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1. A comparison of phylogenomic inference pipelines for low‐coverage whole‐genome sequencing in Formica ants

   https://doi.org/10.1111/syen.12670  

   Zhang, Junxia; Lin, Long; Mu, Yannan; Brelsford, Alan; Purcell, Jessica (January 2025, Systematic Entomology)

   Blaimer, Bonnie (Ed.)

   Abstract A rapid proliferation in the availability of whole genome sequences (WGS), often with relatively low read depth, offers an unprecedented opportunity for phylogenomic advances using publicly available data, but there are several key challenges in applying these data. Using low‐coverage WGS data for the ant species ofFormica, we conducted detailed comparisons on two different analytical pipelines (reference‐based vs. de novo genome assembly), four types of datasets (5‐kbp‐window, ultra‐conserved element [UCE], single‐copy ortholog [BUSCO] and mitogenome), and a series of analytical procedures (e.g. concatenation vs. coalescent analyses) to identify which are robust to typical WGS data. The results show that at a shallow scale of phylogenetic relationships of closely related species 5‐kbp‐windows from the reference‐based pipeline and UCEs from the de novo assemblies are more successful than the BUSCOs in recovering informative markers for phylogenetic inference. Compared with concatenation analyses, coalescent analyses often resulted in disparate deeper relationships in the phylogeny. This study also uncovers evident mito‐nuclear discordance and demonstrates genome‐wide gene conflicts in phylogenetic signals, both pointing to possible incomplete lineage sorting and/or hybridization during the early, rapid radiation ofFormicaants. Divergence dating analyses show that different types of data and analytical methods could result in inconsistent time estimates, highlighting the potential need for multiple approaches to better understand species divergence. The strengths and weaknesses of different analytical pipelines and strategies are discussed. Findings from this study provide valuable insights for large‐scale phylogenomic projects using WGS data. 

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2. Convergent evolution of complex structures for ant–bacterial defensive symbiosis in fungus-farming ants

   https://doi.org/10.1073/pnas.1809332115  

   Li, Hongjie; Sosa-Calvo, Jeffrey; Horn, Heidi A.; Pupo, Mônica T.; Clardy, Jon; Rabeling, Christian; Schultz, Ted R.; Currie, Cameron R. (October 2018, Proceedings of the National Academy of Sciences)

   Evolutionary adaptations for maintaining beneficial microbes are hallmarks of mutualistic evolution. Fungus-farming “attine” ant species have complex cuticular modifications and specialized glands that house and nourish antibiotic-producing Actinobacteria symbionts, which in turn protect their hosts’ fungus gardens from pathogens. Here we reconstruct ant–Actinobacteria evolutionary history across the full range of variation within subtribe Attina by combining dated phylogenomic and ultramorphological analyses. Ancestral-state analyses indicate the ant–Actinobacteria symbiosis arose early in attine-ant evolution, a conclusion consistent with direct observations of Actinobacteria on fossil ants in Oligo-Miocene amber. qPCR indicates that the dominant ant-associated Actinobacteria belong to the genus Pseudonocardia . Tracing the evolutionary trajectories of Pseudonocardia -maintaining mechanisms across attine ants reveals a continuum of adaptations. In Myrmicocrypta species, which retain many ancestral morphological and behavioral traits, Pseudonocardia occur in specific locations on the legs and antennae, unassociated with any specialized structures. In contrast, specialized cuticular structures, including crypts and tubercles, evolved at least three times in derived attine-ant lineages. Conspicuous caste differences in Pseudonocardia -maintaining structures, in which specialized structures are present in worker ants and queens but reduced or lost in males, are consistent with vertical Pseudonocardia transmission. Although the majority of attine ants are associated with Pseudonocardia , there have been multiple losses of bacterial symbionts and bacteria-maintaining structures in different lineages over evolutionary time. The early origin of ant– Pseudonocardia mutualism and the multiple evolutionary convergences on strikingly similar anatomical adaptations for maintaining bacterial symbionts indicate that Pseudonocardia have played a critical role in the evolution of ant fungiculture. 

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

   https://doi.org/10.1111/syen.12678  

   Ward, Philip_S; Fisher, Brian_L; Wernegreen, Jennifer_J; Blaimer, Bonnie_B (May 2025, Systematic Entomology)

   Abstract 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 the 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:Lathidrisgen. n., from the mountains of Mesoamerica;Retalimyrmagen. n., from the Indian Himalayas; andUwarigen. n., from eastern Asia. The species in these new genera were described and placed erroneously inCamponotus. The tribe Camponotini is estimated to have a crown origin in the Eocene (median age 38.4 Ma), with successively younger crown ages forColobopsis(22.5 Ma),Camponotus(18.6 Ma) andPolyrhachis(18.5 Ma). We infer an Australasian or Indomalayan origin for the tribe, with multiple dispersal events to the Afrotropics, Palearctic region, and New World. Phylogenetic analysis of selectedBlochmanniagenes from a subset of 97 camponotine taxa yields results that are largely congruent with the ant host phylogeny, at least for well‐supported nodes, but we find evidence thatBlochmanniafrom some old lineages—especiallyLathidris—may have discordant histories, suggesting possible lability of this symbiosis in the early evolution of camponotine ants. 

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4. Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

   https://doi.org/10.1093/sysbio/syaa054  

   Singhal, Sonal; Colston, Timothy J; Grundler, Maggie R; Smith, Stephen A; Costa, Gabriel C; Colli, Guarino R; Moritz, Craig; Pyron, R Alexander; Rabosky, Daniel L (August 2020, Systematic Biology)

   Ruane, Sara (Ed.)

   Abstract Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).] 

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5. Evolving perspectives in Hymenoptera systematics: Bridging fossils and genomes across time

   https://doi.org/10.1111/syen.12645  

   Zhang, Y_Miles; Bossert, Silas; Spasojevic, Tamara (July 2024, Systematic Entomology)

   Abstract The recent advances in sequencing technologies, phylogenomics and divergence dating methods call for an integrative review of the current state of Hymenoptera systematics. We here explore the impact of these latest developments on the Hymenoptera phylogeny and our understanding of the timing of Hymenoptera evolution, while identifying the current methodological constraints and persistent knowledge gaps that warrant further investigation. Our review highlights the lack of consensus among the backbone phylogeny of Hymenoptera between key phylogenomic studies, as the higher level phylogeny remains unresolved in key nodes such as the relationships among Eusymphyta, the relationships within the Infraorder Proctotrupomorpha and the placements of the superfamilies Ichneumonoidea, Ceraphronoidea and Vespoidea. Furthermore, we underline the huge variation in divergence age estimates for Hymenoptera and detect several major gaps and/or disagreements between the fossil record and available age estimates, either due to the poorly studied fossil record or problematic age estimates, or both. To better understand the timing of Hymenoptera evolution and the role of key diversification factors, we will need continuous efforts to (i) reconcile conflicts among morphological and molecular phylogenies, by improving taxon sampling of underrepresented lineages, applying novel techniques to study morphology, making use of genome‐scale data and critically assessing incongruences in genetic markers; (ii) improve the Hymenoptera fossil record, by exercising integrative taxonomy and bringing together paleontologists and neontologists; and (iii) reconcile age estimates, by relying on tip dating approaches to bridge fossils, morphology and genomes across time. 

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