10.5061/DRYAD.2VM20
Childs, Lauren M.
Harvard University
England, Whitney E.
University of Illinois at Urbana Champaign
Young, Mark J.
Montana State University
Weitz, Joshua S.
Georgia Institute of Technology
Whitaker, Rachel J.
University of Illinois at Urbana Champaign
Data from: CRISPR-induced distributed immunity in microbial populations
Dryad
dataset
2015
Models/simulation
Evolutionary biology
immunity mechanism
Population biology
Host-parasite interaction
Host-viral coevolution
2015-06-13T00:00:00Z
2015-06-13T00:00:00Z
en
https://doi.org/10.1371/journal.pone.0101710
36054 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
In bacteria and archaea, viruses are the primary infectious agents, acting
as virulent, often deadly pathogens. A form of adaptive immune defense
known as CRISPR-Cas enables microbial cells to acquire immunity to viral
pathogens by recognizing specific sequences encoded in viral genomes. The
unique biology of this system results in evolutionary dynamics of host and
viral diversity that cannot be fully explained by the traditional models
used to describe microbe-virus coevolutionary dynamics. Here, we show how
the CRISPR-mediated adaptive immune response of hosts to invading viruses
facilitates the emergence of an evolutionary mode we call distributed
immunity - the coexistence of multiple, equally-fit immune alleles among
individuals in a microbial population. We use an eco-evolutionary modeling
framework to quantify distributed immunity and demonstrate how it emerges
and fluctuates in multi-strain communities of hosts and viruses as a
consequence of CRISPR-induced coevolution under conditions of low viral
mutation and high relative numbers of viral protospacers. We demonstrate
that distributed immunity promotes sustained diversity and stability in
host communities and decreased viral population density that can lead to
viral extinction. We analyze sequence diversity of experimentally
coevolving populations of Streptococcus thermophilus and their viruses
where CRISPR-Cas is active, and find the rapid emergence of distributed
immunity in the host population, demonstrating the importance of this
emergent phenomenon in evolving microbial communities.
Multi-scale model of CRISPR-induced host-viral co-evolutionThis 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.CRISPR_DI_Coevolution_Code_Archive.zip