Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm

Our goal was to describe in more detail the evolutionary history of Gamma and two derived lineages (P.1.1 and P.1.2), which are part of the arms race that SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites under positive selection in 12 genes/ORFs: Spike, N, M, E, ORF1a, ORF1b, ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF10. Some diagnostic sites for Gamma lacked a signature of positive selection in our study, but these were not fixed, apparently escaping the action of purifying selection. Our network analyses revealed branches leading to expanding haplotypes with sites under selection only detected when P.1.1 and P.1.2 were considered. The P.1.2 exclusive haplotype H_5 originated from a non-synonymous mutational step (H3509Y) in H_1 of ORF1a. The selected allele, 3509Y, represents an adaptive novelty involving ORF1a of P.1. Finally, we discuss how phenomena such as epistasis and antagonistic pleiotropy could limit the emergence of new alleles (and combinations thereof) in SARS-COV-2 lineages, maintaining infectivity in humans, while providing rapid response capabilities to face the arms race triggered by host immuneresponses.     

Scaling relationships within the maxillary tooth row of the Felidae, and the absence of the second upper premolar in Lynx

Suggestions that short-faced members of the Felidae tend to lack the second upper premolar (P2) imply a possible shift in scaling associated with the palate and maxillary tooth row in Lynx , which lacks P2, as compared to felids that retain it. This hypothesis is tested using a scaling model that relates the lengths of the palate, and the upper tooth row and its components, to post-palatal skull length in the small to moderately large felids Felis catus (domestic cat), L. canadensis (Canada lynx), F. pardalis (ocelot), and F. concolor (cougar). Scaling relationships of both palate and tooth row length to post-palatal skull length do not differ significantly from isometry in all four species. However, ocelots have a significantly shorter palate and tooth row than lynxes over their overlapping ranges of post-palatal skull length, suggesting that the absence of P2 is not correlated with the length of the face in these species. CI, P3 and P4 tend to be relatively longer in larger felids; none the less, ocelots have a relatively small P3 and lynxes have a proportionately large P4. Because both lynxes and ocelots have a relatively small gap between CI and P3, the absence of P2 is not correlated with available space within the tooth row in adults. However, lynxes also appear to have a relatively long dP3 that almost obliterates the diastema within the deciduous tooth row. The absence of P2 in Lynx may be an engineering artefact that is associated with a shift in proportions within the deciduous toothrow, resulting in inhibition of the development of P2 and dP2 early in ontogeny. Despite the variable occurrence and polymorphism associated with P2 in the Felidae, this character has systematic value within this clade and is a synapomorphy for Lynx.     

Re/Making La Negrita: Culture as an Aesthetic System in Costa Rica

In this article, I examine the production of meaning in the veneration of La Negrita, the black Madonna and patroness of Costa Rica. Both an apparition and an icon, La Negrita is a 20-centimeter, dark-colored statue of the Virgin Mary that appeared to a mulata girl on the outskirts of the colonial city of Cartago in 1635. Throughout the ensuing 400 years, La Negrita has been remade in the image of hegemony, even as the experience of her perceived power has challenged that ideological and coercive project. Through an analysis of this historical progression, I argue for a theory of culture as an aesthetic system, where the egalitarianism of experience is always in conflict with the authoritarianism of meaning.     

Northern Goshawk Habitat: an Intersection of Science,Management, and Conservation

Abstract: We responded to the claim by Greenwald et al. (2005) that the management recommendations for the northern goshawk in the Southwestern United States (MRNG; Reynolds et al. 1992), a food web-based conservation plan that incorporated both northern goshawk (Accipiter gentilis) and multiple prey habitats, may be inadequate to protect goshawks. Greenwald et al. (2005) based this claim on their review of 12 telemetry studies of goshawk habitat selection and 5 nontelemetry studies of the effects of vegetation structure at the home range scale on goshawk nest occupancy and reproduction that appeared after the 1992 publication of the MRNG. Greenwald et al. (2005) summarized their review as showing that 1) goshawks were habitat specialists limited to forests with mature and old-growth structures including large trees, high canopy cover, multiple canopy layering, and abundant woody debris; 2) habitats were not selected on the basis of prey abundance and, therefore, managing for prey habitats diluted goshawk habitats; and 3) selection for openings, edges, and habitat diversity was inconclusive. Our review found that when the studies' respective authors pooled their radiotagged goshawks there were weak to strong selections for old forest structures. However, the studies also documented extensive variation in use of vegetation types and structures by individual goshawks; some avoided openings, edges, young forests, and old forests, whereas others selected for these characteristics. Additionally, by virtue of their wide geographic distribution, the studies showed that the focal populations themselves occurred in a variety of forest types, some with large structural differences. We found no evidence in Greenwald's et al. (2005) review that the MRNG are inadequate to protect goshawks. Rather, the studies reviewed by Greenwald et al. (2005), as well as many studies they missed, supported the MRNG. The suggestion of inadequacy by Greenwald et al. (2005) appeared rooted in misunderstandings of goshawk habitats described in the MRNG, a discounting of the extent of variation in vegetation structural and seral stages used by goshawks, a limited understanding of the extent to which prey limits goshawks, a failure to recognize the dynamic nature of forests, and an incomplete review of the literature. We believe the MRNG are adequate because they maximize the sustainable amount of mature and old forests in goshawk home ranges and specify the kinds and intermixtures of prey habitats within home ranges. Implementation of MRNG should reduce the likelihood that the availability of vegetation structures suited to goshawk nesting and foraging, as well as abundance and availability of prey, will limit goshawk nest occupancy and reproduction.     

Factors Controlling the Abundance and Size Distribution of the Phototrophic Ciliate Myrionecta rubra in Open Waters of the North Atlantic

ABSTRACT. Myrionecta rubra, a ubiquitous planktonic ciliate, has received much attention due to its wide distribution, occurrence as a red tide organism, and unusual cryptophyte endosymbiont. Although well studied in coastal waters, M. rubra is poorly examined in the open ocean. In the Irminger Basin, North Atlantic, the abundance of M. rubra was 0–5 cells/ml, which is low compared with that found in coastal areas. Distinct patchiness (100 km) was revealed by geostatistical analysis. Multiple regression indicated there was little relationship between M. rubra abundance and a number of environmental factors, with the exception of temperature and phytoplankton biomass, which influenced abundance in the spring. We also improve on studies that indicate distinct size classes of M. rubra; we statistically recognise four significantly distinct width classes (5–16, 12–23, 18–27, 21–33 μm), which decrease in abundance with increasing size. A multinomial logistic regression revealed the main variable correlated with this size distribution was ambient nitrate concentration. Finally, we propose a hypothesis for the distribution of sizes, involving nutrients, feeding, and dividing of the endosymbiont.     

Studies in Stomatal Behaviour: VI. AN INVESTIGATION OF THE LIGHT RESPONSES OF WHEAT STOMATA WITH THE ATTEMPTED ELIMINATION OF CONTROL BY THE MESOPHYLL

An apparatus is described enabling light responses of wheatstomata to be followed by periodical porometer readings, betweenwhich the substomatal cavities can be swept with carbon dioxide-freeair forced in through the stomata. This is held to eliminatethe influence of changes in the carbon dioxide content of theintercellular space atmosphere brought about by photosynthesisand respiration in the mesophyll. Using this apparatus in anexperiment of ‘Latin square’ design with 6-foldreplication of three light treatments, a statistically significantresponse to light was found in a leaf area subjected to varyinglight intensities from 90 to 800 f.c. This response was reflectedin a similar significant effect, though of smaller magnitude,occurring in a similarly swept ‘control’ area 2cm. distant and maintained at a constant light intensity of270 f.c, the intervening portion of leaf being illuminated with800 f.c. throughout. It is argued that this transmission ofa light effect from one area to another does not occur via theintercellular spaces, nor by means of carbon dioxide gradientsfrom cell to cell. It is concluded from the data that thereis an indirect effect of light and perhaps also a direct effectupon the guard cells themselves; it is probable that neitherof the two effects concerned operates by reduction of the internalcarbon dioxide content in the guard cells.