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Who is eating what: diet assessment using next generation sequencing
TLDR
The power and pitfalls of NGS diet methods are reviewed, the critical factors to take into account when choosing or designing a suitable barcode are presented and the validation of data accuracy including the viability of producing quantitative data is discussed. Expand
A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks
TLDR
A new genome-wide SNP genotyping array is developed to study patterns of genetic variation in sticklebacks over a wide geographic range, and to scan the genome for regions that contribute to repeated evolution of marine-freshwater or benthic-limnetic species pairs. Expand
DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match
TLDR
It is argued that COI does not contain suitably conserved regions for most amplicon-based metabarcoding applications and available marker choices should be broadened in order to maximize potential in this exciting field of research. Expand
Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces
TLDR
This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first of its kind to quantify the amounts of predator and prey DNA present within individual faecal samples. Expand
Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces
TLDR
The pyrosequencing approach presented significantly expands the capabilities of DNA‐based methods of dietary analysis and is suitable for large‐scale diet investigations on a broad range of animals. Expand
Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions
TLDR
A captive feeding trial to test whether prey DNA could be reliably detected in scat samples from Steller sea lions highlighted an approach that can accurately identify prey species and is not dependent on prey hard parts surviving digestion. Expand
Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?
TLDR
The results highlight that DNA sequences recovered in dietary barcoding studies can provide semi-quantitative information on diet composition, but these data should be given wide confidence intervals. Expand
Studying Seabird Diet through Genetic Analysis of Faeces: A Case Study on Macaroni Penguins (Eudyptes chrysolophus)
TLDR
The ability of the DNA-based approach to detect temporal variation in the diet of macaroni penguins indicates this non-invasive method will be generally useful for monitoring population-level dietary trends in seabirds. Expand
Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?
TLDR
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, and indicate that using relative read abundance information often provides a more accurate view of population‐level diet even with moderate recovery biases incorporated. Expand
Group‐specific polymerase chain reaction for DNA‐based analysis of species diversity and identity in dietary samples
TLDR
A range of group‐specific PCR primers for studying the prey diversity found in predator stomach contents and scats are developed and their application to studying prey diversity and identity in predator diet is described. Expand
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