Pensoft’s ARPHA Publishing Platform integrates with OA Switchboard to streamline reporting to funders of open research

By the time authors open their inboxes to the message their work is online, a similar notification will have also reached their research funder.

Image credit: OA Switchboard.

By the time authors – who have acknowledged third-party financial support in their research papers submitted to a journal using the Pensoft-developed publishing platform: ARPHA – open their inboxes to the congratulatory message that their work has just been published and made available to the wide world, a similar notification will have also reached their research funder.

This automated workflow is already in effect at all journals (co-)published by Pensoft and those published under their own imprint on the ARPHA Platform, as a result of the new partnership with the OA Switchboard: a community-driven initiative with the mission to serve as a central information exchange hub between stakeholders about open access publications, while making things simpler for everyone involved.

All the submitting author needs to do to ensure that their research funder receives a notification about the publication is to select the supporting agency or the scientific project (e.g. a project supported by Horizon Europe) in the manuscript submission form, using a handy drop-down menu. In either case, the message will be sent to the funding body as soon as the paper is published in the respective journal.

“At Pensoft, we are delighted to announce our integration with the OA Switchboard, as this workflow is yet another excellent practice in scholarly publishing that supports transparency in research. Needless to say, funding and financing are cornerstones in scientific work and scholarship, so it is equally important to ensure funding bodies are provided with full, prompt and convenient reports about their own input.”

comments Prof Lyubomir Penev, CEO and founder of Pensoft and ARPHA.

 

“Research funders are one of the three key stakeholder groups in OA Switchboard and are represented in our founding partners. They seek support in demonstrating the extent and impact of their research funding and delivering on their commitment to OA. It is great to see Pensoft has started their integration with OA Switchboard with a focus on this specific group, fulfilling an important need,”

adds Yvonne Campfens, Executive Director of the OA Switchboard.

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About the OA Switchboard:

A global not-for-profit and independent intermediary established in 2020, the OA Switchboard provides a central hub for research funders, institutions and publishers to exchange OA-related publication-level information. Connecting parties and systems, and streamlining communication and the neutral exchange of metadata, the OA Switchboard provides direct, indirect and community benefits: simplicity and transparency, collaboration and interoperability, and efficiency and cost-effectiveness.

About Pensoft:

Pensoft is an independent academic publishing company, well known worldwide for its novel cutting-edge publishing tools, workflows and methods for text and data publishing of journals, books and conference materials.

All journals (co-)published by Pensoft are hosted on Pensoft’s full-featured ARPHA Publishing Platform and published in a way that ensures their content is as FAIR as possible, meaning that it is effortlessly readable, discoverable, harvestable, citable and reusable by both humans and machines.

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Linking FAIR biodiversity data, NEW article collection in BDJ

Supported by the EU-funded Biodiversity Community Integrated Knowledge Library (BiCIKL) project, the collection at Biodiversity Data Journal will provide APC waivers for up to 100 publications

A new article collection, dedicated to linked FAIR biodiversity data was announced by the EU-funded Biodiversity Community Integrated Knowledge Library (BiCIKL) project.

The BiCIKL project is dedicated to building new communities of key research infrastructures, researchers, citizen scientists and other stakeholders by using linked and FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing and identification of taxa, to final publication in advanced, human- and machine-readable, reusable scholarly articles.

Supported by BiCIKL, the upcoming collection at BDJ will provide an exciting opportunity for biodiversity researchers to enjoy free and technologically advanced publication for up to 100 scholarly articles.

The collection will welcome research articles, data papers, software descriptions, and methodological/theoretical papers that demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.

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The journal is still looking for guest editors to join the core team. If you are interested, please let us know at bdj@pensoft.net.

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In this collection, the authors will need to ensure that their narratives comply with the community-agreed standards for terms, ontologies and vocabularies. Additionally, they will be required to use explicit persistent identifiers, where such are available. 

Here are several examples of research questions concerning semantically enriched biodiversity data: 

  1. How linking taxa or OTUs to external data in my study will contribute to a better understanding of the functions and regional/local processes within faunas/floras/mycotas or biotic communities?
  2. How mine and other researchers’ data and narratives (e.g. specimen records, sequences, traits, biotic interactions etc.) can be re-used to support more extensive and data-rich studies? 
  3. How to streamline taxon descriptions and inventories, including such based on genomic and barcoding data? 
  4. How general conclusions, assertions and citations in my article can be expressed in a formal, machine-actionable language? 
  5. Other taxon- or topic-specific research questions that would benefit from richer, semantically enhanced FAIR data.

Conditions for publication and types of articles:

  • Manuscripts must use data from at least two of the BiCIKL’s partnering research infrastructures. Highly welcome are also submissions that include data from research infrastructures that are not part of BiCIKL.
  • Taxonomic papers (e.g. descriptions of new species) must contain persistent identifiers for the holotype, paratypes and the majority of the specimens used in the study.
  • New species descriptions using data associated with a particular Barcode Identification Number (BIN) imported directly from BOLD via the ARPHA Writing Tool are encouraged.
  • Individual specimen records imported directly from BOLD, GBIF or iDigBio into the manuscript are strongly encouraged.
  • Hyperlinked in-text citations of taxon treatments from Plazi’s TreatmentBank are highly welcome.
  • Other terms of value hyperlinked to external resources are encouraged.
  • Tables that list gene accession numbers, specimens and taxon names, should conform to the Biodiversity Data Journal’s guidelines.
  • Theoretical or methodological papers on linking of FAIR biodiversity data are eligible for the BiCIKL collection if they provide examples and use cases.
  • Data papers or software descriptions are eligible if they use data from the BiCIKL’s partnering research infrastructures, or describe tools and services that facilitate access to and linking between FAIR biodiversity data.


You can find full information about the eligibility criteria in the Open Call published on the BiCIKL’s website, or can contact us at bdj@pensloft.net.

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Threatened South American coati found roaming in a large city

Researchers recorded an individual at the Canoas Airbase, one of the last remaining green spaces in a densely urbanized area of a large city in southern Brazil.

You may assume that metropolitan areas are devoid of wildlife, but that is very far from the truth. The remaining green spaces within the urban matrices of large cities can serve as corridors or stepping stones for wild animals. Sometimes, even threatened mammal species end up using them.

On August 12, 2020, a research team from Brazil recorded a South American coati in Canoas, the fourth most populous and densely urbanized city in the southernmost state of Brazil, Rio Grande do Sul. The animal was detected with a camera trap during a Masters research project conducted at the Canoas Airbase, one of the last green spaces remaining in the municipality.

South American Coati at the Canoas airbase in Rio Grande do Sul, Brazil. Video by Diego Floriano da Rocha, Thaís Brauner do Rosario and Cristina Vargas Cademartori

Widely distributed throughout the continent, the South American coati is a medium-sized carnivore living on trees and feeding mainly on small invertebrates and fruits. The species is classified as Vulnerable in Rio Grande do Sul, and it’s considered threatened mainly because of the loss of its forest habitats.

The study that recorded an individual in the urban area was conducted as part of a partnership between the Canoas Airbase and La Salle University. Led by Dr Cristina Vargas Cademartori from La Salle University, the research team was made up of Diego Floriano da Rocha (Doctoral student), Thaís Brauner do Rosario (Masters student), Ana Carolina Pontes Maciel (biologist at the Canoas Airbase), and Duana Suelem Alves (undergraduate student). They described in detail the record and the study area in a paper in the open-access journal Neotropical Biology and Conservation.

The researchers were surprised to find the coati in the midst of a dense urban area. Although the species is not considered threatened in the majority of its area of distribution, its populations have been in decline because of habitat loss and hunting.

“This record confirms the capacity of this species to use environments that have been changed by anthropic activity,” the researchers write in their paper, adding that, because of all the food that humans leave behind, urban environments can in fact favor the establishment of more adaptable species like the coati.

The discovery highlights the importance of urban green spaces for wildlife conservation. “This is very important for defining appropriate conservation measurements for endangered species, especially beyond protected areas,” the authors conclude.

Research article:
da Rocha DF, do Rosario TB, Maciel ACP, Alves DS, Cademartori CV (2022) Record of occurrence of Nasua nasua (Linnaeus, 1766) (Carnivora, Procyonidae) in a densely urbanized area of the city of Canoas, southern Brazil. Neotropical Biology and Conservation 17(2): 111-116. https://doi.org/10.3897/neotropical.17.e81824

In the Atlantic Forest, the lowland tapir is at risk of extinction

Lowland tapir populations in the Atlantic Forest in South America are at risk of almost complete disappearance, scientists have estimated. The main long-term threat to their well-being is population isolation, as hunting and highways keep populations away from each other. Urgent measures need to be taken to connect isolated populations and ensure the long-term conservation of tapirs, warn the authors of a new study published in the open-access journal Neotropical Biology and Conservation.

Lowland tapir populations in the Atlantic Forest in South America are at risk of almost complete disappearance, scientists have estimated. Weighing up to 250 kg, the animal can adapt to most habitats in South America—but its populations continue to decline across its range.

Today, its survival is seriously threatened: it can be found in just 1.78% of its original distributional range in the Atlantic Forest biome, which covers parts of Brazil, Argentina and Paraguay. The main long-term threat to its well-being is population isolation, as hunting and highways keep populations away from each other.

Lowland tapir. Photo by Patricia Medici

Urgent measures need to be taken to connect isolated populations and ensure the long-term conservation of tapirs, warn the authors of a new study on the distribution and conservation status of lowland tapirsin the South American Atlantic Forest, published in the open-access journal Neotropical Biology and Conservation

The research was done by Kevin Flesher, PhD, researcher at the Biodiversity Study Center, Michelin Ecological Reserve, Bahia, and Patrícia Medici, PhD, coordinator of the Lowland Tapir Conservation Initiative, a project developed by the Institute for Ecological Research in Brazil, and chair of the Tapir Specialist Group at the Species Survival Commission in the International Union for Conservation of Nature.

 “Of the 48 tapir populations identified during the study, between 31.3% and 68.8% are demographically unviable (low number of individuals), and between 70.8% and 93.8% of the populations are genetically unviable (low gene flow). Only 3-14 populations are still viable in the long run when both criteria are considered. The evidence suggests that with the appropriate conservation actions, the lowland tapir could be broadly distributed throughout the Atlantic Forest,” says Kevin Flesher. 

Lowland tapir. Photo by Alexander Blanco

“Tapirs have low reproductive potential, including a long reproductive cycle with the birth of just one young after a gestation period of 13-14 months and intervals of up to three years between births. Our populational simulations clearly show how, in the case of small populations, even the loss of a single individual per year can result in rapid extinction of an entire local population,” adds Medici. 

Lowland tapir. Photo by Bill Konstant

Kevin Flesher dedicated 15 years to visiting 93 reserves in the Atlantic Forest, talking to people and analyzing 217 datasets, before he compiled the necessary data to design conservation actions that can ensure the survival of tapirs in the area. 

The states of São Paulo and Paraná in Brazil have the largest number of remaining populations: 14 and 10, respectively. The two largest populations are in Misiones, Argentina, and in the neighboring Iguaçu and Turvo reserves, in Paraná and Rio Grande do Sul, Brazil.

“As far as our knowledge goes, there is no evidence of movement of tapirs between these populations,” points out Medici.

The distance between population fragments, however, is not what is stopping them.

“The central problem is the multiple threats they face while crossing the habitat,” explains Flesher. Highways are one major obstacle that limits the access of tapirs to forests with adequate habitat. “For example, the heavy traffic on highway BR-101 (which cuts the Brazilian Atlantic Forest from North to South) is a death trap to wildlife. Tapirs often die when attempting to cross it,” explains Medici. 

The construction of highways and expansion of traffic in and around natural areas is a serious threat to large tapir populations that might otherwise have the chance to thrive, like those in Misiones, Argentina, and Serra do Mar, Brazil. 

“Roadkill is a significant cause of death in six of the eight reservations in which highways cross tapir populations, and the expansion of the roadway grid in the country threatens to cause population fragmentation in at least four populations,” points out Flesher. This is why finding ways to allow tapirs to cross highways safely is an urgent conservation priority.

Lowland tapir. Photo by Patricia Medici

The results of the study, however, give cause for “cautious optimism” for the future of tapirs in the area: after decades of dedicated conservation efforts, the situation is starting to improve. 

“Despite these continuing challenges for tapir conservation, most populations appear to be stable or increasing and the conservation outlook for the species is better than several decades ago, when the first efforts to protect the species began,” Kevin Flesher concludes.

Research article:

Flesher KM, Medici EP (2022) The distribution and conservation status of Tapirus terrestris in the South American Atlantic Forest. Neotropical Biology and Conservation 17(1): 1-19. https://doi.org/10.3897/neotropical.17.e71867

Man’s best friend could be a jaguar’s next meal: A case study from the Mexican Caribbean

Events of jaguars predating on and attacking dogs are poorly documented throughout the Americas. Researchers from Mexico and Germany report in detail jaguar attacks on 20 dogs at a tourist site in the Mexican Caribbean. In addition, they describe an initiative proposed by locals as well as national and international NGOs to prevent human-jaguar conflicts due to pet predation. The study was published in the open-access journal Neotropical Biology and Conservation.

Mahahual is a small fishing village in the Mexican Caribbean that receives a large number of tourists every year. Over the past 15 years, its population has increased rapidly, and, as a result, people have started to settle in areas away from the main center of the village, sometimes encroaching on jaguar habitats. As most of those people keep guard dogs on their properties, jaguars have taken advantage of this situation by wandering near people’s houses at night, and sometimes those dogs end up as a night-time snack for the big cats.

A jaguar is photographed wandering around houses looking for dogs. Photo by Víctor Rosales

Unlike jaguar attacks on livestock, attacks and predation on other domestic species such as dogs have only been documented anecdotally (through interviews or from remains found in faeces). Such attacks can indeed lead to pet predation conflict, which can ultimately have a negative impact on the jaguar populations. Attachment to pets may lead humans to start killing the big cats, which is of particular concern for an endangered species like the jaguar. Furthermore, it is possible that a wide range of pathogens may be transmitted from dogs to jaguars, further threatening the health of jaguar populations in Mahahual.

A dog injured as a result of a jaguar attack in Mahahual, Quintana Roo, Mexico. Photo by Víctor Rosales

This is why a multidisciplinary team made up of veterinarians, conservationists, locals, NGOs (Aak Mahahual A.C. and International Fund for Animal Welfare (IFAW)) and researchers (El Colegio de la Frontera Sur and Universidad Tecnológica de Calakmul), led by Dr Jonathan Pérez Flores, began investigating the occurrence of jaguar predation and attacks on dogs at the Mexican Caribbean tourist site from almost 10 years ago. Their research was just published in the open-access journal Neotropical Biology and Conservation.

According to their report, the behaviour of Mahahual’s jaguars resembles that of Indian leopards, which have already turned dogs into an important component of their diet, preferring them over livestock. Jaguars and leopards usually attack from a blindside, biting the dogs on the neck or head to avoid counterattacks. Similarly to leopards, jaguars attack at night and kill more dogs during the dry season. This is likely due to the fact that it’s easier for jaguars to hunt dogs than their natural prey: armadillo, lowland paca, brocket deer, white-tailed deer. Furthermore, the latter are less available during the dry season.

One of the night houses built by the people of Mahahual, Aak Mahahual A.C. and International Fund for Animal Welfare (IFAW). Photo by Francisco Rubén Castañeda

In 2017, the people of Mahahual partnered with Aak Mahahual A.C. and IFAW to build protective night houses made of wood and wire mesh meant to keep dogs safe at night. So far, they’ve built 38 such houses to prevent jaguar attacks. Sterilisation and vaccination campaigns have also been intensified since late 2020 to prevent the transmission of diseases between the two species.

Thanks to this study, we now have a better understanding of the adaptability and persistence of jaguars in human-dominated landscapes and the impact of dog predation by jaguars. However, the authors call for more research in the area to help paint the full picture.

Research article:
Carral-García M, Buenrostro I, Weissenberger H, Rosales V, Pérez-Flores J (2021) Dog predation by jaguars in a tourist town on the Mexican Caribbean. Neotropical Biology and Conservation 16(4): 461-474. https://doi.org/10.3897/neotropical.16.e68973

Vibes before it bites: 10 types of defensive behaviour for the False Coral Snake

The False Coral Snake (Oxyrhopus rhombifer) may be capable of recognising various threat levels and demonstrates ten different defensive behaviours, seven of which are registered for the first time for the species. Scientists from the Federal University of Viçosa (Brazil) published their laboratory observation results based on a juvenile specimen in the open-access journal Neotropical Biology and Conservation.

In a recent paper in the open-access journal Neotropical Biology and Conservation, a group of Brazilian scientists from the Federal University of Viçosa (Brazil) published ten different defensive behaviours for the False Coral Snake (Oxyrhopus rhombifer), seven of which are registered for the first time for the species. One of these is reported for the first time for Brazilian snakes.

Evolution shaped anti-predator mechanisms in preys, which can be displayed either with avoidance or defensive behaviours. The current knowledge about such mechanisms are still scarce for many snake species, but it is constantly increasing over the last years. These data are helpful for better understanding of the species ecology, biology and evolution.

The False Coral Snake (O. rhombifer) is a terrestrial snake species with a colouration like the true coral snake . The species has a wide geographic distribution, occurring in Argentina, Paraguay, Uruguay, Bolivia and all Brazilian biomes. Among its previously known anti-predator mechanisms, this species has already shown cloacal discharge, body flattening, struggling, erratic movements and hiding the head.

However, these behaviors were only a small part of what this species is capable of doing to defend itself! In November 2017, a juvenile male  captured in the Atlantic Forest of southeastern Brazil was observed under laboratory settings, where the scientists would simulate a predation attempt with an increasing threat level.

We released the snake on to the laboratory bench and let it notice our presence. The animal remained motionless at first, then performed a pronounced dorsoventral flattening of the anterior part of the body, raised its tail, adopted an S-shaped posture, raised the first third of the body and performed brief body vibrations. Then we approached the snake, which remained with the same posture and body vibrations. When we touched the animal (not handling), it remained with the S-shaped posture, keeping the first third of the body elevated and the dorsoventral flattening (however, less accentuated) and started to display erratic movements, false strikes and locomotor escape. When handled, the snake only struggled,

shares the lead scientist Mr. Clodoaldo Lopes de Assis.

Amongst ten recorded behaviour types only three were among those already registered for this species. Since defensive responses in snakes decrease as body size increases, juveniles exhibit a broader set of defensive behaviour than adults. Because of that, some types of behaviour described in this study might be explained either by physical constraints or stage of development of the individual.

Some types of behaviour resemble the ones of true coral snakes of the genus Micrurus, a group of extremely venomous snakes. Thus, this similarity may be linked with the mimicry hypothesis between these two groups, where harmless false coral snakes take advantage of their similar appearance to the true coral snakes to defend themselves.

Another type of anti-predation mechanism shown — body vibrations — is yet an unknown behaviour for Brazilian snakes and has been recorded for the first time. This type of behaviour is difficult to interpret, but could represent a defensive signal against non-visually orientated predators.

Finally, defensive strategies of the specimen differed according to the threat level imposed: starting from discouraging behaviour up to false bites, erratic movements and locomotor escape.


Some defensive types of behaviour displayed by the juvenile Oxyrhopus rhombifer
Credit: Mr. Clodoaldo Lopes de Assis
License: CC-BY 4.0

O. rhombifer may be capable of recognising different threat levels imposed by predators and adjusting its defensive behaviour accordingly,

highlights Mr. Clodoaldo Lopes de Assis.

Through such simple laboratory observations we can get a sense of how Brazilian snakes are yet poorly known regarding their natural history, where even common species like the false coral snake O. rhombifer can surprise us!

Mr. Clodoaldo Lopes de Assis adds in conclusion.

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Original source:
Lopes de Assis C, José Magalhães Guedes J, Miriam Gomes de Jesus L, Neves Feio R (2020) New defensive behaviour of the false coral snake Oxyrhopus rhombifer Duméril, Bibron & Duméril, 1854 (Serpentes, Dipsadidae) in south-eastern Brazil. Neotropical Biology and Conservation 15(1): 71-76. https://doi.org/10.3897/neotropical.15.e48564

Pensoft welcomes Neotropical Biology & Conservation to its open-access journal portfolio

Eleven studies in the first issue demonstrate the modernized look & feel of the Brazil-born journal, as provided by the scholarly publishing platform ARPHA

Launched by the Brazilian university Unisinos (Universidade do Vale do Rio dos Sinos) in 2006, the open-access, peer-reviewed Neotropical Biology & Conservation moves to the journal family of scholarly publisher and technology provider Pensoft.

Neotropical Biology & Conservation welcomes research and review articles, short communications and commentaries on the biology and behaviour of organisms from the tropical ecoregions of the Americas and the entire South America. Special emphasis is given to papers that demonstrate the application of conservation principles for natural resource management and policy. Manuscripts can be published in Portuguese, as well as English, where an English-language abstract is mandatory.

The journal is published three times a year, with the first 2019 issue already available on the new website. New research papers, part of the second issue, will be out next Monday (15th July).

New website for Neotropical Biology & Conservation

Beyond Neotropical Biology & Conservation‘s new glossy and user-friendly appearance, the Pensoft-developed scholarly platform ARPHA provides its signature fast-track, end-to-end publishing system to the benefit of its users: authors, reviewers and editors alike. Thereby, each submitted manuscript is carried through the review, editing, publication, dissemination and archiving stages without leaving ARPHA’s collaboration-centred online environment. The articles are available in PDF and machine-readable XML formats, so that they are easy to discover, access, cite and reuse.

Editor-in-Chief of Neotropical Biology & Conservation Dr Ana Maria Leal-Zanchet, says:

“It’s an honour for the Editorial board of Neotropical Biology & Conservation that the journal becomes a member of the Pensoft/ARPHA team. This journal was born as Acta Biologica Leopoldensia, which was published by Unisinos between 1979 and 2005. Since 2006 Neotropical Biology & Conservation continued the tradition of this former journal, publishing articles from all around Brazil, and even enhancing its coverage to other parts of the Neotropics. In recent years, the scientific community that uses our journal as a venue to disseminate their research results has been continuously increasing. We maintain our commitment to disseminate scientific findings through open access and to continue pursuing a sustainable international growth. I am sure that the user-friendly ARPHA’s publishing system and the great support of the Pensoft team will please authors, reviewers and the Editorial board of the journal, enhancing the efficiency, quality and swiftness of publishing, as well as the international visibility of Neotropical Biology & Conservation.”

ARPHA’s and Pensoft’s founder and CEO Prof Lyubomir Penev says:

“I’m delighted to welcome Neotropical Biology & Conservation to the Pensoft/ARPHA family, where the journal not only feels at home amongst predominantly biodiversity-themed titles, but also comes to complement another two Brazil-born journals: Check List, which publishes biogeographical data, especially for the use of biodiversity conservation, and Zoologia: mostly focusing on systematics, evolution and taxonomy in the field of Zoology. With this kind of background and the constantly expanding high-tech functions of ARPHA, I’m certain that we are fully equipped to build on the image and success of Neotropical Biology & Conservation.”

What’s on in the first issue?

Amongst the 11 articles in the first issue of Neotropical Biology & Conservation, there is the study by Dr Lucas Porto (Federal University of Rio Grande do Sul) and Dr Ana Maria Rui (Universidade Federal de Pelotas), which observes Crab-eating and Pampas foxes in southern Brazil for a year to compare the diets and habitat uses of the two sympatric species. Curiously, the canids demonstrated a high overlap of their diets at all times, with the exception of autumn.

Another paper, authored by a research team from the Federal Institute of Education, Science and Technology of Goiano and the Federal University of Goiás, describes the frequency, occurrence status and activity period of the most common medium- and large-sized mammals living in the world’s most biodiverse savanna: Brazil’s Cerrado. Namely, subjects of the study were the Giant anteater, Nine-banded armadillo, South American tapir, Crab-eating fox and Lowland paca, where the largest species were found to have the greatest variation in time period of activity.

A collaborative work at the Federal University of PernambucoUniversity of Brasília and the Rural Federal University of Pernambuco, reports important observations of the unexpectedly diverse bat fauna in an urban environment located in the Atlantic Forest, northeastern Brazil. Between May 2006 and April 2007, the researchers captured 950 bats identified to 16 species and five families.

The first 2019 issue of Neotropical Biology and Conservation.

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