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1. Expansion and Accelerated Evolution of 9-Exon Odorant Receptors in Polistes Paper Wasps

   https://doi.org/10.1093/molbev/msab023  

   Legan, Andrew W; Jernigan, Christopher M; Miller, Sara E; Fuchs, Matthieu F; Sheehan, Michael J (February 2021, Molecular Biology and Evolution)

   Agashe, Deepa (Ed.)

   Abstract Independent origins of sociality in bees and ants are associated with independent expansions of particular odorant receptor (OR) gene subfamilies. In ants, one clade within the OR gene family, the 9-exon subfamily, has dramatically expanded. These receptors detect cuticular hydrocarbons (CHCs), key social signaling molecules in insects. It is unclear to what extent 9-exon OR subfamily expansion is associated with the independent evolution of sociality across Hymenoptera, warranting studies of taxa with independently derived social behavior. Here, we describe OR gene family evolution in the northern paper wasp, Polistes fuscatus, and compare it to four additional paper wasp species spanning ∼40 million years of evolutionary divergence. We find 200 putatively functional OR genes in P. fuscatus, matching predictions from neuroanatomy, and more than half of these are in the 9-exon subfamily. Most OR gene expansions are tandemly arrayed at orthologous loci in Polistes genomes, and microsynteny analysis shows species-specific gain and loss of 9-exon ORs within tandem arrays. There is evidence of episodic positive diversifying selection shaping ORs in expanded subfamilies. Values of omega (dN/dS) are higher among 9-exon ORs compared to other OR subfamilies. Within the Polistes OR gene tree, branches in the 9-exon OR clade experience relaxed negative (relaxed purifying) selection relative to other branches in the tree. Patterns of OR evolution within Polistes are consistent with 9-exon OR function in CHC perception by combinatorial coding, with both natural selection and neutral drift contributing to interspecies differences in gene copy number and sequence. 

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2. Water lily ( Nymphaea thermarum ) genome reveals variable genomic signatures of ancient vascular cambium losses

   https://doi.org/10.1073/pnas.1922873117  

   Povilus, Rebecca A.; DaCosta, Jeffrey M.; Grassa, Christopher; Satyaki, Prasad R. V.; Moeglein, Morgan; Jaenisch, Johan; Xi, Zhenxiang; Mathews, Sarah; Gehring, Mary; Davis, Charles C.; et al (March 2020, Proceedings of the National Academy of Sciences)

   For more than 225 million y, all seed plants were woody trees, shrubs, or vines. Shortly after the origin of angiosperms ∼140 million y ago (MYA), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium, the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem, which are produced by apical meristems and retained in nearly all seed plants. Here, we sequenced and assembled a draft genome of the water lilyNymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compared it to genomes from other cambium-bearing and cambium-less lineages (e.g., monocots andNelumbo). This revealed lineage-specific patterns of gene loss and divergence.Nymphaeais characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss ofREVOLUTA, which influences cambial activity in other angiosperms. We also found theNymphaeaand monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids.Nelumbodisplays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent loss of vascular cambium reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent events of trait loss. Our results shed light on the evolution of herbaceousness—one of the key biological innovations associated with the earliest phases of angiosperm evolution. 

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3. Co-expression Gene Networks and Machine-learning Algorithms Unveil a Core Genetic Toolkit for Reproductive Division of Labour in Rudimentary Insect Societies

   https://doi.org/10.1093/gbe/evac174  

   Favreau, Emeline; Geist, Katherine S; Wyatt, Christopher D; Toth, Amy L; Sumner, Seirian; Rehan, Sandra M (January 2023, Genome Biology and Evolution)

   Webster, Matthew (Ed.)

   Abstract The evolution of eusociality requires that individuals forgo some or all their own reproduction to assist the reproduction of others in their group, such as a primary egg-laying queen. A major open question is how genes and genetic pathways sculpt the evolution of eusociality, especially in rudimentary forms of sociality—those with smaller cooperative nests when compared with species such as honeybees that possess large societies. We lack comprehensive comparative studies examining shared patterns and processes across multiple social lineages. Here we examine the mechanisms of molecular convergence across two lineages of bees and wasps exhibiting such rudimentary societies. These societies consist of few individuals and their life histories range from facultative to obligately social. Using six species across four independent origins of sociality, we conduct a comparative meta-analysis of publicly available transcriptomes. Standard methods detected little similarity in patterns of differential gene expression in brain transcriptomes among reproductive and non-reproductive individuals across species. By contrast, both supervised machine learning and consensus co-expression network approaches uncovered sets of genes with conserved expression patterns among reproductive and non-reproductive phenotypes across species. These sets overlap substantially, and may comprise a shared genetic “toolkit” for sociality across the distantly related taxa of bees and wasps and independently evolved lineages of sociality. We also found many lineage-specific genes and co-expression modules associated with social phenotypes and possible signatures of shared life-history traits. These results reveal how taxon-specific molecular mechanisms complement a core toolkit of molecular processes in sculpting traits related to the evolution of eusociality. 

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4. 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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5. Mitochondrial genome fragmentation is correlated with increased rates of molecular evolution

   https://doi.org/10.1371/journal.pgen.1011266  

   Najer, Tomáš; Doña, Jorge; Buček, Aleš; Sweet, Andrew D; Sychra, Oldřich; Johnson, Kevin_P (May 2024, PLOS Genetics)

   Sloan, Daniel (Ed.)

   While mitochondrial genome content and organization is quite diverse across all Eukaryotes, most bilaterian animal mitochondrial genomes (mitogenomes) exhibit highly conserved gene content and organisation, with genes typically encoded on a single circular chromosome. However, many species of parasitic lice (Insecta: Phthiraptera) are among the notable exceptions, having mitogenomes fragmented into multiple circular chromosomes. To better understand the process of mitogenome fragmentation, we conducted a large-scale genomic study of a major group of lice, Amblycera, with extensive taxon sampling. Analyses of the evolution of mitogenome structure across a phylogenomic tree of 90 samples from 53 genera revealed evidence for multiple independent origins of mitogenome fragmentation, some inferred to have occurred less than five million years ago. We leveraged these many independent origins of fragmentation to compare the rates of DNA substitution and gene rearrangement, specifically contrasting branches with fragmented and non-fragmented mitogenomes. We found that lineages with fragmented mitochondrial genomes had significantly higher rates of mitochondrial sequence evolution. In addition, lineages with fragmented mitochondrial genomes were more likely to have mitogenome gene rearrangements than those with single-chromosome mitochondrial genomes. By combining phylogenomics and mitochondrial genomics we provide a detailed portrait of mitogenome evolution across this group of insects with a remarkably unstable mitogenome structure, identifying processes of molecular evolution that are correlated with mitogenome fragmentation. 

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