Biology subjects

Guerra, C. A.

Publications and source records attributed to Guerra, C. A..

11 recordsLinked to original sources

bioRxiv2025

Mosquito Dispersal in Context

Mosquito dispersal plays an important role in mosquito ecology and mosquito-borne pathogen transmission. While reaction-diffusion and patch-based models with simple flux assumptions for emigration have played a predominant role in modeling mosquito dispersal, mosquito behavioral ecology - in particular, the process of searching for resources - is usually ignored by diffusion-based models. We thus set out to analyze mosquito movement using highly mimetic models, to see what we could learn from a different approach. Here, we present two behavioral state microsimulation models, in which mosquitoes are in behavioral states and search for required resources, which are distributed on a landscape. Models of this sort are laborious and challenging to work with, so we developed ramp.micro, an R package to build, solve, analyze, and visualize behavioral state microsimulation models for mosquitoes. Mosquito population dispersal is an emergent feature in these complex systems, so we developed new methods to describe and understand it. We show that population structure might not be revealed by a crude analysis of observed mosquito movement patterns, unless it can somehow account for sequences of flights for mosquitoes in behavioral states trying to accomplish a goal. We also show that even when resources are distributed randomly and uniformly, mosquito populations tend to form highly spatially structured communities. We also show that some heterogeneity in mosquito population densities is attributed to features of a network defined by searching and the spatial distribution of resources. These models highlight the importance of understanding mosquito behavioral states and resource availability in understanding mosquito population dispersal, and they point to the importance of local context. Motivated by these dynamics, spatial models for mosquito ecology and mosquito-borne pathogen transmission would benefit from considering resource availability as a factor affecting mosquito movement and dispersal. Author summaryWe develop highly realistic population dynamic models for mosquito behavioral ecology where mosquitoes move around on landscapes made up of resources located at points in space. The mosquitoes are in behavioral states - blood feeding, egg laying, or sugar feeding - and they end each search at a point where the resource they need can be found. Even with simple assumptions, mosquito populations can be highly structured. Because mosquitoes tend to leave areas that lack a resource, and they tend to stay in areas that have all required resources, the scarcest resources end up determining the structure of mosquito populations.

ecology↗

bioRxiv2024

Regular Plasmodium falciparum importation onto Bioko Island, Equatorial Guinea, hampers malaria elimination from the island

The Bioko Island Malaria Elimination Project (BIMEP) has made significant progress in reducing the prevalence of Plasmodium falciparum on Bioko Island, Equatorial Guinea. However, like other malaria endemic islands like Sao Tome and Principe and Zanzibar, Tanzania, elimination efforts are hampered by imported infections. In an effort to understand the local transmission dynamics and the influence of importation on Bioko Islands P. falciparum population, whole-genome sequences were generated from field samples collected during the BIMEPs 2019 Malaria Indicator Survey (MIS). Within the sub-Saharan African context, we observed Bioko Island parasites did not significantly differentiate from nearby continental neighbors. Among Bioko infections, within-host diversity and the quantity of polyclonal infections appear similar to an area of moderate malaria transmission. However, we observed higher than expected genetic diversity among Bioko parasites, similar to high transmission areas, suggesting imported strains are contributing to transmission on the island. Among Biokos closest geographical neighbors, the flow of parasites with Bioko appeared more pronounced with the Gabonese parasite population, implying more importation may be coming from this region than others. Overall, despite significant investment in malaria control, results illustrate the challenges of eliminating malaria without both interrupting local transmission and accounting for importation from higher transmission areas, likely due to human migration. For there to be sustained progress towards elimination, the BIMEP needs, if feasible, to conduct targeted interventions of outgoing/incoming travelers, and ideally expand malaria control interventions to the continental region of Equatorial Guinea. ImportancePlasmodium falciparum accounts for the majority of malaria deaths globally, with over 500,000 estimated deaths in 2023, predominantly in sub-Saharan Africa, despite strong investment in control and elimination interventions. Incorporating sequencing technologies into malaria surveillance is viewed as a powerful tool to improve control strategies, including identifying parasite transmission pathways. Here, we provide the first genomic characterization of P. falciparum on Bioko Island and Equatorial Guinea since malaria control began in 2004, and use these data to better understand the contribution of neighboring regions to Biokos P. falciparum population. Results highlight the need to account for offisland contributors to transmission and to understand how unmitigated transmission in neighboring regions can hamper progress. This study furthers our understanding of how the flow of parasites between regions impacts infectious disease control and provides foundational genomic data in a previously undescribed region that can be used to inform malaria elimination efforts.

genomics↗

bioRxiv2023

Soil health is linked to primary productivity across Europe

A healthy soil is at the core of sustainable management and policy, but its importance for plant productivity across environmental gradients and land-use types remains poorly understood. To address this gap, we conducted a pan-European field study including 588 sites from 27 countries to investigate the link between soil health and primary productivity across three major land-use types: woodlands, grasslands, and croplands. We found that mean soil health (a composite index based on soil properties, biodiversity, and plant disease control) in woodlands was 31.4% higher than in grasslands, and 76.1% higher than in croplands. Soil health was positively linked to cropland and grassland productivity at the continental scale. Woodland productivity was best explained by climate. Among microbial diversity indicators, we observed a positive association between the richness of Acidobacteria, Firmicutes, and Proteobacteria and primary productivity. Among microbial functional groups, we found that nitrogen-fixing bacteria and mycorrhizal fungi positively related to primary productivity in croplands and grasslands, while plant pathogens showed a negative relationship. Together, our results point to the importance of soil biodiversity and soil health for maintaining primary productivity across contrasting land-use types.

ecology↗

bioRxiv2022

The global distribution and environmental drivers of the soil antibiotic resistome

BackgroundLittle is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earths largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents, and created the first global atlas with the distributions of topsoil ARGs. ResultsWe show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. ConclusionsTogether, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome.

ecology↗

bioRxiv2022

Globally invariant metabolism but density-diversity mismatch in springtails

Soil life supports the functioning and biodiversity of terrestrial ecosystems1, 2. Springtails (Collembola) are among the most abundant soil animals regulating soil fertility and flow of energy through above- and belowground food webs3-5. However, the global distribution of springtail diversity and density, and how these relate to energy fluxes remains unknown. Here, using a global dataset collected from 2,470 sites, we estimate total soil springtail biomass at 29 Mt carbon (threefold higher than wild terrestrial vertebrates6) and record peak densities up to 2 million individuals per m{superscript 2} in the Arctic. Despite a 20-fold biomass difference between tundra and the tropics, springtail energy use (community metabolism) remains similar across the latitudinal gradient, owing to the increase in temperature. Neither springtail density nor community metabolism were predicted by local species richness, which was highest in the tropics, but comparably high in some temperate forests and even tundra. Changes in springtail activity may emerge from latitudinal gradients in temperature, predation7, 8, and resource limitation7, 9, 10 in soil communities. Contrasting temperature responses of biomass, diversity and activity of springtail communities suggest that climate warming will alter fundamental soil biodiversity metrics in different directions, potentially restructuring terrestrial food webs and affecting major soil functions.

ecology↗

bioRxiv2021

Analysis of nucleic acids extracted from rapid diagnostic tests reveals a significant proportion of false positive test results associated with recent malaria treatment

Surveillance programs often use malaria rapid diagnostic tests (RDTs) to determine the proportion of the population carrying parasites in their peripheral blood to assess the malaria transmission intensity. Despite an increasing number of reports on false-negative and false-positive RDT results, there is a lack of systematic quality control activities for RDTs deployed in malaria surveillance programs. Our study provides a larger scale comparative evaluation of RDTs used in the 2018 Malaria Indicator Survey (MIS) conducted on Bioko Island, Equatorial Guinea. We conducted a molecular analysis by extraction of nucleic acids from 1,800 negative and 1,065 positive RDTs followed by qPCR analysis. These results were combined with a dataset collected in a comprehensive questionnaire from each MIS participant. Of the 2,865 RDTs that were collected in 2018 on Bioko Island and analysed in our study, 4.7% had a false-negative result. These false-negative RDT results were associated with low parasite density infections. In a substantial proportion of samples, we identified masked pfhrp2 and pfhrp3 gene deletions in which at least one P. falciparum strain carried a gene deletion. Among all positive RDTs analysed, 28.4% were tested negative by qPCR and therefore considered to be false-positive. Analysing the questionnaire data collected from the participants, this high proportion of false-positive RDT results could be explained by PfHRP2 antigen persistence after recent malaria treatment. We conclude that malaria surveillance depending solely on RDTs needs well-integrated quality control procedures assessing the extend and impact of reduced sensitivity and specificity of RDTs on malaria control programs.

microbiology↗

bioRxiv2020

Measuring the accuracy of gridded human population density surfaces: a case study in Bioko Island, Equatorial Guinea

Geospatial datasets of population are becoming more common in models used for health policy. Publicly-available maps of human population in sub-Saharan Africa make a consistent picture from inconsistent census data, and the techniques they use to impute data makes each population map unique. Each mapping model explains its methods, but it can be difficult to know which map is appropriate for which policy work. Gold-standard census datasets, where available, are a unique opportunity to characterize maps by comparing them with truth. We use census data from Bioko Island, in Equatorial Guinea, to evaluate LandScan (LS), WorldPop (WP), and the High-Resolution Settlement Layer (HRSL). Each layer is compared to the gold-standard using statistical measures to evaluate distribution, error, and bias. We investigated how map choice affects burden estimates from a malaria prevalence model. Specific population layers were able to match the gold-standard distribution at different population densities. LandScan was able to most accurately capture highly urban distribution, HRSL matched best at all other lower population densities and WorldPop performed poorly everywhere. Correctly capturing empty pixels is key, and smaller pixel sizes (100 m vs 1 km) improve this. Normalizing areas based on known district populations increased performance. The use of differing population layers in a malaria model showed a disparity in results around transition points between endemicity levels. The metrics in this paper, some of them novel in this context, characterize how these population maps differ from the gold standard census and from each other. We show that the metrics help understand the performance of a population map within a malaria model. The closest match to the census data would combine LandScan within urban areas and the HRSL for rural areas. Researchers should prefer particular maps if health calculations have a strong dependency on knowing where people are not, or if it is important to categorize variation in density within a city.

ecology↗

bioRxiv2020

Global trends in biodiversity and ecosystem services from 1900 to 2050

Despite the scientific consensus on the extinction crisis and its anthropogenic origin, the quantification of historical trends and of future scenarios of biodiversity and ecosystem services has been limited, due to the lack of inter-model comparisons and harmonized scenarios. Here, we present a multi-model analysis to assess the impacts of land-use and climate change from 1900 to 2050. During the 20th century provisioning services increased, but biodiversity and regulating services decreased. Similar trade-offs are projected for the coming decades, but they may be attenuated in a sustainability scenario. Future biodiversity loss from land-use change is projected to keep up with historical rates or reduce slightly, whereas losses due to climate change are projected to increase greatly. Renewed efforts are needed by governments to meet the 2050 vision of the Convention on Biological Diversity. One Sentence SummaryDevelopment pathways exist that allow for a reduction of the rates of biodiversity loss from land-use change and improvement in regulating services but climate change poses an increasing challenge.

ecology↗

bioRxiv2019

Blind spots in global soil biodiversity and ecosystem function research

Soils harbor a substantial fraction of the worlds biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and governance. Here we identify and characterize the existing gaps in soil biodiversity and ecosystem function data across soil macroecological studies and >11,000 sampling sites. These include significant spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.6% of all sampling sites having a non-systematic coverage of both biodiversity and function datasets. Based on this information, we provide clear priorities to support and expand soil macroecological research.

ecology↗

bioRxiv2019

Pathways of human development threaten biomes protection and their remaining natural vegetation

Protected areas have been one of the most commonly applied conservation tools to prevent ecosystem degradation. International conservation targets have been created to incentivize widespread expansion of protected area networks, but this call might clash with expected future land use change. Here we investigated how future land use trajectories (2015-2090), representing a wide range of plausible future scenarios would impact the remaining areas of primary vegetation under different protection levels across the worlds biomes. We then highlight areas under greater risk of conflict between conservation (highly protected) and land use expansion (high projected change), and areas where these two can better co-exist (lower protection with high projected change and/or high protection with low projected change).\n\nWhile the most positive pathway of development led to the least loss of primary vegetation globally, this was not observed in all biomes. Further, we found no significant correlation between existing extent of protection and average proportion of vegetation loss. Mediterranean Forests, Woodlands & Scrub had the largest projected loss occurring in the highest protected areas. Tropical Forests in Central Africa and the Boreal Forests of North Euro-Asia and Canada emerge as the areas where most projected change occurs, and existing protection is still low. Areas in India and Southeast Asia emerge as potential areas for intervention as they have significant projected loss of primary vegetation, and considerably low protection.\n\nOur results can help inform policy and decision-makers to prevent such conflicts and support the development of management actions. These policy and management actions should target conservation in areas under expected great pressure of change with high ecological value (e.g., composed mainly by primary vegetation), but still not protected. This study also opens the discussion to the future of current protected areas and to the potential to expand the existing network of protected areas.

ecology↗

bioRxiv2019

Global distribution of earthworm diversity

Soil organisms provide crucial ecosystem services that support human life. However, little is known about their diversity, distribution, and the threats affecting them. Here, we compiled a global dataset of sampled earthworm communities from over 7000 sites in 56 countries to predict patterns in earthworm diversity, abundance, and biomass. We identify the environmental drivers shaping these patterns. Local species richness and abundance typically peaked at higher latitudes, while biomass peaked in the tropics, patterns opposite to those observed in aboveground organisms. Similar to many aboveground taxa, climate variables were more important in shaping earthworm communities than soil properties or habitat cover. These findings highlight that, while the environmental drivers are similar, conservation strategies to conserve aboveground biodiversity might not be appropriate for earthworm diversity, especially in a changing climate.\n\nOne sentence summaryGlobal patterns of earthworm diversity, abundance and biomass are driven by climate but patterns differ from many aboveground taxa.

ecology↗