Data from: Dry habitats were crucibles of domestication in the evolution of agriculture in ants

  • S. G. Brady (Contributor)
  • Michael G. Branstetter (Contributor)
  • Ana JeŠovnik (Contributor)
  • Brant C. Faircloth (Contributor)
  • Ted R. Schultz (Contributor)
  • Jeffrey Sosa-Calvo (Contributor)
  • Michael W. Lloyd (Contributor)



The evolution of ant agriculture, as practiced by the fungus-farming “attine” ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The “out-of-the-rainforest” hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining how fungal domestication might have occurred, given that isolation from free-living populations is required. Here, we use phylogenomic data from ultra-conserved element (UCE) loci to reconstruct the evolutionary history of fungus-farming ants, reduce topological uncertainty, and identify the closest non-fungus-growing ant relative. Using the phylogeny we infer the history of attine agricultural systems, habitat preference, and biogeography. Our results show that the out-of-the-rainforest hypothesis is correct with regard to the origin of attine ant agriculture; however, contrary to expectation, we find that the transition from lower to higher agriculture very likely occurred in a seasonally dry habitat, inhospitable to the growth of free-living populations of attine fungal cultivars. We suggest that dry habitats favored the isolation of attine cultivars over the evolutionary time spans necessary for domestication to occur.,Raw illumina reads (SRA BioProject PRJNA379607).Raw illumina reads for all newly sequenced specimens in this study.Alignment supermatrices - filtered, trimmedSeveral of the concatenated supermatrices analyzed in this study. Includes the attine-118t-f75 matrix, attine-119t-f75 matrix, and the attine-118t-f75-base-comp matrix.alignment-supermatrices.zipData partitioning schemesData partitioning schemes for the attine-118t-f75 supermatrix. Includes by-locus, rculster, and kmeans schemes. In RAxML format.attine-118t-f75-partitioning-schames.zipBEAST XML data files.All BEAST XML files used in divergence dating analyses. Five separate DNA matrices were created using 20 randomly selected UCE loci.beast-xml-files.zipBigeography, trait, and diversification rate analysis filesData files and scripts for all biogeography, trait, and diversification rate analyses.biogeo-trait-diversification-files.zipAll phylogenetic treesAll resulting phylogenetic trees generated in this study.phylogenetic-trees.zipSupplementary tablesAll supplementary tables (same as Appendix 1 in paper).supplementary-tables.xlsUCE alignments - unfiltered, untrimmedUCE alignments for the 118t and 119t datasets. Data were aligned using MAFFT, but were not trimmed or filtered. Data from the 119t alignment set were uploaded to GenBank.uce-alignments-untrimmed.zipTrinity assembliesBulk trinity assemblies. Includes newly sequenced samples and samples from previous,
Date made availableApr 12 2017

Cite this