We analyze patterns of gene presence and absence in a maximum likelihood framework with rate parameters for gene gain and loss. Standard methods allow independent gains and losses in different parts of a tree. While losses of the same gene are likely to be frequent, multiple gains need to be considered carefully. A gene gain could occur by horizontal transfer or by origin of a gene within the lineage being studied. If a gene is gained more than once, then at least one of these gains must be a horizontal transfer. A key parameter is the ratio of gain to loss rates, a/v We consider the limiting case known as the infinitely many genes model, where a/v tends to zero and a gene cannot be gained more than once. The infinitely many genes model is used as a null model in comparison to models that allow multiple gains. Using genome data from cyanobacteria and archaea, it is found that the likelihood is significantly improved by allowing for multiple gains, but the average a/v is very small. The fraction of genes whose presence/absence pattern is best explained by multiple gains is only 15% in the cyanobacteria and 20% and 39% in two data sets of archaea. The distribution of rates of gene loss is very broad, which explains why many genes follow a treelike pattern of vertical inheritance, despite the presence of a significant minority of genes that undergo horizontal transfer.
We consider competition between antibiotic producing bacteria, non-producers (or cheaters), and sensitive cells in a two-dimensional lattice model. Previous work has shown that these three cell types can survive in spatial models due to the presence of spatial patterns, whereas coexistence is not possible in a well-mixed system. We extend this to consider the evolution of the antibiotic production rate, assuming that the cost of antibiotic production leads to a reduction in growth rate of the producers. We find that coexistence occurs for an intermediate range of antibiotic production rate. If production rate is too high or too low, only sensitive cells survive. When evolution of production rate is allowed, a mixture of cell types arises in which there is a dominant producer strain that produces sufficient to limit the growth of sensitive cells and which is able to withstand the presence of cheaters in its own species. The mixture includes a range of low-rate producers and non-producers, none of which could survive without the presence of the dominant producer strain. We also consider the case of evolution of antibiotic resistance within the sensitive species. In order for the resistant cells to survive, they must grow faster than both the non-producers and the producers. However, if the resistant cells grow too rapidly, the producing species is eliminated, after which the resistance mutation is no longer useful, and sensitive cells take over the system. We show that there is a range of growth rates of the resistant cells where the two species coexist, and where the production mechanism is maintained as a polymorphism in the producing species and the resistance mechanism is maintained as a polymorphism in the sensitive species.
14We consider competition between antibiotic producing bacteria, non-producers (or cheaters), and 15 sensitive cells in a two-dimensional lattice model. Previous work has shown that these three cell 16 types can survive in spatial models due to the presence of spatial patterns, whereas coexistence is 17 not possible in a well-mixed system. We extend this to consider the evolution of the antibiotic 18 production rate, assuming that the cost of antibiotic production leads to a reduction in growth 19 rate of the producers. We find that coexistence occurs for an intermediate range of antibiotic 20 production rate. If production rate is too high or too low, only sensitive cells survive. When 21 evolution of production rate is allowed, a mixture of cell types arises in which there is a 22 dominant producer strain that produces sufficient to limit the growth of sensitive cells and which 23 is able to withstand the presence of cheaters in its own species. The mixture includes a range of 24 low-rate producers and non-producers, none of which could survive without the presence of the 25 dominant producer strain. We also consider the case of evolution of antibiotic resistance within 26 the sensitive species. In order for the resistant cells to survive, they must grow faster than both 27 the non-producers and the producers. However, if the resistant cells grow too rapidly, the 28 producing species is eliminated, after which the resistance mutation is no longer useful, and 29 sensitive cells take over the system. We show that there is a range of growth rates of the resistant 30 cells where the two species coexist, and where the production mechanism is maintained as a 31 polymorphism in the producing species and the resistance mechanism is maintained as a 32 polymorphism in the sensitive species. Natural environments such as the soil contain many species of antibiotic producing bacteria. 37Antibiotics prevent the growth of sensitive species that would otherwise outcompete the more-38 slowly-growing antibiotic producers. The producers are also vulnerable to competition from non-39 producing "cheats" arising by mutations within the producing species that avoid the metabolic . CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/342600 doi: bioRxiv preprint first posted online Jun.
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