Molecular dietary analysis of two sympatric felids in the Mountains of Southwest China biodiversity hotspot and conservation implications

Xiong, Mengyin; Wang, Dajun; Bu, Hongliang; Shao, Xinning; Zhang, Dan; Li, Sheng; Wang, Rongjiang; Yao, Meng

doi:10.1038/srep41909

Cited by 50 publications

(67 citation statements)

References 47 publications

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“…Many metabarcoding diet studies make use of both %FOO and POO (e.g., Xiong et al, 2017). POO provides a convenient view as each food taxon contributes a percentage of total diet (unlike %FOO which does not sum to 100%).…”

Section: Focalmentioning

confidence: 99%

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

et al. 2018

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Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi-quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa-specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low-level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population-level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.

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Section: Focalmentioning

confidence: 99%

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

et al. 2018

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“…Many metabarcoding diet studies make use of both %FOO and POO (e.g. Xiong et al 2017). POO 187 provides a convenient view since each food taxon contributes a percentage of total diet (unlike 188 %FOO which does not sum to 100%).…”

mentioning

confidence: 99%

Counting with DNA in metabarcoding studies: how should we convert sequence reads to dietary data?

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Thomas

McInnes

et al. 2018

Preprint

157

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“…Other studies have reported far lower success rates from faeces e.g. 47% to 71% in Atlantic puffin (Fratercula arctica) (Bowser et al 2013); 73% in Panthera species (Xiong et al 2017).…”

Section: Buccal Swabs and Dietary Analysesmentioning

confidence: 87%

Metabarcoding-based dietary analysis of hen harrier (Circus cyaneus) in Great Britain using buccal swabs from chicks

2019

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The hen harrier is a heavily persecuted bird of prey in Great Britain since its diet includes Red grouse, a game bird shot in driven and walked-up grouse shooting. Unlike walked-up shooting where shooters walk up moors and flush grouse with dogs, in driven grouse shooting the grouse are driven by beaters towards static shooters. Driven grouse moors (DGMs) are increasingly being managed to sustain high densities of Red grouse intensifying a long-standing conservation conflict between conservationists and grouse moor keepers. A metabarcoding approach was used with degenerate universal cytochrome oxidase I and cytochrome b primers along with hen harrier blocking primers. A novel sampling method was used to detect prey in buccal swab samples from chicks from broods across Great Britain from both managed and unmanaged moorland habitats. This resulted in detection of 62 species of prey across 51 broods with Meadow pipit, Red grouse, Wren, Skylark, and voles being most frequently detected. Frequency of occurrence data and species accumulation curves reveal high incidence of Red grouse and low prey species richness in the diet of hen harriers in DGMs but low incidence of Red grouse and high prey species richness in walked-up and unmanaged moors. Waders were only detected within walked-up and unmanaged moors and not within DGMs where they have been reported to occur at high densities. Regional species detected included endemic species such as the Orkney vole seen only in Orkney. This study represents the first metabarcoding-based dietary analysis in a raptor using buccal swabs.

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Molecular dietary analysis of two sympatric felids in the Mountains of Southwest China biodiversity hotspot and conservation implications

Cited by 50 publications

References 47 publications

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

Counting with DNA in metabarcoding studies: how should we convert sequence reads to dietary data?

Metabarcoding-based dietary analysis of hen harrier (Circus cyaneus) in Great Britain using buccal swabs from chicks

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