Taiana Haag

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.

Phylogenetic relationships among species of the genus Calomys with emphasis on south american lowland taxa

Abstract Calomys Waterhouse, 1837, is one of the most speciose genera of the Phyllotini tribe of the South American sigmodontine rodents. Distributed predominately in southern South America, the genus has been proposed to have originated in the central Andes with further differentiation as subsequent occupations of the lowlands of the continent occurred. In this study, 30 newly obtained sequences of the cytochrome-b gene from specimens collected in Brazil were analyzed in conjunction with data available in GenBank in an attempt to discern the dispersion patterns of this genus in the South American lowlands. The analyses support a scenario where a phyllotine lineage appeared in the Andes and later separated into 2 larger clades. Members of 1 clade remained in the highlands (C. musculinus, C. lepidus, and C. sorellus), experiencing some local differentiation. Members of the 2nd clade invaded the lowlands of South America, especially nonforested biomes, where they underwent intense differentiation resulting in species with wide distributions in the continent. In the lowland clade, the “callosus–venustus” group is more derived, is characterized by a larger body size, and has a broad distribution; differentiation of this group was probably accompanied by some reduction in chromosomal diploid numbers.

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.

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.

Population Genetics of Jaguars (Panthera onca) in the Brazilian Pantanal: Molecular Evidence for Demographic Connectivity on a Regional Scale

Habitat loss and fragmentation are important threats to carnivores worldwide, and can be especially intense for large predators. Jaguars have already been extirpated from over half of their original area of distribution, and few regions still maintain large populations. For these, detailed understanding is crucial for setting appropriate recovery targets in impacted areas. The Pantanal is among the best examples of a region with a large jaguar population in a healthy environment. Here, we analyzed 12 microsatellite loci to characterize genetic diversity and population structure of 52 jaguars sampled in 4 localities of the southern Pantanal, and compared them with prior studies of heavily fragmented populations of the Atlantic Forest. Although we observed some internal structure among the Pantanal localities, our results indicated that this area comprises a single population with high genetic variability. Moreover, our comparative analyses supported the hypothesis that the strong population structure observed in the Atlantic Forest derives from recent, anthropogenic fragmentation. We also observed significant but low levels of genetic differentiation between the Pantanal and Atlantic Forest populations, indicating recent connectivity between jaguars occurring in these biomes. Evidence for admixture between the Pantanal and a population on the western boundary of the Atlantic Forest corroborates the transitional nature of the latter area, where the jaguar population has already been extirpated. Our results can be used to understand jaguar population dynamics in a region that is less disturbed than the Atlantic forest, and to support the design of conservation strategies that maintain and restore natural connectivity among currently isolated areas.Habitat loss and fragmentation are important threats to carnivores worldwide, and can be especially intense for large predators. Jaguars have already been extirpated from over half of their original area of distribution, and few regions still maintain large populations. For these, detailed understanding is crucial for setting appropriate recovery targets in impacted areas. The Pantanal is among the best examples of a region with a large jaguar population in a healthy environment. Here, we analyzed 12 microsatellite loci to characterize genetic diversity and population structure of 52 jaguars sampled in 4 localities of the southern Pantanal, and compared them with prior studies of heavily fragmented populations of the Atlantic Forest. Although we observed some internal structure among the Pantanal localities, our results indicated that this area comprises a single population with high genetic variability. Moreover, our comparative analyses supported the hypothesis that the strong population structure observed in the Atlantic Forest derives from recent, anthropogenic fragmentation. We also observed significant but low levels of genetic differentiation between the Pantanal and Atlantic Forest populations, indicating recent connectivity between jaguars occurring in these biomes. Evidence for admixture between the Pantanal and a population on the western boundary of the Atlantic Forest corroborates the transitional nature of the latter area, where the jaguar population has already been extirpated. Our results can be used to understand jaguar population dynamics in a region that is less disturbed than the Atlantic forest, and to support the design of conservation strategies that maintain and restore natural connectivity among currently isolated areas.

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.

Multiple methods increase detection of large and medium-sized mammals: working with volunteers in south-eastern Oman

We compared the effectiveness of various methods for surveying medium and large wild mammals in southern Oman. Working with volunteers recruited by Biosphere Expeditions, wildlife professionals and local rangers, we used direct observation, camera traps, sign surveys (tracks and/or dung) and molecular scatology to study 66 sampling units of 2 × 2 km (grid cells) in an area of 32 × 36 km during a 4-week period in February–March 2011. Sixteen mammal species were recorded, and the largest numbers of species were recorded by sign surveys and camera traps (both n = 9); sign surveys, direct sightings and DNA scatology recorded species across the largest number of grid cells. For species with a sample size large enough for comparison (i.e. detected in ≥ 8 grid cells), DNA scatology proved most effective for detecting caracal Caracal caracal , signs for hyaena Hyaena hyaena , ibex Capra nubiana , porcupine Hystrix indica and hyrax Procavia capensis , and signs and direct sightings for mountain gazelle Gazella gazella . Clustering, in which records from multiple methods are either adjacent or overlapping, was highest (≥ 76%) for the wolf Canis lupus , porcupine, ibex and gazelle. Our results indicate the best methods to detect and record the distributions of individual species in the study area, and demonstrate the advantage of using multiple methods to reduce the risk of false absences or partial detections. Our findings also highlight the potential of clustering as a means of cross-checking results of observations that are skill-dependent, which is particularly useful when employing a large workforce.