Uncovering species boundaries in the Neotropical ant complex Ectatomma ruidum (Ectatomminae) under the presence of nuclear mitochondrial paralogues

Nuclear mitochondrial (mt) paralogues (numts) are non‐functional fragments of mtDNA integrated into the nuclear genome that can overestimate the number of species in analyses based on mtDNA sequences. As numts have relatively slow mutation rates, they can pass undetected by conventional procedures such as inspecting for internal stop codons, indels or apparent polymorphism in chromatograms. Species boundaries based on mtDNA markers therefore require a thorough assessment of numts, especially in insects, where this phenomenon appears to be relatively frequent. Ectatomma ruidum is a widely distributed Neotropical ant species that is distributed from northern Mexico to northern Brazil. Previous behavioural and molecular evidence suggests that this species actually represents a composite taxon. Here we assessed the species boundaries in E. ruidum based on two mt (COI, cyt b) and one nuclear (H3) marker, as well as on external morphology. Ancient and recent mt paralogues were detected in several specimens, although pre‐PCR dilution of DNA template helped to recover most of the mt orthologues. Based on the congruence found between our species delineation obtained from the mt genealogies and the discriminated morphospecies, we propose that E. ruidum is actually composed of at least three species. Two of these species have a wide geographical distribution in the Neotropics, whereas the remaining one was restricted to localities situated near the Pacific coast in south‐east Mexico. We also found extensive intra‐ and interspecific variation in the barcoding locus. Moreover, the nuclear evidence suggests the existence of hybrids between two of these species in Oaxaca, south‐east Mexico. This study agrees with previous studies of other closely related animal taxa, which have revealed a complex evolutionary history and overlooked species diversity in the latter region.     

Break the pattern: breakpoints in beta diversity of vertebrates are general across clades and suggest common historical causes

The use of correlative analyses might be insufficient to understand the processes that control biodiversity, because the variables accounting for different hypotheses (e.g. current climate, past climate change, post‐glacial dispersal limitation) are mutually correlated. We suggest here that, in order to gain insight, it could be useful to search for latitudinal thresholds that could provide information about qualitative changes in the way biodiversity varies in space. Such tipping points could inform about higher‐level processes that are not reflected in correlative analyses. We test whether similar breakpoints in latitudinal beta‐diversity patterns exist for different vertebrate groups with diverse life histories and dispersal abilities. In birds, bats and non‐volant mammals we find breakpoints similar to those of amphibians. Differences in species composition are mainly due to species replacement from the equator to the breakpoint, but are dominated by nested species losses from the breakpoint to higher latitudes. Thus, marked thresholds discriminate two world regions where different processes appear to drive biodiversity.     

Diversity and trophic structure of insects associated with grains of three maize landraces in San Agustín Loxicha,Oaxaca, Mexico

Diversity and trophic structure of grain insect communities were examined in Olotillo, Nal‐Tel and Comiteco maize landraces cultivated within a milpa agroecosystem by Zapotec ethnic groups in Mexico. Higher insect diversity was expected in Olotillo, whose cultivation comprises a wide variety of agroecosystems, and low insect abundance in Nal‐Tel with small grains and thick testa. Forty Olotillo cobs were collected at low, medium and high elevations, and 40 each of Nal‐Tel at low elevation and Comiteco at high elevation. Cobs were monitored for 30 days under controlled laboratory conditions until all insects emerged. Thickness of testa of 400 grains from each landrace was measured. Community composition and trophic structure were described and standard diversity indices were estimated. A total of 9,708 insects, corresponding to five orders, 24 families and 36 species, were recorded, with six species not previously reported in this region. Insect guilds were composed of 70% phytophages, 22% parasitoids and 8% predators. Species richness was S = 27, 16 and 8 in Olotillo, Comiteco and Nal‐Tel, respectively. Nal‐Tel and Olotillo had the highest diversity index values (H′ = 1.32 and 1.2, respectively) and no significant differences; Comiteco had the lowest value (H′ = 0.65) and differed significantly from the other landraces. Comiteco and Olotillo, which have large grains and thin testa, showed higher insect abundance than Nal‐Tel, which has small grains and thick testa and showed lower abundance. Results support our hypotheses and highlight the role of traditional crop management in insect agrobiodiversity maintenance and conservation.     

Analysis of the volume of fluid (VOF) method for the simulation of the mucus clearance process with CFD

The clearance of mucus through coughing is a complex, multiphase process, which is affected principally by mucus viscosity and airflow velocity; however, it is also critically affected by the thickness of the two layers of mucus—the serous and gel layers—and oscillation level. The present study examines the effects of the latter parameters more closely. To do so, the mucus clearance process is simulated with a transient 3D volume of fluid (VOF) multiphase model in ANSYS Fluent. The model includes mucus’ bilayer properties and a wide range of boundary conditions were tested. The model was analysed in both a straight tube and a realistic trachea. Ultimately, the model was able to both capture air-mucus interface wave evolution and predict the overall behaviour of the clearance process. The results were consistent with experimental clearance data and numerical airflow simulations, which indicates our methodology is appropriate for future studies. Ultimately, the mere presence of the serous layer was found to increase mucus clearance by more than 15 percent. An oscillating flow enhanced clearance by up to 5 percent. Interestingly, interface wave steepness was found to be inversely correlated with mucus thickness, but directly with mucus velocity, which suggests it will be an interesting parameter for further study.     

Sequential development of several RT-qPCR tests using LNA nucleotides and dual probe technology to differentiate SARS-CoV-2 from influenza A and B

Sensitive and accurate RT-qPCR tests are the primary diagnostic tools to identify SARS-CoV-2-infected patients. While many SARS-CoV-2 RT-qPCR tests are available, there are significant differences in test sensitivity, workflow (e.g. hands-on-time), gene targets and other functionalities that users must consider. Several publicly available protocols shared by reference labs and public health authorities provide useful tools for SARS-CoV-2 diagnosis, but many have shortcomings related to sensitivity and laborious workflows. Here, we describe a series of SARS-CoV-2 RT-qPCR tests that are originally based on the protocol targeting regions of the RNA-dependent RNA polymerase (RdRp) and envelope (E) coding genes developed by the Charité Berlin. We redesigned the primers/probes, utilized locked nucleic acid nucleotides, incorporated dual probe technology and conducted extensive optimizations of reaction conditions to enhance the sensitivity and specificity of these tests. By incorporating an RNase P internal control and developing multiplexed assays for distinguishing SARS-CoV-2 and influenza A and B, we streamlined the workflow to provide quicker results and reduced consumable costs. Some of these tests use modified enzymes enabling the formulation of a room temperature-stable master mix and lyophilized positive control, thus increasing the functionality of the test and eliminating cold chain shipping and storage. Moreover, a rapid, RNA extraction-free version enables high sensitivity detection of SARS-CoV-2 in about an hour using minimally invasive, self-collected gargle samples. These RT-qPCR assays can easily be implemented in any diagnostic laboratory and can provide a powerful tool to detect SARS-CoV-2 and the most common seasonal influenzas during the vaccination phase of the pandemic.