First recorded occurrence of the parasitic barnacle (Anelasma squalicola) on a Greenland shark (Somniosus microcephalus) in the Canadian Arctic.

A solitary Anelasma squalicola specimen was collected from the cloaca of a Greenland shark (Somniosus microcephalus), the first time this association has been recorded. The specimen's identity was confirmed through morphological and genetic assessment (mitochondrial markers: COI and control region). A. squalicola is a species typically associated with deep-sea lantern sharks (Etmopteridae) and, until the present observation, had never been observed at a sexually mature size in the absence of a mating partner. Given the reported negative effects of this parasite on its hosts, monitoring Greenland sharks for additional cases is recommended.

Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus.

Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships. We generated a complete A. tricolor chloroplast sequence of 150,027 bp. The three barcoding genes revealed poor inter- and intra-species resolution with low bootstrap support. Whole chloroplast phylogenomics of 59 Amaranthus accessions increased the number of parsimoniously informative sites from 92 to 481 compared to the barcoding genes, allowing improved separation of amaranth species. Our results support previous findings that two geographically independent domestication events of Amaranthus hybridus likely gave rise to several species within the Hybridus complex, namely Amaranthus dubius, Amaranthus quitensis, Amaranthus caudatus, Amaranthus cruentus and Amaranthus hypochondriacus. Poor resolution of species within the Hybridus complex supports the recent and ongoing domestication within the complex, and highlights the limitation of chloroplast data for resolving recent evolution. The weedy Amaranthus retroflexus and Amaranthus powellii was found to share a common ancestor with the Hybridus complex. Leafy amaranth, Amaranthus tricolor, Amaranthus blitum, Amaranthus viridis and Amaranthus graecizans formed a stable sister lineage to the aforementioned species across the phylogenetic trees. This study demonstrates the power of next-generation sequencing data and reference-based assemblies to resolve phylogenies, and also facilitated the identification of unknown Amaranthus accessions from a local genebank. The informative phylogeny of the Amaranthus genus will aid in selecting accessions for breeding advanced genotypes to satisfy global food demand.

Spatial distribution of proteins in the quagga mussel adhesive apparatus.

The invasive freshwater mollusc Dreissena bugensis (quagga mussel) sticks to underwater surfaces via a proteinacious 'anchor' (byssus), consisting of a series of threads linked to adhesive plaques. This adhesion results in the biofouling of crucial underwater industry infrastructure, yet little is known about the proteins responsible for the adhesion. Here the identification of byssal proteins extracted from freshly secreted byssal material is described. Several new byssal proteins were observed by gel electrophoresis. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to characterize proteins in different regions of the byssus, particularly those localized to the adhesive interface. Byssal plaques and threads contain in common a range of low molecular weight proteins, while several proteins with higher mass were observed only in the plaque. At the adhesive interface, a plaque-specific ~8.1 kDa protein had a relative increase in signal intensity compared to the bulk of the plaque, suggesting it may play a direct role in adhesion.

Global phylogeography suggests extensive eucosmopolitanism in Mesopelagic Fishes (Maurolicus: Sternoptychidae).

Fishes in the mesopelagic zone (200-1000 m) have recently been highlighted for potential exploitation. Here we assess global phylogeography in Maurolicus, the Pearlsides, an ecologically important group. We obtained new sequences from mitochondrial COI and nuclear ITS-2 from multiple locations worldwide, representing 10 described species plus an unknown central South Pacific taxon. Phylogenetic analyses identified five geographically distinct groupings, three of which comprise multiple described species. Species delimitation analyses suggest these may represent four species. Maurolicus muelleri and M. australis are potentially a single species, although as no shared haplotypes are found between the two disjunct groups, we suggest maintenance of these as two species. Maurolicus australis is a predominantly southern hemisphere species found in the Pacific, Indian and southern South Atlantic Oceans, comprising five previously allopatric species. M. muelleri (previously two species) is distributed in the North Atlantic and Mediterranean Sea. Maurolicus weitzmani (previously two species) inhabits the eastern equatorial Atlantic, Gulf of Mexico and western North and South Atlantic. Maurolicus mucronatus is restricted to the Red Sea. No Maurolicus have previously been reported in the central South Pacific but we have identified a distinct lineage from this region, which forms a sister group to Maurolicus from the Red Sea.

Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome.

The European freshwater mollusk Dreissena bugensis (quagga mussel), an invasive species to North America, adheres to surfaces underwater via the byssus: a non-living protein 'anchor'. In spite of its importance as a biofouling species, the sequence of the majority of byssal proteins responsible for adhesion are not known, and little genomic data is available. To determine protein sequence information, we utilized next-generation RNA sequencing and de novo assembly to construct a cDNA library of the quagga mussel foot transcriptome, which contains over 200,000 transcripts. Quagga mussel byssal proteins were extracted from freshly induced secretions and analyzed using LC-MS/MS; peptide spectra were matched to the transcriptome to fingerprint the entire protein primary sequences. We present the full sequences of fourteen novel quagga mussel byssal proteins, named Dreissena bugensis foot proteins 4 to 17 (Dbfp4-Dbfp17), and new sequence data for two previously observed byssal proteins Dbfp1 and Dbfp2. Theoretical masses of the newly discovered proteins range from 4.3 kDa to 21.6 kDa. These protein sequences are unique but contain features similar to glue proteins from other species, including a high degree of polymorphism, proteins with repeated peptide motifs, disordered protein structure, and block structures.

De novo innovation allows shark parasitism and global expansion of the barnacle Anelasma squalicola.

The barnacle Anelasma squalicola is a marine epibiont found on members of the species-rich, deep-sea lantern shark family Etmopteridae (Figure 1A) but is unlike any other epibiotic thoracian barnacles [1]. While many barnacle species are associated with various marine animals including turtles and whales, with the exception of Anelasma these all retain a filter-feeding lifestyle and have a commensal relationship with their host; despite often being deeply embedded in the dermis, no other species has been reported as feeding on its host. Although Anelasma is fully equipped with cirri (thoracic appendages), these are no longer used for filter feeding [1]. Instead, Anelasma embeds a stalk with root-like structures into the flesh of the shark (Figure S1C in Supplemental Information, published with this article online) that it uses to parasitize its host. Here, we show that specimens of Anelasma sampled from all over the world show very little genetic differentiation, suggesting that this innovation coincided with a rapid worldwide expansion.

The utility of biological monitoring for manganese in ferroalloy smelter workers in South Africa.

Five hundred and nine workers at a manganese (Mn) smelting works comprising eight production facilities and 67 external controls were studied cross-sectionally. Exposure measures from personal sampling included inhalable dust, cumulative exposure indices (CEI) and average intensity (INT = CEI/years exposed) calculated for the current job at the smelter and also across all jobs held by subjects. Biological exposure was measured by Mn in the blood (MnB) and urine (MnU) and biological effect was measured by serum prolactin. Average lifetime exposure intensity across all jobs ranged from near 0 (0.06 microg/m3) for unexposed external referents to 5 mg/m3. Atmospheric exposures and MnB and MnU distributions were consistent with published data for both unexposed and smelter workers. Associations between biological exposures and groups defined by atmospheric exposures in the current job were substantial for MnB, less so for MnU and absent for serum prolactin. Random sampling of MnB measurements representative of a group of workers with more than 1-2 years of service in the same job and notionally homogenous exposure conditions could serve as a cross-sectional predictor of atmospheric Mn exposure in the current job, as well as for surveillance of Mn exposure trends over time. Correlations at the individual level were only modest for MnB (33% of the variance in log atmospheric Mn intensity in the current job was explained by log MnB), much worse for MnU (only 7%). However, a receiver operating characteristic (ROC) analysis was performed which showed that it is possible to use a MnB cut-off of 10 microg/l (the 95th percentile in the unexposed) to good effect as a screening tool to discriminate between individual exposures exceeding and falling below a relatively strict atmospheric Mn exposure threshold at the ACGIH threshold limit value (TLV) of 0.2 mg/m3. MnU has no utility as a measure of biological exposure nor does serum prolactin as a measure of biological effect.

The nervous system effects of occupational exposure on workers in a South African manganese smelter.

Five hundred and nine production workers at a manganese (Mn) smelting works comprising eight production facilities and 67 external controls were studied cross-sectionally for Mn related neuroehavioural effects. Exposure measures from personal sampling included Mn in inhalable dust as cumulative exposure indices (CEI) and average intensity (INT). Biological exposure and biological effect measures included blood (MnB), urine (MnU) manganese and serum prolactin. Endpoints included items from the Swedish nervous system questionnaire (Q16), World Health Organisation neurobehavioural core test battery (WHO NCTB), Swedish performance evaluation system (SPES), Luria-Nebraska (LN), and Danish product development (DPD) test batteries, and a brief clinical examination. Potential confounders and effect modifiers included age, educational level, alcohol and tobacco consumption, neurotoxic exposures in previous work, past medical history, previous head injury and home language. Associations were evaluated by multiple linear and logistic regression modelling. Modelling assumptions were tested. Average exposure intensity across all jobs ranged from near 0 (0.06 microg/m3) for external controls to 5.08 mg/m3 for inhalable Mn, and was greater than the ACGIH TLV for 69% of subjects. Results from the large number of tests performed resolved into three groups. Group 1 shows differences between external unexposed referents and all the exposed and/or differences between internal low exposed referents and the rest of the exposed but no further exposure-response relationships. It includes the Santa Ana, Benton and digit-span tests from the WHO NCTB; the hand tapping and endurance tapping tests from the SPES; Luria-Nebraska item 2L; questionnaire items tired, depressed, irritated, having to take notes in order to remember things, and subjects' perception that they had sex less often than normal; a test of clinical abnormality; and increased sway under two conditions (eyes open without foot insulation, eyes open with foot insulation). Group 2 shows the presence of a more substantive exposure-response relationship. It consists of only two tests: and includes the WHO digit-symbol test (although the major impact is at low exposure and therefore counterintuitive, arguably placing this test in group 3) and the LN item 1R which has a step to a poorer score at high exposure. Group 3 contains the overwhelming majority of test results (almost all the questionnaire items, almost all the DPD tests including tremor, sway and diadochokinesia, and serum prolactin) which were either null or counterintuitive (did not make sense). The CEI was the strongest predictor of test abnormalities, except for the clinical test which was more strongly associated with blood manganese. Despite a comprehensive range of endpoints, and levels of exposure ranging from environmental to industrial, this large study of Mn workers found little convincing evidence for a continuum of effects, contributing further questions to current debates about the adequacy of the current ACGIH TLV.

Novel proteins identified in the insoluble byssal matrix of the freshwater zebra mussel.

The freshwater zebra mussel, Dreissena polymorpha, is an invasive, biofouling species that adheres to a variety of substrates underwater, using a proteinaceous anchor called the byssus. The byssus consists of a number of threads with adhesive plaques at the tips. It contains the unusual amino acid 3, 4-dihydroxyphenylalanine (DOPA), which is believed to play an important role in adhesion, in addition to providing structural integrity to the byssus through cross-linking. Extensive DOPA cross-linking, however, renders the zebra mussel byssus highly resistant to protein extraction, and therefore limits byssal protein identification. We report here on the identification of seven novel byssal proteins in the insoluble byssal matrix following protein extraction from induced, freshly secreted byssal threads with minimal cross-linking. These proteins were identified by LC-MS/MS analysis of tryptic digests of the matrix proteins by spectrum matching against a zebra mussel cDNA library of genes unique to the mussel foot, the organ that secretes the byssus. All seven proteins were present in both the plaque and thread. Comparisons of the protein sequences revealed common features of zebra mussel byssal proteins, and several recurring sequence motifs. Although their sequences are unique, many of the proteins display similarities to marine mussel byssal proteins, as well as to adhesive and structural proteins from other species. The large expansion of the byssal proteome reported here represents an important step towards understanding zebra mussel adhesion.

Large genomes among caridean shrimp.

Recent genome size estimates for Arctic amphipods have revealed the largest genomes known in the Crustacea. Here we provide additional data for 7 species of caridean shrimp collected from the Canadian Arctic and the Gulf of St. Lawrence. Genome sizes were estimated by flow cytometry and haploid C-values ranged from 8.53 +/- 0.30 pg in Pandalus montagui (Pandalidae) to 40.89 +/- 1.23 pg in Sclerocrangon ferox (Crangonidae). The value for S. ferox represents the largest decapod genome yet recorded and indicates a 38-fold variation in genome size within this order. These data suggest that large genomes may be relatively common in Arctic crustaceans, and underline the need for further comparative studies.

Amphipod genome sizes: first estimates for Arctic species reveal genomic giants.

The genome sizes of 8 species of amphipods collected from the Canadian Arctic were estimated by flow cytometry. Haploid genome sizes ranged from 2.94 +/- 0.04 pg DNA in Acanthostepheia malmgreni (Oedicerotidae) to 64.62 +/- 2.85 pg in Ampelisca macrocephala (Ampeliscidae). The value for Ampelisca macrocephala represents the largest crustacean genome size recorded to date (and also the largest within the Arthropoda) and indicates a 400-fold variation in genome size among crustaceans. The presence of such large genomes within a relatively small sample of Arctic amphipods is striking and highlights the need to further explore the relationships between genome size, development rates, and body size in both Arctic and temperate amphipods.

Cryptic intercontinental colonization in water fleas Daphnia pulicaria inferred from phylogenetic analysis of mitochondrial DNA variation.

The water fleas of the Daphnia pulex complex play a key role in freshwater ecosystems throughout the northern hemisphere. Despite the fact that they have been the subject of study for numerous biological disciplines, their phylogeny and species delimitation remain controversial. We used DNA sequence variation of the mitochondrial ND5 gene to reconstruct the phylogenetic relationships of D. pulicaria Forbes, a widespread member of this complex from North America and Europe. Populations from the two continents respectively split into two evolutionary lineages, Eastern Nearctic and European, which each belong to another main clade within the D. pulex complex (the pulicaria and tenebrosa groups, respectively). Unexpectedly, melanin and carotenoid pigmented D. pulicaria populations from European high-mountain lakes were not allied with the transparent populations inhabiting the same lakes and the lowland ponds and reservoirs throughout Europe, but were included with the samples from Canada and Greenland in the Eastern Nearctic lineage. Until now populations belonging to this lineage were known only from Canada and North Atlantic islands, but not from mainland Europe. Independent data from microsatellite markers supported the genetic distinctiveness of the sympatric carotenoid pigmented and transparent populations and suggested that they may have undergone transition to obligate parthenogenesis, possibly as a consequence of past introgressive hybridization. Two different taxa are therefore confused under the name D. pulicaria in Europe. The close phylogenetic relationships of European populations with those from Canada and Greenland suggest that the Nearctic lineage is of recent origin in Europe via intercontinental dispersal from the North America. It has evolved melanin and carotenoid pigmentation as adaptations against the UV light stress, which enable it to share habitat occupied by the transparent European species. The Nearctic D. pulicaria thus provides a new model for studying successful intercontinental invasion. In general, our study demonstrates that a considerable part of the diversity among widespread taxa of cladoceran crustaceans has been overlooked in morphological taxonomies.

Molecules and morphology: evidence for cryptic hybridization in African Hyalomma (Acari: Ixodidae).

The role of natural hybridization and introgression as part of the evolutionary process is of increasing interest to zoologists, particularly as more examples of gene exchange among species are identified. We present mitochondrial and nuclear sequence data for Hyalomma dromedarii, Hyalomma truncatum, and Hyalomma marginatum rufipes (Acari: Ixodidae) collected from one-humped camels in Ethiopia. These species are well differentiated morphologically and genetically; sequence data from the mitochondrial DNA (mtDNA) cytochrome oxidase I gene indicates 10-14% divergence between the species. However, incongruence between morphology and the mtDNA phylogeny was observed, with multiple individuals of H. dromedarii and H. truncatum present on the same mtDNA lineage as H. marginatum rufipes. Thus, individuals with morphology of H. dromedarii and H. truncatum are indistinguishable from H. marginatum rufipes on the basis of mtDNA. Multiple copies of ITS-2 were subsequently cloned and sequenced for a subset of individuals from the mtDNA phylogeny, representing both 'normal' and 'putative hybrid' individuals. Very low sequence divergence (0.3%) was observed within 'normal' individuals of both H. dromedarii and H. truncatum relative to the 'putative hybrid' individuals (6 and 2.7%, respectively). The pattern of intra-individual variation in ITS-2 within 'putative hybrid' individuals, particularly in H. dromedarii, strongly suggests that gene flow has occurred among these Hyalomma species, but no indication of this is given by the morphology of the individuals.