à la recherche du plus proche ancêtre commun universel

L’application des méthodes de la biologie moléculaire à l’étude des premières étapes de l’évolution a montré que le monde vivant pouvait être divisé en trois domaines : archées, bactéries et eucaryotes. Cette découverte a mis à l’ordre du jour le problème de Luca, le dernier ancêtre commun à tous les organismes cellulaires actuels (thelast universal common ancestor). Ce problème peut être abordé aujourd’hui sur des bases plus solides, grâce à la génomique comparative : celle-ci nous apprend que Luca possédait une membrane cytoplasmique et un appareil de traduction déjà relativement sophistiqué. En revanche, la nature de son génome reste inconnue : faisait-il encore partie du monde à ARN, ou avait-il déjà un génome à ADN ? De nouvelles hypothèses sont avancées, qui font intervenir les virus dans l’apparition de l’ADN et la formation des trois domaines. Connaître Luca est essentiel si nous voulons retracer l’histoire évolutive des mécanismes moléculaires présents chez les organismes actuels.One of the most important outcomes of modern biology has been the demonstration of the unity of life. All living beings are in fact descendants of a unique ancestor commonly referred to as Luca (the Last universal common ancestor). The discovery — nearly 30 years ago by Carl Woese – that present-day life on our planet can be assigned to only three domains: two of prokaryotic nature (Archaea and Bacteria), and one eukaryoyic (Eucarya), has given birth to a new field of investigation aimed at determining the nature of Luca. Today, thanks to the accumulation of genomic data, we can loop back into the past and infer a few characters of Luca by comparing what present-day organisms have in common. For example, it is now clear that Luca was a cellular organism provided with a cytoplasmic membrane, and that it harboured already a quite sophisticated translation apparatus. However, the inference of other characters of Luca from comparative genomics is less straightforward: for instance, a few key molecular mechanisms for DNA replication are non-homologous across the three domains and their distribution is often puzzling. This evidence has been embraced by proponents of the hypothesis that Luca harboured an RNA genome and that its replacement by DNA and the appearance of the corresponding molecular systems would have occurred independently in the three life domains after their divergence. However, an equally likely scenario would be that of a Luca with a DNA genome and of a subsequent replacement of its DNA-replication systems by non-homologous counterparts either in the bacterial or in the archaeal/eukaroytic branch. Nevertheless, including the viral world into the picture of the tree of life may thus provide us with precious insights into our most distant past since the invention and spread potential of viruses may have played a key role in early evolution

An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences

BACKGROUND: The concept of a genomic core, defined as the set of genes ubiquitous in all genomes of a monophyletic group, has become crucial in comparative and evolutionary genomics. However, it is still a matter of debate whether lateral gene transfers (LGT) may affect the components of genomic cores, preventing their use to retrace species evolution. We have recently reconstructed the phylogeny of Archaea by using two large concatenated datasets of core proteins involved in translation and transcription, respectively. The resulting trees were largely congruent, showing that informational gene components of the archaeal genomic core belonging to two distinct molecular systems contain a coherent signal for archaeal phylogeny. However, some incongruence remained between the two phylogenies. This may be due either to undetected LGT and/or to a lack of sufficient phylogenetic signal in the datasets. RESULTS: We present evidence strongly favoring of the latter hypothesis. In fact, we have updated our transcription and translation datasets with five new archaeal genomes for a total of 6384 and 2928 amino acid positions, respectively, and 25 taxa. This increase in taxonomic sampling led to the nearly complete convergence of the transcription-based and translation-based trees on a single phylogenetic pattern for archaeal evolution. In fact, only a single incongruence persisted between the two phylogenies. This concerned Methanopyrus kandleri, whose placement remained strongly biased in the transcription tree due to its above average evolutionary rates, and could not be counterbalanced due to the lack of availability of closely related and/or slower-evolving relatives. CONCLUSION: To our knowledge, this is the first report of evidence that the phylogenetic signal harbored by components of the archaeal translation apparatus is confirmed by additional markers belonging to a second molecular system (i.e. transcription). This rules out the risk of circularity when inferring species evolution by small subunit ribosomal RNA and ribosomal protein sequences, since it has been suggested that concerted LGT may affect these markers. Our results strongly support the existence of a core of proteins that has evolved mainly through vertical inheritance in Archaea, and carries a bona fide phylogenetic signal that can be used to retrace the evolutionary history of this domain. The identification and analysis of additional molecular markers not affected by LGT should continue defining the emerging picture of a genuine phylogenetic core for the third domain of life

A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya

DNA topoisomerase IB (TopoIB) was thought for a long time to be a eukaryotic specific enzyme. A shorter version was then found in viruses and later on in several bacteria, but not in archaea. Here, we show that a eukaryotic-like TopoIB is present in the recently sequenced genomes of two archaea of the newly proposed phylum Thaumarchaeota. Phylogenetic analyses suggest that a TopoIB was present in the last common ancestor of Archaea and Eucarya. This finding indicates that the last common ancestor of Archaea and Eucarya may have harboured a DNA genome

A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes

A large-scale survey of potential recently acquired integrative elements in 119 archaeal and bacterial genomes reveals that many recently acquired genes have originated from integrative element

Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure

<p>Abstract</p> <p>Background</p> <p>As bacteria, motile archaeal species swim by means of rotating flagellum structures driven by a proton gradient force. Interestingly, experimental data have shown that the archaeal flagellum is non-homologous to the bacterial flagellum either in terms of overall structure, components and assembly. The growing number of complete archaeal genomes now permits to investigate the evolution of this unique motility system.</p> <p>Results</p> <p>We report here an exhaustive phylogenomic analysis of the components of the archaeal flagellum. In all complete archaeal genomes, the genes coding for flagellum components are co-localized in one or two well-conserved genomic clusters showing two different types of organizations. Despite their small size, these genes harbor a good phylogenetic signal that allows reconstruction of their evolutionary histories. These support a history of mainly vertical inheritance for the components of this unique motility system, and an interesting possible ancient horizontal gene transfer event (HGT) of a whole flagellum-coding gene cluster between Euryarchaeota and Crenarchaeota.</p> <p>Conclusion</p> <p>Our study is one of the few exhaustive phylogenomics analyses of a non-informational cell machinery from the third domain of life. We propose an evolutionary scenario for the evolution of the components of the archaeal flagellum. Moreover, we show that the components of the archaeal flagellar system have not been frequently transferred among archaeal species, indicating that gene fixation following HGT can also be rare for genes encoding components of large macromolecular complexes with a structural role.</p