DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents

Lopes, Carla Martins; Barba, Marta De; Boyer, Frédéric; Mercier, Céline; Filho, Pedro Joel Silva da Silva; Heidtmann, L M; Galiano, Daniel; Kubiak, Bruno Busnello; Langone, Patrícia Quintana; Garcias, Felipe M.; Gielly, Ludovic; Coissac, Éric; Freitas, Thales Renato Ochotorena de; Taberlet, Pierre

doi:10.1038/hdy.2014.109

Cited by 69 publications

(82 citation statements)

References 34 publications

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“…To ensure fresh scats are collected in the field, some studies have captured or contained animals (Kartzinel & Pringle ; Lopes et al . ), or placed sheets to collect fresh faeces (Deagle et al . ; Vesterinen et al .…”

Section: Discussionmentioning

confidence: 99%

Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates

et al. 2016

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Summary1. DNA metabarcoding of food in animal scats provides a non-invasive dietary analysis method for vertebrates. A variety of molecular approaches can be used to recover dietary DNA from scats; however, many of these also recover non-food DNA. Blocking primers can be used to inhibit amplification of some non-target DNA, but this may not always be feasible, especially when multiple distinct non-target groups are present. 2. We have developed scat collection protocols to optimise the detection of food DNA in vertebrate scat samples. Using shy albatross Thalassarche cauta as a case study, we investigated how DNA amplification success and the proportion of food DNA detected are influenced by both environmental and physiological parameters. We show that both the amount and type of non-target DNA vary with sample freshness, the collection substrate, fasting period and developmental stage of the consumer. 3. Fresh scat samples yielded the highest proportion of food sequences. Collecting scats from dirt substrates reduced the proportion of food DNA and increased the proportion of contaminating DNA. Food DNA detection rates changed throughout the albatross breeding season and related to the time since feeding and the developmental stage of the animal. Fasting albatross produced scats dominated by parasite amplicons in universal PCR analysis, with little food DNA recovered. Samples from very young animals also produced reduced food DNA proportions. 4. Based on our observations, we recommend the following procedures for field scat collections to ensure highquality samples for dietary DNA metabarcoding studies. Ideally, (i) collect fresh scats; (ii) from surfaces with minimal contamination (e.g. rock or ice); (iii) collect scats from animals with minimum time since feeding and avoid fasting animals; (iv) avoid young animals that are not feeding directly (e.g. not weaned or fledged) or target larger/older individuals. The optimised field sampling protocols that we describe will improve the quality of dietary data from vertebrates by focusing on samples most likely to contain food DNA. They will also help minimise contamination issues from non-target DNA and provide standardised field methods in this rapidly expanding area of research.

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Section: Discussionmentioning

confidence: 99%

Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates

et al. 2016

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“…This method has been used to noninvasively study diet in a diverse range of species including Adelie penguins ( Pygoscelis adeliae ; Jarman et al., ), golden‐crowned sifaka ( Propithecus tattersalli ; Quéméré et al., ), subterranean rodents ( Ctenomys sp. ; Lopes et al., ), tapir ( Tapirus terrestris ; Hibert et al., ), brown bears (De Barba et al., ; Elfström et al., ; Valentini et al., ), golden marmots ( Marmota caudata ; Valentini et al., ), African herbivores (Kartzinel et al., ), Hawaiin tree snails ( Achatinella spp. ; O'Rorke et al., ; Price, O'Rorke, Amend, & Hadfield, ), red deer ( Cervus elaphus ; Fløjgaard, De Barba, Taberlet, & Ejrnæs, ) and leopard cats ( Prionailurus bengalensis ; Shehzad et al., ).…”

Section: Questions and Metrics That Can Be Investigated With Mismentioning

confidence: 99%

Genetic and genomic monitoring with minimally invasive sampling methods

Carroll

Bruford

DeWoody

et al. 2018

Evolutionary Applications

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The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD‐seq) require large amounts of high‐quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low‐quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next‐generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.

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“…The study of animal predator diets has an old and rich history in ecology (e.g., Elton, ; Valverde, ), contributing to the understanding of species interactions, food web structure and the mechanisms driving populations and ecosystem dynamics (Layman et al., ; Nielsen, Clare, Hayden, Brett, & Kratina, ). The advent of DNA‐based molecular tools for the identification of complex multitaxa samples, that is metabarcoding, has greatly renewed the interest in dietary studies, particularly due to the high taxonomic resolution offered by this approach (e.g., De Barba et al., ; Kartzinel & Pringle, ; Lopes et al., ). This has been especially relevant to species whose diet is particularly difficult to study, either due to their secretive behaviour (e.g., Shehzad et al., ; Soininen et al., ) or due to difficulties to identify prey in dietary remains such as stomach contents, regurgitates and scats (e.g., Arrizabalaga‐Escudero et al., ; Kaunisto, Roslin, Sääksjärvi, & Vesterinen, ; Mollot et al., ).…”

Section: Introductionmentioning

confidence: 99%

How much is enough? Effects of technical and biological replication on metabarcoding dietary analysis

et al. 2018

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DNA metabarcoding is increasingly used in dietary studies to estimate diversity, composition and frequency of occurrence of prey items. However, few studies have assessed how technical and biological replication affect the accuracy of diet estimates. This study addresses these issues using the European free-tailed bat Tadarida teniotis, involving high-throughput sequencing of a small fragment of the COI gene in 15 separate faecal pellets and a 15-pellet pool per each of 20 bats. We investigated how diet descriptors were affected by variability among (a) individuals, (b) pellets of each individual and (c) PCRs of each pellet. In addition, we investigated the impact of (d) analysing separate pellets vs. pellet pools. We found that diet diversity estimates increased steadily with the number of pellets analysed per individual, with seven pellets required to detect ~80% of prey species. Most variation in diet composition was associated with differences among individual bats, followed by pellets per individual and PCRs per pellet. The accuracy of frequency of occurrence estimates increased with the number of pellets analysed per bat, with the highest error rates recorded for prey consumed infrequently by many individuals. Pools provided poor estimates of diet diversity and frequency of occurrence, which were comparable to analysing a single pellet per individual, and consistently missed the less common prey items. Overall, our results stress that maximizing biological replication is critical in dietary metabarcoding studies and emphasize that analysing several samples per individual rather than pooled samples produce more accurate results.

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DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents

Cited by 69 publications

References 34 publications

Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates

Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates

Genetic and genomic monitoring with minimally invasive sampling methods

How much is enough? Effects of technical and biological replication on metabarcoding dietary analysis

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