Population genetic structure and habitat connectivity for jaguar (Panthera onca) conservation in Central Belize

Background Connectivity among jaguar (Panthera onca) populations will ensure natural gene flow and the long-term survival of the species throughout its range. Jaguar conservation efforts have focused primarily on connecting suitable habitat in a broad-scale. Accelerated habitat reduction, human-wildlife conflict, limited funding, and the complexity of jaguar behaviour have proven challenging to maintain connectivity between populations effectively. Here, we used non-invasive genetic sampling and individual-based conservation genetic analyses to assess genetic diversity and levels of genetic connectivity between individuals in the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We used expert knowledge and scientific literature to develop models of landscape permeability based on circuit theory with fine-scale landscape features as ecosystem types, distance to human settlements and roads to predict the most probable jaguar movement across central Belize. Results We used 12 highly polymorphic microsatellite loci to identify 50 individual jaguars. We detected high levels of genetic diversity across loci (HE = 0.61, HO = 0.55, and NA = 9.33). Using Bayesian clustering and multivariate models to assess gene flow and genetic structure, we identified one single group of jaguars (K = 1). We identified critical areas for jaguar movement that fall outside the boundaries of current protected areas in central Belize. We detected two main areas of high landscape permeability in a stretch of approximately 18 km between Sittee River Forest Reserve and Manatee Forest Reserve that may increase functional connectivity and facilitate jaguar dispersal from and to Cockscomb Basin Wildlife Sanctuary. Our analysis provides important insights on fine-scale genetic and landscape connectivity of jaguars in central Belize, an area of conservation concern. Conclusions The results of our study demonstrate high levels of relatively recent gene flow for jaguars between two study sites in central Belize. Our landscape analysis detected corridors of expected jaguar movement between the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We highlight the importance of maintaining already established corridors and consolidating new areas that further promote jaguar movement across suitable habitat beyond the boundaries of currently protected areas. Continued conservation efforts within identified corridors will further maintain and increase genetic connectivity in central Belize

Population genetic structure and phylogeography of pumas ( Puma concolor)

Pumas are a wide-ranging carnivore and capable of long-distance dispersal, so they should be genetically connected. The dispersal of pumas may be impeded by habitat fragmentation and increased encroachment of humans into suitable puma habitat, though no studies have addressed this issue. Pumas appear to be spatially structured based upon estimates of population subdivision from both mitochondrial DNA and highly polymorphic microsatellite loci. Pumas can be broadly grouped in North, Central (including Mexico), and South American metapopulations, with finer scale subdivision within those metapopulations. The reduced genetic diversity observed in the North American populations, relative to that of Central and South American populations, supports a previous hypothesis (Culver et al., 2000) of recolonization of North America by a founder population from these areas. Genetic diversity indices for these populations suggest pumas are moderately connected and should remain genetically viable for the foreseeable future. However, this study identified a population of pumas inhabiting the areas near the border northeastern Argentina and southwestern Brazil as being genetically isolated due to suitable habitat nearly completely surrounded by agricultural land. Additionally, a population of pumas inhabiting a peninsula on the Pacific coast of Costa Rica was also genetically distinct from surrounding populations, also indicating a lack of connectivity with other pumas. This study suggests that while pumas have viable levels of genetic diversity and connectivity, populations need to be monitored for genetic variability and genetic/geographic connectivity, especially in areas impacted by high levels of human modification. These types of studies will allow for the identification of at-risk populations and ensure the maintenance of dispersal corridors to maintain viable puma populations

Elbrochetal_JAnimEcol_Data

Location data used to create all home ranges and quantify home range overlap

Data from: Spatial overlap in a solitary carnivore: support for the land-tenure, kinship, or resource dispersion hypotheses?

1. There are several alternative hypotheses about the effects of territoriality, kinship, and prey availability on individual carnivore distributions within populations. The first is the land-tenure hypothesis, which predicts that carnivores regulate their density through territoriality and temporal avoidance. The second is the kinship hypothesis, which predicts related individuals will be clumped within populations, and the third is the resource dispersion hypothesis, which suggests that resource richness may explain variable sociality, spatial overlap, or temporary aggregations of conspecifics. 2. Research on the socio-spatial organization of animals is essential in understanding territoriality, intra- and inter-specific competition, and contact rates that influence diverse ecology, including disease transmission between conspecifics and courtship behaviors. 3. We explored these hypotheses with data collected on a solitary carnivore, the cougar (Puma concolor), from 2005 to 2012 in the Southern Yellowstone Ecosystem, Wyoming, USA. We employed 27 annual home ranges for 13 cougars to test whether home range overlap was better explained by land-tenure, kinship, resource dispersion, or some combination of the three. 4. We found support for both the land-tenure and resource dispersion hypotheses, but not for kinship. Cougar sex was the primary driver explaining variation in home range overlap. Males overlapped significantly with females, whereas the remaining dyads (F-F, M-M) overlapped significantly less. In support for the resource dispersion hypothesis, hunting opportunity (the probability of a cougar killing prey in a given location) was often higher in overlapping than in non-overlapping portions of cougar home ranges. In particular, winter hunt opportunity rather than summer hunt opportunity was higher in overlapping portions of female-female and male-female home ranges. 5. Our results may indicate that solitary carnivores are more tolerant of sharing key resources with unrelated conspecifics than previously believed, or at least during periods of high resource availability. Further, our results suggest that the resource dispersion hypothesis, which is typically applied to social species, is applicable in describing the spatial organization of solitary carnivores

Adaptive social strategies in a solitary carnivore

Cost-benefit trade-offs for individuals participating in social behaviors are the basis for current theories on the evolution of social behaviors and societies. However, research on social strategies has largely ignored solitary animals, in which we assume that rare interactions are explained by courtship or territoriality or, in special circumstances, resource distributions or kinship. We used directed network analysis of conspecific tolerance at food sources to provide evidence that a solitary carnivore, the puma (Puma concolor), exhibited adaptive social strategies similar to more social animals. Every puma in our analysis participated in the network, which featured densely connected communities delineated by territorial males. Territorial males also structured social interactions among pumas. Contrary to expectations, conspecific tolerance was best characterized by direct reciprocity, establishing a fitness benefit to individuals that participated in social behaviors. However, reciprocity operated on a longer time scale than in gregarious species. Tolerance was also explained by hierarchical reciprocity, which we defined as network triangles in which one puma (generally male) received tolerance from two others (generally females) that also tolerated each other. Hierarchical reciprocity suggested that males might be cheating females; nevertheless, we suspect that males and females used different fitness currencies. For example, females may have benefited from tolerating males through the maintenance of social niches that support breeding opportunities. Our work contributes evidence of adaptive social strategies in a solitary carnivore and support for the applicability of theories of social behavior across taxa, including solitary species in which they are rarely tested

Data from: Genetic diversity and population structure of Mesoamerican jaguars (Panthera onca): implications for conservation and management

Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of understanding levels of genetic diversity and connectivity to making informed management and conservation decisions with the goal to maintain functional connectivity across the region

Coyotes in New York City Carry Variable Genomic Dog Ancestry and Influence Their Interactions with Humans

Coyotes are ubiquitous on the North American landscape as a result of their recent expansion across the continent. They have been documented in the heart of some of the most urbanized cities, such as Chicago, Los Angeles, and New York City. Here, we explored the genomic composition of 16 coyotes in the New York metropolitan area to investigate genomic demography and admixture for urban-dwelling canids in Queens County, New York. We identified moderate-to-high estimates of relatedness among coyotes living in Queens (r = 0.0–0.5) and adjacent neighborhoods, suggestive of a relatively small population. Although we found low background levels of domestic-dog ancestry across most coyotes in our sample (5%), we identified a male suspected to be a first-generation coyote–dog hybrid with 46% dog ancestry, as well as his two putative backcrossed offspring that carried approximately 25% dog ancestry. The male coyote–dog hybrid and one backcrossed offspring each carried two transposable element insertions that are associated with human-directed hypersociability in dogs and gray wolves. An additional, unrelated coyote with little dog ancestry also carried two of these insertions. These genetic patterns suggest that gene flow from domestic dogs may become an increasingly important consideration as coyotes continue to inhabit metropolitan regions

Response of pumas (Puma concolor) to migration of their primary prey in Patagonia.

Large-scale ungulate migrations result in changes in prey availability for top predators and, as a consequence, can alter predator behavior. Migration may include entire populations of prey species, but often prey populations exhibit partial migration with some individuals remaining resident and others migrating. Interactions of migratory prey and predators have been documented in North America and some other parts of the world, but are poorly studied in South America. We examined the response of pumas (Puma concolor) to seasonal migration of guanacos (Lama guanicoe) in La Payunia Reserve in northern Patagonia Argentina, which is the site of the longest known ungulate migration in South America. More than 15,000 guanacos migrate seasonally in this landscape, and some guanacos also are resident year-round. We hypothesized that pumas would respond to the guanaco migration by consuming more alternative prey rather than migrating with guanacos because of the territoriality of pumas and availability of alternative prey throughout the year at this site. To determine whether pumas moved seasonally with the guanacos, we conducted camera trapping in the summer and winter range of guanacos across both seasons and estimated density of pumas with spatial mark-resight (SMR) models. Also, we analyzed puma scats to assess changes in prey consumption in response to guanaco migration. Density estimates of pumas did not change significantly in the winter and summer range of guanacos when guanacos migrated to and from these areas, indicating that pumas do not follow the migration of guanacos. Pumas also did not consume more alternative native prey or livestock when guanaco availability was lower, but rather fed primarily on guanacos and some alternative prey during all seasons. Alternative prey were most common in the diet during summer when guanacos also were abundant on the summer range. The response of pumas to the migration of guanacos differs from sites in the western North America where entire prey populations migrate and pumas migrate with their prey or switch to more abundant prey when their primary prey migrates

Results of the global STRUCTURE analysis in Mesoamerican jaguars.

<p>The optimal number of genetic clusters (<i>K</i>) in Mesoamerican jaguars (<i>n</i> = 115) applying Bayesian clustering methods in STRUCTURE, version 2.3.4 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162377#pone.0162377.ref047" target="_blank">47</a>] was chosen based on posterior probabilities (mean L(<i>K</i>); A) and delta <i>K</i> (Δ<i>K</i>, mean (|L”(<i>K</i>)|)/SD(L(<i>K</i>)); D) for each <i>K</i> value. SD, standard deviation; L’(<i>K</i>), mean rate of change of the likelihood distribution (B); |L”(<i>K</i>)|, absolute value of the 2^nd order rate of change of the likelihood distribution (C).</p