scholarly journals Using Data Mining and Network Analysis to Infer Arboviral Dynamics: The Case of Mosquito-Borne Flaviviruses Reported in Mexico

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 398
Author(s):  
Jesús Sotomayor-Bonilla ◽  
Enrique Del Callejo-Canal ◽  
Constantino González-Salazar ◽  
Gerardo Suzán ◽  
Christopher R. Stephens
Keyword(s):  
Mosquito Species ◽  
Animal Health ◽  
Biotic Interactions ◽  
Significant Degree ◽  
Identification Algorithm ◽  
Modeling Framework ◽  
Mammal Species ◽  
Transmission Cycle ◽  
Artibeus Lituratus ◽  
Multiple Pathogens

Given the significant impact of mosquito-borne flaviviruses (MBFVs) on both human and animal health, predicting their dynamics and understanding their transmission cycle is of the utmost importance. Usually, predictions about the distribution of priority pathogens, such as Dengue, Yellow fever, West Nile Virus and St. Louis encephalitis, relate abiotic elements to simple biotic components, such as a single causal agent. Furthermore, focusing on single pathogens neglects the possibility of interactions and the existence of common elements in the transmission cycles of multiple pathogens. A necessary, but not sufficient, condition that a mosquito be a vector of a MBFV is that it co-occurs with hosts of the pathogen. We therefore use a recently developed modeling framework, based on co-occurrence data, to infer potential biotic interactions between those mosquito and mammal species which have previously been identified as vectors or confirmed positives of at least one of the considered MBFVs. We thus create models for predicting the relative importance of mosquito species as potential vectors for each pathogen, and also for all pathogens together, using the known vectors to validate the models. We infer that various mosquito species are likely to be significant vectors, even though they have not currently been identified as such, and are likely to harbor multiple pathogens, again validating the predictions with known results. Besides the above “niche-based” viewpoint we also consider an assemblage-based analysis, wherein we use a community-identification algorithm to identify those mosquito and/or mammal species that form assemblages by dint of their significant degree of co-occurrence. The most cohesive assemblage includes important primary vectors, such as A. aegypti, A. albopictus, C. quinquefasciatus, C. pipiens and mammals with abundant populations that are well-adapted to human environments, such as the white-tailed deer (Odocoileus virginianus), peccary (Tayassu pecari), opossum (Didelphis marsupialis) and bats (Artibeus lituratus and Sturnira lilium). Our results suggest that this assemblage has an important role in the transmission dynamics of this viral group viewed as a complex multi-pathogen-vector-host system. By including biotic risk factors our approach also modifies the geographical risk profiles of the spatial distribution of MBFVs in Mexico relative to a consideration of only abiotic niche variables.

Anthropogenic perturbation modifies interactions between mammals and fruits in a tropical forest of southern Mexico

2021 ◽  
Vol 71 (3) ◽  
pp. 311-327
Author(s):  
Mayra Zamora-Espinoza ◽  
Juan Carlos López-Acosta ◽  
Eduardo Mendoza
Keyword(s):  
Daily Activity ◽  
Interaction Strength ◽  
Biotic Interactions ◽  
Camera Traps ◽  
Canis Lupus Familiaris ◽  
Mammalian Fauna ◽  
Mammal Species ◽  
Southern Mexico ◽  
Field Station ◽  
The Impact

Abstract Studies of tropical mammal defaunation highlight the loss of species as well as their reduction in abundance and diversity; however, there is a complex series of effects associated with this anthropogenic disruption, including increases in the relative abundance of disturbance-tolerant mammals and the arrival of alien mammals whose effects on biotic interactions have been poorly studied. We compared the species richness, composition, interaction strength, and patterns of daily activity of mammals that consume the fruits of Pouteria sapota on the forest floor, both inside and outside of the Los Tuxtlas Field Station (LTFS) in Veracruz, southern Mexico. Using camera traps, we recorded eight mammal species interacting with the fruits inside the LTFS ( trees) and nine species interacting outside ( trees). Alien species such as Canis lupus familiaris were recorded both inside and outside of the LTFS, whereas Bos taurus was only recorded outside. Medium-sized generalist mammals were overrepresented both inside and outside of the LTFS, evidencing an impoverishment of the fauna, when compared to the mammal assemblage reported to interact with P. sapota fruits in a more intact forest. The daily activity patterns of the mammals that interacted strongly with P. sapota fruits were different inside and outside the LTFS, particularly in the case of Cuniculus paca. Our results show that the impact of human activity is highly pervasive, directly affecting the mammalian fauna at different levels and indirectly affecting the biotic interactions in which these animals are involved.

scholarly journals The Biodiversity of Water Mites That Prey on and Parasitize Mosquitoes

Diversity ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 226
Author(s):  
Adrian A. Vasquez ◽  
Bana A. Kabalan ◽  
Jeffrey L. Ram ◽  
Carol J. Miller
Keyword(s):  
Mosquito Species ◽  
Biotic Interactions ◽  
Future Research ◽  
Water Mites ◽  
Ecological Functions ◽  
Predator Prey ◽  
Parasitic Mite ◽  
Aquatic Food ◽  
Parasitic Interactions ◽  
Mite Predator

Water mites form one of the most biodiverse groups within the aquatic arachnid class. These freshwater macroinvertebrates are predators and parasites of the equally diverse nematocerous Dipterans, such as mosquitoes, and water mites are believed to have diversified as a result of these predatory and parasitic relationships. Through these two major biotic interactions, water mites have been found to greatly impact a variety of mosquito species. Although these predatory and parasitic interactions are important in aquatic ecology, very little is known about the diversity of water mites that interact with mosquitoes. In this paper, we review and update the past literature on the predatory and parasitic mite–mosquito relationships, update past records, discuss the biogeographic range of these interactions, and add our own recent findings on this topic conducted in habitats around the Laurentian Great Lakes. The possible impact on human health, along with the importance of water mite predator–prey dynamics in aquatic food webs, motivates an increase in future research on this aquatic predator and parasite and may reveal novel ecological functions that these parasitic and predator–prey relationships mediate.

scholarly journals Meta-Transcriptomic Comparison of the RNA Viromes of the Mosquito Vectors Culex pipiens and Culex torrentium in Northern Europe

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1033 ◽  
Author(s):  
Pettersson ◽  
Shi ◽  
Eden ◽  
Holmes ◽  
Hesson
Keyword(s):  
Culex Pipiens ◽  
Evolutionary History ◽  
Rna Viruses ◽  
Mosquito Species ◽  
Animal Health ◽  
Mosquito Vectors ◽  
South Central ◽  
Global Movement ◽  
History Of ◽  
Local Habitat

Mosquitoes harbor an extensive diversity of ‘insect-specific’ RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes, little is known about the diversity and evolutionary history of RNA viruses sampled from mosquitoes in northerly regions. Here, we compared the RNA virome of two common northern mosquito species, Culex pipiens and Culex torrentium, collected in south-central Sweden. Following bulk RNA-sequencing (meta-transcriptomics) of 12 libraries, comprising 120 specimens of Cx. pipiens and 150 specimens of Cx. torrentium, we identified 40 viruses (representing 14 virus families) of which 28 were novel based on phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) protein. Hence, we documented similar levels of virome diversity as in mosquitoes sampled from the more biodiverse lower latitudes. Many viruses were also related to those sampled on other continents, indicative of a widespread global movement and/or long host–virus co-evolution. Although the two mosquito species investigated have overlapping geographical distributions and share many viruses, several viruses were only found at a specific location at this scale of sampling, such that local habitat and geography may play an important role in shaping viral diversity in Culex mosquitoes.

scholarly journals Outbreak of autochthonous cases of malaria in coastal regions of Northeast Brazil: the diversity and spatial distribution of species of Anopheles

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Elainne Christine de Souza Gomes ◽  
Derciliano Lopes da Cruz ◽  
Maria Alice Varjal Melo Santos ◽  
Renata Maria Costa Souza ◽  
Cláudia Maria Fontes de Oliveira ◽  
...  
Keyword(s):  
At Risk ◽  
Spatial Distribution ◽  
Spatial Analysis ◽  
Mosquito Species ◽  
Health Department ◽  
Transmission Cycle ◽  
Imported Case ◽  
Bg Sentinel ◽  
Epidemiology Investigation ◽  
Amazonian Region

Abstract Background Brazil has the fourth highest prevalence of malaria of all countries in the Americas, with an estimated 42 million people at risk of contracting this disease. Although most cases occur in the Amazon region, cases of an autochthonous nature have also been registered in the extra-Amazonian region where Anopheles aquasalis and An. albitarsis are the mosquito species of greatest epidemiological interest. In 2019, the municipality of Conde (state of Paraíba) experienced an epidemic of autochthonous cases of malaria. Here we present preliminary results of an entomological and case epidemiology investigation, in an attempt to correlate the diversity and spatial distribution of species of Anopheles with the autochthonous cases of this outbreak of malaria. Methods Case data were collected using case report forms made available by the Conde Municipal Health Department. The entomological survey was carried out from July to November 2019. The various methods of capture included the use of battery-powered aspirators, mouth aspirators, Shannon traps, BG-Sentinel traps (with and without dry ice) and CDC light traps. Captured mosquitoes were separated, packaged and sent to the laboratory for sexing and molecular identification of the various species of anophelines. The data were tabulated and analyzed using Microsoft Excel. Spatial analysis of the data was performed using ArcGis 10 software. Results In 2019, 20 autochthonous cases and one imported case of malaria caused by Plasmodium vivax were diagnosed, with three cases of relapses. A total of 3713 mosquitoes were collected, of which 3390 were culicines and 323 were anophelines. Nine species of genus Anopheles were identified, with the most abundant being An. aquasalis (38.9%), followed by An. minor (18.2%) and An. albitarsis (9.0%). Spatial analysis of the data showed that the area could be considered to be at risk of malaria cases and that there was a high prevalence of Anopheles. Conclusions The results presented indicate that this extra-Amazonian region has an environment conducive to maintenance of the malaria transmission cycle owing to the wide diversity of Anopheles species. This environment in combination with the high influx of people from endemic areas to the study area provides a perfect setting for the occurrence and maintenance of malaria.

scholarly journals MURCIÉLAGOS (CHIROPTERA) EN ÁREAS VERDES URBANAS DE LA CIUDAD DE TEPIC, NAYARIT, MÉXICO

2020 ◽  
Vol 10 (1) ◽  
pp. 21
Author(s):  
Juan Pablo Ramírez-Silva ◽  
Elsa Jazmín Lugo-Gil
Keyword(s):  
Urban Areas ◽  
Feeding Habits ◽  
Biotic Interactions ◽  
Urban Ecosystem ◽  
Green Spaces ◽  
Ecological Processes ◽  
Artibeus Jamaicensis ◽  
Mexican State ◽  
Artibeus Lituratus ◽  
The City

ResumenLos murciélagos desempeñan un papel fundamental en los ecosistemas, ya que efectúan múltiples interacciones bióticas como la dispersión de semillas, polinización y el control de plagas, además de que poseen hábitos alimenticios muy variados. En Nayarit se han registrado 67 especies de quirópteros, pero ningún estudio se ha enfocado en las zonas urbanas del estado. Nuestro objetivo fue evaluar la diversidad y abundancia de murciélagos en las áreas verdes de la zona urbana de Tepic, Nayarit. Se realizó un muestro en nueve sitios empleando una red de 12 metros, colocada de 18:00 h a 23:00 h., durante el periodo de noviembre del 2015 a noviembre del 2016, en el cual se acumuló un total de 45 horas/red. Se muestrearon tres tipos de hábitat urbanos: plazas, zanjones y parques. Con los datos recabados se estimó el índice de diversidad alfa de Shannon y se realizó una prueba de t modificada por Hutchenson para comparar los distintos ecosistemas. Se registraron tres especies de murciélagos (Artibeus lituratus, Artibeus jamaicensis y Artibeus hirsutus). Los parques resultaron el ecosistema que registró la mayor diversidad y abundancia de murciélagos, mientras que la especie que se documentó con mayor frecuencia fue A. lituratus.Palabras clave: ambientes antropizados, parques urbanos, quirópteros.AbstractThe bats play a fundamental role in the ecological processes of ecosystems, they carry out multiple biotic interactions such as seed dispersers, pollination, and pest control, they also have very varied feeding habits. In the Mexican state of Nayarit have been registered 67 bat species, but no one research has focused on the urban areas. Our objective was to research the species present in the green areas of the city of Tepic, Nayarit. Nine sites were sampled using a 12-meter network, which was placed from 6:00 p.m. to 11:00 p.m. The samplings were carried out from November 2015 to November 2016, for a total of 45 hours/network. Three types of habitat were covered: plazas, zanjon, and parks. We performed the Shannon alpha index to assess diversity and a t-test was used to compare between the different habitats. Three species were registered (Artibeus lituratus, Artibeus jamaicensis and Artibeus hirsutus). The urban ecosystem with the greatest diversity and abundance was the parks and the species that presented the highest frequency in the urban area was A. lituratus.Key words: Anthropized areas, bats, green spaces.

scholarly journals Modeling the role of mortality-based response triggers on the effectiveness of African swine fever control strategies

2021 ◽  
Author(s):  
Gustavo Machado ◽  
Trevor Farthing ◽  
Mathieu Andraud ◽  
Francisco Paulo Nunes Lopes ◽  
Cristina Lanzas
Keyword(s):  
Spatial Distribution ◽  
Animal Movement ◽  
Control Strategies ◽  
Virulent Strain ◽  
Animal Health ◽  
African Swine Fever ◽  
Multiscale Model ◽  
Case Scenario ◽  
Modeling Framework ◽  
Highly Virulent

African swine fever (ASF) is considered the most impactful transboundary swine disease. In the absence of effective vaccines, control strategies are heavily dependent on mass depopulation and movement restrictions. Here we developed a nested multiscale model for the transmission of ASF, combining spatially explicit network model of animal movements with a deterministic compartmental model for the dynamics of two ASF strains within-pixels of 3 km x 3 km, amongst the pig population in one Brazilian state. The model outcomes are epidemic duration, number of secondary infected farms and pigs, and distance of ASF spread. The model also predicted the spatial distribution of ASF epidemics. We analyzed quarantine-based control interventions in the context of mortality trigger thresholds for the deployment of control strategies. The mean epidemic duration of a moderately virulent strain was 11.2 days assuming the first infection is detected (best-case scenario) and 15.9 days when detection is triggered at 10 % mortality. For a highly virulent strain, the epidemic duration was 6.5 days and 13.1 days, respectively. The distance from the source to infected locations and the spatial distribution was not dependent on strain virulence. Under the best-case scenario, we projected an average number of infected farms of 18.79 farms and 23.77 farms for the moderate and highly virulent strains, respectively. At 10% mortality-trigger, the predicted number of infected farms was on average 48.28 farms and 42.97 farms, respectively. We also demonstrated that the establishment of ring quarantine zones regardless of size (i.e., 5 km, 15 km) was outperformed by backward animal movement tracking. The proposed modeling framework provides an evaluation of ASF epidemic potential, providing a ranking of quarantine-based control strategies that could assist animal health authorities in planning the national preparedness and response plan.

scholarly journals Liberating Biodiversity Data From COVID-19 Lockdown: Toward a knowledge hub for mammal host-virus information

2020 ◽  
Vol 4 ◽  
Author(s):  
Nathan Upham ◽  
Donat Agosti ◽  
Jorrit Poelen ◽  
Lyubomir Penev ◽  
Deborah Paul ◽  
...  
Keyword(s):  
Biotic Interactions ◽  
Basic Knowledge ◽  
Deer Mice ◽  
Data Repository ◽  
Ecological Data ◽  
Viral Reservoirs ◽  
Mammal Species ◽  
Biodiversity Knowledge ◽  
Biodiversity Science ◽  
Mammal Host

A deep irony of COVID-19 likely originating from a bat-borne coronavirus (Boni et al. 2020) is that the global lockdown to quell the pandemic also locked up physical access to much basic knowledge regarding bat biology. Digital access to data on the ecology, geography, and taxonomy of potential viral reservoirs, from Southeast Asian horseshoe bats and pangolins to North American deer mice, was suddenly critical for understanding the disease's emergence and spread. However, much of this information lay inside rare books and personal files rather than as open, linked, and queryable resources on the internet. Even the world's experts on mammal taxonomy and zoonotic disease could not retrieve their data from shuttered laboratories. We were caught unprepared. Why, in this digitally connected age, were such fundamental data describing life on Earth not already freely accessible online? Understanding why biodiversity science was unprepared—and how to fix it before the next pandemic—has been the focus of our COVID-19 Taskforce since April 2020 and is continuing (organized by CETAF and DiSSCo). We are a group of museum-based and academic scientists with the goal of opening the rich ecological data stored in natural history collections to the research public. This information is rooted in what may seem an unlikely location—taxonomic names and their historical usages, which are the keys for searching literature and extracting linked ecological data (Fig. 1). This has been the core motivation of our group, enabled by the pioneering efforts of Plazi (Agosti and Egloff 2009) to build tools for literature digitization, extraction, and parsing (e.g., Synospecies, Ocellus) without which biodiversity science would be even less prepared. Our group led efforts to build an additional pipeline from Plazi to the Biodiversity Literature Repository at Zenodo, a free and unlimited data repository (Agosti et al. 2019), and then to GloBI, an open-source database of biotic interactions (Poelen et al. 2014, GloBI 2020). We also developed a direct integration from Pensoft Journals to GloBI, leveraging that publisher’s indexing of computer-readable terms (called semantic metadata; Senderov et al. 2018) to extract mammal host and virus information. Overall, considerable progress was made. In total, 85,492 new interactions were added to GloBI from 14 April to 21 May 2020 (see entire dataset on Zenodo: Poelen et al. 2020). Of those, 28,839 interactions are present when subset to "hasHost", "hostOf", "pathogenOf", "virus", and 4,101 unique name combinations are present after considering mammal species synonymies (from Meyer et al. 2015). Of those interactions, 892 species of mammals and 1,530 unique virus names are involved, which compares to 754 mammals and 586 viruses in the most recent data synthesis (Olival et al. 2017). While these liberated data may still include redundancies, they demonstrate the value of our approach and the expanse of known but digitally unconnected data that remains locked in publications. We can liberate host-virus data from publications, but doing so is expensive and does not scale to the continued influx of new articles that are inadequately digitized. Our efforts make it clear that Pensoft-style semantic publishing should be expanded to all major journals. The pandemic has created an opportunity for re-thinking the way we do science in the digital age. Thankfully, our future is not the past, so we do not have to keep wasting resources to digitially 'rediscover' biodiversity knowledge. We collectively call for changes to the publishing paradigm, so that research findings are directly accessible, citable, discoverable, and reusable for creating complete forms of digital knowledge.

scholarly journals Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions

2019 ◽  
Vol 69 (4) ◽  
pp. 739-755 ◽  
Author(s):  
Ignacio Quintero ◽  
Michael J Landis
Keyword(s):  
Data Augmentation ◽  
Biotic Interactions ◽  
Adaptive Divergence ◽  
Modeling Framework ◽  
Niche Divergence ◽  
Trait Divergence ◽  
Ecological Requirements ◽  
Alternative Scenarios ◽  
Beak Size ◽  
Lineage Diversification

Abstract Biotic interactions are hypothesized to be one of the main processes shaping trait and biogeographic evolution during lineage diversification. Theoretical and empirical evidence suggests that species with similar ecological requirements either spatially exclude each other, by preventing the colonization of competitors or by driving coexisting populations to extinction, or show niche divergence when in sympatry. However, the extent and generality of the effect of interspecific competition in trait and biogeographic evolution has been limited by a dearth of appropriate process-generating models to directly test the effect of biotic interactions. Here, we formulate a phylogenetic parametric model that allows interdependence between trait and biogeographic evolution, thus enabling a direct test of central hypotheses on how biotic interactions shape these evolutionary processes. We adopt a Bayesian data augmentation approach to estimate the joint posterior distribution of trait histories, range histories, and coevolutionary process parameters under this analytically intractable model. Through simulations, we show that our model is capable of distinguishing alternative scenarios of biotic interactions. We apply our model to the radiation of Darwin’s finches—a classic example of adaptive divergence—and find limited support for in situ trait divergence in beak size, but stronger evidence for convergence in traits such as beak shape and tarsus length and for competitive exclusion throughout their evolutionary history. These findings are more consistent with presympatric, rather than postsympatric, niche divergence. Our modeling framework opens new possibilities for testing more complex hypotheses about the processes underlying lineage diversification. More generally, it provides a robust probabilistic methodology to model correlated evolution of continuous and discrete characters. [Bayesian; biotic interactions; competition; data augmentation; historical biogeography; trait evolution.]

scholarly journals Diversity begets diversity in mammal species and human cultures

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marcus J. Hamilton ◽  
Robert S. Walker ◽  
Christopher P. Kempes
Keyword(s):  
Cultural Diversity ◽  
Cultural Evolution ◽  
Biotic Interactions ◽  
Common Currency ◽  
Complex Environments ◽  
Temperature Dependent ◽  
Mammal Species ◽  
Develop Theory ◽  
Underlying Mechanisms ◽  
Kinetics Of

AbstractAcross the planet the biogeographic distribution of human cultural diversity tends to correlate positively with biodiversity. In this paper we focus on the biogeographic distribution of mammal species and human cultural diversity. We show that not only are these forms of diversity similarly distributed in space, but they both scale superlinearly with environmental production. We develop theory that explains that as environmental productivity increases the ecological kinetics of diversity increases faster than expected because more complex environments are also more interactive. Using biogeographic databases of the global distributions of mammal species and human cultures we test a series of hypotheses derived from this theory and find support for each. For both mammals and cultures, we show that (1) both forms of diversity increase exponentially with ecological kinetics; (2) the kinetics of diversity is faster than the kinetics of productivity; (3) diversity scales superlinearly with environmental productivity; and (4) the kinetics of diversity is faster in increasingly productive environments. This biogeographic convergence is particularly striking because while the dynamics of biological and cultural evolution may be similar in principle the underlying mechanisms and time scales are very different. However, a common currency underlying all forms of diversity is ecological kinetics; the temperature-dependent fluxes of energy and biotic interactions that sustain all forms of life at all levels of organization. Diversity begets diversity in mammal species and human cultures because ecological kinetics drives superlinear scaling with environmental productivity.

Mosquito—Virus Interactions

2020 ◽  
pp. 191-214
Author(s):  
Christine M. Reitmayer ◽  
Michelle V. Evans ◽  
Kerri L. Miazgowicz ◽  
Philip M. Newberry ◽  
Nicole Solano ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Mosquito Species ◽  
Animal Health ◽  
Quality Data ◽  
Human Pathogens ◽  
Virus West Nile ◽  
Vector Borne ◽  
Virus Interaction ◽  
Abiotic And Biotic Factors ◽  
Virus Interactions

Vector-borne viruses (arboviruses) are emerging threats to both human and animal health. The global expansion of dengue virus, West Nile virus, chikungunya, and most recently Zika virus are prominent examples of how quickly mosquito-transmitted viruses can emerge and spread. We currently lack high quality data from a diversity of mosquito-arbovirus systems on the specific mosquito and viral traits that drive disease transmission. Further, the factors that contribute to variation in these traits and disease transmission remain largely unidentified. In this chapter, we outline and explore the following: 1. the specific mechanisms governing the outcome of vector-virus interactions 2. how genetic variation across mosquito populations and viral strains, as well as environmental variation in abiotic and biotic factors shape the mosquito-virus interaction and 3. the implications of these interactions for understanding and predicting arbovirus transmission, as well as for control of mosquito species that transmit human pathogens.

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