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

Buglione, Maria; Petrelli, Simona; Notomista, Tommaso; Filippo, Gabriele de; Gregorio, Romano; Fulgione, Domenico

doi:10.1007/s12686-020-01153-9

Cited by 11 publications

(7 citation statements)

References 46 publications

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“…Indeed, the use of gNIS provides practical and ethical method, preferable to other strategies to study animal ecology, that manipulate the individuals, inducing stress and mortality, or require high field effort, such as live-trapping. This is particularly useful when working on elusive species, like hares, or rare and vulnerable species like the endemic Italian hare 25 , 27 . However, faecal DNA is often highly degraded 43 , it contains low template concentration and it carries PCR inhibitors from the environment or the digestive system, reducing the success of the genetic analyses 44 , 45 .…”

Section: Discussionmentioning

confidence: 99%

“…Species assignment was developed using HRM analysis 67 on Rotor-Gene Q 5-Plex (QIAGEN GmbH Valencia, CA, USA) with the Type-it HRM PCR Kit (QIAGEN GmbH Valencia, CA, USA). Experimental protocol and raw data analyses (using Rotor-Gene Q software v. 2.1.0 (QIAGEN GmbH Valencia, CA, USA) were performed following 25 . The assignment of unknown samples to corresponding hare species was made using their resulting melting profile compared to positive controls melting curves.…”

Section: Methodsmentioning

confidence: 99%

“…Moreover, the Italian hare is also threatened by ecological competition with native and exotic lineages of the European hare, a cosmopolitan species intensively restocked as a game species 19 – 21 . Because of these reintroductions, there are some areas in Italy where the Italian hare and the European hare occur in sympatry 19 , 20 , 22 – 25 .…”

Section: Introductionmentioning

confidence: 99%

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

Buglione

Petrelli

Filippo³

et al. 2020

Sci Rep

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Buglione

Petrelli

Filippo³

et al. 2020

Sci Rep

Self Cite

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“…Old spraints were removed the day before each sampling session, with collection taking place the following day in the early morning, to reduce the time interval from defecation to collection. Furthermore, all scats were manipulated with sterilized tools and the samples were placed in a sterile tube together with silica granules to speed up drying ( Wasser et al, 1997 ; Buglione et al, 2020b ).…”

Section: Methodsmentioning

confidence: 99%

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

Buglione

Petrelli

Troiano

et al. 2020

PeerJ

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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.

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Section: Sample Collectionmentioning

confidence: 99%

Peer Review #1 of "The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach (v0.1)"

2020

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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 to resolve 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.

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

Cited by 11 publications

References 46 publications

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

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

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

Peer Review #1 of "The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach (v0.1)"

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