Rapid clade divergence and phyletic gradualism in an interacting particle model of sympatric speciation

The coexistence of cladogenesis, i.e., the branching of lineages along an evolutionary tree as observed in the fossil record, and anagenesis, which is the progressive evolution within populations, lacks a clear explanation. In this study, we examine a simple model that simulates the evolutionary changes occurring within populations inhabiting the same environment in sympatry, and driven by ecological competition. Our model characterizes populations through a set of evolving morphological traits represented by mathematical points within a two-dimensional morphospace. Such points may reproduce or die due to overcrowding, implying competition in morphospace as suggested by the ecological phenomenon of character displacement. By focusing on the morphospace rather than physical space, the model effectively captures the simultaneous evolution of coexisting populations. Central to the model is the delicate balance between the range of competition and the range of reproduction within the morphospace. Interesting patterns emerge when the ratio between the competition to reproducetion ranges, referred to as CR ratio, changes from values slightly smaller to significantly larger than unity. When competition acts over short distances relative to the reproduction range (low CR), the phylogenetic tree takes on a nearly uniform appearance, gradually transforming into a more bush-like structure for slightly higher CR values. With further increases in CR, evolutionary lineages become more discernible, and the morphogenetic pattern shifts from a bush-like shape to a more tree-like arrangement and few branches for very large CRs. At specific time sections, the synthetic phylogenetic tree appears as an assembly of clusters of individuals within the morphospace. These clusters, interpretable as simulated models of species, exhibit distinct separation within the morphospace and are subject to dynamic inter-cluster repulsion. Notably, clusters tend to be resistant to change. They maintain relatively constant abundances while gradually shifting their positions within the morphospace-a phase that aligns with the concept of phyletic gradualism. However, this predictable pattern is occasionally upset by the abrupt divisions into multiple groups, interpreted as cladogenesis events. The intricacies of the splitting process are explored, revealing that in scenarios with large CR values, the splitting can emerge much more rapidly than phyletic changes. This accelerated process of splitting is initiated by one or few individuals at the fringes of a cluster, where competition is minimal. The newly generated cluster then undergoes deformation, swiftly followed by divergence and splitting (seen as branching in the synthetic phylogenetic tree), as if an inherent "repulsion" triggered the division between species. The simple rules implied in the interacting-particle model may provide insight into the coexistence of gradualism and cladogenesis along lineages, illustrating the capacity for rapid shifts during cladogenesis and the more gradual process of anagenesis.

Short-term association between air temperature and mortality in seven cities in Norway: A time series analysis

BACKGROUND

The association between ambient air temperature and mortality has not been assessed in Norway. This study aimed to quantify for seven Norwegian cities (Oslo, Bergen, Stavanger, Drammen, Fredrikstad, Trondheim and Tromsø) the non-accidental, cardiovascular and respiratory diseases mortality burden due to non-optimal ambient temperatures.

METHODS

We used a historical daily dataset (1996-2018) to perform city-specific analyses with a distributed lag non-linear model with 14 days of lag, and pooled results in a multivariate meta-regression. We calculated attributable deaths for heat and cold, defined as days with temperatures above and below the city-specific optimum temperature. We further divided temperatures into moderate and extreme using cut-offs at the 1st and 99th percentiles.

RESULTS

We observed that 5.3% (95% confidence interval (CI) 2.0-8.3) of the non-accidental related deaths, 11.8% (95% CI 6.4-16.4) of the cardiovascular and 5.9% (95% CI -4.0 to 14.3) of the respiratory were attributable to non-optimal temperatures. Notable variations were found between cities and subgroups stratified by sex and age. The mortality burden related to cold dominated in all three health outcomes (5.1%, 2.0-8.1, 11.4%, 6.0-15.4, and 5.1%, -5.5 to 13.8 respectively). Heat had a more pronounced effect on the burden of respiratory deaths (0.9%, 0.2-1.0). Extreme cold accounted for 0.2% of non-accidental deaths and 0.3% of cardiovascular and respiratory deaths, while extreme heat contributed to 0.2% of non-accidental and to 0.3% of respiratory deaths.

CONCLUSIONS

Most of the burden could be attributed to the contribution of moderate cold. This evidence has significant implications for enhancing public-health policies to better address health consequences in the Norwegian setting.

Antibiotic Consumption in a Cohort of Hospitalized Adults with Viral Respiratory Tract Infection

Development of antibiotic resistance, a threat to global health, is driven by inappropriate antibiotic usage. Respiratory tract infections (RTIs) are frequently treated empirically with antibiotics, despite the fact that a majority of the infections are caused by viruses. The purpose of this study was to determine the prevalence of antibiotic treatment in hospitalized adults with viral RTIs, and to investigate factors influencing the antibiotic decision-making. We conducted a retrospective observational study of patients ≥ 18 years, hospitalized in 2015-2018 with viral RTIs. Microbiological data were taken from the laboratory information system and information on antibiotic treatment drawn from the hospital records. To investigate decisions for prescribing antibiotic treatment, we evaluated relevant factors such as laboratory and radiological results, in addition to clinical signs. In 951 cases without secondary bacterial RTIs (median age 73 years, 53% female), 720 (76%) were prescribed antibiotic treatment, most frequently beta-lactamase-sensitive penicillins, but cephalosporins were prescribed as first-line in 16% of the cases. The median length of treatment (LOT) in the patients treated with antibiotics was seven days. Patients treated with antibiotics had an average of two days longer hospital stay compared to patients with no such treatment, but no difference in mortality was found. Our study revealed that there is still a role for antimicrobial stewardship to further improve antibiotic use in patients admitted for viral RTIs in a country with relatively low antibiotic consumption.

Visiting crowded places during the COVID-19 pandemic. A panel study among adult Norwegians

Non-pharmaceutical interventions, including promotion of social distancing, have been applied extensively in managing the COVID-19 pandemic. Understanding cognitive and psychological factors regulating precautionary behavior is important for future management. The present study examines the importance of selected factors as predictors of having visited or intended to visit crowded places. Six online questionnaire-based waves of data collection were conducted in April-October 2020 in a Norwegian panel (≥18 years). Sample size at Wave 1 was 1,400. In the present study, "Visited or intended to visit crowded places" for different types of locations were the dependent variables. Predictors included the following categories of items: Perceived response effectiveness, Self-efficacy, Vulnerability, Facilitating factors and Barriers. Data were analyzed with frequency and percentage distributions, descriptives, correlations, principal components analysis, negative binomial-, binary logistic-, and multiple linear regression, and cross-lagged panel models. Analyses of dimensionality revealed that a distinction had to be made between Grocery stores, a location visited by most, and locations visited by few (e.g., "Pub," "Restaurants," "Sports event"). We merged the latter set of variables into a countscore denoted as "Crowded places." On the predictor side, 25 items were reduced to eight meanscores. Analyses of data from Wave 1 revealed a rather strong prediction of "Crowded places" and weaker associations with "Supermarket or other store for food." Across waves, in multiple negative binomial regression models, three meanscore predictors turned out to be consistently associated with "Crowded places." These include "Response effectiveness of individual action," "Self-efficacy with regard to avoiding people," and "Barriers." In a prospective cross-lagged model, a combined Response effectiveness and Self-efficacy score (Cognition) predicted behavior ("Visited or intended to visit crowded places") prospectively and vice versa. The results of this study suggest some potential to reduce people's visits to crowded locations during the pandemic through health education and behavior change approaches that focus on strengthening individuals' perceived response effectiveness and self-efficacy.

Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway

Neisseria gonorrhoeae multilocus sequence type (ST)-7827 emerged in a dramatic fashion in Norway in the period 2016-2018. Here, we aim to shed light on the provenance and expansion of this ST. ST-7827 was found to be polyphyletic, but the majority of members belonged to a monophyletic clade we termed PopPUNK cluster 7827 (PC-7827). In Norway, both PC-7827 and ST-7827 isolates were almost exclusively isolated from men. Phylogeographical analyses demonstrated an Asian origin of the genogroup, with multiple inferred exports to Europe and the USA. The genogroup was uniformly resistant to fluoroquinolones, and associated with reduced susceptibility to both azithromycin and the extended-spectrum cephalosporins (ESCs) cefixime and ceftriaxone. From a genetic background including the penA allele 13.001, associated with reduced ESC susceptibility, we identified repeated events of acquisition of porB alleles associated with further reduction in ceftriaxone susceptibility. Transmission of the strain was significantly reduced in Norway in 2019, but our results indicate the existence of a recently established global reservoir. The worrisome drug-resistance profile and rapid emergence of PC-7827 calls for close monitoring of the situation.

Is the risk for sexually transmissible infections (STI) lower among women with exclusively female sexual partners compared with women with male partners? A retrospective study based on attendees at a Norwegian STI clinic from 2004 to 2014

BACKGROUND

The prevalence of and the risk for sexually transmissible infections (STIs) for women engaging in same-sex sexual behaviour was investigated among women attending an STI clinic.

METHODS

Data from electronic medical records were reviewed and logistic regression used to estimate the odds ratio (OR) of STIs. Women reporting life-time exclusively female partners (WSW) and women reporting female and male partners (WSWM) were compared with women reporting exclusively male partners (WSM). Outcomes included: Chlamydia trachomatis, Mycoplasma genitalium, Neisseria gonorrhoea, HIV and syphilis.

RESULTS

The study population comprised 103564 women (WSW 641, WSWM 12010 and WSM 90913). Overall prevalence of STIs was 8%. Crude OR of STIs for WSW: 0.56 (95% CI 0.39-0.81), for WSWM: 0.99 (95% CI 0.92-1.06) compared with WSM. Multivariate analysis revealed an interaction effect between same-sex sexual behaviour and smoking. Among non-smokers; WSW adjusted OR was 0.41 (95% CI 0.21-0.80), WSWM adjusted OR was 0.91 (95% CI 0.81-1.02) compared with WSM. Among smokers; WSW adjusted OR was 1.03 (95% CI 0.63-1.67) for WSWM adjusted OR was 1.00 (CI 95% 0.93-1.13), compared with WSM.

CONCLUSION

This study, including the largest cohort of women reporting life-time exclusively female partners in an STI study, shows that WSW generally are at lower risk for acquiring STIs than WSM. Smoking WSW, however, had the same risk for acquiring bacterial STIs as WSM and WSWM. Our study suggests that all WSW should receive the same encouragement to test for STIs as WSM.

Population-level impact, herd immunity, and elimination after human papillomavirus vaccination: a systematic review and meta-analysis of predictions from transmission-dynamic models

BACKGROUND

Modelling studies have been widely used to inform human papillomavirus (HPV) vaccination policy decisions; however, many models exist and it is not known whether they produce consistent predictions of population-level effectiveness and herd effects. We did a systematic review and meta-analysis of model predictions of the long-term population-level effectiveness of vaccination against HPV 16, 18, 6, and 11 infection in women and men, to examine the variability in predicted herd effects, incremental benefit of vaccinating boys, and potential for HPV-vaccine-type elimination.

METHODS

We searched MEDLINE and Embase for transmission-dynamic modelling studies published between Jan 1, 2009, and April 28, 2015, that predicted the population-level impact of vaccination on HPV 6, 11, 16, and 18 infections in high-income countries. We contacted authors to determine whether they were willing to produce new predictions for standardised scenarios. Strategies investigated were girls-only vaccination and girls and boys vaccination at age 12 years. Base-case vaccine characteristics were 100% efficacy and lifetime protection. We did sensitivity analyses by varying vaccination coverage, vaccine efficacy, and duration of protection. For all scenarios we pooled model predictions of relative reductions in HPV prevalence (RRprev) over time after vaccination and summarised results using the median and 10th and 90th percentiles (80% uncertainty intervals [UI]).

FINDINGS

16 of 19 eligible models from ten high-income countries provided predictions. Under base-case assumptions, 40% vaccination coverage and girls-only vaccination, the RRprev of HPV 16 among women and men was 0·53 (80% UI 0·46-0·68) and 0·36 (0·28-0·61), respectively, after 70 years. With 80% girls-only vaccination coverage, the RRprev of HPV 16 among women and men was 0·93 (0·90-1·00) and 0·83 (0·75-1·00), respectively. Vaccinating boys in addition to girls increased the RRprev of HPV 16 among women and men by 0·18 (0·13-0·32) and 0·35 (0·27-0·39) for 40% coverage, and 0·07 (0·00-0·10) and 0·16 (0·01-0·25) for 80% coverage, respectively. The RRprev were greater for HPV 6, 11, and 18 than for HPV 16 for all scenarios investigated. Finally at 80% coverage, most models predicted that girls and boys vaccination would eliminate HPV 6, 11, 16, and 18, with a median RRprev of 1·00 for women and men for all four HPV types. Variability in pooled findings was low, but increased with lower vaccination coverage and shorter vaccine protection (from lifetime to 20 years).

INTERPRETATION

Although HPV models differ in structure, data used for calibration, and settings, our population-level predictions were generally concordant and suggest that strong herd effects are expected from vaccinating girls only, even with coverage as low as 20%. Elimination of HPV 16, 18, 6, and 11 is possible if 80% coverage in girls and boys is reached and if high vaccine efficacy is maintained over time.

FUNDING

Canadian Institutes of Health Research.

A model for global diversity in response to temperature change over geological time scales, with reference to planktic organisms

There are strong propositions in the literature that abiotic factors override biotic drivers of diversity on time scales of the fossil record. In order to study the interaction of biotic and abiotic forces on long term changes, we devise a spatio-temporal discrete-time Markov process model of macroevolution featuring population formation, speciation, migration and extinction, where populations are free to migrate. In our model, the extinction probability of these populations is controlled by latitudinally and temporally varying environment (temperature) and competition. Although our model is general enough to be applicable to disparate taxa, we explicitly address planktic organisms, which are assumed to disperse freely without barriers over the Earth's oceans. While rapid and drastic environmental changes tend to eliminate many species, generalists preferentially survive and hence leave generalist descendants. In other words, environmental fluctuations result in generalist descendants which are resilient to future environmental changes. Periods of stable or slow environmental changes lead to more specialist species and higher population numbers. Simulating Cenozoic diversity dynamics with both competition and the environmental component of our model produces diversity curves that reflect current empirical knowledge, which cannot be obtained with just one component. Our model predicts that the average temperature optimum at which planktic species thrive best has declined over the Neogene, following the trend of global average temperatures.

Dynamics of competing species in a model of adaptive radiation and macroevolution

We present a simple model of adaptive radiation in evolution based on species competition. Competition is found to promote species divergence and branching, and to dampen the net species production. In the model simulations, high taxonomic diversification and branching take place during the beginning of the radiation. The results show striking similarities with empirical data and highlight the mechanism of competition as an important driving factor for accelerated evolutionary transformation.

Combining optical and electrical impedance techniques for quantitative measurement of confluence in MDCK-I cell cultures

A new method combining optical and electrical impedance measurements is described that enables submicroscopic cell movements to be monitored. The cells are grown on small gold electrodes that are transparent to light. This modified electrical cell-substrate impedance sensor (ECIS) allows simultaneous microscopic recording of both growth and motility, thus enabling cell confluence on the electrodes to be systematically correlated to the impedance in regular time intervals of seconds and for extended periods of time. Furthermore, the technique provides an independent measure of monolayer cell densities that we compare to calculated values from a theoretical model. We have followed the attachment and spreading behavior of epithelial Madin-Darby canine kidney strain I (MDCK-I) cell cultures on microelectrodes for up to 40 h. The studies reveal a high degree of correlation between the measured resistance at 4 kHz and the corresponding cell confluence in 4- to 6-h intervals with typical linear cross-correlation factors of r equaling approximately 0.9. In summary, the impedance measured with the ECIS technique provides a good quantitative measure of cell confluence.

Intercellular calcium signalling in cultured renal epithelia: a theoretical study of synchronization mode and pacemaker activity

We investigate a two-dimensional lattice model representation of intercellular Ca2+ signalling in a population of epithelial cells coupled by gap junctions. The model is based on and compared with Ca2+ imaging data from globally bradykinin-stimulated MDCK-I (Madin-Darby canine kidney)-I cell layers. We study large-scale synchronization of relevance to our laboratory experiments. The system is found to express a wealth of dynamics, including quasiperiodic, chaotic and multiply-periodic behaviour for intermediate couplings. We take a particular interest in understanding the role of "pacemaker cells" in the synchronization process. It has been hypothesized that a few highly hormone-sensitive cells control the collective frequency of oscillation, which is close to the natural frequencies (without coupling) of these cells. The model behaviour is consistent with the conjectures of the pacemaker cell hypothesis near the critical coupling where the cells lock onto a single frequency. However, the simulations predict that the frequency in globally connected systems decreases with increasing coupling. It is found that a pacemaker is not defined by its natural frequency alone, but that other intrinsic or local factors must be considered. Inclusion of partly sensitized cells that do not oscillate autonomously in the cell layer increases the coupling necessary for global synchronization. For not excessively high coupling, these cells oscillate irregularly and with distinctive lower frequencies. In summary, the present study shows that the frequency of synchronized oscillations is not dictated by one or few fast-responding cells. The collective frequency is the result of a two-way communication between the phase-advanced pacemaker and its environment.