English: Modeling relic DNA dynamics

(a) The amount of relic DNA in a microbial environment is determined by inputs associated with the mortality of viable individuals with intact DNA and by losses associated with the degradation of relic DNA. If the diversity of sequences contained in the relic DNA pool is sufficiently different from that in the intact DNA pool, then relic DNA may bias estimates of microbial biodiversity (as indicated by different colored boxes) when sampling from the total (intact + relic) DNA pool.
(b) We developed a sampling-based simulation model to explore the effects of mixing intact and relic DNA on estimates of diversity. We populated intact and relic communities with individuals from a lognormal species abundance distribution (SAD). We altered the diversity (i.e., evenness, E) of the relic community by changing the scale parameter of the lognormal distribution describing the SAD. We then sampled and mixed the intact and relic communities so that the relic contribution to total community ranged from 0.01 to 0.96.
(c) To gain mechanistic insight into how bias arises, we created a stochastic process-based model that captures features that influence relic DNA dynamics, including immigration, birth, death, and degradation (a). We simulated a range of degradation rates to achieve relic DNA pool sizes with proportions ranging between 0.05 and 0.95.

To explore how degradation alters the SAD of the relic community, we explored three scenarios. First, we simulated a neutral scenario where relic DNA sequences produced by different species degrade at the same rate. Second, we simulated conditions under which physical, chemical, or biological processes reduce the degradation rate of relic DNA belonging to some species via protection. Third, we simulated “hot spots” where more abundant relic DNA sequences experience higher rates of relic DNA degradation, a condition that may arise in structured habitats where there are patchy distributions of individuals and their metabolic products (i.e., enzymes). We ran simulations for 10,000 time steps and then sampled the intact and relic communities. To quantify bias in diversity (b and c), we calculated “richness ratios” which reflect the number of species in the total DNA pool (intact + relic) divided by the number of species in the intact DNA pool in a simulation.

When values for richness ratios equal 1, relic DNA has no effect on estimates of diversity; when richness ratios are >1, relic DNA overestimates true diversity; and when richness ratios are <1, relic DNA underestimates true diversity.