Bridging the gap between movement data and connectivity analysis using the Time-Explicit Habitat Selection (TEHS) model

BACKGROUND

Understanding how to connect habitat remnants to facilitate the movement of species is a critical task in an increasingly fragmented world impacted by human activities. The identification of dispersal routes and corridors through connectivity analysis requires measures of landscape resistance but there has been no consensus on how to calculate resistance from habitat characteristics, potentially leading to very different connectivity outcomes.

METHODS

We propose a new model, called the Time-Explicit Habitat Selection (TEHS) model, that can be directly used for connectivity analysis. The TEHS model decomposes the movement process in a principled approach into a time and a selection component, providing complementary information regarding space use by separately assessing the drivers of time to traverse the landscape and the drivers of habitat selection. These models are illustrated using GPS-tracking data from giant anteaters (Myrmecophaga tridactyla) in the Pantanal wetlands of Brazil.

RESULTS

The time model revealed that the fastest movements tended to occur between 8 p.m. and 5 a.m., suggesting a crepuscular/nocturnal behavior. Giant anteaters moved faster over wetlands while moving much slower over forests and savannas, in comparison to grasslands. We also found that wetlands were consistently avoided whereas forest and savannas tended to be selected. Importantly, this model revealed that selection for forest increased with temperature, suggesting that forests may act as important thermal shelters when temperatures are high. Finally, using the spatial absorbing Markov chain framework, we show that the TEHS model results can be used to simulate movement and connectivity within a fragmented landscape, revealing that giant anteaters will often not use the shortest-distance path to the destination patch due to avoidance of certain habitats.

CONCLUSIONS

The proposed approach can be used to characterize how landscape features are perceived by individuals through the decomposition of movement patterns into a time and a habitat selection component. Additionally, this framework can help bridge the gap between movement-based models and connectivity analysis, enabling the generation of time-explicit connectivity results.

Behavioral responses of terrestrial mammals to COVID-19 lockdowns

COVID-19 lockdowns in early 2020 reduced human mobility, providing an opportunity to disentangle its effects on animals from those of landscape modifications. Using GPS data, we compared movements and road avoidance of 2300 terrestrial mammals (43 species) during the lockdowns to the same period in 2019. Individual responses were variable with no change in average movements or road avoidance behavior, likely due to variable lockdown conditions. However, under strict lockdowns 10-day 95th percentile displacements increased by 73%, suggesting increased landscape permeability. Animals' 1-hour 95th percentile displacements declined by 12% and animals were 36% closer to roads in areas of high human footprint, indicating reduced avoidance during lockdowns. Overall, lockdowns rapidly altered some spatial behaviors, highlighting variable but substantial impacts of human mobility on wildlife worldwide.

What a few hairs can tell us about the resource use of giant armadillos

Understanding of resource requirements of vulnerable species is key for conservation planning. Here, we used stable carbon (δ¹³ C) and nitrogen isotopes (δ¹⁵ N) of hair from giant armadillos (Priodontes maximus) to understand individual resource use. We collected hair from 19 giant armadillos analyzing 34 samples from the Brazilian Pantanal and compared the resource use between sexes and age classes. We also assessed the relationship of isotopic values with individuals' body mass and the habitat type used. We observed a wide variation in resource use by giant armadillos, showing that individuals consume prey that feeds on distinct resources and occupies different habitat types, indicating that there is individual variation in foraging behavior. Most giant armadillos presented a mixed diet (C₃ /C₄ resources, forests/open areas), but a quarter of individuals had strictly C₄ diets (open areas). Males are more prone to forage on C₄ resources, presenting an isotopic niche 2.6-times larger than that of females. Subadults presented diets more associated with habitats with high arboreal cover (C₃ resources, forests), while adults foraged more in open areas (C₄ resources). This result is mirrored by the positive relationship between δ¹³ C values and body mass, suggesting that larger giant armadillos tend to feed more in open areas. We observed that δ¹³ C values decreased as individuals increased the use of habitats with high arboreal cover. We stress the importance of conserving the natural mosaic in the Pantanal landscape for the species persistence, given that giant armadillos require all habitat types to fulfill their dietary, spatial, and developmental needs.

Forecasting seasonal peaks in roadkill patterns for improving road management

For several species, roadkill is not spatially aggregated on hotspots, having instead a more diffuse pattern along the roads. For such species, management measures such as road passages may be insufficient for effective mitigation, since a large part of the road crossings is likely to occur outside the influence of those structures. One complementary approach could be to implement temporary mitigation actions, such as traffic calming. This requires understanding when roadkill peaks may occur. We tested the feasibility of predicting seasonal peaks of roadkill using data from a 3-year systematic monitoring (78 surveys over ca. 960 km of roads) from eight non-flying vertebrate species from Mato Grosso do Sul, Brazil, with different body size and life history traits (ca. 6400 records from focal species). We modelled the time-series of the roadkill of these species at large scale (state level) using generalized additive mixed models (GAMMs). We used the data of the first 2 years as training datasets, and the information from the third year of surveys as testing datasets to evaluate the prediction performance of models. Overall, the models of species feed with a higher number of records were able to follow reasonably well the variations of roadkill over time, although they were not able to correctly predict the number of collisions. For species with fewer observations, the models presented a poorer goodness-of-fit and prediction ability. Our results suggest that, at least for those species with higher roadkill rates, it can be possible to forecast periods of higher probability of occurring hot-moments of mortality. Such models can provide valuable information to implement seasonal management actions.

Evaluating expert-based habitat suitability information of terrestrial mammals with GPS-tracking data

AIM

Macroecological studies that require habitat suitability data for many species often derive this information from expert opinion. However, expert-based information is inherently subjective and thus prone to errors. The increasing availability of GPS tracking data offers opportunities to evaluate and supplement expert-based information with detailed empirical evidence. Here, we compared expert-based habitat suitability information from the International Union for Conservation of Nature (IUCN) with habitat suitability information derived from GPS-tracking data of 1,498 individuals from 49 mammal species.

LOCATION

Worldwide.

TIME PERIOD

1998-2021.

MAJOR TAXA STUDIED

Forty-nine terrestrial mammal species.

METHODS

Using GPS data, we estimated two measures of habitat suitability for each individual animal: proportional habitat use (proportion of GPS locations within a habitat type), and selection ratio (habitat use relative to its availability). For each individual we then evaluated whether the GPS-based habitat suitability measures were in agreement with the IUCN data. To that end, we calculated the probability that the ranking of empirical habitat suitability measures was in agreement with IUCN's classification into suitable, marginal and unsuitable habitat types.

RESULTS

IUCN habitat suitability data were in accordance with the GPS data (> 95% probability of agreement) for 33 out of 49 species based on proportional habitat use estimates and for 25 out of 49 species based on selection ratios. In addition, 37 and 34 species had a > 50% probability of agreement based on proportional habitat use and selection ratios, respectively.

MAIN CONCLUSIONS

We show how GPS-tracking data can be used to evaluate IUCN habitat suitability data. Our findings indicate that for the majority of species included in this study, it is appropriate to use IUCN habitat suitability data in macroecological studies. Furthermore, we show that GPS-tracking data can be used to identify and prioritize species and habitat types for re-evaluation of IUCN habitat suitability data.

Using a Conflict Framework Analysis to Help Beekeepers and Giant Armadillos (Priodontes maximus) Coexist

Damage caused by wildlife is one reason preventing peaceful coexistence between humans and wildlife. To identify the complexity and scope of human-wildlife interactions and to guide conservation interventions, a theoretical framework has been recently proposed, based on the field of conflict analysis and peacebuilding. Despite its importance, to our knowledge, there are no studies yet testing the framework. We therefore adapted and expanded the framework to investigate a wildlife-people interaction scenario, involving damage by giant armadillos (Priodontes maximus) to apiaries in the Brazilian Cerrado biome of Mato Grosso do Sul state. From August to November 2018, we interviewed 111 beekeepers identified through a mixed random and snowball sampling design to assess at which level of conflict this interaction could be framed, and to identify strategies able to promote coexistence. Analysis of the five key areas of the framework suggested the current human-wildlife interaction is a level one conflict. This means the negative relation between beekeepers and giant armadillos is still not rooted in less visible, more complex social disagreements, but founded in a material dispute: destruction of beehives. We used the findings to create an intervention strategy which involves: (i) the implementation of mitigation strategies that prevent giant armadillos from predating beehives; (ii) a certification scheme to acknowledge beekeepers' efforts to implement the mitigation strategies, and (iii) a Citizen Science Program using an app that enables data gathering for adaptive management, as well as maintains beekeeper engagement. We hope beekeepers-giant armadillos' coexistence will become beneficial rather than a challenge with the novel interventions.

Moderate Genetic Diversity and Demographic Reduction in the Threatened Giant Anteater, Myrmecophaga tridactyla

In general, large mammal species with highly specialized feeding behavior and solitary habits are expected to suffer genetic consequences from habitat loss and fragmentation. To test this hypothesis, we analyzed the genetic diversity distribution of the threatened giant anteater inhabiting a human-modified landscape. We used 10 microsatellite loci to assess the genetic diversity and population structure of 107 giant anteaters sampled in the Brazilian Central-Western region. No genetic population structuring was observed in this region suggesting no gene flow restriction within the studied area. On the other hand, the moderate level of genetic diversity (Ho = 0.54), recent bottleneck detected and inbreeding (F_is, 0.13; p ≤ 0.001) signatures suggest potential impacts on the genetic variation of this Xenarthra. Additionally, a previous demographic reduction was suggested. Thus, considering the increased human-promoted impacts across the entire area of distribution of the giant anteater, our results can illustrate the potential effects of these disturbances on the genetic variation, allowing us to request the long-term conservation of this emblematic species.

Trypanosoma rangeli Genetic, Mammalian Hosts, and Geographical Diversity from Five Brazilian Biomes

Trypanosoma rangeli is a generalist hemoflagellate that infects mammals and is transmitted by triatomines around Latin America. Due to its high genetic diversity, it can be classified into two to five lineages. In Brazil, its distribution outside the Amazon region is virtually unknown, and knowledge on the ecology of its lineages and on host species diversity requires further investigation. Here, we analyzed 57 T. rangeli samples obtained from hemocultures and blood clots of 1392 mammals captured in different Brazilian biomes. The samples were subjected to small subunit (SSU) rDNA amplification and sequencing to confirm T. rangeli infection. Phylogenetic inferences and haplotype networks were reconstructed to classify T. rangeli lineages and to infer the genetic diversity of the samples. The results obtained in our study highlighted both the mammalian host range and distribution of T. rangeli in Brazil: infection was observed in five new species (Procyon cancrivorous, Priodontes maximum, Alouatta belzebul, Sapajus libidinosus, and Trinomys dimidiatus), and transmission was observed in the Caatinga biome. The coati (Nasua nasua) and capuchin monkey (S. libidinosus) are the key hosts of T. rangeli. We identified all four T. rangeli lineages previously reported in Brazil (A, B, D, and E) and possibly two new genotypes.

Zoonotic parasites infecting free-living armadillos from Brazil

Armadillos are specialist diggers and their burrows are used to find food, seek shelter and protect their pups. These burrows can also be shared with dozens of vertebrate and invertebrate species and; consequently, their parasites including the zoonotics. The aim of this study was to diagnose the presence of zoonotic parasites in four wild-caught armadillo species from two different Brazilian ecosystems, the Cerrado (Brazilian savanna) and the Pantanal (wetland). The investigated parasites and their correspondent diseases were: Toxoplasma gondii (toxoplasmosis), Trypanosoma cruzi (Chagas disease), Leishmania spp., (leishmaniasis), Paracoccidioides brasiliensis (Paracoccidioidomicosis) and Mycobacterium leprae (Hansen's disease). Forty-three free-living armadillos from Pantanal and seven road-killed armadillos from the Cerrado were sampled. Trypanosoma cruzi DTU TcIII were isolated from 2 out of 43 (4.65%) armadillos, including one of them also infected with Trypanosoma rangeli. Antibodies anti-T. gondii were detected in 13 out of 43 (30.2%) armadillos. All seven armadillos from Cerrado tested positive for P. brasiliensis DNA, in the lungs, spleen, liver fragments. Also, by molecular analysis, all 43 individuals were negative for M. leprae and Leishmania spp. Armadillos were infected by T. cruzi, T. rangeli, P. brasiliensis and presented seric antibodies to T. gondii, highlighting the importance of those armadillos could have in the epidemiology of zoonotic parasites.

Spatial ecology of the giant armadillo Priodontes maximus in Midwestern Brazil

The giant armadillo (Priodontes maximus) is the largest living armadillo. This naturally rare and poorly known species is endemic to South America and classified as “Vulnerable” by the IUCN. Here we explored aspects of the spatial ecology of P. maximus in Midwestern Brazil to gain insights on its ecology and biology to support conservation efforts. In 8 years, we identified 50 individuals of P. maximus and monitored 23 of them using telemetry methods. To characterize site fidelity and home range, we fitted individual continuous-time movement models and estimated Autocorrelated Kernel Density Estimates. We built a Structural Equation Model to evaluate how home-range area and daily displacement are related to each other, to sampling effort, and to individual characteristics. We estimated home-range overlap between pairs of different sexes using a bias-corrected Bhattacharyya coefficient. Finally, we formulated a canonical density estimation formula to characterize minimum population density. We gathered a total of 12,168 locations of P. maximus. The best-fitted movement models indicated site fidelity for all individuals and a median adult home-range area of 2,518 ha. Median adult daily displacement was 1,651 m. Home-range area scales positively with daily displacement and daily displacement scales positively with body mass. Median home-range overlap between pairs was low (4%) and adult females presented exclusive home ranges among themselves. Median minimum density was 7.65 individuals per 100 km2 (CI = 5.68–10.19 ind/100 km2). Our results are congruent with characterizing P. maximus as a generally asocial species, most likely promiscuous/polygynous, that establishes large, long-term home ranges, which grants the population a naturally low density. Spatial patterns and biological characteristics obtained in this study can be used to guide future conservation strategies for P. maximus in the Pantanal wetlands and elsewhere.

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans-anteaters, sloths, and armadillos-have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data.

Spatial patterns of road mortality of medium–large mammals in Mato Grosso do Sul, Brazil

Context Brazil has one of the richest biodiversity and one of the most extensive road networks in the world. Several negative impacts emerge from this interaction, including wildlife–vehicle collisions (WVC), which may represent a significant source of non-natural mortality in several species. The understanding of the main drivers of WVC is, therefore, crucial to improve the safe coexistence between human needs (transportation of goods and people) and animal populations. Aims We aimed to (1) evaluate the relative influence of land-cover patterns on the distribution of WVC, (2) assess whether WVCs are clustered forming hotspots of mortality, and, if so, (3) evaluate the benefits of mitigating only hotspot sections. Methods We collected WVC data involving medium–large mammals (4–260kg) along three road transects (920km), fortnightly over 1 year (n=1006 records). We used boosted regression trees to relate the WVC locations with a set of environmental variables including a roadkill index, reflecting overall habitat suitability and landscape connectivity, while accounting for spatial autocorrelation effects. We identified hotspots of mortality using Ripley’s K statistic and testing whether data follow a random Poisson distribution correcting for Type I error. Key results We found a strong association between WVC probability and roadkill index for all focal species. Distance to riparian areas, tree cover, terrain ruggedness and distance to urban areas were also important predictors, although to a lesser extent. We detected 21 hotspots of mortality, yet with little spatial overlapping as only four road sections (2%) were classified as hotspot for more than one species. Conclusions Our results supported that WVC mainly occur in road sections traversing areas with more abundant and diverse mammal communities. Hotspots of mortality may provide important information to prioritise road sections for mitigation, but this should be used in complement with roadkill indexes accounting for overall mortality. Implications The results support focusing on hotspots and habitat quality and landscape connectivity for a better assessment of road mortality. At the local scale, a larger number and improved road passages with exclusionary fencing of appropriate mesh size in riparian areas may provide safe crossings for many species and constitute a promising mitigation measure.

Yellow fever impact on brown howler monkeys (Alouatta guariba clamitans) in Argentina: a metamodelling approach based on population viability analysis and epidemiological dynamics

In South America, yellow fever (YF) is an established infectious disease that has been identified outside of its traditional endemic areas, affecting human and nonhuman primate (NHP) populations. In the epidemics that occurred in Argentina between 2007-2009, several outbreaks affecting humans and howler monkeys (Alouatta spp) were reported, highlighting the importance of this disease in the context of conservation medicine and public health policies. Considering the lack of information about YF dynamics in New World NHP, our main goal was to apply modelling tools to better understand YF transmission dynamics among endangered brown howler monkey (Alouatta guariba clamitans) populations in northeastern Argentina. Two complementary modelling tools were used to evaluate brown howler population dynamics in the presence of the disease: Vortex, a stochastic demographic simulation model, and Outbreak, a stochastic disease epidemiology simulation. The baseline model of YF disease epidemiology predicted a very high probability of population decline over the next 100 years. We believe the modelling approach discussed here is a reasonable description of the disease and its effects on the howler monkey population and can be useful to support evidence-based decision-making to guide actions at a regional level.