Insights on the evolution of Coronavirinae in general, and SARS-CoV-2 in particular, through innovative biocomputational resources.

The structural proteins of coronaviruses portray critical information to address issues of classification, assembly constraints, and evolutionary pathways involving host shifts. We compiled 173 complete protein sequences from isolates belonging to the four genera of the subfamily Coronavirinae. We calculate a single matrix of viral distance as a linear combination of protein distances. The minimum spanning tree (MST) connecting the individuals captures the structure of their similarities. The MST re-capitulates the known phylogeny of Coronovirinae. Hosts were mapped onto the MST and we found a non-trivial concordance between host phylogeny and viral proteomic distance. We also study the chimerism in our dataset through computational simulations. We found evidence that structural units coming from loosely related hosts hardly give rise to feasible chimeras in nature. This work offers a fresh way to analyze features of SARS-CoV-2 and related viruses.

Ecoregions, climate, topography, physicochemical, or a combination of all: Which criteria are the best to define river types based on abiotic variables and macroinvertebrates in neotropical rivers?

The baseline conditions for a particular river or stream type are essential to classify aquatic ecosystems based on physical and biological characteristics. In this study, we proposed a river typology for different ecoregions, climate and topography of northwestern Argentina using parameters, and combined key variables to establish reference conditions. A set of geographical, hydro-morphological, hydrological, geological (pedology and sedimentology) and physicochemical variables were measured from different rivers and analyzed with clustering and ordination techniques to develop a typology. We analyzed the correspondence of the physical river conditions and benthic macroinvertebrate assemblages using non-metric multidimensional scaling analysis, dissimilarity among assemblages, ANOSIM approach and envfit analysis in order to make an ecological validation of the classification. Our results allowed us to classify the neotropical rivers studied, according to typological systems adapted from the European Water Framework Directive. The combination of ecoregions and topography along with other variables associated (system B), was better corresponded with biological arrangements. Hence, ecoregions and topography combined turned out to be more precise as a criterion to define river types and their local abiotic and biotic reference conditions. Macroinvertebrate distribution corresponded with the classifications proposed and was related with abiotic features of the rivers. The physical variables as altitude, grain size, water temperature and turbidity were key parameters to develop a schematic model to define river types that could be implemented and tested in other countries of the region. Five river types have been identified, characterized, and included in three large groups: Mountains, Foothills, and Lowlands (Plains). Our results showed that topography and climate are two aspects that strongly influence South American freshwater biota. We propose the schematic model developed in our study as a baseline to define freshwater biomes based on altitude (topography), ecoregions (climate) and biological functional traits at a broad spatial scale (continental or global).