From: Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis
Parameter | Qualitative description | Default values and units |
---|---|---|
\(\left({y}_{i}, {z}_{i}\right)\) | The indispensability (\(y\)) and connectivity (\(z\)) of the \({i}^{th}\) population of transferable genes | Non-negative integers |
\(\Delta {x}_{i}\) | The realized change in \({y}_{i}\) or \({z}_{i}\) over one ancestor–descendant mapping due to gene-host coevolution | \(-1, 0, 1\) |
\(P\left(+1\right)\) | The probability that \(\Delta {x}_{i}=+1\) | \({10}^{-3}\) per mapping |
\(P\left(-1\right)\) | The probability that \(\Delta {x}_{i}=-1\) | \({10}^{-5}\) per mapping |
\(E(\Delta {x}_{i})\) | The expected value of \(\Delta {x}_{i}\) | Expected change per mapping |
\(N\) | The number of populations in the metapopulation of transferable genes | Non-negative integer |
\({N}_{max}\) | The maximum number of populations in the metapopulation of transferable genes | \({10}^{4}\) |
\({\beta }_{N}\) | The expected number of naïve microbial populations a population of transferable genes will enter by HGT over one ancestor–descendant mapping | A Poisson random variable with mean \({\beta }_{N}=\beta \left(1-N{/N}_{max}\right)\) per mapping \(\beta \in \left\{0.06, 0.08\right\}\) |
\(\delta\) | The probability that a microbial host population will be temporarily subjected to the neutral environmental state at some point over one ancestor–descendant mapping | \(0.01\) per mapping |
\({p}_{D}\left({y}_{i}\right)\) | The probability that a population of T will suffer death by gene loss in the neutral environmental state | \(\mathrm{exp}\left(-{y}_{i}s\right)\in \left[\mathrm{0,1}\right], s=0.20\) |
\({p}_{B}\left({z}_{i}\right)\) | The probability that a population of T will reproduce following HGT into a naïve microbial population | \(\mathrm{exp}\left(-{z}_{i}s\right)\in \left[\mathrm{0,1}\right], s=0.20\) |