Microclimate–forage growth linkages across two strongly contrasting precipitation years in a Mediterranean catchment

Given the complex topography of California rangelands, contrasting microclimates affect forage growth at catchment scales. However, documentation of microclimate–forage growth associations is limited, especially in Mediterranean regions experiencing pronounced climate change impacts. To better understand microclimate–forage growth linkages, we monitored forage productivity and root-zone soil temperature and moisture (0–15 and 15–30 cm) in 16 topographic positions in a 10-ha annual grassland catchment in California's Central Coast Range. Data were collected through two strongly contrasting growing seasons, a wet year (2016–17) with 287-mm precipitation and a dry year (2017–18) with 123-mm precipitation. Plant-available soil water storage (0–30 cm) was more than half full for most of the wet year; mean peak standing forage was 2790 kg ha−1 (range: 1597–4570 kg ha−1). The dry year had restricted plant-available water and mean peak standing forage was reduced to 970 kg ha−1 (range: 462–1496 kg ha−1). In the wet year, forage growth appeared energy limited (light and temperature): warmer sites produced more forage across a 3–4°C soil temperature gradient but late season growth was associated with moister sites spanning this energy gradient. In the dry year, the warmest topographic positions produced limited forage across a 10°C soil temperature gradient until late season rainfall in March. Linear models accounting for interactions between soil moisture and temperature explained about half of rapid, springtime forage growth variance. These findings reveal dynamic but clear microclimate–forage growth linkages in complex terrain, and thus, have implications for rangeland drought monitoring and dryland ecosystems modeling under climate change

Habitat‐dependent occupancy and movement in a migrant songbird highlights the importance of mangroves and forested lagoons in Panama and Colombia

Climate change is predicted to impact tropical mangrove forests due to decreased rainfall, sea‐level rise, and increased seasonality of flooding. Such changes are likely to influence habitat quality for migratory songbirds occupying mangrove wetlands during the tropical dry season. Overwintering habitat quality is known to be associated with fitness in migratory songbirds, yet studies have focused primarily on territorial species. Little is known about the ecology of nonterritorial species that may display more complex movement patterns within and among habitats of differing quality. In this study, we assess within‐season survival and movement at two spatio‐temporal scales of a nonterritorial overwintering bird, the prothonotary warbler (Protonotaria citrea), that depends on mangroves and tropical lowland forests. Specifically, we (a) estimated within‐patch survival and persistence over a six‐week period using radio‐tagged birds in central Panama and (b) modeled abundance and occupancy dynamics at survey points throughout eastern Panama and northern Colombia as the dry season progressed. We found that site persistence was highest in mangroves; however, the probability of survival did not differ among habitats. The probability of warbler occupancy increased with canopy cover, and wet habitats were least likely to experience local extinction as the dry season progressed. We also found that warbler abundance is highest in forests with the tallest canopies. This study is one of the first to demonstrate habitat‐dependent occupancy and movement in a nonterritorial overwintering migrant songbird, and our findings highlight the need to conserve intact, mature mangrove, and lowland forests

Modeling the initiation of others into injection drug use, using data from 2,500 injectors surveyed in Scotland during 2008-2009

The prevalence of injection drug use has been of especial interest for assessment of the impact of blood-borne viruses. However, the incidence of injection drug use has been underresearched. Our 2-fold aim in this study was to estimate 1) how many other persons, per annum, an injection drug user (IDU) has the equivalent of full responsibility (EFR) for initiating into injection drug use and 2) the consequences for IDUs' replacement rate. EFR initiation rates are strongly associated with incarceration history, so that our analysis of IDUs' replacement rate must incorporate when, in their injecting career, IDUs were first incarcerated. To do so, we have first to estimate piecewise constant incarceration rates in conjunction with EFR initiation rates, which are then combined with rates of cessation from injecting to model IDUs' replacement rate over their injecting career, analogous to the reproduction number of an epidemic model. We apply our approach to Scotland's IDUs, using over 2,500 anonymous injector participants who were interviewed in Scotland's Needle Exchange Surveillance Initiative during 2008-2009. Our approach was made possible by the inclusion of key questions about initiations. Finally, we extend our model to include an immediate quit rate, as a reasoned compensation for higher-than-expected replacement rates, and we estimate how high initiates' quit rate should be for IDUs' replacement rate to be 1

Spontaneous mutation rate in the smallest photosynthetic eukaryotes

Mutation is the ultimate source of genetic variation, and knowledge of mutation rates is fundamental for our understanding of all evolutionary processes. High throughput sequencing of mutation accumulation lines has provided genome wide spontaneous mutation rates in a dozen model species, but estimates from nonmodel organisms from much of the diversity of life are very limited. Here, we report mutation rates in four haploid marine bacterial-sized photosynthetic eukaryotic algae; Bathycoccus prasinos, Ostreococcus tauri, Ostreococcus mediterraneus, and Micromonas pusilla. The spontaneous mutation rate between species varies from μ = 4.4 × 10−10 to 9.8 × 10−10 mutations per nucleotide per generation. Within genomes, there is a two-fold increase of the mutation rate in intergenic regions, consistent with an optimization of mismatch and transcription-coupled DNA repair in coding sequences. Additionally, we show that deviation from the equilibrium GC content increases the mutation rate by ∼2% to ∼12% because of a GC bias in coding sequences. More generally, the difference between the observed and equilibrium GC content of genomes explains some of the inter-specific variation in mutation rates

High Abundances of Species in Protected Areas in Parts of their Geographic Distributions Colonized during a Recent Period of Climatic Change

It is uncertain whether Protected Areas (PAs) will conserve high abundances of species as their distributions and abundances shift in response to climate change. We analyzed large datasets for 57 butterfly and 42 odonate species (including four that have recently colonized Britain). We found that 73 of 94 species with sufficient data for analysis were more abundant inside than outside PAs in the historical parts of their British distributions, showing that PAs have retained high conservation value. A significant majority (61 of 99 species) was also more abundant inside PAs in regions they have colonized during the last 30–40 years of climate warming. Species with relatively high abundances inside PAs in long-established parts of their distributions were also disproportionately associated with PAs in recently colonized regions, revealing a set of relatively PA-reliant species. Pas, therefore, play a vital role in the conservation of biodiversity as species’ ranges become more dynamic

Direct and indirect causal effects of heterozygosity on fitness-related traits in Alpine ibex

Heterozygosity–fitness correlations (HFCs) are a useful tool to investigate the effects of inbreeding in wild populations, but are not informative in distinguishing between direct and indirect effects of heterozygosity on fitness-related traits. We tested HFCs in male Alpine ibex (Capra ibex) in a free-ranging population (which suffered a severe bottleneck at the end of the eighteenth century) and used confirmatory path analysis to disentangle the causal relationships between heterozygosity and fitness-related traits. We tested HFCs in 149 male individuals born between 1985 and 2009. We found that standardized multi-locus heterozygosity (MLH), calculated from 37 microsatellite loci, was related to body mass and horn growth, which are known to be important fitness-related traits, and to faecal egg counts (FECs) of nematode eggs, a proxy of parasite resistance. Then, using confirmatory path analysis, we were able to show that the effect of MLH on horn growth was not direct but mediated by body mass and FEC. HFCs do not necessarily imply direct genetic effects on fitness-related traits, which instead can be mediated by other traits in complex and unexpected ways

Still armed after domestication? Impacts of domestication and agronomic selection on silicon defences in cereals

Plant phenotypes reflect trade‐offs between competing resource‐intensive physiological processes. A shift in resource allocation, away from anti‐herbivore defences and towards growth and reproduction, is predicted through plant domestication, such that crops are faster growing and higher yielding than their wild ancestors. These changes are hypothesized to have come at the cost of defence investment, leaving crops “disarmed by domestication”. Silicon is the principal anti‐herbivore defence in grasses, including many of our most important staple cereal crops, but the impact of domestication on silicon‐based defences is unknown. We measured the effects of both domestication and modern agronomic selection on growth rate and a suite of anti‐herbivore defences, specifically leaf toughness, silicon and phenolic concentrations. Our comparison of wild, landrace and modern cultivated cereals spanned multiple cereal species, including wheat, barley and maize, sampling eight independent domestication events and five examples of modern agronomic selection. Leaf silicon concentration showed a small, but significant, 10% reduction through domestication, but there was no effect of modern agronomic selection, and phenolic concentration was not affected by either factor. Silicon concentration correlated positively with leaf tensile strength, but negatively with foliar phenolic concentrations, suggesting a trade‐off between chemical and physical defences. Size‐standardized growth rate was independent of domestication status, and did not trade‐off with silicon or phenolic defences. However, modelling showed that relative growth rate slowed more with increasing size in plants with higher silicon levels, so that they reached a smaller final size, implying a cost of silicon‐based defence. We found the opposite pattern for phenolic‐based defence, with increasing phenolic concentrations associated with a greater plant size at maturity, and faster maximum relative growth rates. Silicon‐based defences have been reduced in cereals through domestication, consistent with our predicted costs of these defences to growth. However, modern agronomic selection has not influenced silicon defences in cereal crops and the small decrease in silicon concentration associated with domestication is unlikely to have a major effect on the ability of cereals to withstand a range of abiotic and biotic stresses. These findings have broad implications for crop protection and our understanding of plant trade‐offs

Syndromic surveillance of influenza-like illness in Scotland during the influenza A H1N1v pandemic and beyond

Syndromic surveillance refers to the rapid monitoring of syndromic data to highlight and follow outbreaks of infectious diseases, increasing situational awareness. Such systems are based upon statistical models to described routinely collected health data. We describe a working exception reporting system (ERS) currently used in Scotland to monitor calls received to the NHS telephone helpline, NHS24. We demonstrate the utility of the system to describe the time series data from NHS24 both at an aggregated Scotland level and at the individual health board level for two case studies, firstly during the initial phase of the 2009 Influenza A H1N1v and secondly for the emergence of seasonal influenza in each winter season from 2006/07 and 2010/11. In particular, we focus on a localised cluster of infection in the Highland health board and the ability of the system to highlight this outbreak. Caveats of the system, including the effect of media reporting of the pandemic on the results and the associated statistical issues, will be discussed. We discuss the adaptability and timeliness of the system and how this continues to form part of a suite of surveillance used to give early warnings to public health decision makers

Optimising time-limited non-pharmaceutical interventions for COVID-19 outbreak control

Retrospective analyses of the non-pharmaceutical interventions (NPIs) used to combat the ongoing COVID-19 outbreak have highlighted the potential of optimizing interventions. These optimal interventions allow policymakers to manage NPIs to minimize the epidemiological and human health impacts of both COVID-19 and the intervention itself. Here, we use a susceptible-infectious-recovered (SIR) mathematical model to explore the feasibility of optimizing the duration, magnitude and trigger point of five different NPI scenarios to minimize the peak prevalence or the attack rate of a simulated UK COVID-19 outbreak. An optimal parameter space to minimize the peak prevalence or the attack rate was identified for each intervention scenario, with each scenario differing with regard to how reductions to transmission were modelled. However, we show that these optimal interventions are fragile, sensitive to epidemiological uncertainty and prone to implementation error. We highlight the use of robust, but suboptimal interventions as an alternative, with these interventions capable of mitigating the peak prevalence or the attack rate over a broader, more achievable parameter space, but being less efficacious than theoretically optimal interventions. This work provides an illustrative example of the concept of intervention optimization across a range of different NPI strategies. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'

Substitutions near the hemagglutinin receptor-binding site determine the antigenic evolution of influenza A H3N2 viruses in U.S. swine

Swine influenza A virus is an endemic and economically important pathogen in pigs, with the potential to infect other host species. The hemagglutinin (HA) protein is the primary target of protective immune responses and the major component in swine influenza A vaccines. However, as a result of antigenic drift, vaccine strains must be regularly updated to reflect currently circulating strains. Characterizing the cross-reactivity between strains in pigs and seasonal influenza virus strains in humans is also important in assessing the relative risk of interspecies transmission of viruses from one host population to the other. Hemagglutination inhibition (HI) assay data for swine and human H3N2 viruses were used with antigenic cartography to quantify the antigenic differences among H3N2 viruses isolated from pigs in the United States from 1998 to 2013 and the relative cross-reactivity between these viruses and current human seasonal influenza A virus strains. Two primary antigenic clusters were found circulating in the pig population, but with enough diversity within and between the clusters to suggest updates in vaccine strains are needed. We identified single amino acid substitutions that are likely responsible for antigenic differences between the two primary antigenic clusters and between each antigenic cluster and outliers. The antigenic distance between current seasonal influenza virus H3 strains in humans and those endemic in swine suggests that population immunity may not prevent the introduction of human viruses into pigs, and possibly vice versa, reinforcing the need to monitor and prepare for potential incursions