Can scat-based species identification be a misleading sign of presence? More evidences from northeastern portugal

Abstract

Abstract Species identification of non-invasively collected samples using molecular genetics tools has become an important tool in ecological research. For decades, scat-based ecological studies were almost exclusively rooted in morphological identification of scats, within local context, in the field. However, this approach raised a controversial debate, due to species and context-specific probability of error and lack of validation. In this study, we aimed to test the accuracy of mesocarnivore scats identification, based on morphological criteria, using a carnivore guild in northeastern Portugal as a model and molecular identification as a standard for accuracy of morphological identifications, within local context. While using only expert-based identifications for comparison with molecular identification standard, we have also compared the identifications performed by observers with different levels of experience. We extracted DNA from 63 scats (NE Portugal), which was successfully amplified/sequenced from 83% (n= 52) of the extracts: 38 were molecularly assigned to red fox (Vulpes vulpes), eight to stone marten (Martes foina), two to pine marten (Martes martes) and domestic dog (Canis lupus familiaris) and one to European badger (Meles meles) and common genet (Genetta genetta). There was a tendency for better performance by more experienced researchers, with 67% of scats being correctly assigned, but differences among observers were not significant. Due to the small sample size, only for foxes and stone martens was possible to estimate the error rate in species assignment, based on morphological criteria. False positive rates (% of times a scat was misassigned to a given species) were 4% for fox samples and 62% for stone marten. False negative rates (i.e. the rate at which a scat of a given species was assigned to another species) reached 29% for fox (scats that were initially assigned to stone marten and domestic dog were in fact from fox) and 25% for stone marten (originally misassigned to weasel, Mustela nivalis), respectively. The results support the need to implement molecular methods in ecological studies based on scat identification, so researchers can determine the error rates associated with morphological discrimination to develop accurate monitoring studies. Keywords: Mesocarnivore, Mitochondrial DNA, Monitoring, Non-invasive sampling, Species molecular identification. Resumen La identificacion de especies mediante tecnicas no invasivas, como la genetica molecular, se ha revelado de importancia en la investigacion ecologica. Durante decadas, la identificacion de excrementos en estudios ecologicos se baso casi exclusivamente en la identificacion morfologica de heces, que a menudo tenian en cuenta la informacion sobre el habitat y la ubicacion del excremento. Sin embargo, este enfoque planteaba serios debates, por la elevada probabilidad de error especifico y por la falta de validacion. El objetivo de este estudio es comprobar el grado de precision a la hora de identificar heces de mesocarnivoros mediante criterios morfologicos, validando estos resultados con la identificacion molecular. Mientras utilizamos solo identificaciones realizadas por expertos para comparar con el estandar de identificacion molecular, tambien comparamos las identificaciones realizadas por observadores con diferentes niveles de experiencia. Se extrajo ADN de 63 heces de mesocarnivoros (NE Portugal), de las cuales fue amplificado y secuenciado con exito el 83% (n= 52) de los extractos: 38 se identificaron molecularmente como de zorro (Vulpes vulpes), ocho como de garduna (Martes foina), dos de marta (Martes martes) y perro domestico (Canis lupus familiaris) y uno de tejon (Meles meles) y gineta (Genetta genetta). Debido al pequeno tamano de la muestra, tan solo fue posible estimar la tasa de error de identificacion de excrementos segun criterios morfologicos (% de veces que las heces fueran mal asignadas a una especie determinada en el campo o en el laboratorio) para zorro y garduna: 4% para muestras de zorro y 62% para las de garduna. La tasa de error cuando se asigno el excremento de una especie a otra en el campo o en el laboratorio (confirmada por tecnicas moleculares) alcanzo el 29% para el zorro (heces identificadas inicialmente como de garduna y de perro) y del 25% para la garduna (heces asignadas a comadreja, Mustela nivalis). Los resultados confirman la conveniencia de incluir metodos moleculares en los estudios ecologicos basados en la identificacion de excrementos, de forma que los investigadores puedan determinar la tasa de error asociada con la discriminacion morfologica para desarrollar estudios de monitoreo mas precisos. Palabras clave: ADN mitocondrial, identificacion molecular especies, mesocarnivoro, monitoreo, muestreo no invasivo. DOI: 10.7325/Galemys.2020.A5