Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics.

The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.

The impact of the COVID-19 lockdowns on wildlife-vehicle collisions in the UK.

Wildlife-vehicle collisions (WVCs) cause millions of vertebrate mortalities globally, threatening population viability and influencing wildlife behaviour and survival. Traffic volume and speed can influence wildlife mortality on roads, but roadkill risk is species specific and depends on ecological traits. The COVID-19 pandemic, and associated UK-wide lockdowns, offered a unique opportunity to investigate how reducing traffic volume alters WVC. These periods of reduced human mobility have been coined the 'anthropause'. We used the anthropause to identify which ecological traits may render species vulnerable to WVC. We did this by comparing the relative change in WVC of species with differing traits before and during the anthropause. We used Generalised Additive Model predictions to assess which of the 19 species most frequently observed as WVC in the UK exhibited changes in road mortality during two lockdown periods, March-May 2020 and December 2020-March 2021, relative to the same time periods in previous years (2014-2019). Compositional data analysis was used to identify ecological traits associated with changes in the relative number of observations during lockdown periods compared to previous years. WVC were, across all species, 80% lower during the anthropause than predicted. Compositional data analysis revealed proportionally fewer reports of nocturnal mammals, urban visitors, mammals with greater brain mass and birds with a longer flight initiation distance. Species that have several of these traits, and correspondingly significantly lower than predicted WVC during lockdowns, included badgers Meles meles, foxes Vulpes vulpes, and pheasants, Phasianus colchicus; we posit they stand to benefit most from reduced traffic, and, of the species studied here, have highest mortality under 'normal' traffic levels. This study identifies traits and species that may have experienced a temporary reprieve during the anthropause, and highlights the impacts of traffic-induced mortality on species numbers and ultimately on trait frequency in a road-dominated landscape. By taking advantage of reductions in traffic offered by the anthropause, we can understand how vehicles influence wildlife survival and behaviour and may be exerting a selective force for certain species and traits.

Transmission risk predicts avoidance of infected conspecifics in Trinidadian guppies.

Associating with conspecifics afflicted with infectious diseases increases the risk of becoming infected, but engaging in avoidance behaviour incurs the cost of lost social benefits. Across systems, infected individuals vary in the transmission risk they pose, so natural selection should favour risk-sensitive avoidance behaviour that optimally balances the costs and benefits of sociality. Here, we use the guppy Poecilia reticulata-Gyrodactylus turnbulli host-parasite system to test the prediction that individuals avoid infected conspecifics in proportion to the transmission risk they pose. In dichotomous choice tests, uninfected fish avoided both the chemical and visual cues, presented separately, of infected conspecifics only in the later stages of infection. A transmission experiment indicated that this avoidance behaviour accurately tracked transmission risk (quantified as both the speed at which transmission occurs and the number of parasites transmitting) through the course of infection. Together, these findings reveal that uninfected hosts can use redundant cues across sensory systems to inform dynamic risk-sensitive avoidance behaviour. This correlation between the transmission risk posed by infected individuals and the avoidance response they elicit has implications for the evolutionary ecology of infectious disease, and its explicit inclusion may improve the ability of epidemic models to predict disease spread.

Population dynamics of wild rodents induce stochastic fadeouts of a zoonotic pathogen.

Stochastic processes play an important role in the infectious disease dynamics of wildlife, especially in species subject to large population oscillations. Here, we study the case of a free ranging population of yellow-necked mice (Apodemus flavicollis) in northern Italy, where circulation of Dobrava-Belgrade hantavirus (DOBV) has been detected intermittently since 2001, until an outbreak emerged in 2010. We analysed the transmission dynamics of the recent outbreak using a computational model that accounts for seasonal changes of the host population and territorial behaviour. Model parameters were informed by capture-mark-recapture data collected over 14 years and longitudinal seroprevalence data from 2010 to 2013. The intermittent observation of DOBV before 2010 can be interpreted as repeated stochastic fadeouts after multiple introductions of infectious rodents migrating from neighbouring areas. We estimated that only 20% of introductions in a naïve host population results in sustained transmission after 2 years, despite an effective reproduction number well above the epidemic threshold (mean 4·5, 95% credible intervals, CI: 0·65-15·8). Following the 2010 outbreak, DOBV has become endemic in the study area, but we predict a constant probability of about 4·7% per year that infection dies out, following large population drops in winter. In the absence of stochastic fadeout, viral prevalence is predicted to continue its growth to an oscillating equilibrium around a value of 24% (95% CI: 3-57). We presented an example of invasion dynamics of a zoonotic virus where stochastic fadeout have played a major role and may induce future extinction of the endemic infection.

East-West Divide: temperature and land cover drive spatial variation of Toxoplasma gondii infection in Eurasian otters (Lutra lutra) from England and Wales.

Toxoplasma gondii, a zoonotic parasite of global importance, infects all endothermic vertebrates, with extensive health implications. The prevalence of this parasite is seldom monitored in wildlife. Here, a semi-aquatic species, the Eurasian otter (Lutra lutra) was used as a model to assess the potential effect of climate, land cover and biotic factors on T. gondii seroprevalence in British wildlife. The Sabin-Feldman cytoplasm-modifying dye test identified T. gondii antibodies in 25·5% of blood samples from otters found dead, mainly as road kill, in England and Wales, between 2004 and 2010. Otters in the east of England were more likely to be infected with T. gondii than those in western regions. Land cover and temperature are key determinants of T. gondii infection risk, with more infection in arable areas and lower infection where temperatures are higher. The probability of T. gondii infection increased with host age, reflecting cumulative exposure with time, but there was no association between T. gondii seroprevalence and cause of host death.

Evaluation of Exposure to Brevundimonas diminuta and Pseudomonas aeruginosa during Showering.

This study experimentally assessed bacterial water-to-air partitioning coefficients resulting from showerhead aerosolization of water contaminated with Brevundimonas diminuta or Pseudomonas aeruginosa, and estimated human exposure through inhalation. Dechlorinated tap water was spiked with two cell densities (109 and 1010 CFU l-1) and cycled at three temperatures (10, 25, and 37 or 40ºC) through a full-scale shower system. For reproducibility, spiked water concentrations were intentionally higher than found in natural environments. Three types of samplers measured size distribution and viable concentrations throughout the system. Results indicate low levels of respirable bioaerosols were generated. The ratio of bacterial contaminant that was effectively aerosolized (bacterial water-to-air partitioning coefficient, PC bwa ) was low - averaging 1.13×10-5 L m-3 for B. diminuta and 8.31×10-6 L m-3 for P. aeruginosa. However, the respirable fraction of aerosolized organisms was high, averaging above 94% (in shower) and above 99% (downstream) for both organisms. This study found no significant difference in bioaerosol load for a forward facing versus reverse facing individual. Further, for the average hot shower (33-43°C) the total number of respirable bioaerosols is higher, but the observed culturability of those aerosolized cells is lower when compared to lower temperatures. Bacterial water to air partitioning coefficients were calculated to predict microbial air concentration and these empirical parameters may be used for assessing inhalation as a route of exposure to pathogens in contaminated waters.

Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation.

Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity.

Impacts of climate change on the world's most exceptional ecoregions.

The current rate of warming due to increases in greenhouse gas (GHG) emissions is very likely unprecedented over the last 10,000 y. Although the majority of countries have adopted the view that global warming must be limited to <2 °C, current GHG emission rates and nonagreement at Copenhagen in December 2009 increase the likelihood of this limit being exceeded by 2100. Extensive evidence has linked major changes in biological systems to 20th century warming. The "Global 200" comprises 238 ecoregions of exceptional biodiversity [Olson DM, Dinerstein E (2002) Ann Mo Bot Gard 89:199-224]. We assess the likelihood that, by 2070, these iconic ecoregions will regularly experience monthly climatic conditions that were extreme in 1961-1990. Using >600 realizations from climate model ensembles, we show that up to 86% of terrestrial and 83% of freshwater ecoregions will be exposed to average monthly temperature patterns >2 SDs (2σ) of the 1961-1990 baseline, including 82% of critically endangered ecoregions. The entire range of 89 ecoregions will experience extreme monthly temperatures with a local warming of <2 °C. Tropical and subtropical ecoregions, and mangroves, face extreme conditions earliest, some with <1 °C warming. In contrast, few ecoregions within Boreal Forests and Tundra biomes will experience such extremes this century. On average, precipitation regimes do not exceed 2σ of the baseline period, although considerable variability exists across the climate realizations. Further, the strength of the correlation between seasonal temperature and precipitation changes over numerous ecoregions. These results suggest many Global 200 ecoregions may be under substantial climatic stress by 2100.

AI-based discovery of habitats from museum collections.

Museum collection records are a source of historic data for species occurrence, but little attention is paid to the associated descriptions of habitat at the sample locations. We propose that artificial intelligence methods have potential to use these descriptions for reconstructing past habitat, to address ecological and evolutionary questions.

Low molecular weight fibroblast growth factor-2 signals via protein kinase C and myofibrillar proteins to protect against postischemic cardiac dysfunction.

Among its many biological roles, fibroblast growth factor-2 (FGF2) acutely protects the heart from dysfunction associated with ischemia/reperfusion (I/R) injury. Our laboratory has demonstrated that this is due to the activity of the low molecular weight (LMW) isoform of FGF2 and that FGF2-mediated cardioprotection relies on the activity of protein kinase C (PKC); however, which PKC isoforms are responsible for LMW FGF2-mediated cardioprotection, and their downstream targets, remain to be elucidated. To identify the PKC pathway(s) that contributes to postischemic cardiac recovery by LMW FGF2, mouse hearts expressing only LMW FGF2 (HMWKO) were bred to mouse hearts not expressing PKCα (PKCαKO) or subjected to a selective PKCε inhibitor (εV(1-2)) before and during I/R. Hearts only expressing LMW FGF2 showed significantly improved postischemic recovery of cardiac function following I/R (P < 0.05), which was significantly abrogated in the absence of PKCα (P < 0.05) or presence of PKCε inhibition (P < 0.05). Hearts only expressing LMW FGF2 demonstrated differences in actomyosin ATPase activity as well as increases in the phosphorylation of troponin I and T during I/R compared with wild-type hearts; several of these effects were dependent on PKCα activity. This evidence indicates that both PKCα and PKCε play a role in LMW FGF2-mediated protection from cardiac dysfunction and that PKCα signaling to the contractile apparatus is a key step in the mechanism of LMW FGF2-mediated protection against myocardial dysfunction.

Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland.

Range expansions are extremely common, but have only recently begun to attract attention in terms of their genetic consequences. As populations expand, demes at the wave front experience strong genetic drift, which is expected to reduce genetic diversity and potentially cause 'allele surfing', where alleles may become fixed over a wide geographical area even if their effects are deleterious. Previous simulation models show that range expansions can generate very strong selective gradients on dispersal, reproduction, competition and immunity. To investigate the effects of range expansion on genetic diversity and adaptation, we studied the population genomics of the bank vole (Myodes glareolus) in Ireland. The bank vole was likely introduced in the late 1920s and is expanding its range at a rate of ~2.5 km/year. Using genotyping-by-sequencing, we genotyped 281 bank voles at 5979 SNP loci. Fourteen sample sites were arranged in three transects running from the introduction site to the wave front of the expansion. We found significant declines in genetic diversity along all three transects. However, there was no evidence that sites at the wave front had accumulated more deleterious mutations. We looked for outlier loci with strong correlations between allele frequency and distance from the introduction site, where the direction of correlation was the same in all three transects. Amongst these outliers, we found significant enrichment for genic SNPs, suggesting the action of selection. Candidates for selection included several genes with immunological functions and several genes that could influence behaviour.

Limitations of lymph node ratio, evidence-based benchmarks, and the importance of a thorough lymph node dissection in melanoma.

BACKGROUND: Stage III melanoma is currently stratified by number of lymph nodes (LNs) involved. However, given the variability of LN retrieval counts we hypothesize that lymph node ratio (LNR) may also provide prognostic information. METHODS: Retrospective cohort study of 411 patients with stage III melanoma were divided into two groups based on LNR (<0.15, n = 291 and ≥0.15, n = 120). RESULTS: In multivariate analysis N stage (N3 vs. N1, hazard ratio [HR] = 2.13, p < 0.001), extranodal extension (HR = 1.92, p = 0.002), macrometastasis (HR = 1.70, p = 0.005), non-SLN involvement (HR = 1.65, p = 0.005), risk of N2 disease exceeding 35 % (HR = 1.51, p = 0.03), and LNR ≥0.15 (HR = 1.46, p = 0.03) were associated with overall survival (OS). LNR failed to further stratify stage III melanoma; however, the number of LNs examined was an independent prognostic factor. Patients who had >8 inguinal, >15 axillary, or >20 cervical LNs examined had fewer same nodal basin recurrences (26 [8 %] vs. 20 [20 %], p = 0.0009) and for N1 patients an improved OS (3-year OS 84 % vs. 76 %, 10-year OS 53 % vs. 34 %, p = 0.06) compared with N1 patients who had fewer LNs examined. CONCLUSIONS: LNR is an important prognostic factor in stage III melanoma; however, it was not independent over the current AJCC TNM staging system. Diligence by the surgeon and pathologist to retrieve and examine >8 inguinal, >15 axillary, or >20 cervical LNs is associated with fewer same nodal basin recurrences and improved survival and is critical to reliable prognostication.

Do invasive species perform better in their new ranges?

A fundamental assumption in invasion biology is that most invasive species exhibit enhanced performance in their introduced range relative to their home ranges. This idea has given rise to numerous hypotheses explaining "invasion success" by virtue of altered ecological and evolutionary pressures. There are surprisingly few data, however, testing the underlying assumption that the performance of introduced populations, including organism size, reproductive output, and abundance, is enhanced in their introduced compared to their native range. Here, we combined data from published studies to test this hypothesis for 26 plant and 27 animal species that are considered to be invasive. On average, individuals of these 53 species were indeed larger, more fecund, and more abundant in their introduced ranges. The overall mean, however, belied significant variability among species, as roughly half of the investigated species (N=27) performed similarly when compared to conspecific populations in their native range. Thus, although some invasive species are performing better in their new ranges, the pattern is not universal, and just as many are performing largely the same across ranges.

Neighbourhood and consumer food environment is associated with dietary intake among Supplemental Nutrition Assistance Program (SNAP) participants in Fayette County, Kentucky.

OBJECTIVE: The aim of the study was to determine the association between dietary outcomes and the neighbourhood food environment (street network distance from home to stores) and consumer food environment (Nutrition Environment Measurement Survey-Stores (NEMS-S) audit). DESIGN: The neighbourhood food environment was captured by creating 0?5-mile and 1-mile network distance (street distance) around each participant's home and the nearest food venue (convenience store, grocery store, supermarket, farmers' market and produce stand). The consumer food environment was captured by conducting NEMS-S in all grocery stores/supermarkets within 0?5 and 1 mile of participants' homes. SETTING: Fayette County, KY, USA. SUBJECTS: Supplemental Nutrition Assessment Program (SNAP) participants, n 147. RESULTS: SNAP participants who lived within 0?5 mile of at least one farmers' market/produce stand had higher odds of consuming one serving or more of vegetables (OR56?92; 95% CI 4?09, 11?69), five servings or more of grains (OR51?76; 95% CI 1?01, 3?05) and one serving or more of milk (OR53?79; 95% CI 2?14, 6?71) on a daily basis. SNAP participants who lived within 0?5 mile of stores receiving a high score on the NEMS-S audit reported higher odds of consuming at least one serving of vegetables daily (OR53?07; 95% CI 1?78, 5?31). CONCLUSIONS: Taken together, both the neighbourhood food environment and the consumer food environment are associated with a healthy dietary intake among SNAP participants.

The presence of territorial damselfish predicts choosy client species richness at cleaning stations.

Mutualisms are driven by partners deciding to interact with one another to gain specific services or rewards. As predicted by biological market theory, partners should be selected based on the likelihood, quality, reward level, and or services each partner can offer. Third-party species that are not directly involved in the interaction, however, may indirectly affect the occurrence and or quality of the services provided, thereby affecting which partners are selected or avoided. We investigated how different clients of the sharknose goby (Elacatinus evelynae) cleaner fish were distributed across cleaning stations, and asked what characteristics, relating to biological market theory, affected this distribution. Through quantifying the visitation and cleaning patterns of client fish that can choose which cleaning station(s) to visit, we found that the relative species richness of visiting clients at stations was negatively associated with the presence of disruptive territorial damselfish at the station. Our study highlights, therefore, the need to consider the indirect effects of third-party species and their interactions (e.g., agonistic interactions) when attempting to understand mutualistic interactions between species. Moreover, we highlight how cooperative interactions may be indirectly governed by external partners.

Demographic effects of road mortality on mammalian populations: a systematic review.

In light of rapidly expanding road networks worldwide, there is increasing global awareness of the growing amount of mammalian roadkill. However, the ways in which road mortality affects the population dynamics of different species remains largely unclear. We aimed to categorise the demographic parameters in mammalian populations around the world that are directly or indirectly affected by road mortality, as well as identify the most effective study designs for quantifying population-level consequences of road mortality. We conducted a comprehensive systematic review to synthesise literature published between 2000 and 2021 and out of 11,238 unique studies returned, 83 studies were retained comprising 69 mammalian species and 150 populations. A bias towards research-intensive countries and larger mammals was apparent. Although searches were conducted in five languages, all studies meeting the inclusion criteria were in English. Relatively few studies (13.3%) provided relevant demographic context to roadkill figures, hampering understanding of the impacts on population persistence. We categorised five direct demographic parameters affected by road mortality: sex- and age-biased mortality, the percentage of a population killed on roads per year (values up to 50% were reported), the contribution of roadkill to total mortality rates (up to 80%), and roadkill during inter-patch or long-distance movements. Female-biased mortality may be more prevalent than previously recognised and is likely to be critical to population dynamics. Roadkill was the greatest source of mortality for 28% of studied populations and both additive and compensatory mechanisms to roadkill were found to occur, bringing varied challenges to conservation around roads. In addition, intra-specific population differences in demographic effects of road mortality were common. This highlights that the relative importance of road mortality is likely to be context specific as the road configuration and habitat quality surrounding a population can vary. Road ecology studies that collect data on key life parameters, such as age/stage/sex-specific survival and dispersal success, and that use a combination of methods are critical in understanding long-term impacts. Quantifying the demographic impacts of road mortality is an important yet complex consideration for proactive road management.

Quality of Life and Well-Being for Children and Youth With Special Health Care Needs and their Families: A Vision for the Future.

OBJECTIVES: To fulfill the promise of a life of dignity, autonomy, and independence for children and youth with special health care needs (CYSHCN) and their families, greater value must be assigned to meaningful outcomes, such as quality of life and well-being. METHODS: Despite decades of research, programs, and measurements addressing quality of life and well-being for CYSHCN and their families, there still is no consensus on how to measure, implement, or achieve them. RESULTS: As the US health care system strives to reach the health care goals of safe, efficient, effective, equitable, timely, and patient-centered care, youth and families must be equal partners at all levels of the health care system-from clinical decision making to designing and implementing programs and policies. CONCLUSIONS: The health care system must systematically measure the priorities of CYSHCN and their families. It also must incorporate data on quality of life and well-being when developing services, supports, and systems that help CYSHCN and their families to flourish rather than hindering them.

The prevalence of irritable bowel syndrome in outpatients with bulimia nervosa.

OBJECTIVE: This study examined the prevalence of irritable bowel syndrome (IBS) in patients with bulimia nervosa (BN), and the relationship between these disorders. METHOD: Sixty-four participants with a diagnosis of BN or a related condition were recruited from an outpatient eating disorders service. Questionnaire and interview measures were used to assess bulimic symptoms and attitudes, IBS symptoms, anxiety and depression. Cases of IBS were identified using the Manning criteria. RESULTS: There was a high prevalence of IBS in the patient group (68.8%), but IBS status was not predicted by any of the other variables measured. Patients who met criteria for IBS reported more frequent self-induced vomiting than those who did not (U = 256.0, p = 0.038). DISCUSSION: There is evidence of an high incidence of IBS in outpatients with BN, but the relationship between these conditions remains unclear. Future research should consider possible common risk factors.

Risk factors, correlates, and markers in early-onset bulimia nervosa and EDNOS.

OBJECTIVE: This study aimed to investigate the specific risk factors, correlates, and markers associated with the development of symptomatology of early-onset BN and subclinical BN. METHOD: Two semi-structured interviews were used to examine symptomatology and antecedent factors of bulimic symptoms in a sample of British adolescents. RESULTS: Adolescents with early-onset eating pathology were significantly more likely to report an earlier age of menarche than those developing the disorder at the typical age, and were found to have a different pathway of symptom development. DISCUSSION: Increased awareness of this may help identify those particularly at risk for developing an early-onset of eating pathology.

Passive citizen science: The role of social media in wildlife observations.

Citizen science plays an important role in observing the natural environment. While conventional citizen science consists of organized campaigns to observe a particular phenomenon or species there are also many ad hoc observations of the environment in social media. These data constitute a valuable resource for 'passive citizen science'-the use of social media that are unconnected to any particular citizen science program, but represent an untapped dataset of ecological value. We explore the value of passive citizen science, by evaluating species distributions using the photo sharing site Flickr. The data are evaluated relative to those submitted to the National Biodiversity Network (NBN) Atlas, the largest collection of species distribution data in the UK. Our study focuses on the 1500 best represented species on NBN, and common invasive species within UK, and compares the spatial and temporal distribution with NBN data. We also introduce an innovative image verification technique that uses the Google Cloud Vision API in combination with species taxonomic data to determine the likelihood that a mention of a species on Flickr represents a given species. The spatial and temporal analyses for our case studies suggest that the Flickr dataset best reflects the NBN dataset when considering a purely spatial distribution with no time constraints. The best represented species on Flickr in comparison to NBN are diurnal garden birds as around 70% of the Flickr posts for them are valid observations relative to the NBN. Passive citizen science could offer a rich source of observation data for certain taxonomic groups, and/or as a repository for dedicated projects. Our novel method of validating Flickr records is suited to verifying more extensive collections, including less well-known species, and when used in combination with citizen science projects could offer a platform for accurate identification of species and their location.