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The facilitative effects of “foundation species” on community diversity and composition in alpine systems can be strong, but the strength of these effects often varies along gradients that occur above tree line. Here, we explore the effects of foundation species above and below tree line, a globally consistent and often abrupt climatic and ecological transition. The experiment was developed in Northern Rocky Mountains of Wyoming and Montana, USA, in vegetation with similar herbaceous physiognomies without trees, but containing dominant foundation species with “cushion” morphologies. In these systems, we compared the diversity and structure of plant communities occurring within these foundation species to that in the open at three sites below tree line and three sites above tree line. Above tree line, 69–94% of all species were significantly spatially associated with foundation species, whereas below tree line, 29–62% of the species were associated with foundation species. Similar patterns were observed in species accumulation curves with foundation species affecting the accumulation of species by +17 to +47% above tree line vs. –27 to +24% below tree line. Our results were consistent with the idea that facilitative interactions are more common with greater abiotic stress. However, our results also suggest the possibility that the climatic transition representing tree line might also represent a threshold, rather than a simple linear response, in how foundation species affect community diversity. A much larger sample size is warranted to thoroughly test such thresholds, but the fundamental ecological and physiological transition that plants experience at the climate of the tree line may also be reflected in small-scale species interactions that organize communities. [ABSTRACT FROM PUBLISHER]

Biotic interactions can shape phylogenetic community structure (PCS). However, we do not know how the asymmetric effects of foundation species on communities extend to effects on PCS. We assessed PCS of alpine plant communities around the world, both within cushion plant foundation species and adjacent open ground, and compared the effects of foundation species and climate on alpha (within-microsite), beta (between open and cushion) and gamma (open and cushion combined) PCS. In the open, alpha PCS shifted from highly related to distantly related with increasing potential productivity. However, we found no relationship between gamma PCS and climate, due to divergence in phylogenetic composition between cushion and open sub-communities in severe environments, as demonstrated by increasing phylo-beta diversity. Thus, foundation species functioned as micro-refugia by facilitating less stress-tolerant lineages in severe environments, erasing a global productivity - phylogenetic diversity relationship that would go undetected without accounting for this important biotic interaction. [ABSTRACT FROM AUTHOR]

El uso del método de máxima verosimilitud para estimar modelos de producción Half-Normal con frontera estocástica conlleva algunas dificultades prácticas que tal vez no han sido suficientemente enfatizadas. Usando el software FRONTIER, analizamos el caso en que la estimación sugiere la ausencia de factores aleatorios en el término de error compuesto. Hemos comprobado que existen motivos para pensar que las estimaciones de los parámetros y, sobre todo, sus errores estándar son de dudosa validez. El software LIMDEP no obtiene estimaciones en este caso, ofreciendo un mensaje de error. || Using the maximum likelihood method, in order to estimate Half-Normal stochastic frontier production models, entails several practical difficulties that, perhaps, have not been sufficiently emphasised. In employing FRONTIER software, we analyse the case in which the estimation obtained suggests the absence of random factors in the composite error term. We have proved that there are reasons to doubt the validity of the parameter estimates and especially of its standard errors. On the other hand, no estimation is obtained in the previous situation, with LIMDEP software, but an error message.

In this paper, several identities concerning expectation, variance, covariance, cumulative distribution functions, the coefficient of variation, and the Lorenz curve are obtained and they are used in establishing theoretical results. Furthermore, a graphical representation of the variance is proposed which, together with the aforementioned identities, enables the square of the coeficient of variation to be considered as an equality measure in the sameway as is the Gini index. A study of the similarities between the theoretical expression of the Gini index and the square of the coefficient of variation is also carried out in this paper. || En este trabajo se obtienen diversas identidades relativas a la espezanza, varianza, covarianza, función de distribución acumulada, coeficiente de variación y curva de Lorenz que se usarán para obtener resultados teóricos interesantes. Se construye, además, una representación gráfica de la varianza, la cual, utilizando las propiedades obtenidas, nos indica que el cuadrado del coeficiente de variación se puede considerar como una medida de igualdad, de igual forma que se considera al índice de Gini. En este artículo también se lleva a cabo un estudio de las similitudes entre la expresión teórica delíndice de Gini y el cuadrado del coeficiente de variación.

Background: Coronavirus disease 2019 (COVID-19) infection is a major public health problem in the world and reinfections are becoming more frequent. Our main objective was to describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the capital of Lima and Callao, Peru., Methods: We searched in the Peruvian laboratory information system from April 2020 up to May 2021, looking for cases having 2 positive molecular tests for SARS-CoV-2 with more than 90 days between them. We performed genomic sequencing to the available pairs of samples and described the clinical characteristics, epidemiological impact, and genomic analysis of the confirmed reinfections., Results: There were 1 694 164 people with a positive diagnostic test for SARS-CoV-2 in Lima/Callao during the study period. Of these, 1695 had 2 positive molecular tests with more than 90 days between them. Two hundred eleven had both samples available for genomic analysis according to our selection criteria, and these were retrieved and submitted to sequencing. Thirty cases were confirmed to be SARS-CoV-2 reinfections with 2 different lineages in the 2 episodes. The variant Lambda (C.37) was the most common during the second infection and accounted for 19 (63.3%) of the 30 cases., Conclusions: We report 30 cases of confirmed SARS-CoV-2 reinfections. The Lambda variant was the most common cause of the second infections, in concordance with its predominant circulation during Peru's second wave. This report describes the largest series of confirmed reinfections by SARS-CoV-2 in Latin America.We describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 in Lima and Callao, durante la segunda ola en Peru. The Lambda variant (C.37) was the most common cause of the second infections., (© The Author(s) 2022. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Peru has become one of the countries with the highest mortality rates from the current coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To investigate early transmission events and the genomic diversity of SARS-CoV-2 isolates circulating in Peru in the early COVID-19 pandemic, we analyzed 3472 viral genomes, of which 149 were from Peru. Phylogenomic analysis revealed multiple and independent introductions of the virus likely from Europe and Asia and a high diversity of genetic lineages circulating in Peru. In addition, we found evidence for community-driven transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different regions of Peru., (© 2021 Wiley Periodicals LLC.)

Background: Plant communities of fragmented agricultural landscapes, are subject to patch isolation and scale-dependent effects. Variation in configuration, composition, and distance from one another affect biological processes of disturbance, productivity, and the movement ecology of species. However, connectivity and spatial structuring among these diverse communities are rarely considered together in the investigation of biological processes. Spatially optimised predictor variables that are based on informed measures of connectivity among communities, offer a solution to untangling multiple processes that drive biodiversity., Results: To address the gap between theory and practice, a novel spatial optimisation method that incorporates hypotheses of community connectivity, was used to estimate the scale of effect of biotic and abiotic factors that distinguish plant communities. We tested: (1) whether different hypotheses of connectivity among sites was important to measuring diversity and environmental variation among plant communities; and (2) whether spatially optimised variables of species relative abundance and the abiotic environment among communities were consistent with diversity parameters in distinguishing four habitat types; namely Crop, Edge, Oak, and Wasteland. The global estimates of spatial autocorrelation, which did not consider environmental variation among sites, indicated significant positive autocorrelation under four hypotheses of landscape connectivity. The spatially optimised approach indicated significant positive and negative autocorrelation of species relative abundance at fine and broad scales, which depended on the measure of connectivity and environmental variation among sites., Conclusions: These findings showed that variation in community diversity parameters does not necessarily correspond to underlying spatial structuring of species relative abundance. The technique used to generate spatially-optimised predictors is extendible to incorporate multiple variables of interest along with a priori hypotheses of landscape connectivity. Spatially-optimised variables with appropriate definitions of connectivity might be better than diversity parameters in explaining functional differences among communities., (© 2021. The Author(s).)

Asymptomatic carriers are a likely source of transmission of Neisseria meningitidis to close contacts who are placed at a higher risk for invasive meningococcal disease (IMD). Although N. meningitidis ciprofloxacin-resistance is rare, there have been an increase in the reports of resistant isolates mainly in patients diagnosed with IMD, and little is known about the N. meningitidis ciprofloxacin-resistance in the carrier populations. We performed a pharyngeal carriage study during a 2017 military setting outbreak in Peru, caused by a ciprofloxacin-resistant N. meningitidis B. The isolates analysed came from two hospitalized cases and six asymptomatic carriers. Whole-genome sequence-based analysis was performed and showed that strains carrying the Thr 91 Ile mutation, in the gene encoding for subunit A of DNA gyrase ( gyr A), were responsible for the fluoroquinolone resistance (MICs ≥0.256 µg ml -1 ) and were closely related to highly virulent strains from France, Norway and the UK. Phylogenetic analysis of the gyr A gene revealed that likely these Peruvian isolates acquired resistance through horizontal gene transfer from Neisseria lactamica . Our study provides evidence for the emergence and propagation of ciprofloxacin-resistant N. meningitidis B from asymptomatic carriers, and recommends the introduction of serogroup B vaccines for high-risk populations.

Increasing evidence indicates that in wild ecosystems plant viruses are important ecological agents, and with potential to jump into crops, but only recently have the diversity and population dynamics of wild plant viruses begun to be explored. Theory proposes that biotic factors (e.g., ecosystem biodiversity, host abundance, and host density) and climatic conditions would determine the epidemiology and evolution of wild plant viruses. However, these predictions seldom have been empirically tested. For 3 years, we analyzed the prevalence and genetic diversity of Potyvirus species in preserved riparian forests of Spain. Results indicated that potyviruses were always present in riparian forests, with a novel generalist potyvirus species provisionally named Iberian hop mosaic virus (IbHMV), explaining the largest fraction of infected plants. Focusing on this potyvirus, we analyzed the biotic and climatic factors affecting virus infection risk and population genetic diversity in its native ecosystem. The main predictors of IbHMV infection risk were host relative abundance and species richness. Virus prevalence and host relative abundance were the major factors determining the genetic diversity and selection pressures in the virus population. These observations support theoretical predictions assigning these ecological factors a key role in parasite epidemiology and evolution. Finally, our phylogenetic analysis indicated that the viral population was genetically structured according to host and location of origin, as expected if speciation is largely sympatric. Thus, this work contributes to characterizing viral diversity and provides novel information on the determinants of plant virus epidemiology and evolution in wild ecosystems.

Pseudoalteromonas is a genus of marine bacteria often found in association with other organisms. Although several studies have examined Pseudoalteromonas diversity and their antimicrobial activity, its diversity in tropical environments is largely unexplored. We investigated the diversity of Pseudoalteromonas in marine environments of Panama using a multilocus phylogenetic approach. Furthermore we tested their antimicrobial capacity and evaluated the effect of recombination and mutation in shaping their phylogenetic relationships. The reconstruction of clonal relationships among 78 strains including 15 reference Pseudoalteromonas species revealed 43 clonal lineages, divided in pigmented and non-pigmented strains. In total, 39 strains displayed moderate to high activity against Gram-positive and Gram-negative bacteria and fungi. Linkage disequilibrium analyses showed that the Pseudoalteromonas strains of Panama have a highly clonal structure and that, although present, recombination is not frequent enough to break the association among alleles. This clonal structure is in contrast to the high rates of recombination generally reported for aquatic and marine bacteria. We propose that this structure is likely due to the symbiotic association with marine invertebrates of most strains analyzed. Our results also show that there are several putative new species of Pseudoalteromonas in Panama to be described., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Interactions among species determine local-scale diversity, but local interactions are thought to have minor effects at larger scales. However, quantitative comparisons of the importance of biotic interactions relative to other drivers are rarely made at larger scales. Using a data set spanning 78 sites and five continents, we assessed the relative importance of biotic interactions and climate in determining plant diversity in alpine ecosystems dominated by nurse-plant cushion species. Climate variables related with water balance showed the highest correlation with richness at the global scale. Strikingly, although the effect of cushion species on diversity was lower than that of climate, its contribution was still substantial. In particular, cushion species enhanced species richness more in systems with inherently impoverished local diversity. Nurse species appear to act as a 'safety net' sustaining diversity under harsh conditions, demonstrating that climate and species interactions should be integrated when predicting future biodiversity effects of climate change., (© 2013 John Wiley & Sons Ltd/CNRS.)