Experimental evolution of Dictyostelium discoideum cheating under relaxed selection

Larsen, Tyler1

Published Dec 05, 2023 on Dryad. https://doi.org/10.5061/dryad.kkwh70s97

Data files

Dec 05, 2023 version files 1.67 MB

data_cellcountassay.csv

5.69 KB
data_cheatingassay.csv

47.46 KB
data_slugmigrationassay.csv

1.61 MB
data_sporulationefficiencyassay.csv

2 KB
README.md

4.25 KB

Abstract

Many microbes interact with one another, but the difficulty of directly observing these interactions in nature makes interpreting their adaptive value complicated. The social amoeba Dictyostelium discoideum forms aggregates wherein some cells are sacrificed for the benefit of others. Within chimeric aggregates containing multiple unrelated lineages, cheaters can gain an advantage by undercontributing, but the extent to which wild D. discoideum has adapted to cheat is not fully clear. In this study, we experimentally evolved D. discoideum in an environment where there were no selective pressures to cheat or resist cheating in chimeras. D. discoideum lines grown in this environment evolved reduced competitiveness within chimeric aggregates and reduced ability to migrate during the slug stage. By contrast, we did not observe a reduction in cell number, a trait for which selection was not relaxed. The observed loss of traits that our laboratory conditions had made irrelevant suggests that these traits were adaptations driven and maintained by selective pressures D. discoideum faces in its natural environment. Our results suggest that D. discoideum faces social conflict in nature, and illustrate a general approach that could be applied to searching for social or non-social adaptations in other microbes.

README: Assays of phenotypes of D. discoideum experimentally evolved under relaxed selection

Dataset represents five different assays performed on experimentally evolved D. discoideum lines. 10 wild D. discoideum strains were evolved (as three replicate lines each) under conditions in which the social cycle never occurred. After experimental evolution, the researchers measured various traits of the experimentally evolved lines and compared them to their ancestors. The chief prediction was that traits for which selection had been relaxed (like slug migration and cheating) should tend to decay, while traits that continued to be under selection in the lab (like cell number) should not.

Description of the Data and file structure

The data are in four spreadsheets corresponding to five different assays.

data_cheatingassay:

These data represent the number of fluorescently labelled and total spores within chimeric fruiting bodies inoculated from a 50:50 mixture of a D. discoideum strain of interest (ancestral or experimentally evolved) and a fluorescently labeled control strain RFP-NC28.1.
If no cheating was occurring, 50% of the spores should be fluorescently labelled. If more or fewer are, it indicates one of the strains is undercontributing.
These data correspond to figure 2 in the manuscript.

Column names:

Date - the date of the experiment, naturally (MM/DD/YY)
Strain - D. discoideum strain name, either NC28 or one of 10 wild strains used in the experimental evolution experiment.
Line - For experimental strains, indicates whether the data points are for the ancestor (Anc) or one of three replicate experimentally evolved lines (E1, E2, or E3)
Rep - For separating technical replicates
Filter - Fruiting bodies were grown on small pieces of filter paper, two of which were assayed for each experiment. This column distinguishes those (mostly to help hunt down specific photos if necessary)
Image - Five images were taken for each sample. This column distinguishes those (mostly to help hunt down specific photos if necessary)
Brightfield - A count of the total number of spores, as counted via a brightfield micrograph image. This represents both labeled and unlabeled spores.
Red - A count of the total number of fluorescently labeled spores, as counted via a fluorescence micrograph image.

data_slugmigrationassay:

These data represent the distance travelled by D. discoideum slugs. Cells were inoculated along one end of a nutrient-free plate and given 8 days to move towards a pinhole light source on the opposite end.
These data correspond to figure 3 in the manuscript.

Column names:

Date, Strain, Line - see above
Plate - image names for each photographed plate (to help hunt down specific photos if necessary)
Migration distance - Migration distance (in cm) from starting line, as measured from the photograph.

data_cellcountassay:

These data represent the total number of cells produced after inoculation of spores of ancestral or evolved D. discoideum lines on SM/5 plates.
Data were collected in two separate assays with slightly different purposes and methodology:
For cell count assays, cells were counted prior to aggregation so to eliminate the effect of any differences in sporulation. These data correspond to figure 4 in the manuscript.
For spore count assays, cells were counted after sporulation, and so their number should be affected by any differences that exist between strains in both vegetative cell growth rate and in sporulation. These data correspond to supplementary figure 1 in the manuscript.

Column names -

Strain, Line - see above
Assay - either 'Cell' or 'Spore', to distinguish the two assays described above.
Totalcells - A count of the total cells/spores produced.

data_sporulationefficiencyassay:

These data represent the total number of spores produced after inoculation of vegetative cells of ancestral or evolved D. discoideum lines on non nutrient plates.
These data correspond to supplemental figure 2 in the manuscript.