Comparing the accuracy of PCR-capillary electrophoresis and cuticle microhistological analysis for assessing diet composition in ungulates : a case study with Pyrenean chamois
Espunyes, Johan (Universitat Autònoma de Barcelona. Servei d'Ecopatologia de Fauna Salvatge)
Espunya Prat, M. Carme (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Chaves, Sara (Universitat Autònoma de Barcelona. Servei d'Ecopatologia de Fauna Salvatge)
Calleja Alarcón, Juan Antonio (Centre de Recerca Ecològica i d'Aplicacions Forestals)
Bartolomé, Jordi (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Serrano Ferron, Emmanuel (Universitat Autònoma de Barcelona. Servei d'Ecopatologia de Fauna Salvatge)

Fecha:	2019
Resumen:	The study of diet composition is required to understand the interactions between animal and plant ecosystems. Different non-invasive techniques applied on faecal samples have commonly been used for such purposes, with cuticle microhistological analysis (CMA) and emerging DNA-based methods being the most relevant. In this work, we refined and optimized a qualitative DNA-based approach combining PCR amplification of long trnL(UAA) and ITS2 fragments and capillary electrophoresis (PCR-CE), instead of short trnL(UAA) fragments and massive sequencing technologies commonly reported. To do so, we develope a controlled diet assay using a stabled Pyrenean chamois specimen (Rupicapra pirenaica pyrenaica), which included representative herbaceous and shrubby plant species. We also assessed the impact of sample freshness on the diet determination of this mountain caprinae by exposing faecal samples to the outdoor environment for three weeks. Faecal samples from both experiments were analysed by qualitative PCR-CE and semi-quantitative CMA in order to compare the pros and cons of both approaches. Our results show that all of the offered plant species were detected by both methodologies although CMA overdetected shrubs compared to herbaceous species. At the same time, sample degradation due to sustained climate exposure is a limiting factor for molecular analysis, but not for CMA. Taken all together, our results suggest that the qualitative information obtained by CMA and PCR-CE can be interchangeable when faecal samples are fresh (less than one week after deposition) but, afterwards, molecular analysis underestimates diet composition probably due to DNA degradation. CMA, however, can accurately be used at least three weeks after defecation. Moreover, by combining the results of simultaneous PCR amplification of two complementary genes, this optimized PCR-CE methodology provides a reliable, feasible and more affordable alternative for multiple and routine analyses of complex samples. Neither CMA nor PCR-CE seems to solve comprehensively the quatification of herbivore diets and thus further research needs to be done.
Ayudas:	Ministerio de Economía y Competitividad RYC-2016-2020
Nota:	Altres ajuts: GES/CGL2011-30307
Nota:	Altres ajuts: GES/CGL2015- 70449-R
Nota:	Altres ajuts: GAND/ATC015-AND-2015/2018
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Materia:	Animals salvatges ; Isards ; Aliments ; Hàbits i conducta ; Nutrició ; Pirineus (Serralada)
Publicado en:	PloS one, Vol. 14 Núm. 5 (2019) , ISSN 1932-6203

DOI: 10.1371/journal.pone.0216345
PMID: 31116750

19 p, 1.6 MB

El registro aparece en las colecciones:
Documentos de investigación > Documentos de los grupos de investigación de la UAB > Centros y grupos de investigación (producción científica) > Ciencias de la salud y biociencias > Grupo de investigación Wildlife Ecology & Health
Documentos de investigación > Documentos de los grupos de investigación de la UAB > Centros y grupos de investigación (producción científica) > Ciencias > CREAF (Centre de Recerca Ecològica i d'Aplicacions Forestals)
Documentos de investigación > Documentos de los grupos de investigación de la UAB > Centros y grupos de investigación (producción científica) > Ciencias de la salud y biociencias > Ruminant Research Group (G2R)
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