Assessing reliability of microsatellite genotypes from kit fox faecal samples using genetic and GIS analyses

Noninvasive faecal DNA sampling has the potential to provide a wealth of information necessary for monitoring and managing endangered species while eliminating the need to capture, handle or observe rare individuals. However, scoring problems, and subsequent genotyping errors, associated with this monitoring method remain a great concern as they can lead to misidentification of individuals and biased estimates. We examined a kit fox scat data set (353 scats; 80 genotypes) for genotyping errors using both genetic and GIS analyses, and evaluated the feasibility of combining both approaches to assess reliability of the faecal DNA results. We further checked the appropriateness of using faecal genotypes to study kit fox populations by describing information about foxes that we could deduce from the 'acceptable' scat genotypes, and comparing it to information gathered with traditional field techniques. Overall, genetic tests indicated that our data set had a low rate of genotyping error. Furthermore, examination of distributions of scat locations confirmed our data set was relatively error free. We found that analysing information on sex primer consistency and scat locations provided a useful assessment of scat genotype error, and greatly limited the amount of additional laboratory work that was needed to identify potentially 'false' scores. 'Acceptable' scat genotypes revealed information on sex ratio, relatedness, fox movement patterns, latrine use, and size of home range. Results from genetic and field data were consistent, supporting the conclusion that our data set had a very low rate of genotyping error and that this noninvasive method is a reliable approach for monitoring kit foxes.     

Dispersal of Spores of Mycorrhizal Fungi in Scats of Native Mammals in Tropical Forests of Northeastern Australia

One hundred and thirty-eight scat (faecal) samples from 17 mammal species native to forests of northeastern Queensland were examined for the presence of spores of both ectomycorrhizal and arbuscular mycorrhizal fungi. Spores of mycorrhizal fungi were found in 57 percent of scat samples representing 12 animal species (Aepyprymnus rufescens, Antechinus godmani, Bettongia tropica, Hypsiprymnodon moschatus, Isoodon macrourus, Melomys ceruinipes, Perameles nasuta, Rattus fuscipes, R. tunneyi, Thylogale stigmatica, Trichourur uulperula, Uromys caudimaculatus). Spores were absent in scats of Antechinus stuartii, Dasyurus hallucatus, Dendrolagus lumholtzi, Petaurus australis and Mesembriomys gouldii. Spores of ectomycorrhizal fungi occurred in 38 percent of scats, and all but one of these samples were from Eucalyptus-dominated sclerophyll forests. Based on the frequency and abundance of spores in scats, five mammals were considered active consumers of hypogeous mycorrhizal sporocarps in sclerophyll forests (A. rufescens, B. tropica, I. macrourus, P. nasuta, and U. caudimaculatus). Individual scats of these animals generally contained a range of distinctive spore types. Spores of arbuscular mycorrhizal fungi were found in low abundance in almost 40 percent of scat samples collected, from both sclerophyll forest and rainforest habitats. We suggest that the majoriry of these spores were acquired incidentally through ingestion of soil during foraging activities on the forest floor. Glasshouse inoculation experiments in which seedlings of Eucalyptus grandis and Sorghum bicolor were inoculated with scat material from several species of mammal demonstrated that the spores of ectomycorrhizal and arbuscular mycorrhizal fungi retained some viability and colonized the roots of host-plant seedlings. Insufficient information is known of the ecology of mycorrhizal fungi in Australia's tropical forests to speculate as to the implications of these findings for forest conservation and rehabilitation.     

High occurrence of jellyfish predation by black‐browed and Campbell albatross identified by DNA metabarcoding

Gelatinous zooplankton are a large component of the animal biomass in all marine environments, but are considered to be uncommon in the diet of most marine top predators. However, the diets of key predator groups like seabirds have conventionally been assessed from stomach content analyses, which cannot detect most gelatinous prey. As marine top predators are used to identify changes in the overall species composition of marine ecosystems, such biases in dietary assessment may impact our detection of important ecosystem regime shifts. We investigated albatross diet using DNA metabarcoding of scats to assess the prevalence of gelatinous zooplankton consumption by two albatross species, one of which is used as an indicator species for ecosystem monitoring. Black‐browed and Campbell albatross scats were collected from eight breeding colonies covering the circumpolar range of these birds over two consecutive breeding seasons. Fish was the main dietary item at most sites; however, cnidarian DNA, primarily from scyphozoan jellyfish, was present in 42% of samples overall and up to 80% of samples at some sites. Jellyfish was detected during all breeding stages and consumed by adults and chicks. Trawl fishery catches of jellyfish near the Falkland Islands indicate a similar frequency of jellyfish occurrence in albatross diets in years of high and low jellyfish availability, suggesting jellyfish consumption may be selective rather than opportunistic. Warmer oceans and overfishing of finfish are predicted to favour jellyfish population increases, and we demonstrate here that dietary DNA metabarcoding enables measurements of the contribution of gelatinous zooplankton to the diet of marine predators.     

Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania

The ability to detect the incursion of an invasive species or destroy the last individuals during an eradication program are some of the most difficult aspects of invasive species management. The presence of foxes in Tasmania is a contentious issue with recent structured monitoring efforts, involving collection of carnivore scats and testing for fox DNA, failing to detect any evidence of foxes. Understanding the likelihood that monitoring efforts would detect fox presence, given at least one is present, is therefore critical for understanding the role of scat monitoring for informing the response to an incursion. We undertook trials to estimate the probability of fox scat detection through monitoring by scat‐detector dogs and person searches and used this information to critically evaluate the power of scat monitoring efforts for detecting foxes in the Tasmanian landscape. The probability of detecting a single scat present in a 1‐km² survey unit was highest for scat‐detector dogs searches (0.053) compared with person searches () for each 10 km of search effort. Simulation of the power of recent scat monitoring efforts undertaken in Tasmania from 2011 to 2015 suggested that single foxes would have to be present in at least 20 different locations or fox breeding groups present in at least six different locations, in order to be detected with a high level of confidence (>0.80). We have shown that highly structured detection trials can provide managers with the quantitative tools needed to make judgments about the power of large‐scale scat monitoring programs. Results suggest that a fox population, if present in Tasmania, could remain undetected by a large‐scale, structured scat monitoring program. Therefore, it is likely that other forms of surveillance, in conjunction with scat monitoring, will be necessary to demonstrate that foxes are absent from Tasmania with high confidence.     

Endozoochorous dispersal of forest seeds by carnivorous mammals in Sierra Fría,Aguascalientes, Mexico

Some carnivorous mammals ingest fruit and disperse seeds of forest plant species capable of colonizing disturbed areas in ecosystems. The objective of the present study was to evaluate the dissemination of Arctostaphylos pungens and Juniperus deppeana seeds by the gray fox (Urocyon cinereoargenteus), coyote (Canis latrans), and other carnivores in the Protected Natural Area Sierra Fría, in Aguascalientes, Mexico. Scat collection was undertaken via transects using the direct search method, while the seasonal phenology of A. pungens and J. deppeana was evaluated by recording flower and fruit abundance on both the plant and the surrounding forest floor ground. Seed viability was assessed by optical densitometry via X‐ray and a germination test. It was found that the gray fox, coyote, ringtail (Bassariscus astutus), and bobcat (Lynx rufus) disseminated seeds of A. pungens (212 ± 48.9 seeds/scat) and J. deppeana (23.6 ± 4.9 seeds/scat), since a large proportion of the collected scat of these species contained seeds (28/30 = 93.33%, 12/43 = 27.9%, 6/12 = 50% and 7/25 = 28% respectively). The gray fox, coyote, ringtail, and bobcat presented an average of seed dispersion of both plant species of 185.4 ± 228.7, 4.0 ± 20.0, 12.1 ± 30.4, and 0.8 ± 1.5 per scat; the seed proportions in the gray fox, coyote, ringtail, and bobcat were 89.6/10.4%, 82.3/17.7%, 90.4/9.6%, and 38.1/61.9% for A. pungens and J. deppeana, respectively. The phenology indicated a finding related to the greater abundance of ripe fruit in autumn and winter (p < .01). This coincided with the greater abundance of seeds found in scats during these seasons. Endozoochory and diploendozoochory enhanced the viability and germination of the seeds (p > .05), except in those of A. pungens dispersed by coyote. These results suggest that carnivores, particularly the gray fox, the coyote, and the bobcat, play an important role in forest seed dissemination, and thus forest regeneration, by making both a quantitative and qualitative contribution to the dispersal of the two pioneer species under study.     

Olfactory discrimination in scat-piling lizards

Several lizard species in the Australian scincid genus Egernia havebeen reported to deposit scats in piles. We show that E. striolata,which does produce scat piles, and E. inornata, which does not,can both discriminate their own secretions, on paper substrates, fromthose of unfamiliar conspecifics. This was indicated by elevatedtongue flick rates and more time in contact with the unfamiliarstimulus. This was not just a response to a novel stimulus becausethe secretions from another species (E. stokesii) elicited lowerresponses. When scats were presented, only striolata demonstrateddiscrimination between their own scats and those of unfamiliarconspecifics. This suggests that scats could be used to produceindividual signals, perhaps indicating residence status, in scat-pilingspecies. For striolata the signal from scats became less effectiveas the scats became older, suggesting the need to pile scatsto renew the signal.