Renata Muylaert | Massey University (original) (raw)

Papers by Renata Muylaert

Primeiro release oficial deste tutorial, incluindo um novo passo-a-passo em RMarkDown.

This is the first version of the NeoBat Interactions data paper supplement.

First release of the repo.

First release of the code. How to estimate P-values of network metrics and compare pairs of netwo... more First release of the code. How to estimate P-values of network metrics and compare pairs of networks using Monte Carlo procedures in R Ecological Synthesis Lab (SintECO): https://marcomellolab.wordpress.com. Authors: Renata Muylaert, Pavel Dodonov & Marco Mello. E-mail: renatamuy@gmail.com. How to cite: Muylaert RL, Dodonov P * Mello MAR. 2016. How to estimate P-values of network metrics and compare pairs of networks using Monte Carlo procedures in R. Ecological Synthesis Lab of the University of São Paulo, Brazil. Published on April 25th, 2017 (English version). Run in R 3.3.3 (2017-03-06) -- "Another Canoe". Disclaimer: You may use this script freely for non-comercial purposes at your own risk. We assume no responsibility or liability for the use of this software, convey no license or title under any patent, copyright, or mask work right to the product. We reserve the right to make changes in the software without notification. We also make no representation or warranty t...

Neurotrauma Reports, 2021

This article aims to evaluate the predictive factors of morbidity and mortality in pediatric pati... more This article aims to evaluate the predictive factors of morbidity and mortality in pediatric patients who suffered gunshot wounds to the head. We reviewed a series of 43 patients who were admitted to a referential neurosurgical hospital between 2010 and 2019. Data from 43 patients who underwent a surgical treatment in our institution were collected, and the following parameters were considered in the analysis: the initial Glasgow Coma Scale (GCS), age, sex, bullet entry site, and bullet trajectory. Computed tomography (CT) scans at admission, complications, midline crossing, and Glasgow score scale at the time of discharge (Glasgow Outcome Scale; GOS) were also factored in. Male sex corresponded to 90.7% of cases (N = 39), and 16-17 years of age was the most common age (60.5%). The frontal region was the most common entry site (41.9%), followed by the parietal wall and occipital entry. Penetrating trajectory was shown in 48.8% of cases, perforation/transfixing in 39.5%, and tangential in 11.6%. CT showed that sinking is the most common alteration (74.4%), followed by cerebral contusion (44.2%). According to the GOS, 23.3% died, 23.3% were classified by an unfavorable outcome (GOS, 2-3), and 53.5% a favorable outcome (GOS, 4 and 5). In our study, there was a significant association between the low GCS scores on admission and low GOS (1-3; p = 0.001) at time of discharge. Patients with wounds that crossed the midline also had a significant association with low GOS (p = 0.014) in our clinical experience. We concluded that low GCS scores at admission and children with a wound that crosses the midline are predictive factors of high mortality and morbidity, in our clinical experience.

Philosophical Transactions of the Royal Society B: Biological Sciences, 2021

In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virolo... more In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This artic...

Data cataloguing viral diversity on Earth have been fragmented across sources, disciplines, forma... more Data cataloguing viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open collation, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically-maintained database of vertebrate-virus associations, called The Global Virome in One Network (VIRION). The VIRION database has been assembled through both reconciliation of static datasets and integration of dynamically-updated databases. These data sources are all harmonized against one taxonomic backbone, including metadata on host and virus taxonomic validity and higher classification; additional metadata on sampling methodology and evidence strength are also available in a harmonized format. In total, the VIRION database is the largest open-source, open-access database of its kind, with roughly half a million unique records that include 9,521 resolved virus “species” (of which 1,661 are ICTV ratified), 3,69...

Diversity and Distributions, 2019

This is an open access article under the terms of the Creative Commons Attribution License, which... more This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Viruses, 2019

Background: Hantavirus disease in humans is rare but frequently lethal in the Neotropics. Several... more Background: Hantavirus disease in humans is rare but frequently lethal in the Neotropics. Several abundant and widely distributed Sigmodontinae rodents are the primary hosts of Orthohantavirus and, in combination with other factors, these rodents can shape hantavirus disease. Here, we assessed the influence of host diversity, climate, social vulnerability and land use change on the risk of hantavirus disease in Brazil over 24 years. Methods: Landscape variables (native forest, forestry, sugarcane, maize and pasture), climate (temperature and precipitation), and host biodiversity (derived through niche models) were used in spatiotemporal models, using the 5570 Brazilian municipalities as units of analysis. Results: Amounts of native forest and sugarcane, combined with temperature, were the most important factors influencing the increase of disease risk. Population at risk (rural workers) and rodent host diversity also had a positive effect on disease risk. Conclusions: Land use chang...

Nature Ecology & Evolution, 2019

How are ecological systems assembled? Identifying common structural patterns within complex netwo... more How are ecological systems assembled? Identifying common structural patterns within complex networks of interacting species has been a major challenge in ecology, but researchers have focused primarily on single interaction types aggregating in space or time. Here, we shed light on the assembly rules of a multilayer network formed by frugivory and nectarivory interactions between bats and plants in the Neotropics. By harnessing a conceptual framework known as the integrative hypothesis of specialization, our results suggest that phylogenetic constraints separate species into different layers and shape the network's modules. Then, the network shifts to a nested structure within its modules where interactions are mainly structured by geographic co-occurrence. Finally, organismal traits related to consuming fruits or nectar determine which bat species are central or peripheral to the network. Our results provide insights into how different processes contribute to the assemblage of ecological systems at different levels of organization, resulting in a compound network topology.

PLOS Neglected Tropical Diseases, 2019

Several viruses from the genus Orthohantavirus are known to cause lethal disease in humans. Sigmo... more Several viruses from the genus Orthohantavirus are known to cause lethal disease in humans. Sigmodontinae rodents are the main hosts responsible for hantavirus transmission in the tropical forests, savannas, and wetlands of South America. These rodents can shed different hantaviruses, such as the lethal and emerging Araraquara orthohantavirus. Factors that drive variation in host populations may influence hantavirus transmission dynamics within and between populations. Landscape structure, and particularly areas with a predominance of agricultural land and forest remnants, is expected to influence the proportion of hantavirus rodent hosts in the Atlantic Forest rodent community. Here, we tested this using 283 Atlantic Forest rodent capture records and geographically weighted models that allow us to test if predictors vary spatially. We also assessed the correspondence between proportions of hantavirus hosts in rodent communities and a human vulnerability to hantavirus infection index across the entire Atlantic Forest biome. We found that hantavirus host proportions were more positively influenced by landscape diversity than by a particular habitat or agricultural matrix type. Local small mammal diversity also positively influenced known pathogenic hantavirus host proportions, indicating that a plasticity to habitat quality may be more important for these hosts than competition with native forest dwelling species. We found a consistent positive effect of sugarcane and tree plantation on the proportion of rodent hosts, whereas defaunation intensity did not correlate with the proportion of hosts of potentially pathogenic hantavirus genotypes in the community, indicating that non-defaunated areas can also be hotspots for hantavirus disease outbreaks. The spatial match between host hotspots and human disease vulnerability was 17%, while coldspots matched 20%. Overall, we discovered strong spatial and land use change influences on hantavirus hosts at the landscape level across the Atlantic Forest. Our findings suggest disease surveillance must be reinforced in the southern and southeastern regions of the biome where the highest predicted hantavirus host proportion and levels of vulnerability spatially match.

Introductory paragraphHow are ecological systems assembled? Here, we aim to contribute to answeri... more Introductory paragraphHow are ecological systems assembled? Here, we aim to contribute to answering this question by harnessing the framework of a novel integrative hypothesis. We shed light on the assembly rules of a multilayer network formed by frugivory and nectarivory interactions between bats and plants in the Neotropics. Our results suggest that, at a large scale, phylogenetic trade-offs separate species into different layers and modules. At an intermediate scale, the modules are also shaped by geographic trade-offs. And at a small scale, the network shifts to a nested structure within its modules, probably as a consequence of resource breadth processes. Finally, once the topology of the network is shaped, morphological traits related to consuming fruits or nectar determine which species are central or peripheral. Our results help understand how different processes contribute to the assemblage of ecological systems at different scales, resulting in a compound topology.

Oecologia Australis, 2018

A delimitação geográfica de um bioma engloba questões que envolvem fatores ambientais, como clima... more A delimitação geográfica de um bioma engloba questões que envolvem fatores ambientais, como clima e características da vegetação, além de aspectos políticos. Consequentemente, variações na delimitação de um bioma são recorrentes. A Mata Atlântica é um dos mais importantes hotspots de biodiversidade do mundo e historicamente diversas delimitações territoriais foram propostas para esse bioma. Aqui tivemos como objetivo 1) discutir as quatro principais delimitações e 2) com base nos limites existentes, discutir sua união (Limite Integrativo) e intersecção (Limite Consensual). Os principais limites apresentam áreas consensuais e integrativas de 1,01 e 1,62 milhão km 2 , respectivamente. Cinco regiões de divergência devem ser cuidadosamente avaliadas. Finalmente, sugerimos um debate sobre o uso de limites em estudos ecológicos e sua aplicação em estudos sobre conservação da biodiversidade. Palavras-chave: biogeografia histórica; bioma; distribuição geográfica; floresta tropical; hotspot de biodiversidade. A NOTE ON THE TERRITORIAL LIMITS OF THE ATLANTIC FOREST. The geographic delimitation of a biome encompasses questions that involve environmental factors such as climate and vegetation characteristics as well as political aspects. Consequently, variation on biome delimitation is recurrent. The Atlantic Forest is one of the most important biodiversity hotspots in the world, and historically several territorial delimitations have been proposed for this biome. Here we aim to 1) discuss the four main delimitations and 2) based on the existing limits, discuss their union (Integrative limit) and intersection (Consensual limit). The main limits present consensual and integrative areas of 1.01 and 1.62 million km 2 , respectively. Five regions of divergence must be carefully evaluated. Finally, we suggest a debate about the use of limits in ecological studies and their application in biodiversity conservation studies.

Ecology, 2019

Scientists have long been trying to understand why the Neotropical region holds the highest diver... more Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820–2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities

PLOS Neglected Tropical Diseases, 2018

After obtaining certification of the absence of transmission of the Trypanosoma cruzi by Triatoma... more After obtaining certification of the absence of transmission of the Trypanosoma cruzi by Triatoma infestans in 2006, other native species of protozoan vectors have been found in human dwellings within municipalities of the State of Paraná , Southern Brazil. However, the spatial distribution of T. cruzi vectors and how climatic and landscape combined variables explain the distribution are still poorly understood. The goal of this study was to predict the potential distribution of T. cruzi vectors as a proxy for Chagas disease transmission risk using Ecological Niche Models (ENMs) based on climatic and landscape variables. We hypothesize that ENM based on both climate and landscape variables are more powerful than climate-only or landscape-only models, and that this will be true independent of vector species. A total of 2,662 records of triatomines of five species were obtained by community-based entomological surveillance from 2007 to 2013. The species with the highest number of specimens was Panstrongylus megistus (73%; n = 1,943), followed by Panstrongylus geniculatus (15.4%; 411), Rhodnius neglectus (6.0%; 159), Triatoma sordida (4.5%; 119) and Rhodnius prolixus (1.1%; 30). Of the total, 71.9% were captured at the intradomicile. T. cruzi infection was observed in 19.7% of the 2,472 examined insects. ENMs were generated based on selected climate and landscape variables with 1 km 2 spatial resolution. Zonal statistics were used for classifying the municipalities as to the risk of occurrence of synanthropic triatomines. The integrated analysis of the climate and landscape suitability on triatomines geographical distribution was powerful on generating good predictive models. Moreover, this showed that some municipalities in the northwest, north and northeast of the Paraná state have a higher risk of T. cruzi vector transmission. This occurs because those regions present high climatic and landscape suitability values for occurrence of their vectors. The frequent invasion of houses by infected triatomines clearly indicates a greater risk of transmission of T. cruzi to the inhabitants. More public health attention should be given in the northern areas of the State of

Biological Conservation, 2018

Habitat fragmentation threatens tropical rainforests, which can significantly hinder dispersal in... more Habitat fragmentation threatens tropical rainforests, which can significantly hinder dispersal in species such as arboreal primates. For conservation actions to be effective there must be an understanding of how landscape structure and biological traits shape dispersal. We assessed the effects of landscape, sex and population management (reintroductions and translocations) on gene flow of Leontopithecus rosalia, an endangered arboreal primate living in highly fragmented forests of Brazil. We genotyped 201 individuals using 14 microsatellite loci to answer three questions: (1) How far does L. rosalia disperse? (2) Is dispersal sex-biased? (3) What are the relative contributions of population management, distance, roads and landscape resistance to genetic kinship? We hypothesized that (1) gene flow decrease between more distant sites; (2) males disperse more than females; and (3) management and land-cover resistance (i.e. landscape resistance) are the variables that most influence genetic kinship. We found positive spatial population-structure up to 8 km. The spatial structure was similar between females and males suggesting that they equally contribute to gene flow. Management and landscape resistance best explained genetic kinship, showing that different land-cover types affect the dispersal at different degrees of landscape permeability. We advocate that maintaining more permeable landscapes is essential to ensure dispersal and gene flow of arboreal mammals. Conservation measures in tropical rainforests must take into account not only the habitat amount, but also the degree at which each land useroads, urban areas, agriculture, pasture, isolated trees, and stepping stonesfacilitates or impedes the species dispersal.

Scientific reports, Jan 13, 2018

Bats (Order: Chiroptera) harbor a high diversity of emerging pathogens presumably because their a... more Bats (Order: Chiroptera) harbor a high diversity of emerging pathogens presumably because their ability to fly and social behavior favor the maintenance, evolution, and dissemination of these pathogens. Until 2012, there was only one report of the presence of Hantavirus in bats. Historically, it was thought that these viruses were harbored primarily by rodent and insectivore small mammals. Recently, new species of hantaviruses have been identified in bats from Africa and Asia continents expanding the potential reservoirs and range of these viruses. To assess the potential of Neotropical bats as hosts for hantaviruses and its transmission dynamics in nature, we tested 53 bats for active hantaviral infection from specimens collected in Southeastern Brazil. Part of the hantaviral S segment was amplified from the frugivorous Carollia perspicillata and the common vampire bat Desmodus rotundus. DNA sequencing showed high similarity with the genome of Araraquara orthohantavirus (ARQV), whi...

Primeiro release oficial deste tutorial, incluindo um novo passo-a-passo em RMarkDown.

This is the first version of the NeoBat Interactions data paper supplement.

First release of the repo.

Neurotrauma Reports, 2021

Philosophical Transactions of the Royal Society B: Biological Sciences, 2021

Diversity and Distributions, 2019

Viruses, 2019

Nature Ecology & Evolution, 2019

PLOS Neglected Tropical Diseases, 2019

Oecologia Australis, 2018

Ecology, 2019

PLOS Neglected Tropical Diseases, 2018

Biological Conservation, 2018

Scientific reports, Jan 13, 2018

Este trabalho propôs contribuir com o conhecimento da relação serrapilheira-solo e macroinvertebr... more Este trabalho propôs contribuir com o conhecimento da relação serrapilheira-solo e macroinvertebrados, em microambientes criados por troncos caídos de um bosque de Pinus spp. A decomposição do material orgânico proporciona a liberação dos seus minerais constituintes para uma posterior absorção pelas raízes das plantas. A importância deste ciclo de nutrientes é fundamental para a sustentabilidade de ambientes, como serrapilheira e fauna associada. O objetivo deste trabalho foi o de comparar as comunidades encontradas em troncos caídos em diferentes habitats, e avaliar a resistência e a resiliência destas comunidades de acordo com sua estrutura. O trabalho foi realizado numa área de sub-bosque de Pinus spp na UFSCar. Três coletas foram feitas, a cada sete dias, em seis pontos, sendo três no Interior do sub-bosque e três pontos na Margem, entre o reservatório do Monjolinho e o interior do bosque. As amostras foram obtidas embaixo de troncos caídos e delimitadas por um quadrante e, então, medidas temperatura e umidade. Os macroinvertebrados foram identificados até o nível de Ordem. Foram encontradas 15 ordens, sendo Isopoda a mais representativa. Os demais grupos foram encontrados em menor representatividade, como Solifugae, Opiliones, Lumbricidae, Turbellaria entre outros. Este padrão, com grandes números de táxons raros, refletiu-se num modelo de abundância que segue a série logarítmica, tanto para as comunidades de margem (P=0,963) quanto para as de interior (P=0,882). Neste modelo, a colonização ocorre em intervalos aleatórios de tempo, poucos fatores dominam a ecologia das comunidades e há muitas espécies dominantes e muitas raras. As diferenças em composição entre margem e interior não foram significativas. Uma explicação para isso seria de que nossas definições de Margem e Interior foram arbitrárias e Margem e Interior constituem ambientes similares em relação às variáveis estudadas. Uma explicação alternativa pode ser o baixo número amostral. As comunidades originais não conseguem se restabelecer em uma semana, porém, em quatro troncos as similaridades entre a primeira coleta e a terceira são maiores do que entre primeira coleta e a segunda. Este padrão indica que as comunidades estudadas podem estar em estágio inicial de sucessão, com forte dominância de decompositores e predadores. Troncos caídos de Pinus spp abrigam comunidades de macroinvertebrados diversas, aparentemente estruturadas por poucos fatores proporcionados pelos recursos disponibilizados por estes troncos. Tais comunidades apresentam pouca variação espacial na escala estudada e parecem recompor-se após 15 dias, sugerindo alta resiliência. Desta forma, tais recursos parecem ser importantes para a manutenção da diversidade de macroinvertebrados no chão da floresta, contribuindo para o funcionamento destes ecossistemas através da decomposição de matéria orgânica.

Este roteiro tem por finalidade apresentar noções básicas de como se calcular métricas de paisage... more Este roteiro tem por finalidade apresentar noções básicas de como se calcular métricas de paisagens, considerando formatos vetoriais e/ou matriciais. As instruções foram preparadas para a versão 10.x do ArcGIS (pode funcionar também em versões anteriores). Na prática são utilizadas três extensões. Duas delas tiveram o desenvolvimento coordenado pela equipe do Prof. Rob Rempel (Patch Analyst e Patch Grid Analyst), e terceira é de responsabilidade do Prof. Stefan Lang (V-LATE

Este roteiro tem por finalidade apresentar noções básicas de como se calcular métricas de paisage... more Este roteiro tem por finalidade apresentar noções básicas de como se calcular métricas de paisagens, considerando formatos vetoriais e matriciais. As instruções foram preparadas para a versões 10.x do ArcGIS (pode funcionar também em versões anteriores). São utilizadas três extensões. Duas delas tiveram o desenvolvimento coordenado pela equipe do Prof. Rob Rempel (Patch Analyst e Patch Grid Analyst), e terceira é de responsabilidade do Prof. Stefan Lang (V-LATE = Vector Based Landscape Analysis Tools Extension).