Capacity Building at InBIO for Research and Innovation Using Environmental Metagenomics

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From species detection to population size indexing: the use of sign surveys for monitoring a rare and otherwise elusive small mammal

Publication . Peralta, Dinora; Vaz‑Freire, Teresa; Ferreira, Clara; Mendes, Tiago; Mira, António; Santos, Sara; Alves, Paulo C.; Lambin, Xavier; Beja, Pedro; Paupério, Joana; Pita, Ricardo

Monitoring the occupancy and abundance of wildlife populations is key to evaluate their conservation status and trends. However, estimating these parameters often involves time and resource-intensive techniques, which are logistically challeng- ing or even unfeasible for rare and elusive species that occur patchily and in small numbers. Hence, surveys based on field identification of signs (e.g. faeces, footprints) have long been considered a cost-effective alternative in wildlife monitoring, provided they produce reliable detectability and meaningful indices of population abundance. We tested the use of sign sur- veys for monitoring rare and otherwise elusive small mammals, focusing on the Cabrera vole (Microtus cabrerae) in Portugal. We asked how sampling intensity affects true positive detection of the species, and whether sign abundance is related to population size. We surveyed Cabrera voles’ latrines in 20 habitat patches known to be occupied, and estimated ‘true’ popula- tion size at each patch using DNA-based capture-recapture techniques. We found that a searching rate of ca. 3 min/250m2 of habitat based on adaptive guided transects was sufficient to provide true positive detection probabilities > 0.85. Sign-based abundance indices were at best moderately correlated with estimates of ‘true’ population size, and even so only for search- ing rates > 12 min/250m 2 . Our study suggests that surveys based on field identification of signs should provide a reliable option to estimate occupancy of Cabrera voles, and possibly for other rare or elusive small mammals, but cautions should be exercised when using this approach to infer population size. In case of practical constraints to the use of more accurate methods, a considerable sampling intensity is needed to reliably index Cabrera voles’ abundance from sign surveys.

2023-02Journal article

Open access

Multi-species occupancy modeling reveals methodological and environmental effects on eDNA detection of amphibians in temporary ponds

Publication . Peixoto, Sara; Mota-Ferreira, Mário; Chaves, Cátia; Velo-Antón, Guillermo; Beja, Pedro; Egeter, Bastian

Aquatic environmental DNA is increasingly used for biodiversity monitoring, such as surveying threatened and invasive species. Mainstreaming these methods in practi- cal applications, however, still requires significant standardization and optimisation, namely regarding DNA capture methods. Here we evaluated how filter type (standard disc filters vs high-capacity capsules), number of sampling sites, volume of water fil- tered and environmental factors affected amphibian detection in Mediterranean tem - porary ponds. The study involved water filtering until clogging at one (capsules) and five (discs) sites from 16 small and shallow ponds, where three urodele and seven anu- ran species were recorded through sweep- netting and adult observations. Detection probabilities were estimated from site occupancy models based on replicate sampling and from an adaptation of time-to-detection models relating detection probability to volume of water filtered. Discs filtered relatively small volumes (15–1250 mL), with detection probabilities of the two abundant species (Pelobates cultripes, Hyla meridi- onalis) increasing rapidly with sample size and water volume, reaching almost per- fect detection (0.95) at four and seven discs, and 420 mL and 1860 mL, respectively. However, reaching high detection probabilities for rare species (Pelodytes atlanticus, Pleurodeles waltl, Triturus pygmaeus) would require larger sampling effort than that used in our study. Despite filtering much larger volumes (600–5300 mL), filtering with capsules at a single site per pond provided lower detection probabilities for abun- dant species than filtering with discs at five sites. Rarer species showed no difference between methods, which may be due to small sample sizes and reduced statistical power for species with few detections. The effect of conductivity on species detect- ability was largely negative, while the influence of water clarity varied across species, and pH had no effects. Overall, our results suggest that eDNA amphibian surveys in Mediterranean temporary ponds need to consider filter clogging, heterogeneous DNA distribution, and highly conductive waters

2023-07Journal article

Open access