Evolutionary history, novel lineages, and symbiont coevolution in the ant tribe Camponotini (Hymenoptera: Formicidae)

Many insect groups have acquired obligate microbial symbionts, and the resulting associations can have important ecological and evolutionary consequences. A notable example among ants is the species-rich tribe Camponotini, whose members derive nutritional benefits from a vertically inherited, bacterial endosymbiont Blochmannia. We generate ultraconserved element (UCE) phylogenomic data for 220 ingroup and 5 outgroup taxa to reconstruct a detailed evolutionary history of the Camponotini, including inference of divergence times and dispersal events. Under multiple modes of analysis, including both concatenation and species-tree approaches, we recover a well-supported backbone phylogeny comprising eight lineages: three large genera (Camponotus, Colobopsis, Polyrhachis) and several smaller genera or clusters of genera. Three novel lineages are uncovered that cannot be placed in any existing genus: Lathidris gen. n., from the mountains of Mesoamerica; Retalimyrma gen. n., from the Indian Him..., Phylogenomics
Taxon sampling and UCE data generation
Our taxon set comprises 220 species of Camponotini, representing all genera and most subgenera, and five outgroup species belonging to related genera in the subfamily Formicinae (Table S1). Camponotine ants were sampled roughly in proportion to the number of described species in each genus. Smaller taxon sets were employed for analyses comparing Blochmannia and ant phylogenies.
DNA was extracted from single ants, either adults or pupae, using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) and quantified with a Qubit fluorometer (HS Assay Kit, Life Technologies Inc., Carlsbad, CA). We sheared 5–50 ng input DNA to a target size of ~600 bp using either a Diagenode BioRuptor (Diagenode Inc., Denville, NJ) or QSonica Q800R3-110 (Qsonica Inc., Newtown, CT). This product served as input for the generation of ultraconserved element (UCE) sequence data, following a protocol described by Branstetter et al. (2017a), and involving the fol..., , # Evolutionary history, novel lineages, and symbiont coevolution in the ant tribe Camponotini (Hymenoptera: Formicidae)

[https://doi.org/10.5061/dryad.hx3ffbgqd](https://doi.org/10.5061/dryad.hx3ffbgqd)

## Description of the data and file structure

The data in this repository were collected as part of a phylogenetic study on the ant tribe Camponotini and their *Blochmannia* symbionts, based on ultraconserved element (UCE) phylogenomic data for 225 ant species and selected genes from 97 symbiont taxa. We also estimated the divergence times and biogeographic history of the ants and examined patterns of coevolution between the two symbiotic partners.

Sequence data from target capture and WGS from ants were combined and assembled into contigs using SPAdes, and subsequently processed with Phyluce to filter out ultraconserved element loci. Alignment of matrices was performed with Mafft in Phyluce. Poor quality sequence regions were trimmed further using the program Spruceup. Partitioning ...