Who is who? High Resolution Melting analysis to discern between hare species using non-invasive sampling

The wildcat (Felis s. silvestris) in the Mediterranean forest: sighting through photo-trapping and non-invasive hair collection for genetic purposes

The European wildcat (Felis silvestris silvestris) is a mesocarnivore species widely distributed in Europe, from Eastern Europe to Portugal and from Scotland to Italy. Recent biogeographical studies of wildcat populations have endeavoured to assess in detail the various issues that pose a threat to this species, including hybridization with domestic cats. The use of non-invasive sampling methods supported by photo-trapping and some attractants has made it possible to gather genetic material for the detection of native wildcats in locally threatened populations, some of which live in the Iberian Peninsula. Testimonies of naturalists, hunters and farm workers led our team to choose specific areas in two large territories of Mediterranean forests where the presence of wildcats has been historically attested: the Almonte River basin and the Sierra de San Pedro Mountains. Between 2014 and 2018, non-invasive hair sampling was performed using valerian (Valeriana officinalis) as an attractant and supported by photo-trapping to guarantee the collection of genuine biological material (hair samples). The hair samples were genetically assessed by sequencing the nuclear gene IRBP (interphotoreceptor retinoid-binding protein) and the mtDNA gene ND4 (NADH dehydrogenase subunit 4). Despite the low density of wildcats, this combined protocol proved to be an applicable tool for detecting the presence of elusive wildcats and other mesocarnivore species in this remote region of southern Europe. In addition, non-invasive hair trapping contributes to the collection of genetic material from current wildcat populations. This procedure could enhance future management actions focused on collecting quality individualized biological material.

Application of real-time PCR for the identification of the endangered species Galemys pyrenaicus through faecal samples

BACKGROUND

Currently, many micromammals are important targets for study. The endangered Galemys pyrenaicus is an outstanding example. Globally, their populations have suffered a substantial decline in last 20 years. In the surveyed area, the capture of desman is legally forbidden due to the high conservation concerns. Reason by non-invasive sampling through faeces is proposed for its monitoring. Furthermore, the confusion between faeces from desman and Mediterranean water shrews must be considered. Thus, the aim of this study was focused on developing RT-PCR assays to determine the presence of Galemys pyrenaicus and N. a. anomalus from non-invasive samples.

METHODS AND RESULTS

The study was conducted in the mountains of the System Central of Extremadura (Spain). A total of 186 samples were collected from 2018 to 2021 by experts where historically reported and/or our previous studies confirmed their presence. RT-PCR assays using hydrolysis probes were designed to detect genetic material from both desman and Mediterranean water shrews and its specificity was confirmed. The reliability of the method was further assessed by PCR sequencing of mitochondrial Cyb and d-loop, resulting fully compatible with the RT-PCR approach. Intraspecific phylogenetic relationship was reported to improve knowledge about mtDNA variability in the desman from the Central System.

CONCLUSIONS

We demonstrated that RT-PCR gives a gold opportunity to further map the species using faeces which minimizes disturbance and reports both population status and individual presence. Cost-effective RT-PCR combined with field-collected faeces allows us to better investigate the full range of occurrence of the species.

Contribution to the ecology of the Italian hare (Lepus corsicanus)

The Italian hare (Lepus corsicanus) is endemic to Central-Southern Italy and Sicily, classified as vulnerable due to habitat alterations, low density and fragmented populations and ecological competition with the sympatric European hare (Lepus europaeus). Despite this status, only few and local studies have explored its ecological features. We provided some key traits of the ecological niche of the Italian hare as well as its potential distribution in the Italian peninsula. All data derived from genetically validated presences. We generated a habitat suitability model using maximum entropy distribution model for the Italian hare and its main competitor, the European hare. The dietary habits were obtained for the Italian hare with DNA metabarcoding and High-Throughput Sequencing on faecal pellets. The most relevant environmental variables affecting the potential distribution of the Italian hare are shared with the European hare, suggesting a potential competition. The variation in the observed altitudinal distribution is statistically significant between the two species.The diet of the Italian hare all year around includes 344 plant taxa accounted by 62 families. The Fagaceae, Fabaceae, Poaceae, Rosaceae and Solanaceae (counts > 20,000) represented the 90.22% of the total diet. Fabaceae (60.70%) and Fagaceae (67.47%) were the most abundant plant items occurring in the Spring/Summer and Autumn/Winter diets, respectively. The Spring/Summer diet showed richness (N = 266) and diversity index values (Shannon: 2.329, Evenness: 0.03858, Equitability: 0.4169) higher than the Autumn/Winter diet (N = 199, Shannon: 1.818, Evenness: 0.03096, Equitability: 0.3435). Our contribution adds important information to broaden the knowledge on the environmental (spatial and trophic) requirements of the Italian hare, representing effective support for fitting management actions in conservation planning.

The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach

Background

The Eurasian otter (Lutra lutra) underwent a strong decline in large areas of the Central-Western part of its distribution range, during the second half of the twentieth century. In Italy, only residual fragmented nuclei survive in the Central-Southern part of the peninsula. Nowadays, the otter is one of the most endangered mammals in Italy, and increasing the knowledge about the ecology of this species is a key step in defining fitting management strategies. Here we provide information about the diet of otter on the Agri river system, one of the most important presence sites in Italy, to understand both the species’ food requirements and the impact on fish communities.

Methods

DNA metabarcoding and High Throughput Sequencing were used on DNA extracted from spraints. We amplified DNA with a primer set for vertebrates, focusing efforts on the bulk of the otter’s diet (fishes and amphibians).

Results

Our findings showed that the diet of the otter was dominated by cyprinids (97.77%, and 99.14% of fishes), while amphibians represented 0.85% of the sequences analyzed. Results are in general accordance with previous studies based on morphological characterization; however, molecular analyses allow the resolving of some morphological uncertainties. Although the study area offers a very wide range of available prey, the diet of the otters shows marked selectivity. We highlighted a variation in prey consumed, in accordance with the typology of water system (i.e., river, lake, tributary). Some of the preys found in the diet were alien species introduced by man for sport fishing. Our findings could help define strategies useful for the conservation of the otter population in Southern Italy, suggesting management actions directed at avoiding fish community alterations through illegal stockings without severe controls on their taxonomic status. These introductions could result in a general reduction in the diversity of the otter’s preys, affecting its predatory behavior.