The first complete mitochondrial genome of a parasitic isopod supports Epicaridea Latreille, 1825 as a suborder and reveals the less conservative genome of isopods

The complete mitochondrial genome sequence of the holoparasitic isopod Gyge ovalis (Shiino, 1939) has been determined. The mitogenome is 14,268 bp in length and contains 34 genes: 13 protein-coding genes, two ribosomal RNA, 19 tRNA and a control region. Three tRNA genes (trnE, trnI and trnS1) are missing. Most of the tRNA genes show secondary structures which derive from the usual cloverleaf pattern except for trnC which is characterised by the loss of the DHU-arm. Compared to the isopod ground pattern and Eurydice pulchra Leach, 1815 (suborder Cymothoida Wägele, 1989), the genome of G. ovalis shows few differences, with changes only around the control region. However, the genome of G. ovalis is very different from that of non-cymothoidan isopods and reveals that the gene order evolution in isopods is less conservative compared to other crustaceans. Phylogenic trees were constructed using maxiumum likelihood and Bayesian inference analyses based on 13 protein-coding genes. The results do not support the placement of G. ovalis with E. pulchra and Bathynomus sp. in the same suborder; rather, G. ovalis appears to have a closer relationship to Ligia oceanica (Linnaeus, 1767), but this result suggests a need for more data and further analysis. Nevertheless, these results cast doubt that Epicaridea Latreille, 1825 can be placed as an infraorder within the suborder Cymothoida, and Epicaridea appears to also deserve subordinal rank. Further development of robust phylogenetic relationships across Isopoda Latreille, 1817 will require more genetic data from a greater diversity of taxa belonging to all isopod suborders.     

The Australian fresh water isopod (Phreatoicidea: Isopoda) allows insights into the early mitogenomic evolution of isopods

The complete mitochondrial (mt) genome sequence of the Australian fresh water isopod Eophreatoicus sp.-14 has been determined. The new species is a member of the taxon Phreatoicidea, a clade of particular interest, as it is often regarded as the sister group to all other Isopoda. Although the overall genome organization of Eophreatoicus sp.-14 conforms to the typical state of Metazoa—it is a circular ring of DNA hosting the usual 37 genes and one major non-coding region—it bears a number of derived characters that fall within the scope of “genome morphology”. Earlier studies have indicated that the isopod mitochondrial gene order is not as conserved as that of other crustaceans. Indeed, the mt genome of Eophreatoicus sp.-14 shows an inversion of seven genes (including cox1), which is as far as we know unique. Even more interesting is the derived arrangement of nad1, trnL(CUN), rrnS, control region, cob, trnT, nad5 and trnF that is shared by nearly all available isopod mt genomes. A striking feature is the close proximity of the rearranged genes to the mt control region. Inferable gene translocation events are, however, more suitable to trace the evolution of mt genomes. Genes like nad1/trnL(CUN) and nad5/trnF, which retained their adjacent position after being rearranged, were most likely translocated together. A very good example for the need to understand the mechanisms of translocations is the remolding of trnL(UUR) to trnL(CUN). Both tRNA genes are adjacent and have a high sequence similarity, probably the result of a gene duplication and subsequent anticodon mutation. Modified secondary structures were found in three tRNAs of Eophreatoicus sp.-14, which are all characterized by the loss of the DHU-arm. This is common to crustaceans for tRNA Serine(AGY), while the arm-loss in tRNA Cysteine within Malacostraca is only shared by other isopods. Modification of the third tRNA, Isoleucine, is not known from any other related species. Nucleotide frequencies of genes have been found to be indirectly correlated to the orientation of the mitochondrial replication process. In Eophreatoicus sp.-14 and in other Isopoda the associated nucleotide bias is inversed to the state of other Malacostraca. This is a strong indication for an inversion of the control region that most likely evolved in the isopod ancestor.     

A well‐preserved isopod from the Middle Jurassic of southern Germany and implications for the isopod fossil record

A new isopod species, Eonatatolana geisingensis gen. et sp. nov., is described from Middle Jurassic shallow‐water sediments of southern Germany. It shows not only the almost completely preserved dorsal morphology but, in addition, details of the cephalic appendages, the pereiopods, pleopods and uropods. The presence of ambulatory pereiopods I–VII of a wide tridentate mandibular incisor with prominently developed posteriormost tooth and a narrow frontal lamina indicates that the new species belongs to the subfamily Conilerinae of family Cirolanidae within the suborder Cymothoida. It is closer to the species of the modern genus NatatolanaBruce than to any fossil isopod hitherto described. The isopod fossil record as well as current practices of isopod taxonomy in palaeontology are discussed, and the facies distribution and fossilization of isopods is reviewed with examples from the Jurassic.     

Phylogeographic patterns of a lower intertidal isopod in the Gulf of California and the Caribbean and comparison with other intertidal isopods

A growing body of knowledge on the diversity and evolution of intertidal isopods across different regions worldwide has enhanced our understanding on biological diversification at the poorly studied, yet vast, sea–land interface. High genetic divergences among numerous allopatric lineages have been identified within presumed single broadly distributed species. Excirolana mayana is an intertidal isopod that is commonly found in sandy beaches throughout the Gulf of California. Its distribution in the Pacific extends from this basin to Colombia and in the Atlantic from Florida to Venezuela. Despite its broad distribution and ecological importance, its evolutionary history has been largely neglected. Herein, we examined phylogeographic patterns of E. mayana in the Gulf of California and the Caribbean, based on maximum‐likelihood and Bayesian phylogenetic analyses of DNA sequences from four mitochondrial genes (16S rDNA, 12S rDNA, cytochrome oxidase I gene, and cytochrome b gene). We compared the phylogeographic patterns of E. mayana with those of the coastal isopods Ligia and Excirolana braziliensis (Gulf of California and Caribbean) and Tylos (Gulf of California). We found highly divergent lineages in both, the Gulf of California and Caribbean, suggesting the presence of multiple species. We identified two instances of Atlantic–Pacific divergences. Some geographical structuring among the major clades found in the Caribbean is observed. Haplotypes from the Gulf of California form a monophyletic group sister to a lineage found in Venezuela. Phylogeographic patterns of E. mayana in the Gulf of California differ from those observed in Ligia and Tylos in this region. Nonetheless, several clades of E. mayana have similar distributions to clades of these two other isopod taxa. The high levels of cryptic diversity detected in E. mayana also pose challenges for the conservation of this isopod and its fragile environment, the sandy shores.     

An appraisal of the fossil record for the Cirolanidae (Malacostraca: Peracarida: Isopoda: Cymothoida), with a description of a new cirolanid isopod crustacean from the early Miocene of the Vienna Basin (Western Carpathians)

Abstract:  Isopod crustaceans are rarely preserved in the fossil record. Herein, an appraisal of the fossil record for the cirolanid isopods is presented. Five genera are briefly discussed, including Bathynomus, Brunnaega, Palaega, Pseudopalaega and Cirolana. A key for the cirolanid genera known to date from the fossil record is provided based mostly on pleotelson characters. From the early Miocene of the Slovak part of the Vienna Basin, Cirolana feldmanni sp. nov. is described being only the fifth fossil Cirolana species known to date and one of the few with preserved appendages. The material exhibits preservation suggesting biphasic moulting; the mode of preservation suggests a rather short time between shedding the posterior and anterior parts of the exoskeleton instead of hours or even days known in extant taxa. As no subsequent transport or physical disturbance was inferred, the specimens can be stated as in situ preservation. From the palaeoecological point of view, it is concluded that Cirolana feldmanni sp. nov. is the first unequivocal fossil deep‐water Cirolana as suggested by the accompanied fauna.     

Thaumamermis cosgrovei n. gen., n. sp. (Mermithidae: Nematoda) parasitizing terrestrial isopods (Isopoda: Oniscoidea)

Summary A new mermithid nematode, Thaumamermis cosgrovei n. gen., n. sp. (Mermithidae: Nematoda) was found parasitizing two terrestrial isopods (Isopoda: Oniscoidea) in California. The hosts, Armadillidium vulgare (Latr.) (a pillbug) and Porcellio scaber (Latr.) (a sowbug) represent the first cases of isopods attacked by mermithid nematodes. The genus Thaumamermis can be distinguished from all previously described mermithids by the extremely dimorphic spicules, one being short and broad and the other long and filiform. It has been discovered that the nematodes are infected with an iridiovirus which commonly destroys the isopod hosts. ac]19800917     

High‐contiguity genome assembly of the chemosynthetic gammaproteobacterial endosymbiont of the cold seep tubeworm Lamellibrachia barhami

Symbiotic relationships between vestimentiferan tubeworms and chemosynthetic Gammaproteobacteria build the foundations of many hydrothermal vent and hydrocarbon seep ecosystems in the deep sea. The association between the vent tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has become a model system for symbiosis research in deep‐sea vestimentiferans, while markedly fewer studies have investigated symbiotic relationships in other tubeworm species, especially at cold seeps. Here we sequenced the endosymbiont genome of the tubeworm Lamellibrachia barhami from a cold seep in the Gulf of California, using short‐ and long‐read sequencing technologies in combination with Hi‐C and Dovetail Chicago libraries. Our final assembly had a size of ~4.17 MB, a GC content of 54.54%, 137X coverage, 4153 coding sequences, and a CheckM completeness score of 97.19%. A single scaffold contained 99.51% of the genome. Comparative genomic analyses indicated that the L. barhami symbiont shares a set of core genes and many metabolic pathways with other vestimentiferan symbionts, while containing 433 unique gene clusters that comprised a variety of transposases, defence‐related genes and a lineage‐specific CRISPR/Cas3 system. This assembly represents the most contiguous tubeworm symbiont genome resource to date and will be particularly valuable for future comparative genomic studies investigating structural genome evolution, physiological adaptations and host‐symbiont communication in chemosynthetic animal‐microbe symbioses.     

Granivory in terrestrial isopods

Abstract Granivory (seed feeding) evolved in many animal groups. Field observations hint at the existence of granivory in terrestrial isopods (Crustacea: Isopoda: Oniscidea), for which it was previously unknown. In this paper granivory in terrestrial isopods is addressed for the first time, focusing on (i) seed acceptance in the presence of plant litter and (ii) size as a constraint for acceptance and consumption. In a laboratory choice experiment, Armadillidium vulgare consumed seeds of Capsella bursa‐pastoris and Poa annua when plant litter was present. In a no‐choice experiment, seeds of seven plant species were offered to four isopod species giving 13 combinations in total [A. vulgare (seven species of seeds), Oniscus asellus (two), Porcellio scaber (two), and Porcellionides pruinosus (two)]. The tested isopods differed in their acceptance (proportion of individuals consuming seeds) and consumption (both number and amount of seeds eaten) of seed species. Size as a constraint was demonstrated in A. vulgare offered Cirsium arvense seed, since the probability that this large seed was eaten increased with body size of the isopod. In the other 10 seed–isopod pairs, seed consumption increased linearly with isopod body size. Granivory is thus widespread in terrestrial isopods, although the tendency to eat seeds differs between species.     

Urstylidae – a new family of abyssal isopods (Crustacea: Asellota) and its phylogenetic implications

We report three new species of isopod crustaceans that belong to a rare higher taxon of asellote Isopoda. This taxon does not fit into current classifications. The isopods occurred in abyssal soft sediments, near manganese nodules, and in the vicinity of hydrothermal vents. Given their wide spatial occurrence across the Atlantic and Pacific Oceans, a cosmopolitan distribution is assumed. A cladistic analysis revealed a close relationship with the Macrostylidae, a common representative of the deep‐sea macrofauna. Analyses of character evolution across the Janiroidea showed sufficient synapomorphies to justify the erection of U rstylis gen. nov. and the new family Urstylidae based on the three new species. All taxa are described in this paper. Urstylidae is characterized, amongst other apomorphies, by an elongate habitus with spade‐like head; uropods are long, styliform; one pleonite is free; antennal merus and carpus are relatively short; the first pereopod is carpo‐propodosubchelate, and more robust and shorter than pereopod II. Several characters, such as the pereopods’ posterior scale‐like claw that basally encloses the distal sensilla may be interpreted as ancestral when compared to the situation in the highly derived Macrostylidae. © 2014 The Linnean Society of London     

The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep‐sea environment

The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.     

Genomes of the wild beets Beta patula and Beta vulgaris ssp. maritima

We present draft genome assemblies of Beta patula, a critically endangered wild beet endemic to the Madeira archipelago, and of the closely related Beta vulgaris ssp. maritima (sea beet). Evidence‐based reference gene sets for B. patula and sea beet were generated, consisting of 25 127 and 27 662 genes, respectively. The genomes and gene sets of the two wild beets were compared with their cultivated sister taxon B. vulgaris ssp. vulgaris (sugar beet). Large syntenic regions were identified, and a display tool for automatic genome‐wide synteny image generation was developed. Phylogenetic analysis based on 9861 genes showing 1:1:1 orthology supported the close relationship of B. patula to sea beet and sugar beet. A comparative analysis of the Rz2 locus, responsible for rhizomania resistance, suggested that the sequenced B. patula accession was rhizomania susceptible. Reference karyotypes for the two wild beets were established, and genomic rearrangements were detected. We consider our data as highly valuable and comprehensive resources for wild beet studies, B. patula conservation management, and sugar beet breeding research.     

Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications

In this study, we analyse the evolutionary dynamics and phylogenetic implications of gene order rearrangements in five newly sequenced mitochondrial (mt) genomes and four published mt genomes of isopod crustaceans. The sequence coverage is nearly complete for four of the five newly sequenced species, with only the control region and some tRNA genes missing, while in Janira maculosa only two thirds of the genome could be determined. Mitochondrial gene order in isopods seems to be more plastic than that in other crustacean lineages, making all nine known mt gene orders different. Especially the asellote Janira is characterized by many autapomorphies. The following inferred ancestral isopod mt gene order exists slightly modified in modern isopods: nad1, tnrL1, rrnS, control region, trnS1, cob, trnT, nad5, trnF. We consider the inferred gene translocation events leading to gene rearrangements as valuable characters in phylogenetic analyses. In this first study covering major isopod lineages, potential apomorphies were identified, e.g., a shared relative position of trnR in Valvifera. We also report one of the first findings of homoplasy in mitochondrial gene order, namely a shared relative position of trnV in unrelated isopod lineages. In addition to increased taxon sampling secondary structure, modification in tRNAs and GC-skew inversion may be potentially fruitful subjects for future mt genome studies in a phylogenetic context.     

Molecular Phylogeny and Surface Morphology of Thiriotia hyperdolphinae n. sp. and Cephaloidophora oradareae n. sp. (Gregarinasina,Apicomplexa) Isolated from a Deep Sea Oradarea sp. (Amphipoda) in the West Pacific

In an effort to broaden our understanding of the biodiversity and distribution of gregarines infecting crustaceans, this study describes two new species of gregarines, Thiriotia hyperdolphinae n. sp. and Cephaloidophora oradareae n. sp., parasitizing a deep sea amphipod (Oradarea sp.). Amphipods were collected using the ROV Hyper‐Dolphin at a depth of 855 m while on a cruise in Sagami Bay, Japan. Gregarine trophozoites and gamonts were isolated from the gut of the amphipod and studied with light and scanning electron microscopy, and phylogenetic analysis of 18S rDNA. Thiriotia hyperdolphinae n. sp. was distinguished from existing species based on morphology, phylogenetic position, as well as host niche and geographic locality. Cephaloidophora oradareae n. sp. distinguished itself from existing Cephaloidophora, based on a difference in host (Oradarea sp.), geographic location, and to a certain extent morphology. We established this latter new species with the understanding that a more comprehensive examination of diversity at the molecular level is necessary within Cephaloidophora. Results from the 18S rDNA molecular phylogeny showed that T. hyperdolphinae n. sp. was positioned within a clade consisting of Thiriotia spp., while C. oradareae n. sp. grouped within the Cephaloidophoridae. Still, supplemental genetic information from gregarines infecting crustaceans will be needed to better understand relationships within this group of apicomplexans.     

An evolutionary timescale for terrestrial isopods and a lack of molecular support for the monophyly of Oniscidea (Crustacea: Isopoda)

The marine metazoan fauna first diversified in the early Cambrian, but terrestrial environments were not colonized until at least 100 million years later. Among the groups of organisms that successfully colonized land is the crustacean order Isopoda. Of the 10,000 described isopod species, ~ 3,600 species from the suborder Oniscidea are terrestrial. Although it is widely thought that isopods colonized land only once, some studies have failed to confirm the monophyly of Oniscidea. To infer the evolutionary relationships among isopod lineages, we conducted phylogenetic analyses of nuclear 18S and 28S and mitochondrial COI genes using maximum-likelihood and Bayesian methods. We also analyzed a second data set comprising all of the mitochondrial protein-coding genes from a smaller sample of isopod taxa. Based on our analyses using a relaxed molecular clock, we dated the origin of terrestrial isopods at 289.5 million years ago (95% credibility interval 219.6–358.9 million years ago). These predate the known fossil record of these taxa and coincide with the formation of the supercontinent Pangaea and with the diversification of vascular plants on land. Our results suggest that the terrestrial environment has been colonized more than once by isopods. The monophyly of the suborder Oniscidea was not supported in any of our analyses, conflicting with classical views based on morphology. This draws attention to the need for further work on this group of isopods.     

Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats

Vesicomyid clams of the subfamily Pliocardinae are among the dominant chemosymbiotic bivalves found in sulfide‐rich deep‐sea habitats. Plastic morphologies and present molecular data could not resolve taxonomic uncertainties. The complete mitochondrial (mt) genomes will provide more data for comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group, and help to clarify generic classifications. In this study, we analyze the features and evolutionary dynamics of mt genomes from three Archivesica species (Archivesica sp., Ar. gigas and Ar. pacifica) pertaining to subfamily Pliocardinae. Sequence coverage is nearly complete for the three newly sequenced mt genomes, with only the control region and some tRNA genes missing. Gene content, base composition, and codon usage are highly conserved in these pliocardiin species. Comparative analysis revealed the vesicomyid have a relatively lower ratio of Ka/Ks, and all 13 protein‐coding genes (PGCs) are under strong purifying selection with a ratio of Ka/Ks far lower than one. Minimal changes in gene arrangement among vesicomyid species are due to the translocation trnaG in Isorropodon fossajaponicum. Additional tRNA genes were detected between trnaG and nad2 in Abyssogena mariana (trnaL3), Ab. phaseoliformis (trnaS3), and Phreagena okutanii (trnaM2), and display high similarity to other pliocardiin sequences at the same location. Single base insertion in multiple sites of this location could result in new tRNA genes, suggesting a possible tRNA arising from nongeneic sequence. Phylogenetic analysis based on 12 PCGs (excluding atp8) supports the monophyly of Pliocardiinae. These nearly complete mitogenomes provide relevant data for further comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group of chemosymbiotic bivalves.     

Evidence for Permo-Triassic colonization of the deep sea by isopods

The deep sea is one of the largest ecosystems on Earth and is home to a highly diverse fauna, with polychaetes, molluscs and peracarid crustaceans as dominant groups. A number of studies have proposed that this fauna did not survive the anoxic events that occurred during the Mesozoic Era. Accordingly, the modern fauna is thought to be relatively young, perhaps having colonized the deep sea after the Eocene/Oligocene boundary. To test this hypothesis, we performed phylogenetic analyses of nuclear ribosomal 18S and 28S and mitochondrial cytochrome oxidase I and 16S sequences from isopod crustaceans. Using a molecular clock calibrated with multiple isopod fossils, we estimated the timing of deep-sea colonization events by isopods. Our results show that some groups have an ancient origin in the deep sea, with the earliest estimated dates spanning 232–314 Myr ago. Therefore, anoxic events at the Permian–Triassic boundary and during the Mesozoic did not cause the extinction of all the deep-sea fauna; some species may have gone extinct while others survived and proliferated. The monophyly of the ‘munnopsid radiation’ within the isopods suggests that the ancestors of this group evolved in the deep sea and did not move to shallow-water refugia during anoxic events.     

The Halomonhystera disjuncta population is homogeneous across the Håkon Mosby mud volcano (Barents Sea) but is genetically differentiated from its shallow‐water relatives

The deep sea has a high biodiversity and a characteristic bathyal fauna. Earlier evidence suggested that at least some shallow‐water species invaded the ecosystem followed by radiation leading to endemic deep‐sea lineages with a genetic and/or morphological similarity to their shallow‐water counterparts. The nematode Halomonhystera disjuncta has been reported from shallow‐water habitats and the deep sea [Håkon Mosby mud volcano (HMMV)], but the morphological features and the phylogenetic relationships between deep‐sea and shallow‐water representatives remain largely unknown. Furthermore, nothing is known about the genetic structure of the H. disjuncta population within the HMMV. This study is the first integrative approach in which the morphological and phylogenetic relationships between a deep‐sea and shallow‐water free‐living nematode species are investigated. To elucidate the phylogenetic relationships, we analysed the mitochondrial gene Cytochrome oxidase c subunit I (COI) and three nuclear ribosomal genes (Internal Transcribed Spacer region, 18S and the D2D3 region of 28S). Our results show that deep‐sea nematodes comprise an endemic lineage compared to the shallow‐water representatives with different morphometric features. COI genetic divergence between the deep‐sea and shallow‐water specimens ranges between 19.1% and 25.2%. Taking these findings into account, we conclude that the deep‐sea form is a new species. amova revealed no genetic structure across the HMMV, suggesting that nematodes are able to disperse efficiently in the mud volcano.