Phylogenomics Resolves Evolutionary Relationships among Ants, Bees, and Wasps

Abstract

Eusocial behavior has arisen in few animal groups, most notably in the aculeate Hymenoptera, a clade comprising ants, bees, and stinging wasps [1-4]. Phylogeny is crucial to understanding the evolution of the salient features of these insects, including eusociality [5]. Yet the phylogenetic relationships among the major lineages of aculeate Hymenoptera remain contentious [6-12]. We address this problem here by generating and analyzing genomic data for a representative series of taxa. We obtain a single well-resolved and strongly supported tree, robust to multiple methods of phylogenetic inference. Apoidea (spheciform wasps and bees) and ants are sister groups, a novel finding that contradicts earlier views that ants are closer to ectoparasitoid wasps. Vespid wasps (paper wasps, yellow jackets, and relatives) are sister to all other aculeates except chrysidoids. Thus, all eusocial species of Hymenoptera are contained within two major groups, characterized by transport of larval provisions and nest construction, likely prerequisites for the evolution of eusociality. These two lineages are interpolated among three other clades of wasps whose species are predominantly ectoparasitoids on concealed hosts, the inferred ancestral condition for aculeates [2]. This phylogeny provides a new framework for exploring the evolution of nesting, feeding, and social behavior within the stinging Hymenoptera.

AMAS: a fast tool for alignment manipulation and computing of summary statistics

“…3c0f1), and amino acid alignments of 5,214 exons from 19 wasp taxa from Johnson et al (2013) (datadryad.org/resource/doi:10.5061/dryad.jt440).…”

“…Phyutility allows concatenation only to the sequential NEXUS format. AMAS concatenation times ranged from about 2 seconds for the smallest data set of Johnson et al (2013) to about 22 seconds for Jarvis et al (2014) data, outperforming the other two programs by a factor of 30 or more. A comparison of times taken for concatenating the smallest data set of 5,214 amino acid loci from Johnson et al (2013) is presented in Figure 1A.…”

“…Here I compare the performance of both to AMAS. FASconCAT-G worked on the amino acid alignments of Johnson et al (2013) and Misof et al (2014) data sets, concatenating the former in over 70 seconds and the latter in about 260 seconds. This program also allows simultaneous computation of alignment summaries during concatenation.…”

“…FASconCAT-G crashed with an error when attempting to read in the nucleotide FASTA files of Jarvis et al (2014) UCE and exon data sets. Phyutility was able to concatenate all of the four FASTA data sets, in times of about 10 minutes for the smallest data set of 5,214 amino acid loci of Johnson et al (2013) to over 200 minutes for the largest data set of 8,295 exons from Jarvis et al (2014). Phyutility allows concatenation only to the sequential NEXUS format.…”

“…FASconCAT-G (Kück and Longo, 2014) also calculates alignment statistics but it is significantly slower than AMAS. The total time taken for FASconCAT-G for concatenation and summary computing on the smallest data set of Johnson et al (2013) was >500 seconds, while AMAS concatenates this data set in 2 seconds and outputs summaries in another 30 seconds (Figure 1). …”