Ana Carolina Srbek-Araujo

Development and testing of an optimized method for DNA-based identification of jaguar ( Panthera onca ) and puma ( Puma concolor ) faecal samples for use in ecological and genetic studies

The elusive nature and endangered status of most carnivore species imply that efficient approaches for their non-invasive sampling are required to allow for genetic and ecological studies. Faecal samples are a major potential source of information, and reliable approaches are needed to foster their application in this field, particularly in areas where few studies have been conducted. A major obstacle to the reliable use of faecal samples is their uncertain species-level identification in the field, an issue that can be addressed with DNA-based assays. In this study we describe a sequence-based approach that efficiently distinguishes jaguar versus puma scats, and that presents several desirable properties: (1) considerably high amplification and sequencing rates; (2) multiple diagnostic sites reliably differentiating the two focal species; (3) high information content that allows for future application in other carnivores; (4) no evidence of amplification of prey DNA; and (5) no evidence of amplification of a nuclear mitochondrial DNA insertion known to occur in the jaguar. We demonstrate the reliability and usefulness of this approach by evaluating 55 field-collected samples from four locations in the highly fragmented Atlantic Forest biome of Brazil and Argentina, and document the presence of one or both of these endangered felids in each of these areas.

A biodiversity hotspot losing its top predator: The challenge of jaguar conservation in the Atlantic Forest of South America

The jaguar is the top predator of the Atlantic Forest (AF), which is a highly threatened biodiversity hotspot that occurs in Brazil, Paraguay and Argentina. By combining data sets from 14 research groups across the region, we determine the population status of the jaguar and propose a spatial prioritization for conservation actions. About 85% of the jaguar’s habitat in the AF has been lost and only 7% remains in good condition. Jaguars persist in around 2.8% of the region, and live in very low densities in most of the areas. The population of jaguars in the AF is probably lower than 300 individuals scattered in small sub-populations. We identified seven Jaguar Conservation Units (JCUs) and seven potential JCUs, and only three of these areas may have ≥50 individuals. A connectivity analysis shows that most of the JCUs are isolated. Habitat loss and fragmentation were the major causes for jaguar decline, but human induced mortality is the main threat for the remaining population. We classified areas according to their contribution to jaguar conservation and we recommend management actions for each of them. The methodology in this study could be used for conservation planning of other carnivore species.

The Red-Billed Curassow (Crax blumenbachii): Social Organization, and Daily Activity Patterns

Abstract We studied the Red-billed Currasow (Crax blumenbachii) in Vale Natural Reserve, Linhares, Espírito Santo State, Brazil, using camera traps. We found the Red-billed Curassow present in the entire area of the reserve (∼ 22,000 ha) during 40 months of camera trapping (2005–2008). Most records were of single individuals, especially males, but pairs and even groups of individuals were also recorded. Males were paired with one and two females, suggesting polygyny in the species. The species was recorded throughout the day with one peak from 0500 to 0600 hrs and another after 1600 hrs. The daily activity pattern was similar for males and females. The number and widespread nature of the records suggests the local population of this species may be higher than previously thought.

Population status of the jaguar Panthera onca in one of its last strongholds in the Atlantic Forest

Remaining jaguar Panthera onca populations in the Atlantic Forest are restricted to eight regions, and all populations appear to be declining. We report on the status of one of the last populations in south-eastern Brazil. We monitored this population with camera traps during June 2005–January 2013 in Vale Natural Reserve. We estimated an abundance of 9 ± SE 1.98 jaguars (95% CI 9–17) and a population density of 3.22 ± SE 1.58 individuals per 100 km 2 (95% CI 1.29–7.98). Annual survival probability over a 5-year interval was 78% (95% CI 58–98) and the recapture probability was 62% (95% CI 42–79). Although our results are among the highest densities reported for the jaguar in this biome, the future of the population is threatened by genetic deterioration and local threats, including the expansion of an existing highway and depletion of the jaguars native prey base as a result of poaching, and will depend upon urgent implementation of conservation actions. The necessary actions include establishing gene flow with other compatible populations, increasing surveillance against poaching, continuing population monitoring of jaguars and their main prey species, and implementing mitigation measures in relation to the impacts of the highway on local fauna.

Daily and Seasonal Activity Patterns of the Solitary Tinamou (Tinamus solitarius) in the Atlantic Forest of Southeastern Brazil

ABSTRACT The Solitary Tinamou (Tinamus solitarius) is endemic to the Atlantic Forest. Little information is available about this bird species because of its low conservation priority and cryptic habits. Hunting and habitat loss are the main threats to the species, which is regionally threatened in southern and southeastern Brazil. We used camera traps installed along unpaved roads, at edges with roads, and in the forest interior in one of the last large remnants of the lowland Brazilian Atlantic Forest in southeastern Brazil to determine daily and seasonal activity patterns of the Solitary Tinamou. We obtained 256 records between June 2005 and December 2013 (sampling effort = 14,316 cameras-day). Solitary Tinamous were mainly observed away from roads, confirming the tendency of the species to occur more frequently in areas with greater canopy cover. Our data confirmed that photoperiod may influence daily activity patterns of the Solitary Tinamou, as the duration of daylight differs among the seasons. The species showed a total of 16 hrs of daily activity during the wet season with two main activity peaks during the day (0500 and 1800) and an intervening smaller peak (1300). During the dry season, the species showed a shorter duration of daily activity (13 hrs), and the activity peaks occurred either 2 hrs later or 1 hr earlier. Despite the difference in daily activity patterns between seasons, the number of records obtained was proportional to the sampling effort at each season, and the records were not correlated with climatic variables. The species was most often recorded between August and January, a time span that coincided with its reproductive period. It was less often recorded between March and May, a finding that could be related to the timing of the post-nuptial molting period. Our data serve to enhance current knowledge of activity patterns of T. solitarius and may be used in future studies relating temporal niche partitioning by the Solitary Tinamou with other frugivores or between the species and its predators.

Abundance of tegu lizards ( Tupinambis merianae ) in a remnant of the Brazilian Atlantic forest

We investigated the abundance of the tegu lizard ( Tupinambis merianae ) in a 21 787 ha Brazilian Atlantic forest fragment (Reserva Natural Vale, RNV). This remnant has a highly irregular perimeter and an extensive network (126 km) of internal unpaved roads. We hypothesized that the high proportion of these edge habitats might benefit active heliothermic lizards like tegus due to greater incidence of sunlight. We estimated population density using the program DISTANCE, and compared sighting frequency of tegus along twelve 500 m long transects located at three distances (25, 200 and 400 m) from the nearest unpaved road or fragment edge. We found no significant differences in sighting frequency among the three distances (Chi-square; χ 2 = 4.308; P = 0.116) and no significant association between edge distance and edge type (internal, external) ( G test adjusted; G 2 = 0.617; P = 0.734). However, as the test comparing distances had relatively low power we assumed that the experimental evidence was not strong enough to prove lack of an edge effect. The estimated density (0.63±0.13 lizard/ha) is within the range of densities found on Brazilian islands where tegus have proliferated to the point of becoming a threat to ground nesting birds and turtles. We caution, however, that the absence of published data on other non-island sites prevents us from concluding that the species has an abnormally high density in RNV.

Worrisome isolation: noninvasive genetic analyses shed light on the critical status of a remnant jaguar population

Many carnivore species, particularly felids, are sensitive to land use changes and may disappear from landscapes with reduced natural habitat and increased fragmentation. The jaguar (Panthera onca) is highly affected by these factors and is particularly endangered in the Atlantic Forest (AF) of South America, one of the most threatened biomes in the world. We used noninvasive fecal sampling and microsatellite markers to investigate the genetic diversity of jaguars in one of the last remnant populations of this species in the entire coastal AF. This section of the biome is highly fragmented. We observed low levels of genetic diversity (HO = 0.621, HE = 0.532, AR = 3.195), and estimated a small effective size for the population (Ne = 7.9 individuals). We performed comparative analyses incorporating data from previously surveyed populations located farther inland (interior AF), revealing that the coastal population studied shows significant genetic differentiation. Our results support a scenario of anthropogenic, drift-induced differentiation among jaguar populations in small AF fragments, affecting both the interior and coastal components of this biome. Despite its low diversity, we detected putatively unique alleles present in the coastal population, supporting its importance in the context of maintaining the remaining genetic variability of jaguars in the AF. Our results highlight the urgent need to implement coordinated conservation actions for jaguars in this highly impacted biome, including management interventions that foster the restoration of genetic connectivity among isolated remnant populations.

ATLANTIC MAMMAL TRAITS: a data set of morphological traits of mammals in the Atlantic Forest of South America

Measures of traits are the basis of functional biological diversity. Numerous works consider mean species-level measures of traits while ignoring individual variance within species. However, there is a large amount of variation within species and it is increasingly apparent that it is important to consider trait variation not only between species, but also within species. Mammals are an interesting group for investigating trait-based approaches because they play diverse and important ecological functions (e.g., pollination, seed dispersal, predation, grazing) that are correlated with functional traits. Here we compile a data set comprising morphological and life history information of 279 mammal species from 39,850 individuals of 388 populations ranging from -5.83 to -29.75 decimal degrees of latitude and -34.82 to -56.73 decimal degrees of longitude in the Atlantic forest of South America. We present trait information from 16,840 individuals of 181 species of non-volant mammals (Rodentia, Didelphimorphia, Carnivora, Primates, Cingulata, Artiodactyla, Pilosa, Lagomorpha, Perissodactyla) and from 23,010 individuals of 98 species of volant mammals (Chiroptera). The traits reported include body mass, age, sex, reproductive stage, as well as the geographic coordinates of sampling for all taxa. Moreover, we gathered information on forearm length for bats and body length and tail length for rodents and marsupials. No copyright restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.