Sean Gary Brady

• PhD
• Chair at Smithsonian Institution

We present the first global molecular phylogenetic hypothesis for the family Eurytomidae, a group of chalcidoid wasps with diverse biology, with a representative sampling (197 ingroups and 11 outgroups) that covers all described subfamilies, and 70% of the known genera. Analyses of 962 Ultra-Conserved Elements (UCEs) with concatenation (IQ-TREE) an...

During the past two decades, the phylogenetic relationships and higher-level classification of the subfamily Rogadinae have received relevant contributions based on Sanger, mitogenome and genome-wide nuclear DNA sequence data. These studies have helped to update the circumscription and tribal classification of this subfamily, with six tribes curren...

Despite significant advances in alpha level taxonomy in the past few decades, the higher-level phylogeny of flat wasps (Hyme-noptera, Bethylidae) remains poorly explored. Herein we provide the first phylogenomic assessment of the family based on data from ultraconserved elements for 96 species in 61 genera of the family, with material from 29 count...

Modern genomic techniques have enabled the generation of phylogenetic datasets of unprecedented scale. However, there are also troves of molecular data accumulated from past studies using Sanger sequencing, often at fine taxonomic scales. Combining both sources of data is an obviously appealing possibility, but it can also lead to inconsistency due...

The subfamilies Amicrocentrinae and Dirrhopinae (Hymenoptera, Braconidae) are two small, monogeneric braconid subfamilies whose species exclusively attack lepidopteran larvae. The phylogenetic placement of Amicrocentrinae as a member of the helconoid complex of subfamilies has been supported by morphological and nuclear Sanger sequence data. The su...

Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that...

Mitochondrial (mtDNA) genes have served as widely utilised genetic loci for phylogenetic and phylogeographic studies of animals. However, the phylogenetic performance of many mtDNA genes has not been empirically evaluated across lineages within hymenopteran wasps. To address this question, we assembled and analysed mitogenomic data from social wasp...

The use of DNA barcoding has revolutionised biodiversity science, but its application depends on the existence of comprehensive and reliable reference libraries. For many poorly known taxa, such reference sequences are missing even at higher-level taxonomic scales. We harvested the collections of the Smithsonian’s National Museum of Natural History...

The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of the most diverse animal lineages, but whether specific key innovations have contributed to its diversification is still unknown. We assembled the largest time-calibrated phylogeny of Hymenoptera to date and investigated the origin and possible correlation of particular morpho...

Biogeographic patterns in the Southern Hemisphere have largely been attributed to vicariant processes, but recent studies have challenged some of the classic examples of this paradigm. The parasitoid wasp subfamily Labeninae has been hypothesized to have a Gondwanan origin, but the lack of divergence dating analysis and the discovery of a putative...

Capturing phylogenetic signal from a massive radiation can be daunting. The superfamily Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. Chalcidoidea are mostly parasitoid wasps that until now included 27 families, 87 subfamilies and as many as 500,000 estimated species. We comb...

Aim The standard latitudinal diversity gradient (LDG), in which species richness decreases from equator to pole, is a pervasive pattern observed in most organisms. Some lineages, however, exhibit inverse LDGs. Seemingly problematic, documenting and studying contrarian groups can advance understanding of LDGs generally. Here, we identify one such co...

The parasitoid lifestyle is largely regarded as a key innovation that contributed to the evolutionary success and extreme species richness of the order Hymenoptera. Understanding the phylogenetic history of hyperdiverse parasitoid groups is a fundamental step in elucidating the evolution of biological traits linked to parasitoidism. We used a genom...

The mining bees (Andrenidae) are a major bee family of over 3000 described species with a nearly global distribution. They are a particularly significant component of northern temperate ecosystems and are critical pollinators in natural and agricultural settings. Despite their ecological and evolutionary significance, our knowledge of the evolution...

Summarizing individual gene trees to species phylogenies using two-step coalescent methods is now a standard strategy in the field of phylogenomics. However, practical implementations of summary methods suffer from gene tree estimation error, which is caused by various biological and analytical factors. Greatly understudied is the choice of gene tr...

Bees of the tribes Biastini, Neolarrini, and Townsendiellini are cleptoparasites in the subfamily Nomadinae (Hymenoptera, Apidae) and parasitize solitary bees. Understanding their phylogenetic relationships has proven difficult for many decades. Previous research yielded ambiguous results because of conflicting phylogenetic signals of larval and ad...

Background: Parasitoidism, a specialized life strategy in which a parasite eventually kills its host, is frequently found within the insect order Hymenoptera (wasps, ants and bees). A parasitoid lifestyle is one of two dominant life strategies within the hymenopteran superfamily Cynipoidea, with the other being an unusual plant-feeding behavior kno...

The Neotropical realm harbours unparalleled species richness and hence has challenged biologists to explain the cause of its high biotic diversity. Empirical studies to shed light on the processes underlying biological diversification in the Neotropics are focused mainly on vertebrates and plants, with little attention to the hyperdiverse insect fa...

Eulophidae is a hyper-diverse family of chalcidoid wasps with 324 genera, about 5300 described species and probably thousands of others to be described. Until now, the absence of unequivocal morphological apomorphies and the low resolution provided by the handful of Sanger sequenced genes have hampered the reconstruction of phylogenetic relationshi...

Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be...

Recent technical advances combined with novel computational approaches promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid...

Knowledge of the internal phylogeny and evolutionary history of ants (Formicidae), the world's most species-rich clade of eusocial organisms, has dramatically improved since the advent of molecular phylogenetics. A number of relationships at the subfamily level, however, remain uncertain. Key unresolved issues include placement of the root of the a...

Two increasingly popular approaches to reconstruct the Tree of Life involve whole transcriptome sequencing and the target capture of ultraconserved elements (UCEs). Both methods can be used to generate large, multigene datasets for analysis of phylogenetic relationships in non-model organisms. While targeted exon sequencing across divergent lineage...

The use of metal ions to harden the tips and edges of ovipositors is known to occur in many hymenopteran species. However, species using the ovipositor for delivery of venom, which occurs in the aculeate hymenoptera (stinging wasps, ants, and bees) remains uninvestigated. In this study, scanning electron microscopy coupled with energy-dispersive X-...

The author would like to correct the errors in the publication of the original article. The corrected details are given below for your reading.

Levels of diversity vary strikingly among different phylogenetic lineages of ants. Rapid radiations in early ant evolution have often proven difficult to resolve with traditional Sanger-sequencing data sets of modest size. We provide a phylogenomic perspective on the evolution of the hyperdiverse ant tribe Crematogastrini by analyzing sequence data...

The evolution of reversed sexual dichromatism and aposematic coloration have long been of interest to both theoreticians and empiricists. Yet despite the potential connections between these phenomena, they have seldom been jointly studied. Large carpenter bees (genus Xylocopa) are a promising group for such comparative investigations as they are a...

Chalcid wasps are one of the most diverse lineages of Hymenoptera also highly disparate in terms of morphologies and biologies. The evolutionary relationships among Chalcidoidea have remained virtually untested. No multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology with appropriate sampling. Here w...

Phylogeographic studies have sought to explain the genetic imprints of historical climatic changes and geographic barriers within the Brazilian Atlantic Forest (AF) biota, and consequently two processes of diversification (refugia and barriers) have been proposed. Additionally, there is evidence that eustatic changes influenced the biogeographic hi...

Knowledge of the internal phylogeny and evolutionary history of ants (Formicidae), the world’s most species-rich clade of eusocial organisms, has dramatically improved since the advent of molecular phylogenetics. A number of relationships at the subfamily level, however, remain uncertain. Key unresolved issues include placement of the root of the a...

The evolution of ant agriculture, as practised by the fungus-farming "attine" ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in Sou...

The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of hymenopteran insects, encompassing over 70,000 described species and a diversity of life history traits, including ectoparasitism, cleptoparasitism, predation, pollen feeding (bees [Anthophila] and Masarinae), and eusociality (social vespid wasps, ants, and some bees) [1...

Female army ants cannot fly, making them very poor dispersers across water barriers. This dependence on terrestrial corridors motivated the investigation by Winston et al. (2017), published in this issue of Molecular Ecology, into the role of Panamanian isthmus formation in the diversification of Eciton army ants. Complete closure of this isthmus o...

Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher mo...

Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs) from 51 large carpenter bee specimens (genus Xylo...

Additional trees from analyses including outgroups. (A) Maximum likelihood best tree of 51 Xylocopa specimens, based on 828 UCE loci and 268566 bp (50% matrix), with values from bootstrap analysis mapped onto this tree. (B) Maximum Likelihood best tree of 51 Xylocopa specimens, based on 123 UCE loci and 42753 bp (70% matrix), with values from boots...

Collection data of Xylocopa specimens included in the study. Summary of collection information for the 51 Xylocopa specimens sequenced in this study, including USNMENT voucher number, collection date, country, locality and coordinates. All information has been transcribed from label data and amended for clarity. Wherever possible, localities have b...

The importance of taxon sampling in phylogenetic accuracy is a topic of active debate. We investigated the role of taxon sampling in causing incongruent results between two recent phylogenomic studies of stinging wasps (Hymenoptera: Aculeata), a diverse lineage that includes ants, bees and the majority of eusocial insects. Using target enrichment o...

The attine ant-fungus agricultural symbiosis evolved over tens of millions of years, producing complex societies with industrial-scale farming analogous to that of humans. Here we document reciprocal shifts in the genomes and transcriptomes of seven fungus-farming ant species and their fungal cultivars. We show that ant subsistence farming probably...

Supplementary Figures 1 - 18, Supplementary Tables 1 - 29, Supplementary Methods and Supplementary References

Number of annotated fungal genes in each CAZy family

Gene/transcript accessions, ortholog assignments, and inferred positively selected gene families for the sequenced attine ants and fungal cultivars

Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher mo...

Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher mo...

Acropyga ants are a widespread clade of small subterranean formicines that live in obligate symbiotic associations with root mealybugs. We generated a data set of 944 loci of ultraconserved elements (UCEs) to reconstruct the phylogeny of 41 representatives of 23 Acropyga species using both concatenation and species-tree approaches. We investigated...

Background Ultraconserved elements (UCEs) have been successfully used in phylogenomics for a variety of taxa, but their power in phylogenetic inference has yet to be extensively compared with that of traditional Sanger sequencing data sets. Moreover, UCE data on invertebrates, including insects, are sparse. We compared the phylogenetic informativen...

Ant communities in tropical forests may be governed by varying assembly mechanisms, depending on the particular habitat investigated. We compared phylogenetic diversity and structure across two forest biomes (dry and humid) and two vertical layers (arboreal and terricolous) in ant communities in Madagascar, and assessed the influence of invasive sp...

A central goal of biology is to uncover the genetic basis for the origin of new phenotypes. A particularly effective approach is to examine the genomic architecture of species that have secondarily lost a phenotype with respect to their close relatives. In the eusocial Hymenoptera, queens and workers have divergent phenotypes that may be produced v...

Fungus-farming (attine) ant agriculture is made up of five known agricultural systems characterized by remarkable symbiont fi- delity in which five phylogenetic groups of ants faithfully cultivate five phylogenetic groups of fungi. Here we describe the first case of a lower- attine ant cultivating a higher-attine fungus based on our discovery of a...

The Neotropical Region harbors high biodiversity and many studies on mammals, reptiles, amphibians and avifauna have investigated the causes for this pattern. However, there is a paucity of such studies that focus on Neotropical insect groups. Synoeca de Saussure, 1852 is a Neotropical swarm-founding social wasp genus with five described species th...

Table S1Family, species, collection identifier, collection year, collection country, collection method, voucher identifier, voucher depository, total amount of extract DNA, amount of DNA input to library preparation, post-enrichment method, and MiSeq run of all samples used for target enrichment. Table S2 Species, genome assembly, genome assembly s...

This study investigates the evolutionary history of a hyperdiverse clade, the ant subfamily Myrmicinae (Hymenoptera: Formicidae), based on analyses of a data matrix comprising 251 species and 11 nuclear gene fragments. Under both maximum likelihood and Bayesian methods of inference, we recover a robust phylogeny that reveals six major clades of Myr...

A new genus and species of Eucoilinae, Rovnoeucoila tympanomorpha Buffington and Perkovsky, from a Rovno Amber inclusion, is described. This new taxon differs from extant eucoilines by having a clearly segmented metasoma and singular flagellomere morphology in the antenna. The new taxon is included in the re-analysis of a fossil calibrated, relaxed...

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci collected across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes rema...

Background Army ants are dominant invertebrate predators in tropical and subtropical terrestrial ecosystems. Their close relatives within the dorylomorph group of ants are also highly specialized predators, although much less is known about their biology. We analyzed molecular data generated from 11 nuclear genes to infer a phylogeny for the major...

The predominantly Holarctic bee genus Osmia Panzer is species-rich and behaviourally diverse. A robust phylogeny of this genus is important for understanding the evolution of the immense variety of morphological and behavioural traits exhibited by this group. We infer a phylogeny of Osmia using DNA sequence data obtained from three nuclear genes (e...

Insecticide resistance is a model phenotype that can be used to investigate evolutionary processes underlying the spread of alleles across a global landscape, while offering valuable insights into solving the problems that resistant pests present to human health and agriculture. Pyrethroids are one of the most widely used classes of insecticides wo...

Locations where house flies were collected. (PDF)

Intron haplotypes, GenBank Accession numbers and locations where each haplotype was observed. (PDF)

In the past decade, Houston, Texas has been virtually overrun by an unidentified ant species, the sudden appearance and enormous population sizes and densities of which have received national media attention. The Rasberry Crazy Ant, as it has become known due to its uncertain species status, has since spread to neighboring states and is still a maj...

Molecular data and GenBank accession numbers. (XLSX)

Morphometric data. For specimens where GPS coordinates were not provided on the label (indicated by an asterisk), when possible we estimated the GPS data based on the collection information. Specimens highlighted in red were excluded from DAPC due to missing data points. (XLS)

Hymenoptera exhibit an incredible diversity of phenotypes, the result of ~240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resources are designed to facilitate accessible a...

A major problem in evolutionary biology is explaining the success of mutualism. Solving this problem requires understanding the level of fidelity between interacting partners. Recent studies have proposed that fungus-growing ants and their fungal cultivars are the products of 'diffuse' coevolution, in which single ant and fungal species are not exc...

We examine the phylogenetic relationships of Figitidae and discuss host use within this group in light of our own and previously published divergence time data. Our results suggest Figitidae, as currently defined, is not monophyletic. Further-more, Mikeiinae and Pycnostigminae are sister-groups, nested adjacent to Thrasorinae, Plectocynipinae and E...

Aim The evolutionary history of bees is presumed to extend back in time to the Early Cretaceous. Among all major clades of bees, Colletidae has been a prime example of an ancient group whose Gondwanan origin probably precedes the complete break‐up of Africa, Antarctica, Australia and South America, because modern lineages of this family occur prima...

The ant genus Prenolepis (Hymenoptera: Formicidae) is the nominal member of the recently established Prenolepis genus‐group within the subfamily Formicinae. Our molecular phylogenetic analyses using fragments from five nuclear genes (arginine kinase, carbomoylphosphate synthase, elongation factor 1‐alpha F1, elongation factor 1‐alpha F2, wingless)...

This paper serves as an introduction to a world monographic series addressing the species-level taxonomy of the ant genus Nylanderia. This series will consist of several regionally based taxonomic revisions. The systematics and biology of Nylanderia are discussed in a global context, and a diagnosis of the genus is given. Several morphological feat...

This paper serves as an introduction to a world monographic series addressing the species-level taxonomy of the ant genus Nylanderia. This series will consist of several regionally based taxonomic revisions. The systematics and biology of Nylanderia are discussed in a global context, and a diagnosis of the genus is given. Several morphological feat...

The bee-family Halictidae has enormous behavioural diversity, including multiple origins of eusociality, cleptoparasitism, and multiple reversals to solitary behaviour. We use a phylogenetic approach to examine social evolution in the Halictini, which is the largest and most behaviourally diverse tribe. We report results from two datasets; a datase...

We provide diagnostic morphological characters to help distinguish males and females of the following species of Nomada: N. augustiana Mitchell, N. bethunei Cockerell, N. fervida Smith, N. fragariae Mitchell, N. lehighensis Cockerell, N. texana Cresson, and N. tiftonensis Cockerell. Based on morphological and DNA barcoding evidence we newly synonym...

Ants (Hymenoptera: Formicidae) are conspicuous organisms in most terrestrial ecosystems, often attaining high levels of abundance and diversity. In this study, we investigate the evolutionary history of a major clade of ants, the subfamily Dolichoderinae, whose species frequently achieve ecological dominance in ant communities. This group has also...

We investigated the phylogeny and taxonomy of the Prenolepis genus-group, a clade of ants we define within the subfamily Formicinae comprising the genera Euprenolepis, Nylanderia, gen. rev., Paraparatrechina, gen. rev. & stat. nov., Paratrechina, Prenolepis and Pseudolasius. We inferred a phylogeny of the Prenolepis genus-group using DNA sequence d...

Maximum likelihood phylogeny of Blochmannia, estimated with outgroups. Taxa are labeled by the ant host from which the bacterial gene was amplified. The topology reflects the majority-rule consensus tree of 100 bootstrap replicates. In this rooted tree, bootstrap values ≥70% are marked. (All unmarked nodes have bootstrap values of 50%-69%.) Outgrou...

MacClade file (nexus format) of the 16S rDNA sequence alignment analyzed here. Ambiguous (excluded) regions in the alignment are marked as character sets. Sequences used in phylogenetic analyses are marked as distinct taxon sets.

Database matches for 52 new bacterial 16S rDNA sequences obtained in this study. The vast majority of sequences most closely matched a published Blochmannia 16S rDNA sequence in NCBI (compared using BLASTn) and/or the Ribosomal Database Project (RDP; compared using SeqMatch).

Maximum likelihood phylogeny of gamma-Proteobacteria, estimated from a region of the 16S rDNA gene. Within Blochmannia, taxa are labeled by the ant host from which the bacterial gene was amplified. The topology reflects the majority-rule consensus tree of 100 bootstrap replicates. Bootstrap values ≥70% are marked. (All unmarked nodes have bootstrap...

Maximum likelihood phylogeny of Blochmannia, estimated without outgroups. Taxa are labeled by the ant host from which the bacterial gene was amplified. The topology reflects the majority-rule consensus tree of 100 bootstrap replicates. In this unrooted tree, only bootstrap values of deep nodes are marked. Otherwise, relationships resemble those in...

Bacterial endosymbiosis has a recurring significance in the evolution of insects. An estimated 10-20% of insect species depend on bacterial associates for their nutrition and reproductive viability. Members of the ant tribe Camponotini, the focus of this study, possess a stable, intracellular bacterial mutualist. The bacterium, Blochmannia, was fir...

This article derives from a society-wide symposium organized by Timothy Bradley and Adriana Briscoe and presented at the 2009 annual meeting of the Society for Integrative and Comparative Biology in Boston, Massachusetts. David Grimaldi provided the opening presentation in which he outlined the major evolutionary events in the formation and subsequ...