Denis Alessio Sana

The effect of habitat fragmentation on the genetic structure of a top predator: loss of diversity and high differentiation among remnant populations of Atlantic Forest jaguars (Panthera onca)

Habitat fragmentation may disrupt original patterns of gene flow and lead to drift‐induced differentiation among local population units. Top predators such as the jaguar may be particularly susceptible to this effect, given their low population densities, leading to small effective sizes in local fragments. On the other hand, the jaguar’s high dispersal capabilities and relatively long generation time might counteract this process, slowing the effect of drift on local populations over the time frame of decades or centuries. In this study, we have addressed this issue by investigating the genetic structure of jaguars in a recently fragmented Atlantic Forest region, aiming to test whether loss of diversity and differentiation among local populations are detectable, and whether they can be attributed to the recent effect of drift. We used 13 microsatellite loci to characterize the genetic diversity present in four remnant populations, and observed marked differentiation among them, with evidence of recent allelic loss in local areas. Although some migrant and admixed individuals were identified, our results indicate that recent large‐scale habitat removal and fragmentation among these areas has been sufficiently strong to promote differentiation induced by drift and loss of alleles at each site. Low estimated effective sizes supported the inference that genetic drift could have caused this effect within a short time frame. These results indicate that jaguars’ ability to effectively disperse across the human‐dominated landscapes that separate the fragments is currently very limited, and that each fragment contains a small, isolated population that is already suffering from the effects of genetic drift.

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.

Participatory networks for large-scale monitoring of large carnivores: pumas and jaguars of the Upper Paraná Atlantic Forest

Most large carnivores are secretive and threatened, and these characteristics pose problems for research on, and monitoring of, these species across extensive areas. Participatory monitoring, however, can be a useful tool for obtaining long-term data across large areas. Pumas Puma concolor and jaguars Panthera onca are the largest predators in the threatened Upper Parana Atlantic Forest. To survey the presence of these two species we established a participatory network of volunteers and a partnership with researchers in the three countries that share the Upper Parana Atlantic Forest (Argentina, Brazil and Paraguay). We trained participants in simple methods of collecting faeces and track imprints of large felids. Between 2002 and 2008 > 100 volunteers helped with monitoring, obtaining 1,633 records identified as pumas or jaguars across c. 92,890 km 2 . We confirmed jaguar presence in a large section of the Misiones Green Corridor in Argentina and in the largest protected areas of Brazil and Paraguay. Pumas exhibited a wider distribution, being recorded throughout Misiones province in Argentina and in some areas of Brazil and Paraguay where jaguars were not detected. Both species, and especially jaguars, were detected mainly in the few remaining medium and large forest fragments in this Forest. Although these carnivores are often in conflict with local people, their charisma and cultural significance makes them flagship species that motivated the participation of volunteers and institutions. Participatory monitoring allowed coverage of a vast area at relatively low cost whilst enhancing collaborative management policies among people and institutions from three countries.

Selection of habitat by the jaguar, Panthera onca (Carnivora: Felidae), in the upper Paraná River, Brazil

We used data from VHF and GPS radio-tagged jaguars, Panthera onca (Linnaeus, 1758) to quantify jaguar habitat selection and how adult individuals in the Upper Parana River region selected among the available habitat types. We followed the framework in which animals make decisions about resource use at hierarchical stages, namely selection of home range within a study area (second-order selection) and selection of patches within a home range (third-order selection). We quantified habitat preferences at two orders of selection with respect to habitat types and to test the null hypothesis that habitat utilization by jaguars was random at both study sites. Using compositional analysis, we assessed habitat selection by jaguars at second- and third-orders of selection. Jaguars consistently preferred dense marshes and primary forests, and avoided human-dominated areas such as intensively managed open pastures. Although the avoidance of disturbed and developed habitat types by jaguars is not surprising, this is the first study to document it. If small protected areas, such as the ones already existing in the Upper Parana region, are to sustain jaguar populations they, must include and protect as many primary forests and marshlands as possible, so that jaguars can disperse, hunt wild prey and take care of their cubs without being disturbed. What is urgently needed in these jaguar-protected areas is the creation of larger protected areas that can sustain jaguars in their favored habitat.

Geographic distribution and food habits of Leopardus tigrinus and L. geoffroyi (Carnivora, Felidae) at their geographic contact zone in southern Brazil

The objective of this study is to define the geographic distribution of Leopardus tigrinus and L. geoffroyi in one of the few regions of South America where they co-occur, the state of Rio Grande do Sul (RS), in southernmost Brazil. We compiled 133 records for both species and constructed a distribution map, which shows sharp geographic segregation between them. Leopardus tigrinus was found to be associated more with forested ecoregions in the northern part of the state, while L. geoffroyi records were mainly associated with open habitats of the Pampas biome in southern RS. We present data on the diet of these two species that indicate trophic niche separation between them in this region of geographic contact. Our results thus suggest that these species exhibit ecological partitioning with respect to habitat and prey, and that these factors may influence the observed pattern of limited spatial overlap in this region.

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.

Molecular tracking of jaguar melanism using faecal DNA

Major evolutionary questions remain elusive due to persistent difficulties in directly studying the genetics of variable phenotypes in natural populations. Many phenotypic variants may be of adaptive relevance, and thus important to consider in the context of conservation genetics. However, since the dynamics of these traits is usually poorly understood in the wild, their incorporation in conservation strategies is difficult to accomplish. For animals which exhibit intriguing phenotypic variation but are difficult to track in the wild, innovative approaches are required to investigate such issues. Here we demonstrate that non-invasive DNA sampling can be used to study the genetics and ecology of melanism in the jaguar, by directly genotyping the molecular polymorphism underlying this coloration trait. These results open new prospects for the in-depth investigation of this polymorphism, and highlight the broader potential of non-invasive DNA-based phenotype tracking for wildlife in general.

Molecular evidence for a recent demographic expansion in the puma (Puma concolor) (Mammalia, Felidae)

The puma is an iconic predator that ranges throughout the Americas, occupying diverse habitats. Previous phylogeographic analyses have revealed that it exhibits moderate levels of genetic structure across its range, with few of the classically recognized subspecies being supported as distinct demographic units. Moreover, most of the species’ molecular diversity was found to be in South America. To further investigate the phylogeographic structure and demographic history of pumas we analyzed mtDNA sequences from 186 individuals sampled throughout their range, with emphasis on South America. Our objectives were to refine the phylogeographic assessment within South America and to investigate the demographic history of pumas using a coalescent approach. Our results extend previous phylogeographic findings, reassessing the delimitation of historical population units in South America and demonstrating that this species experienced a considerable demographic expansion in the Holocene, ca. 8,000 years ago. Our analyses indicate that this expansion occurred in South America, prior to the hypothesized re-colonization of North America, which was therefore inferred to be even more recent. The estimated demographic history supports the interpretation that pumas suffered a severe demographic decline in the Late Pleistocene throughout their distribution, followed by population expansion and re-colonization of the range, initiating from South America.

Genetic studies in representatives of genusRhipidomys (Rodentia, Sigmodontinae) from Brazil

Karyotypic polymorphism of five taxa of the rodent genusRhipidomys from the Brazilian Amazon and Cerrado biomes was analysed.Rhipidomys nitela Thomas, 1901 from Amazon has 2n=48, FN=68. The other species, all have 2n=44, but can be separated into two groups, one with high FNs (76, 80) and the other with low FNs (48, 52). Two cytotypes ofR. mastacalis (Lund, 1840) with high FNs were trapped in four localities of the Cerrado, showing 19 and 17 biarmed autosomes, respectively. A low FN (48) was observed inR. leucodactylus (Tschudi, 1844) in two localities of the Cerrado and FN=52 in one locality in the Cerrado and the Amazon. All taxa with 2n=44 have a medium-sized acrocentric X chromosome and a small Y.Rhipidomys nitela is different from the species with 2n=44 by presenting a heterochromatic short arm of the X chromosome. In all karyotypes analysed, the nucleolus organizer regions were located in the short arms of two to six pairs and the (T2AG3)n telomeric probes hybridizedin situ in both the short and long arms of all pairs of the karyotypes.