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  1. Abstract Background

    The barnacles are a group of >2,000 species that have fascinated biologists, including Darwin, for centuries. Their lifestyles are extremely diverse, from free-swimming larvae to sessile adults, and even root-like endoparasites. Barnacles also cause hundreds of millions of dollars of losses annually due to biofouling. However, genomic resources for crustaceans, and barnacles in particular, are lacking.


    Using 62× Pacific Biosciences coverage, 189× Illumina whole-genome sequencing coverage, 203× HiC coverage, and 69× CHi-C coverage, we produced a chromosome-level genome assembly of the gooseneck barnacle Pollicipes pollicipes. The P. pollicipes genome is 770 Mb long and its assembly is one of the most contiguous and complete crustacean genomes available, with a scaffold N50 of 47 Mb and 90.5% of the BUSCO Arthropoda gene set. Using the genome annotation produced here along with transcriptomes of 13 other barnacle species, we completed phylogenomic analyses on a nearly 2 million amino acid alignment. Contrary to previous studies, our phylogenies suggest that the Pollicipedomorpha is monophyletic and sister to the Balanomorpha, which alters our understanding of barnacle larval evolution and suggests homoplasy in a number of naupliar characters. We also compared transcriptomes of P. pollicipes nauplius larvae and adults and found that nearly one-half of the genes in the genome are differentially expressed, highlighting the vastly different transcriptomes of larvae and adult gooseneck barnacles. Annotation of the genes with KEGG and GO terms reveals that these stages exhibit many differences including cuticle binding, chitin binding, microtubule motor activity, and membrane adhesion.


    This study provides high-quality genomic resources for a key group of crustaceans. This is especially valuable given the roles P. pollicipes plays in European fisheries, as a sentinel species for coastal ecosystems, and as a model for studying barnacle adhesion as well as its key position in the barnacle tree of life. A combination of genomic, phylogenetic, and transcriptomic analyses here provides valuable insights into the evolution and development of barnacles.

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  2. Supplementary descriptions are provided for six poorly known species of Caligus, based on a study of type and other material carried out by the late Roger F. Cressey but never published. As part of that study new illustrations were produced by Hillary Boyle Cressey who has kindly made these previously unpublished drawings available to this paper. The present account also contains critical re-assessments of the validity of several other species of Caligus Müller, 1785. It is proposed to recognise that: C. glacialis Gadd, 1910 and C. raniceps Heegaard, 1943 are junior subjective synonyms of the type species C. curtus Müller, 1785 and we consider the published geographical locality given for C. raniceps by Heegaard (1943) to be erroneous; C. guerini Guiart, 1913 is a junior subjective synonym of C. elongatus von Nordmann, 1832; C. mordax Leigh-Sharpe, 1934 is a junior subjective synonym of C. coryphaenae Steenstrup & Lütken, 1861; C. lessonius Risso, 1826 is not a caligid and is probably a junior synonym of the pandarid Demoleus heptapus (Otto, 1821); C. clavatus Kirtisinghe, 1964 is a junior subjective synonym of C. sphyraeni Pillai, 1963; C. rotundigenitalis Yü, 1933 is a junior subjective synonym of C. torpedinis Heller, 1865; C. hyalinae Heegaard, 1966 is a junior subjective synonym of C. chelifer Wilson, 1905; C. biseriodentatus, Shen, 1957 is a junior subjective synonym of C. pauliani Nuñes-Ruivo & Fourmanoir, 1956; and C. cornutus Heegaard, 1962 can be formally treated as a junior subjective synonym of C. lobodes (Wilson, 1911) because the name C. cornutus belongs with the male holotype; the female allotype collected by Heegaard (1962) remains unidentified. We also conclude that C. mebachii Marukawa, 1927 was based on a young male of Euryphorus brachypterus (Gerstaecker, 1853) and a male of Caligus coryphaenae Steenstrup & Lütken, 1861 which was mistakenly identified as the female. A lectotype is designated for C. mebachii and this species is treated as a synonym of Euryphorus brachypterus. It is noted that C. hamatus Heegaard, 1955 is conspecific with, and has priority over, C. undulatus Shen & Li, 1959. However, given that C. undulatus is a high profile and well known species, frequently recorded from across the Pacific, Indian and Atlantic oceans, a case has been submitted to the ICZN to grant precedence of C. undulatus over C. hamatus. We reject the transfer of Chalimus tenuis Leidy, 1889 to Caligus by Fowler (1912) on the basis of lack of evidence supporting the transfer, and return it to Chalimus, where it can be treated as a species inquirendum within a genus that is no longer considered as valid. We consider that C. alalongae Krøyer, 1863 and C. gracilis Dana, 1852 are species inquirenda. Caligus truttae is a nomen nudum because Giard (1890) provided no morphological information or illustration associated with the new name. 
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    Free, publicly-accessible full text available October 30, 2024
  3. Pupko, Tal (Ed.)
    Abstract The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species and half of animal biomass. It has been the subject of several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans. We show small changes in taxon sampling have large impacts on phylogenetic estimation. By analyzing identical orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due primarily to the effects of taxon sampling on the phylogenetic reconstruction method. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the maximum likelihood trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda nested within Allotriocarida with high support and recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this latter clade, which we collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocarida. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample in future studies. 
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    Free, publicly-accessible full text available August 1, 2024
  4. Teaching biology laboratories remotely presents unique problems and challenges for instructors. Microscopic examination of specimens, as is common in parasitology labs, is especially difficult given the limited quantity of teaching specimens and the need for each student to have access to a microscope at their remote location. Observing images of parasites on the internet coupled with written exercises, while useful, is unrepresentative of real-world laboratory or field conditions. To provide a more realistic microscopy-centered synchronous experience for our parasitology class during the coronavirus pandemic, we used a smartphone mounted on a student microscope to livestream examination of parasite specimens to remote students via the Webex meeting app. This allowed two instructors, working from separate locations, to present and narrate the view of the specimens through the microscope in real time to the remotely located class. While less than ideal, livestreaming microscopic views of parasite specimens together with simultaneous instructor narration provided a reasonable remote substitute for a hands-on parasitology lab experience. 
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  5. The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine metazoans, mostly as parasites. Unfortunately, our understanding of copepod evolutionary relationships is relatively limited in part because of their extremely divergent morphology, sparse taxon sampling in molecular phylogenetic analyses, a reliance on only a handful of molecular markers, and little taxonomic overlap between phylogenetic studies. Here, a synthesis tree method is used to integrate published phylogenies into a more comprehensive tree of copepods by leveraging phylogenetic and taxonomic data. A literature review in this study finds fewer than 500 species of copepods have been sampled in molecular phylogenetic studies. Using the Open Tree of Life platform, those taxa that have been sampled in previous phylogenetic studies are grafted together and combined with the underlying copepod taxonomic hierarchy from the Open Tree of Life Taxonomy to make a synthesis phylogeny of all copepod species. Taxon sampling with respect to molecular phylogenetic analyses is reviewed for all orders of copepods and shows only 3% of copepod species have been sampled in phylogenetic studies. The resulting synthesis phylogeny reveals copepods have transitioned to a parasitic lifestyle on at least 14 occasions. We examine the underlying phylogenetic, taxonomic, and natural history data supporting these transitions to parasitism; review the species diversity of each parasitic clade; and identify key areas for further phylogenetic investigation. 
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