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Abstract The deep connection between Indigenous communities and nature plays a pivotal role in biodiversity conservation. Ethiopia, one of Africa's priority countries for bird conservation, harbours 821 bird species and 83 ethnic groups of Indigenous people. However, cultural and spiritual ties between Indigenous peoples and bird species remain largely unexplored. This is particularly true for remote Indigenous communities such as the Nuer. Relying on preexisting bird survey data, we conducted focussed group discussions and semi‐structured interviews with Indigenous Nuer in western Ethiopia to explore human–bird interactions and documented associated traditional ecological knowledge and considered their conservation implications. We found that Nuers have strong ties with birds. In Nuer community, birds are collectively known by three interchangeable terms: ‘gaatkuoth’ to mean sacred children of god, ‘kuoth’ meaning bearers of spirit and ‘diit’ symbols of human twins (since birds nurture multiple offspring, they associate the incidence of twins in human with birds). We identified 71 culturally important bird species that were used in seven different use categories. Among these species, 10 were used as bushmeat, five for traditional medicine, eight as fish indicators, seven as omens (believed to indicate upcoming misfortunes), three as amulets (believed to protect against danger when bird's body parts are used as necklaces and bracelets), three as season indicators and 45 for their scenic beauty. An informant consensus factor for species in all use categories was >90%, except for the scenic value, indicating a high homogeneity of knowledge about species uses. Bird species with multiple uses have significant cultural values among locals, emphasizing the need to understand these values in conservation efforts. Nuer traditional systems regulate the direct use of birds including for bushmeat. Hunting is permitted only by impoverished households during severe food shortages and is prohibited for those with a history of twins in their ancestry. The Nuer people exhibit a profound cultural connection to birds, viewing them as sacred and spiritually valuable beings. This deep‐seated reverence and traditional knowledge highlight the importance of integrating Indigenous perspectives into bird conservation strategies to enhance their effectiveness and respect cultural values. Read the free Plain Language Summary for this article on the Journal blog.

Understanding the effects of variation in resource availability and habitat disturbance on the ecology of mammals is vital for successful conservation management. In this study, we examined how human disturbances, resource availability and elevation gradients influence mammal assemblages in both managed coffee forest and natural forest of the Belete-Gera National Forest Priority Area, southwestern Ethiopia. We surveyed mammals using motion-detecting infrared camera traps in 90 locations for a total of 4142 camera days. We measured distance from main roads and settlements as disturbance factors, and distance from water sources, key grazing sites, and forest edges and woody plant diversity as resource variables. We assessed the mammal assemblages in coffee forest and natural forests using generalized linear models. Further, we used linear modelling to compare the relationships of mammal detection rates by feeding guilds and body size to resource variables. In total, we recorded 8815 videos identifying 23 different mammal species. The mammal assemblages in coffee forests were negatively associated with increasing distances from key grazing sites, water sources, and elevation. In contrast, the association with increasing distance from the road and woody plant diversity was positive. In addition, herbivores and large (25–200 kg) and very large (≥200 kg) mammals, were all negatively associated with increasing distance from the natural forest edges. With the conversion of natural forest to coffee forest and the intensification of coffee forest management, sustainable management of key grazing sites, water sources, and diverse woody plant species will be essential to the conservation of mammals. In addition, to ensure mammal conservation, adjacent natural forests around coffee forests should also be protected.

Abstract Geographical distribution and diversity patterns of bird species are influenced by climate change. The Rouget's rail (Rougetius rougetii) is a ground‐dwelling endemic bird species distributed in Ethiopia and Eritrea. It is a near‐threatened species menaced by habitat loss, one of the main causes of population declines for bird species. The increasing effects of climate change may further threaten the species’ survival. So far, the spatial distribution of this species is not fully documented. With this study, we develop current potential suitable habitat and predict the future habitat shift of R. rougetii based on environmental data such as bioclimatic variables, population density, vegetation cover, and elevation using 10 algorithms. We evaluated the importance of environmental factors in shaping the bird's distribution and how it shifts under climate change scenarios. We used 182 records of R. rougetii from Ethiopia and nine bioclimatic, population density, vegetation cover, and elevation variables to run the 10 model algorithms. Among 10 algorithms, eight were selected for ensembling models according to their predictive abilities. The current suitable habitats for R. rougetii were predicted to cover an area of about 82,000 km2 despite being highly fragmented. The model suggested that temperature seasonality (bio4), elevation, and mean daily air temperatures of the driest quarter (bio9) contributed the most to delimiting suitable areas for this species. R. rougetii is sensitive to climate change associated with elevation, which leads shrinking distribution of suitable areas. The projected spatial and temporal pattern of habitat loss of R. rougetii suggests the importance of climate change mitigation and implementing long‐term conservation and management strategies for this threatened endemic bird species.

Multiannual population cycles of small mammals are of interest within population biology. We propose an approach for multidimensional autoregressive (AR) time series and analyse monitoring data on grey-sided voles (Myodes rufocanus) in Japan to investigate one or possibly multiple multiannual cycles that drive population dynamics. Temperature, through modifying rodent communities, is found to be a key factor shaping population dynamics. Warmer areas are the main habitat for other rodent species resulting in low vole abundance/dominance, as opposed to higher vole dominance in colder areas—a pattern associated with the AR structure and population cycle. Vole populations in simple rodent communities exhibit an AR(2) cycle of 2–3 years. In areas with complex rodent communities, vole dynamics follows an AR(4) process and a combination of two cycles with different lengths. The AR structure varies in relatively small spatial scales, thus widening the scope of AR analyses needed. Historically, vole abundance increased in the late 1970s and decreased from the 1980s, with warm winters shown to be associated with the decline of vole abundance in the AR(4) populations. This significant association between the AR order, population dynamics, temperature and rodent community provides insights into the declining trends observed in rodent populations of the Northern Hemisphere.

Abstract Habitat suitability models have become a valuable tool for wildlife conservation and management, and are frequently used to better understand the range and habitat requirements of rare and endangered species. In this study, we employed two habitat suitability modeling techniques, namely Boosted Regression Tree (BRT) and Maximum Entropy (Maxent) models, to identify potential suitable habitats for the endangered mountain nyala (Tragelaphus buxtoni) and environmental factors affecting its distribution in the Arsi and Ahmar Mountains of Ethiopia. Presence points, used to develop our habitat suitability models, were recorded from fecal pellet counts (n = 130) encountered along 196 randomly established transects in 2015 and 2016. Predictor variables used in our models included major landcover types, Normalized Difference Vegetation Index (NDVI), greenness and wetness tasseled cap vegetation indices, elevation, and slope. Area Under the Curve model evaluations for BRT and Maxent were 0.96 and 0.95, respectively, demonstrating high performance. Both models were then ensembled into a single binary output highlighting an area of agreement. Our results suggest that 1864 km2 (9.1%) of the 20,567 km2 study area is suitable habitat for the mountain nyala with land cover types, elevation, NDVI, and slope of the terrain being the most important variables for both models. Our results highlight the extent to which habitat loss and fragmentation have disconnected mountain nyala subpopulations. Our models demonstrate the importance of further protecting suitable habitats for mountain nyala to ensure the species' conservation.

Abstract The incidence of plague has rebounded in the Americas, Asia, and Africa alongside rapid globalization and climate change. Previous studies have shown local climate to have significant nonlinear effects on plague dynamics among rodent communities. We analyzed an 18-year database of plague, spanning 1998 to 2015, in the foci of Mongolia and China to trace the associations between marmot plague and climate factors. Our results suggested a density-dependent effect of precipitation and a geographic location-dependent effect of temperature on marmot plague. That is, a significantly positive relationship was evident between risk of plague and precipitation only when the marmot density exceeded a certain threshold. The geographical heterogeneity of the temperature effect and the contrasting slopes of influence for the Qinghai-Tibet Plateau (QTP) and other regions in the study (nQTP) were primarily related to diversity of climate and landscape types.

As an adaptive biological trait, group size may offer a useful metric for monitoring the welfare of wildlife species affected by their environmental surroundings. Here, we examine the drivers that cause variation in group size of the endangered mountain nyala (Tragelaphus buxtoni), including a range of natural ecological factors as well as the density of livestock. For this purpose, we collected data along transect lines during both wet and dry seasons focusing on the hitherto poorly studied populations in the Arsi Mountains National Park, Munessa-Kuke Controlled Hunting Area and Muktar Mountain Forest Reserve, which are managed for multiple use of a variety of natural resources. We found group sizes to be an average of 6.3, 4.4 and 4.1 individuals in the Arsi Mountains, Munessa-Kuke and Muktar Mountain study areas, respectively, and a combination of livestock density and habitat visibility explained as much as 74% of the variation in group size. We propose that whereas group size increases with forage availability (as measured by Normalized Difference Vegetation Index -NDVI) and in open habitats (probably due to a switch in antipredator strategy), the presence of livestock also has an independent, negative impact on group size because of the associated disturbance. The findings contribute to understanding the environmental drivers of variation in group size in social antelopes, particularly highlighting the need to improve livestock management to help conservation of species at risk.

Climate warming has substantially advanced the timing of spring leaf-out of woody species at middle and high latitudes, albeit with large differences. Insights in the spatial variation of this climate warming response may therefore help to constrain future trends in leaf-out and its impact on energy, water and carbon balances at global scales. In this study, we used in situ phenology observations of 38 species from 2067 study sites, distributed across the northern hemisphere in China, Europe and the United States, to investigate the latitudinal patterns of spring leaf-out and its sensitivity (ST, advance of leaf-out dates per degree of warming) and correlation (RT, partial correlation coefficient) to temperature during the period 1980–2016. Across all species and sites, we found that ST decreased significantly by 0.15 ± 0.02 d °C−1 °N−1, and RT increased by 0.02 ± 0.001 °N−1 (both at P < 0.001). The latitudinal patterns in RT and ST were explained by the differences in requirements of chilling and thermal forcing that evolved to maximize tree fitness under local climate, particularly climate predictability and summed precipitation during the pre-leaf-out season. Our results thus showed complicated spatial differences in leaf-out responses to ongoing climate warming and indicated that spatial differences in the interactions among environmental cues need to be embedded into large-scale phenology models to improve the simulation accuracy.

Summary: Ensuring global food security and environmental sustainability is dependent upon the contribution of the world’s hundred million smallholder farms, but the contributions of smallholder farms to global agricultural greenhouse gas (GHG) emissions have been understudied. We developed a localized agricultural life cycle assessment (LCA) database to calculate GHG emissions and made the first extensive assessment of the smallholder farms’ GHG emission reduction potentials by coupling crop and livestock production (CCLP), a redesign of current practices toward sustainable agriculture in China. CCLP can reduce the GHG emission intensity by 17.67%, with its own feed and manure returning to the field as an essential path. Scenario analysis verified that greater GHG emission reduction (28.09%–41.32%) will be achieved by restructuring CCLP. Therefore, this mixed farming is a mode with broader benefits to provide sustainable agricultural practices for reducing GHG emissions fairly.

There is a growing view in conservation science that traditional ways to evaluate publications, researchers, and projects are too slow. This has led to a rise in the use of altmetrics, which are metrics based on social media data, news pieces, blogs, and more. Here we examine altmetric data linked to nearly 10,000 papers published in 23 conservation journals, exploring five issues that represent some of the challenges associated with using social media data in evaluating conservation. We discuss whether social media activity reflects meaningful engagement, and how easily individuals can manipulate scores by using bots or simply through active personal networks or institutional promotion services. Our analysis shows a highly skewed distribution of altmetric scores where most papers have such low scores that the scores likely convey little meaningful information. Examining scores that would be considered meritorious, we find that papers where the first author was male have higher scores than papers led by a woman, suggesting a gender bias in altmetric scores. Finally, this data set reveals regional differences that correspond with access to different social media platforms. Metrics, like altmetrics, may have a role to play when making rapid evaluations. However, such metrics should only be used after careful deliberation and should not be influenced by institutions looking for shortcuts, by companies looking to advance profits, or by individuals seeking to promote themselves, rather than generating meaningful engagement in scholarship and conservation action. Scholarly and conservation activities should be judged on the quality of their contributions, which will require the input of experts and direct contact with impacted communities.

Summary: The flourishing logistics in both developed and emerging economies leads to huge greenhouse gas (GHG) emissions; however, the emission fluxes are poorly constrained. Here, we constructed a spatial network of logistic GHG emissions based on multisource big data at continental scale. GHG emissions related to logistics transportation reached 112.14 Mt CO2-equivalents (CO2e), with seven major urban agglomerations contributing 63% of the total emissions. Regions with short transport distances and well-developed road infrastructure had relatively high emission efficiency. Underlying value flow of the commodities is accompanied by logistics carbon flow along the supply chain. The main driving factors affecting GHG emissions are driving speed and gross domestic product. It may mitigate GHG emissions by 27.50–1162.75 Mt CO2e in 15 years if a variety of energy combinations or the appropriate driving speed (65–70 km/h) is adopted. The estimations are of great significance to make integrated management policies for the global logistics sector.

Abstract The plague of 1630–1632 was one of the deadliest plague epidemics to ever hit Northern Italy, and for many of the affected regions, it was also the last. While accounts on plague during the early 1630s in Florence and Milan are frequent, much less is known about the city of Imola. We analyzed the full skeletal assemblage of four mass graves (n = 133 individuals) at the Lazaretto dell’Osservanza, which date back to the outbreak of 1630–1632 in Imola and evaluated our results by integrating new archival sources. The skeletons showed little evidence of physical trauma and were covered by multiple layers of lime, which is characteristic for epidemic mass mortality sites. We screened 15 teeth for Yersinia pestis aDNA and were able to confirm the presence of plague in Imola via metagenomic analysis. Additionally, we studied a contemporaneous register, in which a friar recorded patient outcomes at the lazaretto during the last year of the epidemic. Our multidisciplinary approach combining historical, osteological and genomic data provided a unique opportunity to reconstruct an in-depth picture of the last plague of Imola through the city's main lazaretto.

The number of COVID-19 confirmed cases rapidly grew since the SARS-CoV-2 virus was identified in late 2019. Due to the high transmissibility of this virus, more countries are experiencing the repeated waves of the COVID-19 pandemic. However, with limited manufacturing and distribution of vaccines, control measures might still be the most critical measures to contain outbreaks worldwide. Therefore, evaluating the effectiveness of various control measures is necessary to inform policymakers and improve future preparedness. In addition, there is an ongoing need to enhance our understanding of the epidemiological parameters and the transmission patterns for a better response to the COVID-19 pandemic. This review focuses on how various models were applied to guide the COVID-19 response by estimating key epidemiologic parameters and evaluating the effectiveness of control measures. We also discuss the insights obtained from the prediction of COVID-19 trajectories under different control measures scenarios.

Abstract Despite a substantial number of COVID‐19 related research papers published, it remains unclear as to which factors are associated with the observed variation in global transmission and what are their relative levels of importance. This study applies a rigorous statistical framework to provide robust estimations of the factor effects for a global and integrated perspective on this issue. We developed a mixed effect model exploring the relative importance of potential factors driving COVID‐19 transmission while incorporating spatial and temporal heterogeneity of spread. We use an integrated data set for 87 countries across six continents for model specification and fitting. The best model accounts for 70.4% of the variance in the data analyzed: 10 fixed effect factors explain 20.5% of the variance, random temporal and spatial effects account for 50% of the variance. The fixed effect factors are classified into climatic, demographic and disease control groups. The explained variance in global transmission by the three groups are 0.6%, 1.1%, and 4.4% respectively. The high proportion of variance accounted for by random effects indicated striking differences in temporal transmission trajectories and effects of population mobility among the countries. In particular, the country‐specific mobility‐transmission relationship turns out to be the most important factor in explaining the observed global variation of transmission in the early phase of COVID‐19 pandemic.

Behavioral responses in wildlife due to human activities may often go unnoticed but have significant effects on population viability. This is a particular concern with endangered species characterized by small population sizes. From June 2016 to May 2017, we measured the effects of human activities on daily the activity budget and home range size of mountain nyala (Tragelaphus buxtoni), an endemic antelope of the Ethiopian highlands. We tracked two groups of mountain nyala from two study sites that differ in the level of human activities; Adaba-Dodola Community Conservation Area (Adaba-Dodola CCA) and Arsi Mountains National Park (Arsi Mountains NP). Our results showed that the time spent on vigilance and movement was dramatically higher in Adaba-Dodola Community CCA, where human presence is significant, than in Arsi Mountains NP, whereas the opposite was true for time spent foraging and resting. In addition, mean home range size (95% KDE) was significantly larger for the Adaba-Dodola CCA group (13 ± 7.4 km2) than for the Arsi Mountains NP group (6.3 ± 2.7 km2) covering larger areas during the dry season (18.7 ± 6.9 km2) than the wet season (4.9 ± 1.0 km2). The finding that increased investment in vigilance and movement trade-off against the restorative behaviors of foraging and resting in human-disturbed areas have implications for conservation managements; specifically, it underscores the need to (i) establish the fitness consequences of behavioral changes, and (ii) monitoring behavioral change in the disturbed population with the aim of bringing it closer to the undisturbed baseline. The study highlights the importance of protected areas, limiting human activities and monitoring the behavioral change of endangered species in human-disturbed areas.

Since its first identification in 1894 during the third pandemic in Hong Kong, there has been significant progress in understanding the lifestyle of Yersinia pestis , the pathogen that is responsible for plague. Although we now have some understanding of the pathogen’s physiology, genetics, genomics, evolution, gene regulation, pathogenesis and immunity, there are many unknown aspects of the pathogen and its disease development. Here, we focus on some of the knowns and unknowns related to Y. pestis and plague. We notably focus on some key Y. pestis physiologic and virulence traits that are important for its mammal-flea-mammal life cycle, but also its emergence from the enteropathogen, Yersinia pseudotuberculosis . Some aspects of the genetic diversity of Y. pestis , the distribution and ecology of plague, as well as the medical countermeasures to protect our population are also provided. Lastly, we present some biosafety and biosecurity information related to Y. pestis and plague.

Yersinia pestis, the causative agent of plague, can change its biofilm production to influence the dynamics of flea-borne transmission. Here, the authors sequence Y. pestis isolates sampled over 40 years in China and show evidence for climate-associated selection on rpoZ to increase biofilm production.

Abstract Background The availability of preferred habitats determines the spatial and temporal distribution of herbivores in savanna ecosystems. Understanding habitat preference of a targeted wildlife species is crucial for developing effective conservation strategies. Habitat preference of large grazers in connection to grass height and post-fire effect has been debated for the last century. Here, we examined the effects of season, grass height and burning on the habitat preference on Swayne’s hartebeest (Alcelaphus buselaphus swaynei) in Maze National Park. Data for seasonal habitat selection were collected using both direct observation along established transect lines and pellet counting using permanently established plots. Every month, we measured grass height commonly preferred by Swayne’s hartebeest in grassland habitat. Starting from the first week of burning, we recorded the abundance of Swayne’s hartebeest in both burned and unburned grassland patches. Results From detected pellets, 94.3% were recorded in the grassland habitat indicating that other habitat types are less used despite their extensive cover > 50% of the Park. During wet and early dry seasons, Swayne’s hartebeest exclusively preferred grassland habitat. We found that 85.2% (n = 1079) and 85.3% (n = 593) of individuals observed in areas with a grass height below 30 cm during wet and early-dry seasons, respectively; while 70.9% (n = 2288) preferred grass height below 30 cm during the dry season. The density of Swayne’s hartebeest in burned grassland area was higher than unburned grassland areas up to 150 days since burning. However, in unburned grassland areas, the density was initially low but showed increasing trend for consecutive days, reaching similar density with burned areas after 150 days since burning. Conclusion Swayne’s hartebeest exclusively preferred grassland habitat, particularly during wet and early-dry seasons, shortest available grass height in all seasons and were attracted to burned grassland areas. Our results suggested that fire played an important role in maintaining habitat quality in grassland, and that management should continue using controlled burning as a tool for the conservation of Swayne’s hartebeest. However, we remain cautious of our findings given the paucity of information regarding other confounding factors and the absence of long-term data on fire disturbance.

Risk estimates are important measures for the study and practice of conservation ecology. Here, the authors show that such estimates can be substantially biased, and propose an approach to improve accuracy.

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has been characterized by unprecedented rates of spatio-temporal spread. Here, we summarize the main events in the pandemic's timeline and evaluate what has been learnt by the public health community. We also discuss the implications for future public health policy and, specifically, the practice of epidemic control. We critically analyze this ongoing pandemic's timeline and contrast it with the 2002–2003 SARS outbreak. We identify specific areas (e.g., pathogen identification and initial reporting) wherein the international community learnt valuable lessons from the SARS outbreak. However, we also identify the key areas where international public health policy failed leading to the exponential spread of the pandemic. We outline a clear agenda for improved pandemic control in the future.

Populations of large mammals have declined at alarming rates, especially in areas with intensified land use where species can only persist in small habitat fragments. To support conservation planning, we developed habitat suitability models for the Walia ibex (Capra walie), an endangered wild goat endemic to the Simen Mountains, Ethiopia. We calibrated several models that differ in statistical properties to estimate the spatial extent of suitable habitats of the Walia ibex in the Simen Mountains, as well as in other parts of the Ethiopian highlands to assess potentially suitable areas outside the current distribution range of the species. We further addressed the potential consequences of future climate change using a climate model with four emission scenarios. Model projections estimated the potential suitable habitat under current climate to 501–672 km2 in Simen and 6,251–7,732 km2 in other Ethiopian mountains. Under projected climate change by 2,080, the suitable habitat became larger in Simen but smaller in other parts of Ethiopia. The projected expansion in Simen is contrary to the general expectation of shrinking suitable habitats for high-elevation species under climate warming and may partly be due to the ruggedness of these particular mountains. The Walia ibex has a wide altitudinal range and is able to exploit very steep slopes, allowing it to track the expected vegetation shift to higher altitudes. However, this potential positive impact may not last long under continued climate warming, as the species will not have much more new space left to colonize. Our study indicates that the current distribution range can be substantially increased by reintroducing and/or translocating the species to other areas with suitable habitat. Indeed, to increase the viability and prospects for survival of this flagship species, we strongly recommend human-assisted reintroduction to other Ethiopian mountains. Emulating the successful reintroduction of the Alpine ibex that has spread from a single mountain in Italy to its historical ranges of the Alps in Europe might contribute to saving the Walia ibex from extinction.

Summary: Background: Until broad vaccination coverage is reached and effective therapeutics are available, controlling population mobility (ie, changes in the spatial location of a population that affect the spread and distribution of pathogens) is one of the major interventions used to reduce transmission of SARS-CoV-2. However, population mobility differs across locations, which could reduce the effectiveness of pandemic control measures. Here we assess the extent to which socioeconomic factors are associated with reductions in population mobility during the COVID-19 pandemic, at both the city level in China and at the country level worldwide. Methods: In this retrospective, observational study, we obtained anonymised daily mobile phone location data for 358 Chinese cities from Baidu, and for 121 countries from Google COVID-19 Community Mobility Reports. We assessed the intra-city movement intensity, inflow intensity, and outflow intensity of each Chinese city between Jan 25 (when the national emergency response was implemented) and Feb 18, 2020 (when population mobility was lowest) and compared these data to the corresponding lunar calendar period from the previous year (Feb 5 to March 1, 2019). Chinese cities were classified into four socioeconomic index (SEI) groups (high SEI, high–middle SEI, middle SEI, and low SEI) and the association between socioeconomic factors and changes in population mobility were assessed using univariate and multivariable linear regression. At the country level, we compared six types of mobility (residential, transit stations, workplaces, retail and recreation, parks, and groceries and pharmacies) 35 days after the implementation of the national emergency response in each country and compared these to data from the same day of the week in the baseline period (Jan 3 to Feb 6, 2020). We assessed associations between changes in the six types of mobility and the country's sociodemographic index using univariate and multivariable linear regression. Findings: The reduction in intra-city movement intensity in China was stronger in cities with a higher SEI than in those with a lower SEI (r=–0·47, p

The development of vaccines has opened a way to lower the public health and societal burden of COVID-19 pandemic. To achieve sustainable gains in the long term, switching the vaccination from one target group to a more diverse portfolio should be planned appropriately. We lay out a general mathematical framework for comparing alternative vaccination roll-out strategies for the year to come: single focus groups: (i-a) the high-risk older age groups and (i-b) the core-sociable groups; and two focus groups: (ii-a) mixed vaccination of both the high-risk and core-sociable groups simultaneously and (ii-b) cyclic vaccination switching between groups. Featuring analyses of all relevant data including age pyramids for 15 representative countries with diverse social mixing patterns shows that mixed strategies that result in both direct and indirect protection of high-risk groups may be better for the overall societal health impact of COVID-19 vaccine roll-out. Of note, over time switching the priority from high-risk older age groups to core-sociable groups responsible for heightened circulation and thus indirect risk may be increasingly advantageous.

Since COVID-19 spread globally in early 2020 and was declared a pandemic by the World Health Organization (WHO) in March, many countries are managing the local epidemics effectively through intervention measures that limit transmission. The challenges of immigration of new infections into regions and asymptomatic infections remain. Standard deterministic compartmental models are inappropriate for sub- or peri-critical epidemics (reproductive number close to or less than one), so individual-based models are often used by simulating transmission from an infected person to others. However, to be realistic, these models require a large number of parameters, each with its own set of uncertainties and lack of analytic tractability. Here, we apply stochastic age-structured Leslie theory with a long history in ecological research to provide some new insights to epidemic dynamics fuelled by external imports. We model the dynamics of an epidemic when R0 is below one, representing COVID-19 transmission following the successful application of intervention measures, and the transmission dynamics expected when infections migrate into a region. The model framework allows more rapid prediction of the shape and size of an epidemic to improve scaling of the response. During an epidemic when the numbers of infected individuals are rapidly changing, this will help clarify the situation of the pandemic and guide faster and more effective intervention.

Climate change may contribute to the spatio-temporal occurrence of disasters. Long-term studies of either homogeneous or heterogeneous responses of historical disasters to climate change are, however, limited by the quality and quantity of the available proxy data. Here we reconstruct spatio-temporal patterns of five types of disasters in China during the period AD 1368–1911. Our analyses of these time series reveal that warmer temperatures decreased the occurrence of disasters in the monsoon-affected parts of central-east China, but it increased the frequency and intensity of disasters along the boundary of arid and humid conditions in parts of southwest and northeast China, probably driven by the interplay among monsoon, westerlies, polar vortex and variation of temperature. Moreover, we show that drought and flood events had cascading effects on the occurrences of locust outbreaks, famine and human epidemics. Our findings suggest that climate can contribute to the spatio-temporal occurrence of disasters, and therefore may contribute to an improvement of China's regional to national risk management of future climate and environmental change.

In this paper, we establish the explicit connection between deterministic trait-based population-level models (in the form of partial differential equations) and species-level models (in the form of ordinary differential equations), in the context of eco-evolutionary systems. In particular, by starting from a population-level model of density distributions in trait space, we derive what amounts to an extension of the typical models at the species level known from adaptive dynamics literature, to account not only for abundance and mean trait values, but also explicitly for trait variances. Thus, we arrive at an explicitly polymorphic model at the species level. The derivations make precise the relationship between the parameters in the two classes of models and allow us to distinguish between notions of fitness on the population and species levels. Through a formal stability analysis, we see that exponential growth of an eigenvalue in the trait covariance matrix corresponds to a breakdown of the underlying assumptions of the species-level model. In biological terms, this may be interpreted as a speciation event: that is, we obtain an explicit notion of the blow-up of the variance of (possibly a linear combination of) traits as a precursor to speciation. Moreover, since evolutionary volatility of the mean trait value is proportional to trait variance, this provides a notion that species at the cusp of speciation are also the most adaptive. We illustrate these concepts and considerations using a numerical simulation.

Yersinia pestis, the bacterial causative agent of plague, remains an important threat to human health. Plague is a rodent-borne disease that has historically shown an outstanding ability to colonize and persist across different species, habitats, and environments while provoking sporadic cases, outbreaks, and deadly global epidemics among humans. Between September and November 2017, an outbreak of urban pneumonic plague was declared in Madagascar, which refocused the attention of the scientific community on this ancient human scourge. Given recent trends and plague's resilience to control in the wild, its high fatality rate in humans without early treatment, and its capacity to disrupt social and healthcare systems, human plague should be considered as a neglected threat. A workshop was held in Paris in July 2018 to review current knowledge about plague and to identify the scientific research priorities to eradicate plague as a human threat. It was concluded that an urgent commitment is needed to develop and fund a strong research agenda aiming to fill the current knowledge gaps structured around 4 main axes: (i) an improved understanding of the ecological interactions among the reservoir, vector, pathogen, and environment; (ii) human and societal responses; (iii) improved diagnostic tools and case management; and (iv) vaccine development. These axes should be cross-cutting, translational, and focused on delivering context-specific strategies. Results of this research should feed a global control and prevention strategy within a "One Health" approach.

Emerging infectious diseases are one of the greatest public health challenges. Approximately three-quarters of these diseases are of animal origin. These diseases include classical zoonoses maintained in humans only via transmission from other vertebrates (e.g., rabies) and those initiated by a successful one-off zoonotic event (host-switch) in conjunction with efficient human-to-human transmission (e.g., H1N1 influenza). Here, we provide a systematic review, in conjunction with a meta-analysis and spatial risk modeling, to identify the major characteristics of past epidemics of animal origin and predict areas with high future disease emergence risk. Countermeasures against future pandemics of animal origin must focus on several key mechanisms. First, the eco-epidemiological contexts favoring spillover events must be clearly establish. Second, pathogen surveillance must be scaled up, particularly in taxa and/or eco-geographic areas with high disease emergence risk. Third, successful spillover risk must be mitigated through proactive strategies to interrupt animal-to-human transmission chains. Fourth, to decrease epidemic potential and prevent epidemics from becoming pandemics, improved source identification and real-time spatial tracking of diseases are crucial. Finally, because pandemics do not respect international borders, enhancing international collaboration is critical to improving preparedness and response.

Abstract Background Species with a restricted geographic distribution, and highly specialized habitat and dietary requirements, are particularly vulnerable to extinction. The Bale monkey (Chlorocebus djamdjamensis) is a little-known arboreal, bamboo-specialist primate endemic to the southern Ethiopian Highlands. While most Bale monkeys inhabit montane forests dominated by bamboo, some occupy forest fragments where bamboo is much less abundant. We used mitochondrial DNA (mtDNA) sequences to analyse the genetic structure and evolutionary history of Bale monkeys covering the majority of their remaining distribution range. We analysed 119 faecal samples from their two main habitats, continuous forest (CF) and fragmented forests (FF), and sequenced 735 bp of the hypervariable region I (HVI) of the control region. We added 12 orthologous sequences from congeneric vervets (C. pygerythrus) and grivets (C. aethiops) as well as animals identified as hybrids, previously collected in southern Ethiopia. Results We found strong genetic differentiation (with no shared mtDNA haplotypes) between Bale monkey populations from CF and FF. Phylogenetic analyses revealed two distinct and highly diverged clades: a Bale monkey clade containing only Bale monkeys from CF and a green monkey clade where Bale monkeys from FF cluster with grivets and vervets. Analyses of demographic history revealed that Bale monkey populations (CF and FF) have had stable population sizes over an extended period, but have all recently experienced population declines. Conclusions The pronounced genetic structure and deep mtDNA divergence between Bale monkey populations inhabiting CF and FF are likely to be the results of hybridization and introgression of the FF population with parapatric Chlorocebus species, in contrast to the CF population, which was most likely not impacted by hybridization. Hybridization in the FF population was probably enhanced by an alteration of the bamboo forest habitat towards a more open woodland habitat, which enabled the parapatric Chlorocebus species to invade the Bale monkey's range and introgress the FF population. We therefore propose that the CF and FF Bale monkey populations should be managed as separate units when developing conservation strategies for this threatened species.

Abstract Background Understanding the effects of habitat modification on the feeding strategies of threatened species is essential to designing effective conservation management plans. Bale monkeys (Chlorocebus djamdjamensis) are endemic to the rapidly shrinking montane forests of the southern Ethiopian Highlands. Most populations inhabit continuous bamboo forest subsisting largely on the young leaves and shoots of a single species of bamboo. Because of habitat disturbance in recent decades, however, there are now also several dozen small populations inhabiting isolated forest fragments where bamboo has been degraded. During 12-months, we assessed Bale monkey responses to habitat degradation by comparing habitat composition, phenological patterns, and feeding ecology in a largely undisturbed continuous forest (Continuous groups A and B) and in two fragments (Patchy and Hilltop groups). Results We found that habitat quality and food availability were much lower in fragments than in continuous forest. In response to the relative scarcity of bamboo in fragments, Bale monkeys spent significantly less time feeding on the young leaves and shoots of bamboo and significantly more time feeding on non-bamboo young leaves, fruits, seeds, stems, petioles, and insects in fragments than in continuous forest. Groups in fragments also broadened their diets to incorporate many more plant species (Patchy: ≥ 47 and Hilltop: ≥ 35 species)—including several forbs, graminoids and cultivated crops—than groups in continuous forest (Continuous A: 12 and Continuous B: 8 species). Nevertheless, bamboo was still the top food species for Patchy group (30% of diet) as well as for both continuous forest groups (mean = 81%). However, in Hilltop group, for which bamboo was especially scarce, Bothriochloa radicans (Poaceae), a grass, was the top dietary species (15% of diet) and bamboo ranked 10th (2%). Conclusions We demonstrate that Bale monkeys are more dietarily flexible than previously thought and able to cope with some degradation of their primary bamboo forest habitat. However, crop raiding and other terrestrial foraging habits more common among fragment groups may place them at greater risk of hunting by humans. Thus, longitudinal monitoring is necessary to evaluate the long-term viability of Bale monkey populations in fragmented habitats.

Abstract Background Anthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium Bacillus anthracis. The dormant B. anthracis spores become vegetative after ingestion by grazing mammals. After killing the host, B. anthracis cells return to the soil where they sporulate, completing the lifecycle of the bacterium. Here we present the first study describing temporal microbial soil community changes in Etosha National Park, Namibia, after decomposition of two plains zebra (Equus quagga) anthrax carcasses. To circumvent state-associated-challenges (i.e. vegetative cells/spores) we monitored B. anthracis throughout the period using cultivation, qPCR and shotgun metagenomic sequencing. Results The combined results suggest that abundance estimation of spore-forming bacteria in their natural habitat by DNA-based approaches alone is insufficient due to poor recovery of DNA from spores. However, our combined approached allowed us to follow B. anthracis population dynamics (vegetative cells and spores) in the soil, along with closely related organisms from the B. cereus group, despite their high sequence similarity. Vegetative B. anthracis abundance peaked early in the time-series and then dropped when cells either sporulated or died. The time-series revealed that after carcass deposition, the typical semi-arid soil community (e.g. Frankiales and Rhizobiales species) becomes temporarily dominated by the orders Bacillales and Pseudomonadales, known to contain plant growth-promoting species. Conclusion Our work indicates that complementing DNA based approaches with cultivation may give a more complete picture of the ecology of spore forming pathogens. Furthermore, the results suggests that the increased vegetation biomass production found at carcass sites is due to both added nutrients and the proliferation of microbial taxa that can be beneficial for plant growth. Thus, future B. anthracis transmission events at carcass sites may be indirectly facilitated by the recruitment of plant-beneficial bacteria.

Abstract Background The African wolf, for which we herein recognise Canis lupaster Hemprich and Ehrenberg, 1832 (Symbolae Physicae quae ex Itinere Africam Borealem er Asoam Occidentalem Decas Secunda. Berlin, 1833) as the valid species name (we consider the older name Canis anthus Cuvier, 1820 [Le Chacal de Sénégal, Femelle. In: Geoffroy St.-Hilaire E, Cuvier F, editors. Histoire Naturelle des Mammifères Paris, A. Belin, 1820] a nomen dubium), is a medium-sized canid with wolf-like characters. Because of phenotypic similarity, specimens of African wolf have long been assigned to golden jackal (Canis aureus Linnaeus, 1758 [Systema Naturae per Regna Tria Naturae, Secundum Classes, Ordines, Genera, Species, cum Characteribus, Differentiis, Synonymis, Locis. Tomus I. Editio decima, reformata, 1758]). Results Here we provide, through rigorous morphological analysis, a species description for this taxonomically overlooked species. Through molecular sequencing we assess its distribution in Africa, which remains uncertain due to confusion regarding possible co-occurrence with the Eurasian golden jackal. Canis lupaster differs from all other Canis spp. including the golden jackal in its cranial morphology, while phylogenetically it shows close affinity to the Holarctic grey wolf (Canis lupus Linnaeus, 1758 [Systema Naturae per Regna Tria Naturae, Secundum Classes, Ordines, Genera, Species, cum Characteribus, Differentiis, Synonymis, Locis. Tomus I. Editio decima, reformata, 1758]). All sequences generated during this study clustered with African wolf specimens, consistent with previous data for the species. Conclusions We suggest that the estimated current geographic range of golden jackal in Africa represents the African wolf range. Further research is needed in eastern Egypt, where a hybrid zone between Eurasian golden jackal and African wolf may exist. Our results highlight the need for improved studies of geographic range and population surveys for the taxon, which is classified as ‘least concern’ by the IUCN due to its erroneous identification as golden jackal. As a species exclusively distributed in Africa, investigations of the biology and threats to African wolf are needed.

Seoul hantavirus (SEOV) has recently raised concern by causing geographic range expansion of hemorrhagic fever with renal syndrome (HFRS). SEOV infections in humans are significantly underestimated worldwide and epidemic dynamics of SEOV-related HFRS are poorly understood because of a lack of field data and empirically validated models. Here, we use mathematical models to examine both intrinsic and extrinsic drivers of disease transmission from animal (the Norway rat) to humans in a SEOV-endemic area in China. We found that rat eradication schemes and vaccination campaigns, but below the local elimination threshold, could diminish the amplitude of the HFRS epidemic but did not modify its seasonality. Models demonstrate population dynamics of the rodent host were insensitive to climate variations in urban settings, while relative humidity had a negative effect on the seasonality in transmission. Our study contributes to a better understanding of the epidemiology of SEOV-related HFRS, demonstrates asynchronies between rodent population dynamics and transmission rate, and identifies potential drivers of the SEOV seasonality.

Plague remains a threat to public health and is considered as a re-emerging infectious disease today. Rodents play an important role as major hosts in plague persistence and driving plague outbreaks in natural foci; however, few studies have tested the association between host diversity in ecosystems and human plague risk. Here we use zero-inflated generalized additive models to examine the association of species richness with human plague presence (where plague outbreaks could occur) and intensity (the average number of annual human cases when they occurred) in China during the Third Pandemic. We also account for transportation network density, annual precipitation levels and human population size. We found rodent species richness, particularly of rodent plague hosts, is positively associated with the presence of human plague. Further investigation shows that species richness of both wild and commensal rodent plague hosts are positively correlated with the presence, but only the latter correlated with the intensity. Our results indicated a positive relationship between rodent diversity and human plague, which may provide suggestions for the plague surveillance system.

Delimiting populations is crucial for conserving threatened species. Using genome-wide data from the whole of Antarctica, Cristofari et al.show that Emperor penguins are organised into a single global population that have shared demography since the late Quarternary.

Climate change is projected to increase the aridity of semi-arid ecosystems, including Mongolian grasslands (MG), which provide ecosystem services that support food supply and pastoralist lifestyle. Here, we conducted a grid-scale (0.5° × 0.5°) probabilistic risk assessment of MG under climate change for 40 years (1976–2015) based on probability theory. We evaluated changes of risk (impacts) and vulnerability of MG to drought between the recent two decades R20 = 1996–2015 and the previous two decades P20 = 1976–1995. The risk is quantified as the product of the probability of hazardous drought and ecosystem vulnerability. The probability of hazardous drought is defined from the Standardized Precipitation–Evapotranspiration Index. Vulnerability is defined as the expected differences of key ecosystem variables between years with and without hazardous conditions. The ecosystem variables are productivity (peak aboveground biomass, net primary productivity, and leaf area index) and root-zone plant-available soil moisture, simulated with a process-based vegetation model Organizing Carbon and Hydrology in Dynamic Ecosystems-Grassland Management validated with field observations of biomass and soil moisture. Results reveal that MG experienced more frequent hazardous droughts with rapid warming and slight drying during R20 aggravated by ever-increasing grazing intensity (34% compared to P20), which resulted in a reduction in soil water availability and grassland productivity, particularly in northeastern areas (20%–65%). The risk of drought to productivity increased by 10% between P20 and R20 over extended areas, particularly in northcentral and northeast Mongolia. The increase in the risk to MG was mainly caused by climate change-induced increase in the probability of hazardous drought and, to a lesser extent, by the increasing vulnerability. Recent droughts modify the risk to grasslands, particularly in northcentral and northeast Mongolia, suggesting that these regions need strategic management for both adaptation and ecosystem conservation to cope with climate change impacts.

Hantaviruses can cause hantavirus pulmonary syndrome (HPS) in the Americas and hemorrhagic fever with renal syndrome (HFRS) in Eurasia. In recent decades, repeated outbreaks of hantavirus disease have led to public concern and have created a global public health burden. Hantavirus spillover from natural hosts into human populations could be considered an ecological process, in which environmental forces, behavioral determinants of exposure, and dynamics at the human-animal interface affect human susceptibility and the epidemiology of the disease. In this review, we summarize the progress made in understanding hantavirus epidemiology and rodent reservoir population biology. We mainly focus on three species of rodent hosts with longitudinal studies of sufficient scale: the striped field mouse (Apodemus agrarius, the main reservoir host for Hantaan virus [HTNV], which causes HFRS) in Asia, the deer mouse (Peromyscus maniculatus, the main reservoir host for Sin Nombre virus [SNV], which causes HPS) in North America, and the bank vole (Myodes glareolus, the main reservoir host for Puumala virus [PUUV], which causes HFRS) in Europe. Moreover, we discuss the influence of ecological factors on human hantavirus disease outbreaks and provide an overview of research perspectives.

Despite ongoing efforts to control transmission, rabies prevention remains a challenge in many developing countries, especially in rural areas of China where re-emerging rabies is under-reported due to a lack of sustained animal surveillance. By taking advantage of detailed genomic and epidemiological data for the re-emerging rabies outbreak in Yunnan Province, China, collected between 1999 and 2015, we reconstruct the demographic and dispersal history of domestic dog rabies virus (RABV) as well as the dynamics of dog-to-dog and dog-to-human transmission. Phylogeographic analyses reveal a lower diffusion coefficient than previously estimated for dog RABV dissemination in northern Africa. Furthermore, epidemiological analyses reveal transmission rates between dogs, as well as between dogs and humans, lower than estimates for Africa. Finally, we show that reconstructed epidemic history of RABV among dogs and the dynamics of rabid dogs are consistent with the recorded human rabies cases. This work illustrates the benefits of combining phylogeographic and epidemic modelling approaches for uncovering the spatiotemporal dynamics of zoonotic diseases, with both approaches providing estimates of key epidemiological parameters.