Towards automated long-term acoustic monitoring of endangered river dolphins: a case study in the Brazilian Amazon floodplains.

Using passive acoustic monitoring (PAM) and convolutional neural networks (CNN), we monitored the movements of the two endangered Amazon River dolphin species, the boto (Inia geoffrensis) and the tucuxi (Sotalia fluviatilis) from main rivers to floodplain habitats (várzea) in the Mamirauá Reserve (Amazonas, Brazil). We detected dolphin presence in four main areas based on the classification of their echolocation clicks. Using the same method, we automatically detected boat passages to estimate a possible interaction between boat and dolphin presence. Performance of the CNN classifier was high with an average precision of 0.95 and 0.92 for echolocation clicks and boats, respectively. Peaks of acoustic activity were detected synchronously at the river entrance and channel, corresponding to dolphins seasonally entering the várzea. Additionally, the river dolphins were regularly detected inside the flooded forest, suggesting a wide dispersion of their populations inside this large area, traditionally understudied and particularly important for boto females and calves. Boats overlapped with dolphin presence 9% of the time. PAM and recent advances in classification methods bring a new insight of the river dolphins' use of várzea habitats, which will contribute to conservation strategies of these species.

AMAZONIA CAMTRAP: A data set of mammal, bird, and reptile species recorded with camera traps in the Amazon forest.

The Amazon forest has the highest biodiversity on Earth. However, information on Amazonian vertebrate diversity is still deficient and scattered across the published, peer-reviewed, and gray literature and in unpublished raw data. Camera traps are an effective non-invasive method of surveying vertebrates, applicable to different scales of time and space. In this study, we organized and standardized camera trap records from different Amazon regions to compile the most extensive data set of inventories of mammal, bird, and reptile species ever assembled for the area. The complete data set comprises 154,123 records of 317 species (185 birds, 119 mammals, and 13 reptiles) gathered from surveys from the Amazonian portion of eight countries (Brazil, Bolivia, Colombia, Ecuador, French Guiana, Peru, Suriname, and Venezuela). The most frequently recorded species per taxa were: mammals: Cuniculus paca (11,907 records); birds: Pauxi tuberosa (3713 records); and reptiles: Tupinambis teguixin (716 records). The information detailed in this data paper opens up opportunities for new ecological studies at different spatial and temporal scales, allowing for a more accurate evaluation of the effects of habitat loss, fragmentation, climate change, and other human-mediated defaunation processes in one of the most important and threatened tropical environments in the world. The data set is not copyright restricted; please cite this data paper when using its data in publications and we also request that researchers and educators inform us of how they are using these data.

Hematology and Serum Chemistry of Free-Ranging Jaguars (Panthera onca) from a Floodplain Forest Site in Amazonia, Brazil.

We provide hematologic and biochemical information for 13 jaguars (Panthera onca) from the Amazon. Most showed increased lymphocytes, monocytes, eosinophils, aspartate aminotransferase, and alanine aminotransferase; all individuals showed lower mean red blood cell (RBC) counts compared to findings from other biomes. Males had a significantly higher RBC count and alkaline phosphatase than did females.

Environmental and anthropogenic factors synergistically affect space use of jaguars.

Large terrestrial carnivores have undergone some of the largest population declines and range reductions of any species, which is of concern as they can have large effects on ecosystem dynamics and function.1-4 The jaguar (Panthera onca) is the apex predator throughout the majority of the Neotropics; however, its distribution has been reduced by >50% and it survives in increasingly isolated populations.5 Consequently, the range-wide management of the jaguar depends upon maintaining core populations connected through multi-national, transboundary cooperation, which requires understanding the movement ecology and space use of jaguars throughout their range.6-8 Using GPS telemetry data for 111 jaguars from 13 ecoregions within the four biomes that constitute the majority of jaguar habitat, we examined the landscape-level environmental and anthropogenic factors related to jaguar home range size and movement parameters. Home range size decreased with increasing net productivity and forest cover and increased with increasing road density. Speed decreased with increasing forest cover with no sexual differences, while males had more directional movements, but tortuosity in movements was not related to any landscape factors. We demonstrated a synergistic relationship between landscape-scale environmental and anthropogenic factors and jaguars' spatial needs, which has applications to the conservation strategy for the species throughout the Neotropics. Using large-scale collaboration, we overcame limitations from small sample sizes typical in large carnivore research to provide a mechanism to evaluate habitat quality for jaguars and an inferential modeling framework adaptable to the conservation of other large terrestrial carnivores.

Total mercury in wild felids occurring in protected areas in the central Brazilian Amazon

This is the first study to investigate mercury (Hg) contamination in felid species in the Brazilian Amazon. We collected 26 fur samples from wild felids of four species (Puma concolor, Panthera onca, Leopardus pardalis and Leopardus wiedii) occurring in the Mamirauá and Amanã sustainable development reserves, in the state of Amazonas. Samples were from museum specimens, except for five P. onca samples collected from free-living individuals. Total Hg concentrations ranged from 0.12 to 48.1 µg g-1. Concentrations of Hg did not differ significantly between museum specimens and live individuals of P. onca, but varied significantly among species, with significantly higher concentrations for P. onca and L. pardalis, which could be related to factors such as diet and habitat. (AU)

Wild dogs at stake: deforestation threatens the only Amazon endemic canid, the short-eared dog (Atelocynus microtis).

The persistent high deforestation rate and fragmentation of the Amazon forests are the main threats to their biodiversity. To anticipate and mitigate these threats, it is important to understand and predict how species respond to the rapidly changing landscape. The short-eared dog Atelocynus microtis is the only Amazon-endemic canid and one of the most understudied wild dogs worldwide. We investigated short-eared dog habitat associations on two spatial scales. First, we used the largest record database ever compiled for short-eared dogs in combination with species distribution models to map species habitat suitability, estimate its distribution range and predict shifts in species distribution in response to predicted deforestation across the entire Amazon (regional scale). Second, we used systematic camera trap surveys and occupancy models to investigate how forest cover and forest fragmentation affect the space use of this species in the Southern Brazilian Amazon (local scale). Species distribution models suggested that the short-eared dog potentially occurs over an extensive and continuous area, through most of the Amazon region south of the Amazon River. However, approximately 30% of the short-eared dog's current distribution is expected to be lost or suffer sharp declines in habitat suitability by 2027 (within three generations) due to forest loss. This proportion might reach 40% of the species distribution in unprotected areas and exceed 60% in some interfluves (i.e. portions of land separated by large rivers) of the Amazon basin. Our local-scale analysis indicated that the presence of forest positively affected short-eared dog space use, while the density of forest edges had a negative effect. Beyond shedding light on the ecology of the short-eared dog and refining its distribution range, our results stress that forest loss poses a serious threat to the conservation of the species in a short time frame. Hence, we propose a re-assessment of the short-eared dog's current IUCN Red List status (Near Threatened) based on findings presented here. Our study exemplifies how data can be integrated across sources and modelling procedures to improve our knowledge of relatively understudied species.

Dissemination of COVID-19 in cities and riverine communities in Central Amazonia / Disseminação da COVID-19 em cidades e comunidades ribeirinhas da Amazônia Central

The population of small towns and riverine communities in Amazonia are extremely vulnerable to COVID-19 due to the absence of basic health care infrastructure in the region. The objective of this study was to (1) evaluate the effect of social distancing measures in the dissemination of COVID-19 in small towns, and (2) to estimate the impact of reducing contact between rural and urban populations on the contamination of riverine communities of Central Amazon. Our results indicate that social distancing can significantly reduce the speed of dissemination of COVID-19 in the population of small towns. However, we also observed that even in towns with intense actions to combat COVID-19, social distancing is below the ideal 70% isolation mark. Regarding the contamination of riverine communities, we observed that the reduction in the number of visits and duration of stay, as well as the interruption of visits during the five weeks with larger probability of contamination has major impact on delaying the arrival of COVID-19 in these vulnerable populations. We recommend that, given the low effectiveness of social distancing measures and the rapid contamination of urban populations, each municipality should evaluate implementing more restrictive measures such as a full or partial lockdown. Our results also suggest that three measures can be effective in delaying the arrival of COVID-19 in riverine communities of Amazonia: (1) the reduction in the number of visits that each community makes to a town, (2) the reduction in duration of each visit, and (3) avoiding visits during the five weeks with the largest number of infected people in towns. It is imperative that implementation of any of the restrictive measures suggested in this publication be accompanied by a vast communication campaign as well as social assistance actions for the rural population and poor families of small towns to guarantee their basic needs for survival.

As populações da Amazônia são extremamente vulneráveis à COVID-19 devido ao intenso fluxo entre as localidades rurais e as sedes municipais e à falta de infraestrutura de saúde básica adequada na região. O objetivo deste estudo foi (1) avaliar o efeito da medida de distanciamento social sobre a disseminação da COVID-19 em sedes municipais e (2) estimar o impacto da redução do contato entre a população rural e urbana sobre a contaminação de localidades rurais da Amazônia Central, região do Médio Solimões. Nossos resultados indicam que o distanciamento social pode reduzir significativamente a velocidade de contaminação da população em sedes municipais. No entanto, mesmo em sedes municipais com atividade intensa no combate à COVID-19, o distanciamento social está muito abaixo do ideal de 70%. Observamos também que a redução do número de visitas e do tempo de permanência durante cada visita, além da interrupção do fluxo durante as cinco semanas com maior probabilidade infecção têm impacto marcante sobre a velocidade de chegada da COVID-19 nas localidades rurais. Recomendamos que, dada a baixa efetividade de medidas de distanciamento social e o rápido contágio nas sedes municipais, cada município avalie a implementação de lockdown. Nossos resultados sugerem também que três medidas podem ser eficientes em atrasar a chegada da COVID-19 às localidades rurais: (1) a redução no número de visitas que cada uma faz a um centro urbano, (2) a redução do tempo de permanência durante cada visita e (3) evitar qualquer ida às sedes municipais durante as cinco semanas com maior número de pessoas infectadas. Destacamos que todas as medidas restritivas sugeridas precisam ser acompanhadas por uma ampla campanha de conscientização e ações de assistência à população rural e às famílias mais carentes das sedes municipais para garantir acesso a itens básicos para sua sobrevivência.

Habitat use of the ocelot (Leopardus pardalis) in Brazilian Amazon.

Amazonia forest plays a major role in providing ecosystem services for human and sanctuaries for wildlife. However, ongoing deforestation and habitat fragmentation in the Brazilian Amazon has threatened both. The ocelot is an ecologically important mesopredator and a potential conservation ambassador species, yet there are no previous studies on its habitat preference and spatial patterns in this biome. From 2010 to 2017, twelve sites were surveyed, totaling 899 camera trap stations, the largest known dataset for this species. Using occupancy modeling incorporating spatial autocorrelation, we assessed habitat use for ocelot populations across the Brazilian Amazon. Our results revealed a positive sigmoidal correlation between remote-sensing derived metrics of forest cover, disjunct core area density, elevation, distance to roads, distance to settlements and habitat use, and that habitat use by ocelots was negatively associated with slope and distance to river/lake. These findings shed light on the regional scale habitat use of ocelots and indicate important species-habitat relationships, thus providing valuable information for conservation management and land-use planning.

Jaguar movement database: a GPS-based movement dataset of an apex predator in the Neotropics.

The field of movement ecology has rapidly grown during the last decade, with important advancements in tracking devices and analytical tools that have provided unprecedented insights into where, when, and why species move across a landscape. Although there has been an increasing emphasis on making animal movement data publicly available, there has also been a conspicuous dearth in the availability of such data on large carnivores. Globally, large predators are of conservation concern. However, due to their secretive behavior and low densities, obtaining movement data on apex predators is expensive and logistically challenging. Consequently, the relatively small sample sizes typical of large carnivore movement studies may limit insights into the ecology and behavior of these elusive predators. The aim of this initiative is to make available to the conservation-scientific community a dataset of 134,690 locations of jaguars (Panthera onca) collected from 117 individuals (54 males and 63 females) tracked by GPS technology. Individual jaguars were monitored in five different range countries representing a large portion of the species' distribution. This dataset may be used to answer a variety of ecological questions including but not limited to: improved models of connectivity from local to continental scales; the use of natural or human-modified landscapes by jaguars; movement behavior of jaguars in regions not represented in this dataset; intraspecific interactions; and predator-prey interactions. In making our dataset publicly available, we hope to motivate other research groups to do the same in the near future. Specifically, we aim to help inform a better understanding of jaguar movement ecology with applications towards effective decision making and maximizing long-term conservation efforts for this ecologically important species. There are no costs, copyright, or proprietary restrictions associated with this data set. When using this data set, please cite this article to recognize the effort involved in gathering and collating the data and the willingness of the authors to make it publicly available.

Spatial patterns of medium and large size mammal assemblages in várzea and terra firme forests, Central Amazonia, Brazil.

Várzea forests account for 17% of the Amazon basin and endure an annual inundation that can reach 14 m deep during 6-8 months. This flood pulse in combination with topography directly influences the várzea vegetation cover. Assemblages of several taxa differ significantly between unflooded terra firme and flooded várzea forests, but little is known about the distribution of medium and large sized terrestrial mammals in várzea habitats. Therefore, our goal was to understand how those habitats influence mammalian species distribution during the dry season. Specifically, we: (1) compared the species composition between a terra firme (Amanã Sustainable Development Reserve) and a várzea forest (Mamirauá Sustainable Development Reserve); and (2) tested the influence of the várzea habitat classes on the number of records, occurrence and species composition of mammalian assemblages. The sampling design in each reserve consisted of 50 baited camera trap stations, with an overall sampling effort of 5015 camera trap days. We used Non-Metric Multidimension Scaling (NMDS) to compare species composition between terra firme and várzea forests, and used Generalized Linear Models (GLM) to assess how habitat types and a habitat diversity index affect mammal distributions. We recorded 21 medium and large sized mammalian species, including 20 species in terra firme and only six in várzea (3443 records). Flood pulse and isolation in várzea forest drove the dissimilarity between these two forest types. In várzea forest, medium size mammals, in general, avoided habitats associated with long flooding periods, while jaguars (Panthera onca) appeared to prefer aquatic/terrestrial transition zones. Habitats that remain dry for longer periods showed more mammalian occurrence, suggesting that dispersion via soil is important even for semi-arboreal species. This is the first study to evaluate differential use of várzea habitats by terrestrial mammalian assemblages.

Ticks (Acari: Ixodidae) of the state of Amazonas, Brazil.

The tick fauna of Brazil is currently composed by 72 species. The state of Amazonas is the largest of Brazil, with an area of ≈ 19% of the Brazilian land. Besides its vast geographic area, only 19 tick species have been reported for Amazonas. Herein, lots containing ticks from the state of Amazonas were examined in three major tick collections from Brazil. A total of 5933 tick specimens were examined and recorded, comprising 2693 males, 1247 females, 1509 nymphs, and 484 larvae. These ticks were identified into the following 22 species: Amblyomma cajennense sensu lato, Amblyomma calcaratum, Amblyomma coelebs, Amblyomma dissimile, Amblyomma dubitatum, Amblyomma geayi, Amblyomma goeldii, Amblyomma humerale, Amblyomma latepunctatun, Amblyomma longirostre, Amblyomma naponense, Amblyomma oblongoguttatum, Amblyomma ovale, Amblyomma rotundatum, Amblyomma scalpturatum, Amblyomma varium, Dermacentor nitens, Haemaphysalis juxtakochi, Ixodes cf. Ixodes fuscipes, Ixodes luciae, Rhipicephalus microplus, Rhipicephalus sanguineus sensu lato. Ticks were collected from 17 (27.4%) out of the 62 municipalities that currently compose the state of Amazonas. The following four species are reported for the first time in the state of Amazonas: A. coelebs, A. dubitatum, H. juxtakochi, and Ixodes cf. I. fuscipes. The only tick species previously reported for Amazonas and not found in the present study is Amblyomma parvum. This study provides a great expansion of geographical and host records of ticks for the state of Amazonas, which is now considered to have a tick fauna composed by 23 species. It is noteworthy that we report 1391 Amblyomma nymphs that were identified to 13 different species.

Ticks (Acari: Ixodidae) of the state of Amazonas, Brazil

The tick fauna of Brazil is currently composed by 72 species. The state of Amazonas is the largest of Brazil, with an area of ae 19% of the Brazilian land. Besides its vast geographic area, only 19 tick species have been reported for Amazonas. Herein, lots containing ticks from the state of Amazonas were examined in three major tick collections from Brazil. A total of 5933 tick specimens were examined and recorded, comprising 2693 males, 1247 females, 1509 nymphs, and 484 larvae. These ticks were identified into the following 22 species: Amblyomma cajennense sensu lato, Amblyomma calcaratum, Amblyomma coelebs, Amblyomma dissimile, Amblyomma dubitatum, Amblyomma geayi, Amblyomma goeldii, Amblyomma humerale, Amblyomma latepunctatun, Amblyomma longirostre, Amblyomma naponense, Amblyomma oblongoguttatum, Amblyomma ovale, Amblyomma rotundatum, Amblyomma scalpturatum, Amblyomma varium, Dermacentor nitens, Haemaphysalis juxtakochi, Ixodes cf. Ixodes fuscipes, Ixodes luciae, Rhipicephalus microplus, Rhipicephalus sanguineus sensu lato. Ticks were collected from 17 (27.4%) out of the 62 municipalities that currently compose the state of Amazonas. The following four species are reported for the first time in the state of Amazonas: A. coelebs, A. dubitatum, H. juxtakochi, and Ixodes cf. I. fuscipes. The only tick species previously reported for Amazonas and not found in the present study is Amblyomma parvum. This study provides a great expansion of geographical and host records of ticks for the state of Amazonas, which is now considered to have a tick fauna composed by 23 species. It is noteworthy that we report 1391 Amblyomma nymphs that were identified to 13 different species.

Ticks (Acari: Ixodidae) of the state of Amazonas, Brazil

The tick fauna of Brazil is currently composed by 72 species. The state of Amazonas is the largest of Brazil, with an area of ae 19% of the Brazilian land. Besides its vast geographic area, only 19 tick species have been reported for Amazonas. Herein, lots containing ticks from the state of Amazonas were examined in three major tick collections from Brazil. A total of 5933 tick specimens were examined and recorded, comprising 2693 males, 1247 females, 1509 nymphs, and 484 larvae. These ticks were identified into the following 22 species: Amblyomma cajennense sensu lato, Amblyomma calcaratum, Amblyomma coelebs, Amblyomma dissimile, Amblyomma dubitatum, Amblyomma geayi, Amblyomma goeldii, Amblyomma humerale, Amblyomma latepunctatun, Amblyomma longirostre, Amblyomma naponense, Amblyomma oblongoguttatum, Amblyomma ovale, Amblyomma rotundatum, Amblyomma scalpturatum, Amblyomma varium, Dermacentor nitens, Haemaphysalis juxtakochi, Ixodes cf. Ixodes fuscipes, Ixodes luciae, Rhipicephalus microplus, Rhipicephalus sanguineus sensu lato. Ticks were collected from 17 (27.4%) out of the 62 municipalities that currently compose the state of Amazonas. The following four species are reported for the first time in the state of Amazonas: A. coelebs, A. dubitatum, H. juxtakochi, and Ixodes cf. I. fuscipes. The only tick species previously reported for Amazonas and not found in the present study is Amblyomma parvum. This study provides a great expansion of geographical and host records of ticks for the state of Amazonas, which is now considered to have a tick fauna composed by 23 species. It is noteworthy that we report 1391 Amblyomma nymphs that were identified to 13 different species.

Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages.

Space Use and Movement of a Neotropical Top Predator: The Endangered Jaguar.

Accurately estimating home range and understanding movement behavior can provide important information on ecological processes. Advances in data collection and analysis have improved our ability to estimate home range and movement parameters, both of which have the potential to impact species conservation. Fitting continuous-time movement model to data and incorporating the autocorrelated kernel density estimator (AKDE), we investigated range residency of forty-four jaguars fit with GPS collars across five biomes in Brazil and Argentina. We assessed home range and movement parameters of range resident animals and compared AKDE estimates with kernel density estimates (KDE). We accounted for differential space use and movement among individuals, sex, region, and habitat quality. Thirty-three (80%) of collared jaguars were range resident. Home range estimates using AKDE were 1.02 to 4.80 times larger than KDE estimates that did not consider autocorrelation. Males exhibited larger home ranges, more directional movement paths, and a trend towards larger distances traveled per day. Jaguars with the largest home ranges occupied the Atlantic Forest, a biome with high levels of deforestation and high human population density. Our results fill a gap in the knowledge of the species' ecology with an aim towards better conservation of this endangered/critically endangered carnivore-the top predator in the Neotropics.

Ocelot (Leopardus pardalis) Density in Central Amazonia.

Ocelots (Leopardus pardalis) are presumed to be the most abundant of the wild cats throughout their distribution range and to play an important role in the dynamics of sympatric small-felid populations. However, ocelot ecological information is limited, particularly for the Amazon. We conducted three camera-trap surveys during three consecutive dry seasons to estimate ocelot density in Amanã Reserve, Central Amazonia, Brazil. We implemented a spatial capture-recapture (SCR) model that shared detection parameters among surveys. A total effort of 7020 camera-trap days resulted in 93 independent ocelot records. The estimate of ocelot density in Amanã Reserve (24.84 ± SE 6.27 ocelots per 100 km2) was lower than at other sites in the Amazon and also lower than that expected from a correlation of density with latitude and rainfall. We also discuss the importance of using common parameters for survey scenarios with low recapture rates. This is the first density estimate for ocelots in the Brazilian Amazon, which is an important stronghold for the species.