Human disturbance has contrasting effects on niche partitioning within carnivore communities

Among species, coexistence is driven partly by the partitioning of available resources. The mechanisms of coexistence and competition among species have been a central topic within community ecology, with particular focus on mammalian carnivore community research. However, despite growing concern regarding the impact of humans on the behaviour of species, very little is known about the effect of humans on species interactions. The aim of this review is to establish a comprehensive framework for the impacts of human disturbance on three dimensions (spatial, temporal and trophic) of niche partitioning within carnivore communities and subsequent effects on both intraguild competition and community structure. We conducted a systematic review of the literature on carnivore niche partitioning (246 studies) and extracted 46 reported effects of human disturbance. We found evidence that human disturbance impacts resource partitioning, either positively or negatively, in all three niche dimensions. The repercussions of such variations are highly heterogeneous and differ according to both the type of human disturbance and how the landscape and/or availability of resources are affected. We propose a theoretical framework of the three main outcomes for the impacts of human disturbance on intraguild competition and carnivore community structure: (i) human disturbance impedes niche partitioning, increasing intraguild competition and reducing the richness and diversity of the community; (ii) human disturbance unbalances niche partitioning and intraguild competition, affecting community stability; and (iii) human disturbance facilitates niche partitioning, decreasing intraguild competition and enriching the community. We call for better integration of the impact of humans on carnivore communities in future research on interspecific competition.

Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore

Background

Different population trajectories are expected to impact the signature of neutral and adaptive processes at multiple levels, challenging the assessment of the relative roles of different microevolutionary forces. Here, we integrate adaptive and neutral variability patterns to disentangle how adaptive diversity is driven under different demographic scenarios within the Iberian wolf (Canis lupus) range. We studied the persistent, the expanding and a small, isolated group within the Iberian wolf population, using 3 MHC class II genes (DRB1, DQA1, and DQB1), which diversity was compared with 39 microsatellite loci.

Results

Both the persistent and the expanding groups show evidence of balancing selection, revealed by a significant departure from neutrality at MHC loci, significant higher observed and expected heterozygosity and lower differentiation at MHC than at neutral loci, and signs of positive selection. However, despite exhibiting a significantly higher genetic diversity than the isolated group, the persistent group did not show significant excess of MHC heterozygotes. The expanding group, while showing a similar level of genetic diversity than the persistent group, displays by contrast a significant excess of MHC heterozygotes, which is compatible with the heterozygote advantage mechanism. Results are not clear regarding the role of drift and selection in the isolated group due to the small size of this population. Although diversity indices of MHC loci correspond to neutral expectations in the isolated group, accelerated MHC divergence, revealed by a higher differentiation at MHC than neutral loci, may indicate diversifying selection.

Conclusion

Different selective pressures were observed in the three different demographic scenarios, which are possibly driven by different selection mechanisms to maintain adaptive diversity.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1420-5) contains supplementary material, which is available to authorized users.

Gray wolf mortality patterns in Wisconsin from 1979 to 2012

Starting in the 1970s, many populations of large-bodied mammalian carnivores began to recover from centuries of human-caused eradication and habitat destruction. The recovery of several such populations has since slowed or reversed due to mortality caused by humans. Illegal killing (poaching) is a primary cause of death in many carnivore populations. Law enforcement agencies face difficulties in preventing poaching and scientists face challenges in measuring it. Both challenges are exacerbated when evidence is concealed or ignored. We present data on deaths of 937 Wisconsin gray wolves (Canis lupus) from October 1979 to April 2012 during a period in which wolves were recolonizing historic range mainly under federal government protection. We found and partially remedied sampling and measurement biases in the source data by reexamining necropsy reports and reconstructing the numbers and causes of some wolf deaths that were never reported. From 431 deaths and disappearances of radiocollared wolves aged > 7.5 months, we estimated human causes accounted for two-thirds of reported and reconstructed deaths, including poaching in 39-45%, vehicle collisions in 13%, legal killing by state agents in 6%, and nonhuman causes in 36-42%. Our estimate of poaching remained an underestimate because of persistent sources of uncertainty and systematic underreporting. Unreported deaths accounted for over two-thirds of all mortality annually among wolves > 7.5 months old. One-half of all poached wolves went unreported, or > 80% of poached wolves not being monitored by radiotelemetry went unreported. The annual mortality rate averaged 18% ± 10% for monitored wolves but 47% ± 19% for unmonitored wolves. That difference appeared to be due largely to radiocollaring being concentrated in the core areas of wolf range, as well as higher rates of human-caused mortality in the periphery of wolf range. We detected an average 4% decline in wolf population growth in the last 5 years of the study. Because our estimates of poaching risk and overall mortality rate exceeded official estimates after 2012, we present all data for transparency and replication. More recent additions of public hunting quotas after 2012 appear unsustainable without effective curtailment of poaching. Effective antipoaching enforcement will require more accurate estimates of poaching rate, location, and timing than currently available. Independent scientific review of methods and data will improve antipoaching policies for large carnivore conservation, especially for controversial species facing high levels of human-induced mortality.

Intensity of space use reveals conditional sex-specific effects of prey and conspecific density on home range size

Home range (HR) size variation is often linked to resource abundance, with sex differences expected to relate to sex‐specific fitness consequences. However, studies generally fail to disentangle the effects of the two main drivers of HR size variation, food and conspecific density, and rarely consider how their relative influence change over spatiotemporal scales. We used location data from 77 Eurasian lynx (Lynx lynx) from a 16‐year Scandinavian study to examine HR sizes variation relative to prey and conspecific density at different spatiotemporal scales. By varying the isopleth parameter (intensity of use) defining the HR, we show that sex‐specific effects were conditional on the spatial scale considered. Males had larger HRs than females in all seasons. Females' total HR size declined as prey and conspecific density increased, whereas males' total HR was only affected by conspecific density. However, as the intensity of use within the HR increased (from 90% to 50% isopleth), the relationship between prey density and area showed opposing patterns for females and males; for females, the prey density effect was reduced, while for males, prey became increasingly important. Thus, prey influenced the size of key regions within male HRs, despite total HR size being independent of prey density. Males reduced their HR size during the mating season, likely to remain close to individual females in estrous. Females reduced their HR size postreproduction probably because of movement constrains imposed by dependent young. Our findings highlight the importance of simultaneously considering resources and intraspecific interactions as HR size determinants. We show that sex‐specific demands influence the importance of prey and conspecific density on space use at different spatiotemporal scales. Thus, unless a gradient of space use intensity is examined, factors not related to total HR size might be disregarded despite their importance in determining size of key regions within the HR.

A New Method for Noninvasive Genetic Sampling of Saliva in Ecological Research

Noninvasive samples for genetic analyses have become essential to address ecological questions. Popular noninvasive samples such as faeces contain degraded DNA which may compromise genotyping success. Saliva is an excellent alternative DNA source but scarcity of suitable collection methods makes its use anecdotal in field ecological studies. We develop a noninvasive method of collection that combines baits and porous materials able to capture saliva. We report its potential in optimal conditions, using confined dogs and collecting saliva early after deposition. DNA concentration in saliva extracts was generally high (mean 14 ng μl^-1). We correctly identified individuals in 78% of samples conservatively using ten microsatellite loci, and 90% of samples using only eight loci. Consensus genotypes closely matched reference genotypes obtained from hair DNA (99% of identification successes and 91% of failures). Mean genotyping effort needed for identification using ten loci was 2.2 replicates. Genotyping errors occurred at a very low frequency (allelic dropout: 2.3%; false alleles: 1.5%). Individual identification success increased with duration of substrate handling inside dog’s mouth and the volume of saliva collected. Low identification success was associated with baits rich in DNA-oxidant polyphenols and DNA concentrations <1 ng μl^-1. The procedure performed at least as well as other noninvasive methods, and could advantageously allow detection of socially low-ranked individuals underrepresented in sources of DNA that are involved in marking behaviour (faeces or urine). Once adapted and refined, there is promise for this technique to allow potentially high rates of individual identification in ecological field studies requiring noninvasive sampling of wild vertebrates.

Revisiting food-based models of territoriality in solitary predators

Food availability is considered a major factor determining spacing behaviour in territorial species, especially for females. Theoretically, spatial overlap (considered the opposite of territoriality) and food availability are related in a nonlinear manner (hypothesized inverted-U function), with high overlap levels at the extremes of a food availability gradient and low overlap at intermediate levels of this gradient. Similar patterns are expected for encounter frequencies owing to its expected correlation with spatial overlap. However, these predictions have rarely been tested in highly structured social systems on a broad gradient of food availability, which implicitly requires experimental manipulation. We test these predictions in a solitary, territorial and trophic specialist, the Iberian lynx Lynx pardinus, taking advantage of a three-decade data set of spatial behaviour in different scenarios of food availability (i.e. rabbit density). In contrast with expectations, home range overlap among resident females was low (median overlap index = 0.08, range 0-0.57) and core area overlap was nearly nil (median overlap index = 0, range 0-0.22) throughout the entire gradient of prey availability. Furthermore, spatial associations between pairs of females were negligible regardless marked variation in prey availability. Therefore, we did not find support for a model of flexible lynx territoriality driven by food availability. Our results suggest that the exclusive use of space in the Iberian lynx was not related to food. Lack of influence of prey availability on lynx territoriality may be adaptive to cope with the consequences of frequent drought-induced periods of prey scarcity or other disturbance typically affecting wild rabbit populations in Mediterranean environments. Thus, lynx would adopt an obstinate strategy of territoriality that consists in defending exclusive areas across a broad range of resource availability ensuring an exclusive access to the minimum amount of prey necessary for survival and eventually reproduction even during periods of prey scarcity. However, we found signs that territoriality was influenced by lynx density in a nonlinear fashion. Our results suggest the occurrence of population regulation through territoriality in this species.

Genetics at the verge of extinction: insights from the Iberian lynx

Population viability might become compromised by the loss of genetic diversity and the accumulation of inbreeding resulting from population decline and fragmentation. The Iberian lynx (Lynx pardinus) provides a paradigmatic example of a species at the verge of extinction, and because of the well-documented and different demographic histories of the two remaining populations (Doñana and Andújar), it provides the opportunity to evaluate the performance of analytical methods commonly applied to recently declined populations. We used mitochondrial sequences and 36 microsatellite markers to evaluate the current genetic status of the species and to assess the genetic signatures of its past history. Mitochondrial diversity was extremely low with only two haplotypes, alternatively fixed in each population. Both remnant populations have low levels of genetic diversity at microsatellite markers, particularly the population from Doñana, and genetic differentiation between the two populations is high. Bayesian coalescent-based methods suggest an earlier decline starting hundreds of years ago, while heterozygosity excess and M-ratio tests did not provide conclusive and consistent evidence for recent bottlenecks. Also, a model of gene flow received overwhelming support over a model of pure drift. Results that are in conflict with the known recent demography of the species call for caution in the use of these methods, especially when no information on previous demographic history is available. Overall, our results suggest that current genetic patterns in the Iberian lynx are mainly the result of its recent decline and fragmentation and alerts on possible genetic risks for its persistence. Conservation strategies should explicitly consider this threat and incorporate an integrated genetic management of wild, captive and re-introduced populations, including genetic restoration through translocations.

Feline leukemia virus outbreak in the critically endangered Iberian lynx (Lynx pardinus): high-throughput sequencing of envelope variable region A and experimental transmission

The Iberian lynx is the most endangered felid species. During winter/spring 2006/7, a feline leukemia virus (FeLV) outbreak of unexpected virulence killed about 2/3 of the infected Iberian lynxes. All FeLV-positive animals were co-infected with feline hemoplasmas. To further characterize the Iberian lynx FeLV strain and evaluate its potential virulence, the FeLV envelope gene variable region A (VRA) mutant spectrum was analyzed using the Roche 454 sequencing technology, and an in vivo transmission study of lynx blood to specified-pathogen-free cats was performed. VRA mutations indicated weak apolipoprotein B mRNA editing enzyme and catalytic polypeptide-like cytidine deaminase (APOBEC) restriction of FeLV replication, and variants characteristic of aggressive FeLV strains, such as FeLV-C or FeLV-A/61C, were not detected. Cats exposed to FeLV/Candidatus Mycoplasma haemominutum-positive lynx blood did not show a particularly severe outcome of infection. The results underscore the special susceptibility of Iberian lynxes to infectious diseases.

Competitive asymmetries in the use of supplementary food by the endangered Iberian lynx (Lynx pardinus)

Background

As a conservation tool, supplementary feeding programs may be directed to specific individuals or sectors of the target population whose productivity or survival is thought to be limited by food scarcity. However, the use of supplemental food by different sex and age classes has received little attention. We studied individual variation in the access of the endangered Iberian lynx (Lynx pardinus) to supplementary food.

Methodology/Principal Findings

From 5349 pictures taken with automatic cameras placed in 25 feeding stations, we identified 28 individuals whose sex and age were known. All individuals known to live in areas subjected to supplementation regularly visited feeding stations. Food consumption was not proportional to expected variations in energy demand within sex and age classes. Food consumption by males was higher than by females, and increased with age, in agreement with a despotic distribution. Food consumption also increased with lynx body mass, and this pattern held for individuals sharing the same breeding territories. The access of inferior competitors increased with the number of feeding stations available within lynx territories.

Conclusions/Significance

All lynx exposed to food supplementation made a regular use of extra food but individuals predicted to be competitively dominant visited stations more frequently than subordinates of the same breeding territory. Our results suggest that insufficient provision of supplementary food could restrict the access of juveniles, or even adult females, to feeding stations. Limited consumption by these target individuals may compromise the efficiency of the supplementary feeding programme at the population level, in endangered species that, as the Iberian lynx, exhibit marked sexual dimorphism in body size.

Feline leukemia virus infection: a threat for the survival of the critically endangered Iberian lynx (Lynx pardinus)

The Iberian lynx (Lynx pardinus) is considered the most endangered felid species in the world. To date, less than 200 animals remain in the wild. Low numbers and genetic uniformity may contribute to render this species particularly susceptible to infectious diseases. Different pathogens have been identified in Iberian lynxes; including several feline bacterial and viral agents. Within a 6-month period starting in December 2006, 12 lynxes living in the northern part of the Doñana area were found to be infected with feline leukemia virus (FeLV). Eleven of these animals were antigenemic, and four of them died in the wild in less than 6 months since the first infected animal had been discovered. The remaining viremic lynxes were captured and allocated to a quarantine center to stop the spread of the infection. An additional three animals died shortly in the quarantine center due to acute anemic disease. Sequencing of the envelope surface unit gene revealed a common origin for the FeLV found in all lynxes. The sequences were closely related to FeLV-A/61E, originally isolated from cats in the USA. Our data demonstrate that, similarly to FeLV, the introduction of a new or particularly pathogenic infection brought into the small population of Iberian lynxes by other wild carnivores or feral cats and dogs roaming in the same habitats have severe consequences. It could result in epidemics that have the potential to eradicate the entire lynx population.

Levels of heavy metals and metalloids in critically endangered Iberian lynx and other wild carnivores from Southern Spain

The Iberian lynx (Lynx pardinus) is the most endangered felid in the world with a wild population which probably stands at less than 200 individuals inhabiting two areas in Southern Spain (Doñana and Sierra Morena) that are known to have been contaminated by heavy metals and metalloids due to a long history of mining activities. This contamination may pose a threat to long term conservation efforts and hence, the concentrations of seven elements (As, Se, Cd, Zn, Cu, Pb, Hg) were determined in the liver, muscle and bone of 9 lynx, as well as 17 red foxes (Vulpes vulpes), 11 Egyptian mongooses (Herpestes ichneumon), 4 common genets (Genetta genetta) and 1 Eurasian badger (Meles meles). The mean concentrations found were below the threshold levels indicative of chronic intoxication in all the species studied. In general, genet and red fox were species with the highest concentrations of several elements in Doñana, whilst Iberian lynx had the lowest levels of most of them. Lynx from Sierra Morena had significantly higher concentrations of bone Pb (2.05 microg/g d.w.) than those from Doñana (0.13 microg/g d.w.), probably due to the mineralised underlying geology and/or the abandoned mine workings in Sierra Morena. Egyptian mongoose presented liver concentrations of Hg up to 9.7 microg/g d.w. A strong relationship between Hg and Se levels was found in liver and muscle samples of all the studied species, especially in mongoose. In conclusion, levels of the studied elements do not appear to represent a significant threat for the lynx or for the other carnivores studied. However, given the critical status of the Iberian lynx, a continuous monitoring scheme remains necessary.

Ectoparasites of the endangered Iberian lynx Lynx pardinus and sympatric wild and domestic carnivores in Spain

Ectoparasites can cause important skin disorders in animals and can also transmit pathogens. The Iberian lynx Lynx pardinus has been stated to be the most endangered felid in the world and such vector-borne pathogens may threaten its survival. We surveyed 98 wild carnivores (26 Iberian lynxes, 34 red foxes Vulpes vulpes, 24 Egyptian mongooses Herpestes ichneumon, 11 common genets Genetta genetta, two Eurasian badgers Meles meles, one polecat Mustela putorius) and 75 domestic but free-ranging carnivores (46 cats Felis catus, 29 dogs Canis familiaris) from June 2004 to June 2006 in the two areas where the last lynx metapopulations survive: Sierra Morena and Doñana (Andalusia, southern Spain). A total of 65% of lynxes were parasitized (50% by ticks, 19% by fleas, 4% by lice, 31% by hippoboscid flies), as were 75% of foxes (58%, 60%, 0%, 19%), 71% of mongooses (50%, 4%, 46%, 0%), 54% of genets (18%, 36%, 0%, 0%), 30% of cats (22%, 14%, 0%, 2%), and 7% of dogs (surveyed only for ticks). Both badgers presented ticks, fleas and lice. Five species of ixodid ticks (Rhipicephalus pusillus Gil Collado, Rhipicephalus turanicus Pomerantzev and Matikashvili, Ixodes ricinus (Linnaeus), Ixodes hexagonus Leach and Ixodes ventalloi Gil Collado; and Hyalomma sp.), four species of fleas (Ctenocephalides canis Curtis, Pulex irritans Linnaeus, Spilopsyllus cuniculi (Dale), Xenopsylla cunicularis Smit), three species of chewing lice (Felicola (Felicola) inequalis (Piaget), Trichodectes (Trichodectes) melis (Fabricius), and Felicola (Lorisicola) isidoroi Pérez and Palma), and one species of hippoboscid fly (Hippobosca longipennis (Fabricius)) were found. We did not detect any cases of mange. Hippobosca longipennis is a new record for Spanish wildlife, and all the flea species are new records for the Iberian lynx. Fleas were more frequent on lynxes and foxes in winter than in spring. Rhipicephalus spp. were more frequent on cats in spring than in any other season. These and other epidemiological findings are discussed with respect to the conservation of the Iberian lynx.