Phylogenomic species delimitation and host‐symbiont coevolution in the fungus‐farming ant genus SericomyrmexMayr (Hymenoptera: Formicidae): ultraconserved elements (UCEs) resolve a recent radiation

Abstract

Abstract. Ants in the Neotropical genus Sericomyrmex Mayr cultivate fungi for food. Both ants and fungi are obligate, coevolved symbionts. The taxonomy of Sericomyrmex is problematic because the morphology of the worker caste is generally homogeneous across all of the species within the genus, species limits are vague, and the relationships between them are unknown. We used ultraconserved elements (UCEs) as genome-scale markers to reconstruct evolutionary history and to infer species boundaries in Sericomyrmex. We recovered an average of ∼990 UCE loci for 88 Sericomyrmex samples from across the geographical range of the genus as well as for five outgroup taxa. Using maximum likelihood and species-tree approaches, we recovered nearly identical topologies across datasets with 50-95% matrix completeness. We identify nine species-level lineages in Sericomyrmex, including two new species. This is less than the previously described 19 species, even accounting for two species for which we had no UCE samples, which brings the total number of Sericomyrmex species to 11. Divergence-dating analyses recovered 4.3 Ma as the crown-group age estimates for Sericomyrmex, indicating a recent, rapid radiation. We also sequenced mitochondrial cytochrome oxidase subunit I (COI) for 125 specimens. Resolution and support for clades in our COI phylogeny are weak, indicating that COI is not an appropriate species-delimitation tool. However, taxa within species consistently cluster together, suggesting that COI is useful as a species identification ('DNA barcoding') tool. We also sequenced internal transcribed spacer (ITS) and large subunit (LSU) for 32 Sericomyrmex fungal cultivars. The fungal phylogeny confirms that Sericomyrmex fungi are generalized higher-attine cultivars, interspersed with Trachymyrmex-associated fungal species, indicating cultivar sharing and horizontal transfer between these two genera. Our results indicate that UCEs offer immense potential for delimiting and resolving relationships of problematic, recently diverged species.

The molecular phylogenetics ofTrachymyrmexForel ants and their fungal cultivars provide insights into the origin and coevolutionary history of ‘higher‐attine’ ant agriculture

“…One prior phylogeny, resulting from a maximum‐parsimony analysis of 50 morphological characters of the worker caste (Brandão & Mayhé‐Nunes, ), supports the monophyly of Trachymyrmex . By contrast, a phylogeny based on larval morphology (Schultz & Meier, ), three multilocus molecular phylogenies (Schultz & Brady, ; Sosa‐Calvo et al ., , ), and four genome‐scale phylogenies (Nygaard et al ., ; Branstetter et al ., ; Ješovnik et al ., ; Li et al ., ) all reconstruct Trachymyrmex as a paraphyletic grade in which the ancestor of the sister genera Xerolitor and Sericomyrmex , as well as the ancestor of the leaf‐cutting genera Atta and Acromyrmex , arise from within a paraphyletic Trachymyrmex .…”

Biogeography of mutualistic fungi cultivated by leafcutter ants

“…(), Ješovnik et al. () and Mueller et al. (in review) that higher‐attine fungi fall into two groups, a genetically homogenous group of Clade‐A fungi ( L. gongylophorus ) and a more diverse group of Clade‐B fungi that is subdivided into at least six distinct subclades (Figure ).…”

Ants in Australia’s Monsoonal Tropics: CO1 Barcoding Reveals Extensive Unrecognised Diversity

“…All four CO1 trees showed moderate (70)(71)(72)(73)(74)(75)(76)(77)(78)(79)(80)(81)(82)(83)(84)(85)(86)(87)(88)(89) to high (≥90) Bayesian posterior probability at the tips, while basal node support was generally lower and poorly resolved in all except Camponotus. Some poorly resolved clades were nested among other better supported clades (e.g., Cardiocondyla and Camponotus), and were supported by differences in locality and morphology.…”

“…However, we are confident that CO1 analysis has provided a reliable indication of diversity within our target taxa. This has been shown to be the case even if CO1 analysis has not got all species exactly correct (e.g., [89]). Moreover, sequenced-based methods such as ABGD and PTP have been shown to result in consistent species estimates across multiple genes [90,91].…”