Extracting abundance information from DNA ‐based data

The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, multiple sources of bias and noise in sampling and processing combine to inject error into DNA-based data sets. To understand how to extract abundance information, it is useful to distinguish two concepts. (i) Within-sample across-species quantification describes relative species abundances in one sample. (ii) Across-sample within-species quantification describes how the abundance of each individual species varies from sample to sample, such as over a time series, an environmental gradient or different experimental treatments. First, we review the literature on methods to recover across-species abundance information (by removing what we call "species pipeline biases") and within-species abundance information (by removing what we call "pipeline noise"). We argue that many ecological questions can be answered with just within-species quantification, and we therefore demonstrate how to use a "DNA spike-in" to correct for pipeline noise and recover within-species abundance information. We also introduce a model-based estimator that can be used on data sets without a physical spike-in to approximate and correct for pipeline noise.

The Time Value of Leaf Area

When a plant invests in construction of a leaf, the revenue-stream that accrues is shaped by three variables: first, the light-capture area per milligram dry mass invested, analogous to a potential rate of return on investment; second, the longevity of the leaf, analogous to the expected duration of the revenue stream; and third, a time-discount rate, quantifying the fact that light-capture area deployed in the immediate future is more valuable to the plant than the same area deployed at some later time. Recent comparative data make it possible to quantify the cross-species trade-off between the first variable and the second variable. Here we develop an approach through which the consequences of the third variable, the time-discount rate, can be related to the trade-off between the first variable and the second variable. The approach involves an equal-benefit set, the cross-species equivalent of a fitness set. A wide spread of strategies is actually observed to coexist in vegetation, from low to high light capture area per gram and, correspondingly, from high to low leaf longevity. The coexistence suggests that the different observed strategies do not have a clear-cut advantage over the other. The equal-benefit set can be used to investigate what levels of time discount would make it the case that neither the highest-longevity nor the highest light-capture area per milligram strategies would have a clear advantage over the other, with regard to the time-discounted value of the revenue stream generated per milligram invested in leaf.

The Time Value of Leaf Area

When a plant invests in construction of a leaf, the revenue-stream that accrues is shaped by three variables: first, the light-capture area per milligram dry mass invested, analogous to a potential rate of return on investment; second, the longevity of the leaf, analogous to the expected duration of the revenue stream; and third, a time-discount rate, quantifying the fact that light-capture area deployed in the immediate future is more valuable to the plant than the same area deployed at some later time. Recent comparative data make it possible to quantify the cross-species trade-off between the first variable and the second variable. Here we develop an approach through which the consequences of the third variable, the time-discount rate, can be related to the trade-off between the first variable and the second variable. The approach involves an equal-benefit set, the cross-species equivalent of a fitness set. A wide spread of strategies is actually observed to coexist in vegetation, from low to high light capture area per gram and, correspondingly, from high to low leaf longevity. The coexistence suggests that the different observed strategies do not have a clear-cut advantage over the other. The equal-benefit set can be used to investigate what levels of time discount would make it the case that neither the highest-longevity nor the highest light-capture area per milligram strategies would have a clear advantage over the other, with regard to the time-discounted value of the revenue stream generated per milligram invested in leaf.