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Data from: Multi-scale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin

When using this data, please cite the original article:

Childs LM, Held NL, Young MJ, Whitaker RJ, Weitz JS (2012) Multi-scale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin. Evolution, online in advance of print. doi:10.1111/j.1558-5646.2012.01595.x

Additionally, please cite the Dryad data package:

Childs LM, Held NL, Young MJ, Whitaker RJ, Weitz JS (2012) Data from: Multi-scale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin. Dryad Digital Repository. doi:10.5061/dryad.gc2260qm
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Dryad Package Identifier doi:10.5061/dryad.gc2260qm    153 views  
Abstract The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered type of adaptive immune defense in bacteria and archaea that functions via directed incorporation of viral and plasmid DNA into host genomes. Here, we introduce a multi-scale model of dynamic coevolution between hosts and viruses in an ecological context that incorporates CRISPR immunity principles. We analyze the model to test whether and how CRISPR immunity induces host and viral diversification and the maintenance of many coexisting strains. We show that hosts and viruses coevolve to form highly diverse communities. We observe the punctuated replacement of extant strains, so that populations have very low similarity compared over the long term. However in the short term, we observe evolutionary dynamics consistent with both incomplete selective sweeps of novel strains and the recurrence of previously rare strains. Coalitions of multiple dominant host strains are predicted to arise because host strains can have nearly identical immune phenotypes mediated by CRISPR defense albeit with different genotypes. We close by discussing how our explicit eco-evolutionary model of CRISPR immunity can help guide efforts to understand the drivers of diversity seen in microbial communities where CRISPR systems are active.
Keywords Models/Simulations, Coevolution, Population Biology, Competition,
Date Deposited 2012-01-26T19:04:38Z
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Multi-Scale Model of CRISPR-Induced Coevolutionary Dynamics    21 views   13 downloads View File Details
This code presents a flexible framework for considering the co-evolutionary dynamics of hosts and viruses which interact via a CRISPR immune mechanism. The code is written in Matlab. Instructions on how to utilize the code including an example file are found in the README file.
Download: README.txt ( 1.493Kb )
Download: CRISPRCoevol_Code_Childs_etal_Evolution2012.zip ( 25.21Kb )
To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data.  


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