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Abstract The ant genus Tapinoma Foerster, 1850 is a moderately diverse group (81 valid species) that occurs worldwide. It includes the tramp species T. melanocephalum, whose evolutionary history, biogeographic origin, and population limits remain unclear. Here, we present a time-calibrated phylogeny and a biogeographic history inference of the genus based on thousands of Ultraconserved Element (UCE) loci. Focusing on T. melanocephalum, we used single nucleotide polymorphisms from UCE loci and COI sequences to analyze species boundaries based on nuclear and mitochondrial DNA. We recovered a monophyletic Tapinoma with an estimated crown age corresponding to middle Eocene (49.4 to 34.4 Ma). Phylogenomic data differentiated T. melanocephalum from T. jandai, a recently established species based on morphology, and revealed that the 2 species diverged ∼12 Ma. Population genetic analyses identified considerable molecular divergence among sampled T. melanocephalum populations, and a heterogeneous genetic structure, showing a weak relationship between genetic differentiation and geographic distance. A phylogeographic comparison of habitat preferences of T. melanocephalum revealed an ecological shift from undisturbed to urban environments, a phenomenon which may have facilitated its ubiquitous and global distribution. Our study presents the first phylogenomic framework for this globally distributed ant genus and molecularly delineates a worldwide pest ant species. 

Abstract Accurate species delimitation is critical to identifying the conservation status of species. Molecular species delimitation methods have revealed previously unrecognized cryptic species across the taxonomic spectrum. However, studies vary in the molecular markers selected, analytical approaches used, and taxon sampling, which sometimes results in conflicting conclusions. One example of such a conflict is seen in the species delimitation analyses of the western bumble bee,Bombus occidentalis. This species was once an abundant insect pollinator in western North America but has declined severely since the mid 1990s and is predicted to continue to diminish under even optimistic future climate scenarios. Complicating this conservation crisis, the species status ofB. occidentalishas varied over time, with most recent studies recognizing one or two species. Previous studies that used molecular methods to address this question focused on a Bayesian phylogeny of the mitochondrialcytochrome oxidase I(COI) gene. Phylogenetic studies that focus on a single gene are criticized for misrepresenting the evolutionary history of species because nuclear and mitochondrial genomes, and even some genes within them, may have different evolutionary patterns. We tested a two species hypothesis of theB. occidentaliscomplex using nuclear (ultraconserved elements) and mitochondrial (COI) markers to infer maximum likelihood and Bayesian phylogenies for the taxa. We present our results and conclusions from eight species delimitation methods. Based on the genomic, morphological and geographic differences between the taxa we find support for the two species hypothesis, withB. occidentalisandB. mckayias separate species. We discuss the strengths and limitations of each genetic dataset and delimitation method, make recommendations for best practices, and highlight opportunities for equitable knowledge and technology development for phylogenomics in conservation biology. 

Abstract The New World army ants (Hymenoptera: Formicidae) comprise the 5 genera of the Eciton species group, and together they are important keystone predators in tropical and subtropical environments. Generic boundaries in the group have been considered solid and stable for nearly 100 years. Workers of the widespread and diverse genus Neivamyrmex are readily separable from the other 4 genera by lacking a subapical tooth on the tarsal claw, while males can be separated with genitalic characters. The genus Labidus is also widespread and is often abundant, with several species that are conspicuous surface foragers. The least known species of Labidus is L. mars, the workers of which have the tarsal tooth but otherwise share many traits with some Neivamyrmex, being completely eyeless and subterranean. This led us to question its generic placement. Here, we used ultraconserved element (UCE) phylogenomics to show that Labidus mars belongs to the genus Neivamyrmex. All phylogenies, inferred using multiple partitioning schemes and a species tree analysis, recovered the same topology, placing Labidus mars workers within Neivamyrmex. Sequenced males of L. mars were found to be within Labidus and thus incorrectly associated with L. mars. Based on these results and review of key specimens, including types, the following taxonomic changes are made: Neivamyrmex mars (Forel 1912) is a new combination; Labidus nero (Santschi 1930) (rev. stat.) is a male-based taxon revived from synonymy under L. mars; and L. denticulatus (Borgmeier 1955) (new stat.), a male-based taxon and former subspecies of L. mars, is raised to species. 

Abstract We present the first chromosome-level genome assembly for Bombus pensylvanicus, a historically widespread native pollinator species that was distributed across eastern North America but has subsequently undergone declines in range area and local relative abundance. This species has been of significant interest as a model for understanding both patterns and possible causes of bumble bee decline in the region, including the role of genetic variation. Here we present a chromosome-level reference genome assembled using Pacific Biosciences singe-molecule HiFi sequences and Hi-C data and annotated using evidence derived from RNA sequencing of multiple tissue types. The B. pensylvanicus genome has a total length of ∼352.6 Mb and was assembled into a total of 224 scaffolds, with 19 primary pseudomolecules representing putative chromosomes and an N50 = 14.872 Mb. Annotation with the Eukaryotic Genome Annotation Pipeline—External (EGAPx) identified 11,411 genes (10,263 protein coding), and BUSCO analysis of 5,991 Hymenoptera-specific BUSCO groups indicated a completeness for the proteins of 99.0% (98.6% single-copy, 0.5% duplicated) and for the genome of 98.5% (98.2% single-copy, 0.3% duplicated). We present synteny analyses with other recently assembled Bombus genomes representing different subgenera and examine the distribution of repetitive regions of the genome relative to the distribution of genes and noncoding RNAs. 

Obligatory ant–plant symbioses often appear to be single evolutionary shifts within particular ant lineages; however, convergence can be revealed once natural history observations are complemented with molecular phylogenetics. Here, we describe a remarkable example of convergent evolution in an ant–plant symbiotic system. Exclusively arboreal,Myrmelachistaspecies can be generalized opportunists nesting in several plant species or obligately symbiotic, live-stem nesters of a narrow set of plant species. Instances of specialization withinMyrmelachistaare known from northern South America and throughout Middle America. In Middle America, a diverse radiation of specialists occupies understory treelets of lowland rainforests. The morphological and behavioural uniformity of specialists suggests that they form a monophyletic assemblage, diversifying after a single origin of specialization. Using ultraconserved element phylogenomics and ancestral state reconstructions, we show that shifts from opportunistic to obligately symbiotic evolved independently in South and Middle America. Furthermore, our analyses support a remarkable case of convergence within the Middle American radiation, with two independently evolved specialist clades, arising nearly simultaneously from putative opportunistic ancestors during the late Pliocene. This repeated evolution of a complex phenotype suggests similar mechanisms behind trait shifts from opportunists to specialists, generating further questions about the selective forces driving specialization. 

The genus-level classification of the ant subfamily Ponerinae (Hymenoptera: Formicidae) is revised based on a comprehensive phylogenomic analysis of more than 2,300 ultraconserved element (UCE) loci across 1,170 sampled specimens representing 1,020 taxa (600 valid species and 420 morphospecies) and all described ponerine genera known from workers. While most previously defined genus groups are recovered as monophyletic, several genera are shown to be polyphyletic or paraphyletic. To resolve these inconsistencies, four new genera are described:Boltonoponegen. nov.,Makebaponegen. nov.,Subiridoponegen. nov., andSritoponeragen. nov.Xiphopeltastat. rev.is revalidated andEuponerais restricted by expandingFisheroponeto absorb a paraphyletic assemblage.Mesoponerais split into four lineages, resulting in transfers toMakebapone,Subiridopone, andXiphopelta.Iroponerasyn. nov.is synonymized underCryptoponeand additional new synonymies at both the generic and species levels are established. Morphological diagnoses are revised for each affected genus, and updated species lists and new combinations are provided. The updated classification recognizes 54 valid genera within Ponerinae and acknowledges an additional lineage that will be formally described in a subsequent publication. To support identification and comparative studies, revised keys to all extant Ponerinae genera are provided, presented by biogeographic region (African and Malagasy, Palearctic–Indomalaya–Australasia, and New World). This classification is intended to provide a stable, phylogenetically informed framework for future research on ponerine ants. 

Comparative genomic studies of social insects suggest that changes in gene regulation are associated with evolutionary transitions in social behavior, but the activity of predicted regulatory regions has not been tested empirically. We used STARR-seq, a high-throughput enhancer discovery tool, to identify and measure the activity of enhancers in the socially variable sweat bee,Lasioglossum albipes. We identified over 36,000 enhancers in theL. albipesgenome from three social and three solitary populations. Many enhancers were identified in only a subset ofL. albipespopulations, revealing rapid divergence in regulatory regions within this species. Population-specific enhancers were often proximal to the same genes across populations, suggesting compensatory gains and losses of regulatory regions may preserve gene activity. We also identified 1182 enhancers with significant differences in activity between social and solitary populations, some of which are conserved regulatory regions across species of bees. These results indicate that social trait variation inL. albipesis driven both by the fine-tuning of ancient enhancers as well as lineage-specific regulatory changes. Combining enhancer activity with population genetic data revealed variants associated with differences in enhancer activity and identified a subset of differential enhancers with signatures of selection associated with social behavior. Together, these results provide the first empirical map of enhancers in a socially flexible bee and highlight links between cis-regulatory variation and the evolution of social behavior. 

Abstract Coloration is an important phenotypic trait for taxonomic studies and has been widely used for identifying insect species and populations. However, coloration can be a poor diagnostic character for insect species that exhibit high polymorphism in this trait, which can lead to over-splitting of taxonomic units. In orchid bees, color variation has been interpreted by different taxonomists as either polymorphism associated with Müllerian mimicry complexes or diagnostic traits for species identification. Despite this uncertainty, integrative approaches that incorporate multiple independent datasets to test the validity of hair coloration as a character that identifies independent evolutionary units have not been used. Here, we use phylogenomic data from Ultraconserved Elements (UCEs) to explore whether color phenotypes in the widespread orchid bee species complexes Eulaema meriana and Eulaema bombiformis (Hymenoptera: Apidae: Euglossini) correspond to independent lineages or polymorphic trait variation within species. We find that lineages within both species are structured according to geography and that color morphs are generally unassociated with evolutionarily independent groups except for populations located in the Atlantic Forest of Brazil. We conclude that there is compelling evidence that E. atleticana and E. niveofasciata are subspecies of E. meriana and E. bombiformis, respectively, and not different species as previously suggested. Therefore, we recognize Eulaema meriana atleticanacomb. n. and Eulaema bombiformis niveofasciatacomb. n. and discuss their morphological characteristics. We make recommendations on the use of color traits for orchid bee taxonomy and discuss the significance of subspecies as evolutionary units relevant for conservation efforts.