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1. Mining Ultraconserved Elements From Transcriptome and Genome Data to Explore the Phylogenomics of the Free-living Lice Suborder Psocomorpha (Insecta: Psocodea)

   https://doi.org/10.1093/isd/ixac010  

   Saenz Manchola, Oscar Fernando ; Samacá Sáenz, Ernesto ; Virrueta Herrera, Stephany ; D’Alessio, Lorenzo Mario ; García Aldrete, Alfonso Nerí ; Johnson, Kevin P ( July 2022 , Insect Systematics and Diversity)

   Yoshizawa, Kazunori (Ed.)

   Abstract The order Psocodea includes the two historically recognized groups Psocoptera (free-living bark lice) and Phthiraptera (parasitic lice) that were once considered separate orders. Psocodea is divided in three suborders: Trogiomorpha, Troctomorpha, and Psocomorpha, the latter being the largest within the free-living groups. Despite the increasing number of transcriptomes and whole genome sequence (WGS) data available for this group, the relationships among the six known infraorders within Psocomorpha remain unclear. Here, we evaluated the utility of a bait set designed specifically for parasitic lice belonging to suborder Troctomorpha to extract UCE loci from transcriptome and WGS data of 55 bark louse species and explored the phylogenetic relationships within Psocomorpha using these UCE loci markers. Taxon sampling was heavily focused on the families Lachesillidae and Elipsocidae, whose relationships have been problematic in prior phylogenetic studies. We successfully recovered a total of 2,622 UCE loci, with a 40% completeness matrix containing 2,081 UCE loci and an 80% completeness matrix containing 178 UCE loci. The average number of UCE loci recovered for the 55 species was 1,401. The WGS data sets produced a larger number of UCE loci (1,495) on average than the transcriptome data sets (972). Phylogenetic relationships reconstructed with Maximum Likelihoodmore »and coalescent-based analysis were concordant regarding the paraphyly of Lachesillidae and Elipsocidae. Branch support values were generally lower in analyses that used a fewer number of loci, even though they had higher matrix completeness.« less
2. Phylogenomics and the evolution of hemipteroid insects

   https://doi.org/10.1073/pnas.1815820115  

   Johnson, Kevin P. ; Dietrich, Christopher H. ; Friedrich, Frank ; Beutel, Rolf G. ; Wipfler, Benjamin ; Peters, Ralph S. ; Allen, Julie M. ; Petersen, Malte ; Donath, Alexander ; Walden, Kimberly K. O. ; et al ( November 2018 , Proceedings of the National Academy of Sciences)

   Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for futuremore »studies of the group.

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3. Phylogenomic Interrogation Revives an Overlooked Hypothesis for the Early Evolution of the Bee Family Apidae (Hymenoptera: Apoidea), With a Focus on the Subfamily Anthophorinae

   https://doi.org/10.1093/isd/ixac022  

   Orr, Michael C. ; Branstetter, Michael G. ; Straka, Jakub ; Yuan, Feng ; Leijs, Remko ; Zhang, Dan ; Zhou, Qingsong ; Zhu, Chao-Dong ; Almeida, ed., Eduardo ( August 2022 , Insect Systematics and Diversity)

   Despite recent advances in phylogenomics, the early evolution of the largest bee family, Apidae, remains uncertain, hindering efforts to understand the history of Apidae and establish a robust comparative framework. Confirming the position of Anthophorinae—a diverse, globally distributed lineage of apid bees—has been particularly problematic, with the subfamily recovered in various conflicting positions, including as sister to all other Apidae or to the cleptoparasitic Nomadinae. We aimed to resolve relationships in Apidae and Anthophorinae by combining dense taxon sampling, with rigorous phylogenomic analysis of a dataset consisting of ultraconserved elements (UCEs) acquired from multiple sources, including low-coverage genomes. Across a diverse set of analyses, including both concatenation and species tree approaches, and numerous permutations designed to account for systematic biases, Anthophorinae was consistently recovered as the sister group to all remaining Apidae, with Nomadinae sister to (Apinae, [Xylocopinae, Eucerinae]). However, several alternative support metrics (concordance factors, quartet sampling, and gene genealogy interrogation) indicate that this result should be treated with caution. Within Anthophorinae, all genera were recovered as monophyletic, following synonymization of Varthemapistra with Habrophorula. Our results demonstrate the value of dense taxon sampling in bee phylogenomics research and how implementing diverse analytical strategies is important for fully evaluatingmore »results at difficult nodes.

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4. New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships

   https://doi.org/10.1038/s41598-019-56728-w  

   Kocot, Kevin M. ; Poustka, Albert J. ; Stöger, Isabella ; Halanych, Kenneth M. ; Schrödl, Michael ( January 2020 , Scientific Reports)

   Relationships among the major lineages of Mollusca have long been debated. Morphological studies have considered the rarely collected Monoplacophora (Tryblidia) to have several plesiomorphic molluscan traits. The phylogenetic position of this group is contentious as morphologists have generally placed this clade as the sister taxon of the rest of Conchifera whereas earlier molecular studies supported a clade of Monoplacophora + Polyplacophora (Serialia) and phylogenomic studies have generally recovered a clade of Monoplacophora + Cephalopoda. Phylogenomic studies have also strongly supported a clade including Gastropoda, Bivalvia, and Scaphopoda, but relationships among these taxa have been inconsistent. In order to resolve conchiferan relationships and improve understanding of early molluscan evolution, we carefully curated a high-quality data matrix and conducted phylogenomic analyses with broad taxon sampling including newly sequenced genomic data from the monoplacophoranLaevipilina antarctica. Whereas a partitioned maximum likelihood (ML) analysis using site-homogeneous models recovered Monoplacophora sister to Cephalopoda with moderate support, both ML and Bayesian inference (BI) analyses using mixture models recovered Monoplacophora sister to all other conchiferans with strong support. A supertree approach also recovered Monoplacophora as the sister taxon of a clade composed of the rest of Conchifera. Gastropoda was recovered as the sister taxon of Scaphopoda in most analyses, which wasmore »strongly supported when mixture models were used. A molecular clock based on our BI topology dates diversification of Mollusca to ~546 MYA (+/− 6 MYA) and Conchifera to ~540 MYA (+/− 9 MYA), generally consistent with previous work employing nuclear housekeeping genes. These results provide important resolution of conchiferan mollusc phylogeny and offer new insights into ancestral character states of major mollusc clades.

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5. Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data

   https://doi.org/10.1093/sysbio/syz064  

   Opatova, Vera ; Hamilton, Chris A. ; Hedin, Marshal ; De Oca, Laura Montes ; Král, Jiři ; Bond, Jason E. ; Wiegmann, ed., Brian ( December 2019 , Systematic Biology)

   The infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here, we present a comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae. We employ 472 loci obtained through anchored hybrid enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We sampled nearly all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providingmore »insights to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). Three families Entypesidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY), and one subfamily Australothelinae (NEW SUBFAMILY) are newly proposed. Such a major rearrangement in classification, recognizing nine newly established family-level rank taxa, is the largest the group has seen in over three decades. [Biogeography; molecular clocks; phylogenomics; spider web foraging; taxonomy.]

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