DOI: 10.5061/dryad.983r5
title: Data from: Fine-scale spatial ecology drives kin selection relatedness among cooperating amoebae

description: Cooperation among microbes is important for traits as diverse as
 antibiotic resistance, pathogen virulence, and sporulation. The
 evolutionary stability of cooperation against “cheater” mutants depends
 critically on the extent to which microbes interact with genetically
 similar individuals. The causes of this genetic social structure in
 natural microbial systems, however, are unknown. Here we show that social
 structure among cooperative Dictyostelium amoebae is driven by the
 population ecology of colonization, growth, and dispersal acting at
 spatial scales as small as fruiting bodies themselves. Despite the fact
 that amoebae disperse while grazing, all it takes to create substantial
 genetic clonality within multicellular fruiting bodies is a few
 millimeters distance between the cells colonizing a feeding site. Even
 adjacent fruiting bodies can consist of different genotypes. Soil
 populations of amoebae are sparse and patchily distributed at millimeter
 scales. The fine-scale spatial structure of cells and genotypes can thus
 account for the otherwise unexplained high genetic uniformity of spores in
 fruiting bodies from natural substrates. These results show how a full
 understanding of microbial cooperation requires understanding ecology and
 social structure at the small spatial scales microbes themselves
 experience.
description: Data: Spatial
 distribution of D. discoideum in soilAbundance of
 Dictyostelium discoideum isolates in small soil samples collected along
 transects. See Fortunato et al (2003) Mol Ecol 12:1031 and Gilbert et al
 (2012) Proc Roy Soc Lond B 279:2619.data-soil-density.txtAnalysis: Spatial distribution of D. discoideum in soilAnalyze and visualize spatial distribution of Dictyostelium discoideum amoebae among soil samples. Script for use with R environment for statistical computing.analysis-soil-density.RData: D. discoideum plaque growthGrowth of Dictyostelium discoideum plaques on bacterial lawnsdata-plaque-growth.txtAnalysis: D. discoideum plaque growthAnalyze and visualize growth of Dictysotelium discoideum plaques on Klebsiella lawns. Script for use with R environment for statistical computing.analysis-plaque-growth.RData: Transect of D. discoideum fruiting bodies across two intersecting plaquesDistribution of genotypes along transect of D. discoideum fruiting bodies across two intersecting plaques.data-plaque-transect.txtAnalysis: Transect of D. discoideum fruiting bodies across two intersecting plaquesAnalyze and visualize distribution of genotypes along transect of Dictyostelium discoideum fruiting bodies across two intersecting plaques. Script for use with R environment for statistical computing.analysis-plaque-transect.RAnalysis: D. discoideum flow cytometryParse flow cytometry .fcs files to determine number and proportion of fluorescent/nonfluorescent Dictyostelium discoideum cells. Script for use with R environment for statistical computing.count_dicty_cells.RData: D. discoideum fruiting bodies sampled from petri plateGenotype composition of individual Dictyostelium discoideum fruiting bodies sampled from across surface of petri plate. Generated by analysis of flow cytometry data.data-relatedness.txtAnalysis: D. discoideum fruiting bodies sampled from petri plateAnalyze and visualize distribution of Dictyostelium discoideum genotypes in individual fruiting bodies sampled from across surface of petri plates. Script for use with R environment for statistical computing.analysis-relatedness.RData: Germination of D. discoideum spores on bacterial lawnsNumber of plaques observed on bacterial lawns inoculated with known number of Dictyostelium discoideum spores.data-germination.txtData: D. discoideum inoculaGenotype composition of Dictyostelium discoideum samples used to inoculate bacterial lawns. Generated by analysis of flow cytometry data.data-inocula.txtData: Flow cytometry of fruiting bodies from transect across plaquesRaw flow cytometry data (FCS format) from Dictyostelium discoideum fruiting bodies sampled along transect crossing two plaques.fcs-files-transect.zipData: Flow cytometry of D. discoideum inocula and all-RFP controlsRaw flow cytometry data (FCS format) of Dictyostelium discoideum spores (1) inoculated onto bacterial lawns and (2) sampled from fruiting bodies on plates only inoculated with RFP-labelled amoebae.fcs-files-controls.zipData: Flow cytometry of D. discoideum fruiting bodies sampled from across plateRaw flow cytometry data (FCS format) of Dictyostelium discoideum spores sampled from fruiting bodies on plates inoculated with mix of wild type and RFP-labelled amoebae.fcs-files-relatedness.zipData: D. discoideum microscopyIndividual and composited images of Dictyostelium discoideum fruiting bodies.dicty-images.zip