Recent advances in phylogenomics allow for the use of large amounts of genetic information in phylogenetic inference. Ideally, the increased resolution and accuracy of such inferences facilitate improved understanding of macroevolutionary processes. Here, we integrate ultraconserved elements (UCEs) with fossil and biogeographic range data to explore diversification and geographic range evolution in the diverse turtle ant genus Cephalotes Latreille, 1802 (Hymenoptera: Formicidae). We focus on the potential role of the uplift of the Panamanian land bridge and the putative ephemeral GAARlandia land bridge linking South America and the Antilles in shaping evolution in this group. Our phylogenetic analyses provide new resolution to the backbone of the turtle ant phylogeny. We further found that most geographic range shifts between South America and Central America regions were temporally consistent with the development of the Panamanian land bridge, while we did not find support for the GAARlandia land bridge. Additionally, we did not infer any shifts in diversification rates associated with our focal land bridges, or any other historical events (we inferred a single diversification rate regime across the genus). Our findings highlight the impact of the Panamanian land bridge for Cephalotes geographic range evolution as well as the influence of taxonomic sampling on macroevolutionary inferences.

Family Cortinariaceae currently includes only one genus, Cortinarius, which is the largest Agaricales genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus Cortinarius contains a lot of morphological variation, and its complexity has led many taxonomists to specialize in particular on infrageneric groups. The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level. Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups. We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species. In addition, a wider 5-locus analysis of 245 species, from the Northern and Southern Hemispheres, was also done. Based on our results, a classification of the family Cortinariaceae into ten genera—Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius, Cystinarius, Volvanarius, Hygronarius, Mystinarius, and Austrocortinarius—is proposed. Seven genera, 10 subgenera, and four sections are described as new to science and five subgenera are introduced as new combinations in a new rank. In addition, 41 section names and 514 species names are combined in new genera and four lecto- and epitypes designated. The position of Stephanopus in suborder Agaricineae remains to be studied. Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to produce -omics data in species-rich groups. The -omics data was produced from fungarium specimens up to 21 years old, demonstrating the value of museum specimens in the study of the fungal tree of life. This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.

The evolutionary history of fungus-farming ants has been the subject of multiple morphological, molecular phylogenetic, and phylogenomic studies. Due to its rarity, however, the phylogenetic position, natural history, and fungal associations of the monotypic genus Paramycetophylax Kusnezov have remained enigmatic. Here we report the first excavations of colonies of Paramycetophylax bruchi (Santschi) and describe its nest architecture and natural history. Utilizing specimens from these collections, we generated ultraconservedelement (UCE) data to determine the evolutionary position of Paramycetophylax within the fungus-farming ants and ribosomal ‘fungal barcoding’ ITS sequence data to identify the fungal cultivar. A maximum-likelihood phylogenomic analysis indicates that the genus Paramycetophylax is the sister group of the yeast-cultivating Cyphomyrmex rimosus group, an unexpected result that renders the genus Cyphomyrmex Mayr paraphyletic. A Bayesian divergence-dating analysis indicates that Paramycetophylax diverged from its sister group around 36 mya (30–42 mya, HPD) in the late Eocene-early Oligocene, a period of global cooling, expansion of grasslands, and large-scale extinction of tropical organisms. Bayesian analysis of the fungal cultivar ITS gene fragment indicates that P. bruchi practices lower agriculture and that the cultivar grown by P. bruchi belongs to the Clade 1 group of lower-attine fungi, a clade that, interestingly, also includes the C. rimosus-group yeast cultivars. Based on these results, we conclude that a better understanding of P. bruchi and its fungal cultivar, including whole-genome data, is critical for reconstructing the origin of yeast agriculture, a major transition in the evolution of fungus-farming ants.

Uncovering the evolutionary history of the subfamilies Ectatomminae and Heteroponerinae, or ectaheteromorphs, is key to understanding a major branch of the ant tree of life. Despite their diversity and ecological importance, phylogenetic relationships in the group have not been well explored. One particularly suitable tool for resolving phylogeny is the use of ultraconserved elements (UCEs), which have been shown to be ideal markers at a variety of evolutionary time scales. In the present study, we enriched and sequenced 2,127 UCEs from 135 specimens of ectaheteromorph ants and investigated phylogeny using a variety of model-based phylogenomic methods.Trees recovered from partitioned maximum-likelihood and species-tree analyses were well resolved and largely congruent.The results are consistent with an expanded concept of Ectatomminae that now includes the subfamily Heteroponerinae new synonym and its single tribe Heteroponerini new combination. Eleven monophyletic groups are recognized as genera: Acanthoponera, Alfaria status revived, Boltonia Camacho and Feitosa new genus, Ectatomma, Gnamptogenys, Heteroponera, Holcoponera status revived, Poneracantha status revived, Rhytidoponera, Stictoponera status revived, and Typhlomyrmex. The new phylogenetic framework and classification proposed here will shed light on the study of Ectatomminae taxonomy and systematics, as well as on the morphological evolution of the groups that it comprises.