Gene Ontology (GO) distributions by level, by species.

<p>Gene Ontology (GO) distributions by level, by species.</p

Functional annotation.

<p>Percentages of BLAST-hits, annotated sequences, mapped sequences, and no-BLAST hits for each species.</p

Phylogenomics and Divergence Dating of Fungus-Farming Ants (Hymenoptera: Formicidae) of the Genera <i>Sericomyrmex</i> and <i>Apterostigma</i>

<div><p>Fungus-farming ("attine") ants are model systems for studies of symbiosis, coevolution, and advanced eusociality. A New World clade of nearly 300 species in 15 genera, all attine ants cultivate fungal symbionts for food. In order to better understand the evolution of ant agriculture, we sequenced, assembled, and analyzed transcriptomes of four different attine ant species in two genera: three species in the higher-attine genus <i>Sericomyrmex</i> and a single lower-attine ant species, <i>Apterostigma megacephala</i>, representing the first genomic data for either genus. These data were combined with published genomes of nine other ant species and the honey bee <i>Apis mellifera</i> for phylogenomic and divergence-dating analyses. The resulting phylogeny confirms relationships inferred in previous studies of fungus-farming ants. Divergence-dating analyses recovered slightly older dates than most prior analyses, estimating that attine ants originated 53.6–66.7 million of years ago, and recovered a very long branch subtending a very recent, rapid radiation of the genus <i>Sericomyrmex</i>. This result is further confirmed by a separate analysis of the three <i>Sericomyrmex</i> species, which reveals that 92.71% of orthologs have 99% - 100% pairwise-identical nucleotide sequences. We searched the transcriptomes for genes of interest, most importantly <i>argininosuccinate synthase</i> and <i>argininosuccinate lyase</i>, which are functional in other ants but which are known to have been lost in seven previously studied attine ant species. Loss of the ability to produce the amino acid arginine has been hypothesized to contribute to the obligate dependence of attine ants upon their cultivated fungi, but the point in fungus-farming ant evolution at which these losses occurred has remained unknown. We did not find these genes in any of the sequenced transcriptomes. Although expected for <i>Sericomyrmex</i> species, the absence of arginine anabolic genes in the lower-attine ant <i>Apterostigma megacephala</i> strongly suggests that the loss coincided with the origin of attine ants.</p></div

Crown-group and stem-group age estimates.

<p>In units of million years ago, with standard error given in parentheses. An asterisk (*) indicates a posterior probability of 1.</p

Gene searches.

<p>Number of gene copies and isoforms per species.</p

Time-calibrated phylogeny of attine ants.

<p>Highlighted taxa are novel transcriptomes obtained for this study. This topology was recovered in both ML and Bayesian analysis. Asterisks (*) at nodes indicate bootstrap values of 100 and posterior probabilities of 1.0. Green error bars at nodes indicate minimum and maximum age estimates; the time scale at the bottom is in million of years.</p

Specimen data.

<p>Specimen data.</p