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1. Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

   https://doi.org/10.1093/molbev/msab038  

   Ontano, Andrew Z; Gainett, Guilherme; Aharon, Shlomi; Ballesteros, Jesús A; Benavides, Ligia R; Corbett, Kevin F; Gavish-Regev, Efrat; Harvey, Mark S; Monsma, Scott; Santibáñez-López, Carlos E; et al (February 2021, Molecular Biology and Evolution)

   Pupko, Tal (Ed.)

   Abstract Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones. 

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2. Target Capture Methods Offer Insight into the Evolution of Rapidly Diverged Taxa and Resolve Allopolyploid Homeologs in the Fern Genus Polypodium s.s.

   https://doi.org/10.1600/036364423X16758873924135  

   Mendez-Reneau, Jonas; Gordon Burleigh, J.; Sigel, Erin M. (March 2023, Systematic Botany)

   Abstract— Like many fern lineages comprising reticulate species complexes, Polypodium s.s. (Polypodiacaeae) has a history shaped by rapid diversification, hybridization, and polyploidy that poses substantial challenges for phylogenetic inference with plastid and single-locus nuclear markers. Using target capture probes for 408 nuclear loci developed by the GoFlag project and a custom bioinformatic pipeline, SORTER, we constructed multi-locus nuclear datasets for diploid temperate and Mesoamerican species of Polypodium and five allotetraploid species belonging to the well-studied Polypodium vulgare complex. SORTER employs a clustering approach to separate putatively paralogous copies of targeted loci into orthologous matrices and haplotype phasing to infer allopolyploid haplotypes across loci, resulting in datasets amenable to both concatenated maximum likelihood and multi-species coalescent phylogenetic analyses. By comparing phylogenies derived from maximum likelihood and multi-species coalescent analyses of unphased and phased datasets, as well as evaluating discordance among gene trees and species trees, we recover support for incomplete lineage sorting within Polypodium s.s., novel relationships among diploid taxa of the Polypodium vulgare complex and its Mesoamerican sister clade, and the placement of several Polypodium species within other genera. Additionally, we were able to infer well-supported phylogenies that identified the hypothesized progenitors of the allotetraploid species, indicating that SORTER is an effective and accurate tool for reconstructing homeolog haplotypes of allopolyploids in fern taxa and other non-model organisms from target capture data. 

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3. Phylogenomic relationships of bioluminescent elateroids define the ‘lampyroid’ clade with clicking Sinopyrophoridae as its earliest member

   https://doi.org/10.1111/syen.12451  

   Kusy, Dominik; He, Jin‐Wu; Bybee, Seth M.; Motyka, Michal; Bi, Wen‐Xuan; Podsiadlowski, Lars; Li, Xue‐Yan; Bocak, Ladislav (August 2020, Systematic Entomology)

   Abstract Bioluminescence has been hypothesized as aposematic signalling, intersexual communication and a predatory strategy, but origins and relationships among bioluminescent beetles have been contentious. We reconstruct the phylogeny of the bioluminescent elateroid beetles (i.e. Elateridae, Lampyridae, Phengodidae and Rhagophthalmidae), analysing genomic data ofSinopyrophorusBi & Li, and in light of our phylogenetic results, we erect Sinopyrophoridae Bi & Li,stat.n. as a clicking elaterid‐like sister group of the soft‐bodied bioluminescent elateroid beetles, that is, Lampyridae, Phengodidae and Rhagophthalmidae. We suggest a single origin of bioluminescence for these four families, designated as the ‘lampyroid clade’, and examine the origins of bioluminescence in the terminal lineages of click beetles (Elateridae). The soft‐bodied bioluminescent lineages originated from the fully sclerotized elateroids as a derived clade with clickingSinopyrophorusand Elateridae as their serial sister groups. This relationship indicates that the bioluminescent soft‐bodied elateroids are modified click beetles. We assume that bioluminescence was not present in the most recent common ancestor of Elateridae and the lampyroid clade and it evolved among this group with some delay, at the latest in the mid‐Cretaceous period, presumably in eastern Laurasia. The delimitation and internal structure of the elaterid‐lampyroid clade provides a phylogenetic framework for further studies on the genomic variation underlying the evolution of bioluminescence. 

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4. A New Paramoeba Isolate From Florida Exhibits a Microtubule‐Bound Endosymbiont Closely Associated With the Host Nucleus

   https://doi.org/10.1111/jeu.70011  

   Tekle, Yonas I; Smith, Atira R; McGinnis, Michael; Ghebezadik, Saron; Patel, Priyal (May 2025, Journal of Eukaryotic Microbiology)

   ABSTRACT The generaParamoebaandNeoparamoeba, within the family Paramoebidae (order Dactylopodida), are distinguished by their dactylopodial pseudopodia and the presence of an intracellular eukaryotic symbiont, thePerkinsela‐like organism (PLO). Taxonomic classification within these genera has been challenging due to overlapping morphological traits and close phylogenetic relationships.Theyare marine, with some playing significant roles as parasites. Notably, they have been implicated in sea urchin mass mortality events and are known causative agents of Amoebic Gill Disease (AGD) in fish. Despite their ecological and economic importance, many aspects of their diversity, biology, evolution, and host interactions remain poorly understood. In this study, we describe a novel amoeba species,Paramoeba daytonin. sp., isolated from Daytona Beach, Florida. Morphological and molecular analyses confirm its placement within theParamoebaclade, closely related toP. eilhardi,P. karteshi, andP. aparasomata. Phylogenetic assessments using 18S rDNA (18S) and Cytochrome c Oxidase I (COI) markers demonstrate the limitations of the 18S gene for species delineation, highlighting COI as a more reliable genetic marker for this group. Additionally, observations on PLO morphology, movement, and microtubule association provide insights into the endosymbiotic relationship, reinforcing the need for further research into this unique eukaryote‐eukaryote symbiosis. 

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5. In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies

   https://doi.org/10.3389/ffunb.2021.716385  

   Montoliu-Nerin, Merce; Sánchez-García, Marisol; Bergin, Claudia; Kutschera, Verena Esther; Johannesson, Hanna; Bever, James D.; Rosling, Anna (September 2021, Frontiers in Fungal Biology)

   Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales. 

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