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  1. Abstract

    Larval feeding by the moth genusOgmograptis(Bucculatricidae: Lepidoptera) creates one of the most iconic features of the Australian bush—the ‘scribbles’ found on smooth‐barkedEucalyptus. The taxonomic history ofOgmograptishas been challenging, with members of the genus being initially described in four different genera representing three different superfamilies. While prior phylogenetic analysis has placedOgmograptiswithin the Bucculatricidae, these findings were not strongly supported and there was poor resolution of the early diverging, non‐Apoditrysia superfamilies thatOgmograptishas been assigned to by different authors. As a consequence, the unique larval biology of scribbly moths cannot yet be interpreted in an evolutionary context. Phylogenomic analysis of whole mitochondrial (mt) genome data forOgmograptis, related non‐Apoditrysia and taxa representing the superfamily‐level diversity of the order strongly supports its placement within the Bucculatricidae, a monophyletic Gracillarioidea and a clade of Gracillarioidea + Yponomeutoidea that was sister to the Apoditrysia. The hypermetamorphic larval development inOgmograptiscan thus be interpreted as an elaboration of the ancestral pattern of the clade Gracillarioidea + Yponomeutoidea that has specialised for phellogen/callus feeding within the bark. The utility of mt genomes for deep‐level phylogenetic study of the Lepidoptera is reviewed against prior multi‐locus and nuclear phylogenomic datasets. Mt phylogenomic analyses are sensitive to analytical methods and the inclusion versus exclusion of high‐variability data partitions for deep‐level relationships, already shown to be uncertain by multi‐locus or nuclear phylogenomic analyses, in particular relationships between apoditrysian and obtectomeran superfamilies. While mt genomes are ideal for examining the relationships of rare, physically small or difficult to collect taxa such asOgmograptis, due to the low technical hurdles to collecting whole genomes, continued attention to the analytical sensitivities of phylogenies that use this data source is needed to reliably advance our understanding of deep lepidopteran evolution.

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  2. Abstract

    Sequencing high molecular weight (HMW) DNA with long-read and linked-read technologies has promoted a major increase in more complete genome sequences for nonmodel organisms. Sequencing approaches that rely on HMW DNA have been limited to larger organisms or pools of multiple individuals, but recent advances have allowed for sequencing from individuals of small-bodied organisms. Here, we use HMW DNA sequencing with PacBio long reads and TELL-Seq linked reads to assemble and annotate the genome from a single individual feather louse (Brueelia nebulosa) from a European Starling (Sturnus vulgaris). We assembled a genome with a relatively high scaffold N50 (637 kb) and with BUSCO scores (96.1%) comparable to louse genomes assembled from pooled individuals. We annotated a number of genes (10,938) similar to the human louse (Pediculus humanus) genome. Additionally, calling phased variants revealed that the Brueelia genome is more heterozygous (∼1%) then expected for a highly obligate and dispersal-limited parasite. We also assembled and annotated the mitochondrial genome and primary endosymbiont (Sodalis) genome from the individual louse, which showed evidence for heteroplasmy in the mitogenome and a reduced genome size in the endosymbiont compared to its free-living relative. Our study is a valuable demonstration of the capability to obtain high-quality genomes from individual small, nonmodel organisms. Applying this approach to other organisms could greatly increase our understanding of the diversity and evolution of individual genomes.

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  3. Abstract

    The mitochondrial genomes (mitogenomes) of bilaterian animals are highly conserved structures that usually consist of a single circular chromosome. However, several species of parasitic lice (Insecta: Phthiraptera) possess fragmented mitogenomes, where the mitochondrial genes are present on separate, circular chromosomes. Nevertheless, the extent, causes, and consequences of this structural variation remain poorly understood. Here, we combined new and existing data to better understand the evolution of mitogenome fragmentation in major groups of parasitic lice. We found strong evidence that fragmented mitogenomes evolved many times within parasitic lice and that the level of fragmentation is highly variable, including examples of heteroplasmic arrangements. We also found a significant association between mitochondrial fragmentation and signatures of relaxed selection. Mitochondrial fragmentation was also associated with changes to a lower AT%, possibly due to differences in mutation biases. Together, our results provide a significant advance in understanding the process of mitogenome fragmentation and provide an important perspective on mitochondrial evolution in eukaryotes.

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    Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice. 
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  6. PLEASE CONTACT AUTHORS IF YOU CONTRIBUTE AND WOULD LIKE TO BE LISTED AS A CO-AUTHOR. (this message will be removed some time weeks/months after the first publication)

    Terrestrial Parasite Tracker indexed biotic interactions and review summary.

    The Terrestrial Parasite Tracker (TPT) project began in 2019 and is funded by the National Science foundation to mobilize data from vector and ectoparasite collections to data aggregators (e.g., iDigBio, GBIF) to help build a comprehensive picture of arthropod host-association evolution, distributions, and the ecological interactions of disease vectors which will assist scientists, educators, land managers, and policy makers. Arthropod parasites often are important to human and wildlife health and safety as vectors of pathogens, and it is critical to digitize these specimens so that they, and their biotic interaction data, will be available to help understand and predict the spread of human and wildlife disease.

    This data publication contains versioned TPT associated datasets and related data products that were tracked, reviewed and indexed by Global Biotic Interactions (GloBI) and associated tools. GloBI provides open access to finding species interaction data (e.g., predator-prey, pollinator-plant, pathogen-host, parasite-host) by combining existing open datasets using open source software.

    If you have questions or comments about this publication, please open an issue at or contact the authors by email.

    The creation of this archive was made possible by the National Science Foundation award "Collaborative Research: Digitization TCN: Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease," Award numbers DBI:1901932 and DBI:1901926

    Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics.

    GloBI Data Review Report

    Datasets under review:
     - University of Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner. accessed via on 2022-06-24T14:02:48.801Z
     - Academy of Natural Sciences Entomology Collection for the Parasite Tracker Project accessed via on 2022-06-24T14:04:22.091Z
     - Bernice Pauahi Bishop Museum, J. Linsley Gressitt Center for Research in Entomology accessed via on 2022-06-24T14:04:37.692Z
     - Texas A&M University, Biodiversity Teaching and Research Collections accessed via on 2022-06-24T14:06:40.154Z
     - Brigham Young University Arthropod Museum accessed via on 2022-06-24T14:06:51.420Z
     - California Academy of Sciences Entomology accessed via on 2022-06-24T14:07:16.371Z
     - Clemson University Arthropod Collection accessed via on 2022-06-24T14:07:40.925Z
     - Denver Museum of Nature and Science (DMNS) Parasite specimens (DMNS:Para) accessed via on 2022-06-24T14:08:00.730Z
     - Field Museum of Natural History IPT accessed via on 2022-06-24T14:18:51.995Z
     - Illinois Natural History Survey Insect Collection accessed via on 2022-06-24T14:19:37.563Z
     - UMSP / University of Minnesota / University of Minnesota Insect Collection accessed via on 2022-06-24T14:20:27.232Z
     - Milwaukee Public Museum Biological Collections Data Portal accessed via on 2022-06-24T14:20:46.185Z
     - Museum for Southern Biology (MSB) Parasite Collection accessed via on 2022-06-24T15:16:07.223Z
     - The Albert J. Cook Arthropod Research Collection accessed via on 2022-06-24T16:09:40.702Z
     - Ohio State University Acarology Laboratory accessed via on 2022-06-24T16:10:00.281Z
     - Frost Entomological Museum, Pennsylvania State University accessed via on 2022-06-24T16:10:07.741Z
     - Purdue Entomological Research Collection accessed via on 2022-06-24T16:10:26.654Z
     - Texas A&M University Insect Collection accessed via on 2022-06-24T16:10:58.496Z
     - University of California Santa Barbara Invertebrate Zoology Collection accessed via on 2022-06-24T16:12:29.854Z
     - University of Hawaii Insect Museum accessed via on 2022-06-24T16:12:41.408Z
     - University of New Hampshire Collection of Insects and other Arthropods UNHC-UNHC accessed via on 2022-06-24T16:12:59.500Z
     - Scott L. Gardner and Gabor R. Racz (2021). University of Nebraska State Museum - Parasitology. Harold W. Manter Laboratory of Parasitology. University of Nebraska State Museum. accessed via on 2022-06-24T16:13:06.914Z
     - Data were obtained from specimens belonging to the United States National Museum of Natural History (USNM), Smithsonian Institution, Washington DC and digitized by the Walter Reed Biosystematics Unit (WRBU). accessed via on 2022-06-24T16:13:38.013Z
     - US National Museum of Natural History Ixodes Records accessed via on 2022-06-24T16:13:45.666Z
     - Price Institute of Parasite Research, School of Biological Sciences, University of Utah accessed via on 2022-06-24T16:13:54.724Z
     - University of Wisconsin Stevens Point, Stephen J. Taft Parasitological Collection accessed via on 2022-06-24T16:14:04.745Z
     - Giraldo-Calderón, G. I., Emrich, S. J., MacCallum, R. M., Maslen, G., Dialynas, E., Topalis, P., … Lawson, D. (2015). VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic acids research, 43(Database issue), D707–D713. doi:10.1093/nar/gku1117. accessed via on 2022-06-24T16:14:11.965Z
     - WIRC / University of Wisconsin Madison WIS-IH / Wisconsin Insect Research Collection accessed via on 2022-06-24T16:14:29.743Z
     - Yale University Peabody Museum Collections Data Portal accessed via on 2022-06-24T16:23:29.289Z

    Generated on:

    GloBI's Elton 0.12.4 

    Note that all files ending with .tsv are files formatted 
    as UTF8 encoded tab-separated values files.

    Included in this review archive are:

      This file.

      Summary across all reviewed collections of total number of distinct review comments.

      Summary by reviewed collection of total number of distinct review comments.

      Summary of number of indexed interaction records by institutionCode and collectionCode.

      All review comments by collection.

      All indexed interactions for all reviewed collections.

      All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.

      Details on the datasets under review.

      Program used to update datasets and generate the review reports and associated indexed interactions.
      Source datasets used by elton.jar in process of executing the script.
      Program used to generate the report

      Log file generated as part of running the script

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  7. 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 future studies of the group.

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