Data from: The relationship between spatial structure and the maintenance of diversity in microbial populations

France, Michael T.

Forney, Larry J.

Published Feb 12, 2020 on Dryad. https://doi.org/10.5061/dryad.5670c6n

Cite this dataset

France, Michael T.; Forney, Larry J. (2020). Data from: The relationship between spatial structure and the maintenance of diversity in microbial populations [Dataset]. Dryad. https://doi.org/10.5061/dryad.5670c6n

Abstract

Spatial structure is pervasive in the microbial world, yet we know little about how it influences the evolution of microbial populations. It is thought that spatial structure limits the scale of competitive interactions and protracts selective sweeps. This may allow microbial populations to simultaneously explore multiple evolutionary paths. But how structured must a microbial population be before this effect is realized? We used experimental and simulation studies to explore the relationship between spatial structure and the maintenance of diversity. The degree of spatial structure experienced by Escherichia coli metapopulations was manipulated by varying the migration rate between its component subpopulations. Each subpopulation was inoculated with an equal number of two equally fit genotypes and their frequencies in 12 subpopulations were determined during 150 generations of evolution. We observed that the frequency of the ‘loser’ genotypes decreased exponentially as the migration rate between the subpopulations was increased and that higher frequencies of the “loser” genotypes were maintained in structured metapopulations. These results demonstrate that structured microbial populations can evolve along multiple evolutionary trajectories even when migration rates between the subpopulations are relatively high.

Usage notes

Variant_abundance_gen150

Frequency of the cycloserine resistant and sensitive variants in each subpopulation after 150 generations of evolution in environments with varying degrees of spatial structure.

gen150_variant_abundance.xlsx

subpopulation_growth_kinetics_data

File contains growth kinetic parameters for each subpopulation at 0, 50, 100, and 150 generations of evolution. Parameters were estimated using the R package "grofit" from OD600 measures over a 24 hour period at 15 minute intervals. Plates were incubated at 37 and shaking.

growth_kinetics_data.xlsx

simulation_ouput_data

File contains the data output from 1000s of replicate metapopulation evolution simulations under varying degrees of spatial structure and mutation rates. Every 250 generations of the evolution the simulation recorded: Average fitness, variance in fitness across the metapopulation, frequency of the minor allele, and variance in frequeny of the minor allele. Variance was estimated from the 12 subpopulations values of fitness or minor allele frequency.

simulation_data_all.xlsx

sas_analysis_code

Contains the SAS code used to analyze the data.

evol_metapopulation_sim.py

Simulation for evolution of metapopulations experiencing differing degrees of spatial structure (migration rate). Simulation was written in python 2.7. Input parameters that can be varied appear in line 577 and include: migration rate, mutation rate, population size, generations of evolution, and number of replicates.

structured_evol_v2.py