Many biodiversity studies make use of metabarcoding, an approach which combines high-throughput sequencing (HTS) with DNA barcoding to characterise organisms in complex mixtures (e.g. in eDNA or bulk samples). The approach is also used to study animal diet by analysing food DNA in faecal samples. One features of HTS is that it provides counts of DNA sequences and therefore has the potential to provide not only a qualitative list, but also a quantitative assessment of what DNA is present. But what do these counts mean and do they reflect biomass of metazoans in a sample? Is it reasonable to use read proportions to retrieve semi-quantitative information, or should we work strictly with presence/absence datasets? Here, we explore how sequence counts are used in metabarcoding studies and discuss results from our research on animal diet (seals and seabirds) and zooplankton communities. We point out that summaries based on frequency of occurrence data have their own biases and argue that in some situations the quantitative interpretation of count data can be justified. We also outline our use of correction factors to account for taxa-specific recovery biases and the inclusion of internal standards to enable quantitative comparisons between samples.
Many biodiversity studies make use of metabarcoding, an approach which combines high-throughput sequencing (HTS) with DNA barcoding to characterise organisms in complex mixtures (e.g. in eDNA or bulk samples). The approach is also used to study animal diet by analysing food DNA in faecal samples. One features of HTS is that it provides counts of DNA sequences and therefore has the potential to provide not only a qualitative list, but also a quantitative assessment of what DNA is present. But what do these counts mean and do they reflect biomass of metazoans in a sample? Is it reasonable to use read proportions to retrieve semi-quantitative information, or should we work strictly with presence/absence datasets? Here, we explore how sequence counts are used in metabarcoding studies and discuss results from our research on animal diet (seals and seabirds) and zooplankton communities. We point out that summaries based on frequency of occurrence data have their own biases and argue that in some situations the quantitative interpretation of count data can be justified. We also outline our use of correction factors to account for taxa-specific recovery biases and the inclusion of internal standards to enable quantitative comparisons between samples.
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