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Synthetic and semi-synthetic fibre ingestion by mesopelagic fishes from Tristan da Cuhna and St Helena, South Atlantic
No full textAs part of the Blue Belt Programme, a marine survey of British Overseas Territories funded by the UK Government, RRS Discovery trawled at depths of between the surface and 1000m around Tristan da Cuhna and St Helena. Fishes were examined for microplastic ingestion.
This work was supported by the National Environmental Research Council [grant number NE/L002485/1] with co-sponsorship from a Fishmongers' Company Fisheries Charity Trust CASE Partnership. Specimens were collected onboard RRS Discover as part of the Blue Belt Programme, which is funded by the UK Government in collaboration with CEFAS and BAS.
Mesopelagic fishes were sampled around Tristan da Cunha and St Helena in the South Atlantic from the RRS Discovery at depths down to 1000 m. Sampling was part of the Blue Belt Programme, a marine survey of British Overseas Territories funded by the United Kingdom Government. Thirteen species of mesopelagic fishes identified from 30 specimens were compared with two species (two specimens) collected from rock pools or surface water near the shore. The digestive tracts of all fishes were examined for microplastics. Additionally, one specimen of Opostomias micripnus (Günther, 1878) was analyzed after recovery from the stomach of a commercially fished species, Hyperoglyphe antarctica (Carmichael, 1819). One specimen of Anoplogaster cornuta was found to have ingested a bearded sea devil (Linophryne sp.), a cock-eyed squid (Histioteuthis sp.), a bolitaenid octopus, Japetella diaphana, remains of unidentifiable fish, crustaceans, and possibly salps. These prey items were also examined for microfibres. Both Histioteuthis sp. and Linophryne sp. had ingested fibers and these were considered “ingested particles” for A. cornuta. Neither shallow water dwelling species had ingested microplastics, whilst 11 of the 13 studied mesopelagic species were found to be contaminated. Overall, 66.7% of mesopelagic fishes were found to contain microfibres. Anthropogenic fibers were common especially viscose, a semi-synthetic material which is associated with sanitary products as well as other items.Copyright © 2021 McGoran, Maclaine, Clark and Morritt. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.NHM Repositor
Assessing gaps in reporting non-target mortality in island rodent eradication operations
Get PDFEradicating invasive species is a key part of island restoration, and can reverse the devastating impacts on native biota. Rodents are one of the most widespread invasive species, found on 80% of oceanic island systems, but have been removed from hundreds of islands through the application of anticoagulant-treated cereal bait. While such eradication operations are often net positive events for island ecosystems over the long-term, some native biota are also susceptible, resulting in short-term non-target mortality. One of the most widely distributed groups of birds, rails and allies (Rallidae) are highly adaptable, often endemic, and are known often to suffer mortality during rodent eradication operations, to varying degrees. Our goal was determine if the year of eradication or the size of the island predicted whether non-target mortalities were reported, including those that were true absences of mortality. We examined 122 eradication operations on 81 islands with rails present from 1983 to 2015, and found 78% with no reported information on non-target mortality using our search criteria. We found non-target mortality reporting has decreased over time, and there was no relationship with island size. Post-operational monitoring of eradication operations should thoroughly record non-target mortality to improve our understanding of factors affecting non-target mortality, and the efficacy of mitigation measures.Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The attached file is the published pdf.NHM Repositor
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
Get PDFIn the quest to reconstruct the Tree of Life, researchers have increasingly turned to phylogenomics, the inference of phylogenetic relationships using genome-scale data (Box 1). Mesmerized by the sustained increase in sequencing throughput, many phylogeneticists entertained the hope that the incongruence frequently observed in studies using single or a few genes [1] would come to an end with the generation of large multigene datasets. Yet, as so often happens, reality has turned out to be far more complex, as three recent large-scale analyses, one published in PLoS Biology [2–4], make clear. The studies, which deal with the early diversification of animals, produced highly incongruent (Box 2) findings despite the use of considerable sequence data (see Figure 1). Clearly, merely adding more sequences is not enough to resolve the inconsistencies. Here, taking these three studies as a case in point, we discuss pitfalls that the simple addition of sequences cannot avoid, and show how the observed incongruence can be largely overcome and how improved bioinformatics methods can help reveal the full potential of phylogenomics.© 2011 Philippe et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published pdf.NHM Repositor
The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758
No full textCopyright: © 2020 Mead D et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.We present a genome assembly from an individual male Sciurus vulgaris (the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.Copyright: © 2020 Mead D et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The attached file is the published pdf.NHM Repositor
Connectivity and zebra mussel invasion offer short‐term buffering of eutrophication impacts on floodplain lake landscape biodiversity
Get PDFAim
To investigate if connectivity and zebra mussel (Dreissena polymorpha) occurrence can mitigate effects of eutrophication in a lowland lake landscape.
Location
Upper Lough Erne, Northern Ireland, UK.
Methods
Data on environment, macrophytes and invertebrates were assembled for three basins of a large central lake and its satellite floodplain lakes via field surveys and palaeolimnological analyses. Space–time interaction analyses of palaeoecological data were compared pre‐1950 and post‐1950. Multivariate analyses examined how connectivity, environment and zebra mussels influenced contemporary lake communities, and explain their divergence from historical communities in the past.
Results
Pre‐1950, we found high community variation across sites and low within‐lake variation in macrophytes, but progressive eutrophication accentuated within‐lake community variation after 1950. Partitioning analysis showed larger effects of connectivity than nutrient enrichment on contemporary macrophyte composition, while local effects structured invertebrate communities. Three clusters of lakes were revealed according to variation in macrophyte composition, isolation from the central lake and nutrient enrichment: Group 1– the central lake and six nearby lakes were meso‐eutrophic (TP = 66.7 ± 47.6 μg/L; TN = 0.79 ± 0.41 mg/L) and had the highest zebra mussel abundances and organismal biodiversity; Group 2– Eight eutrophic (TP = 112±36.6 μg/L; TN = 1.25 ± 0.5 mg/L) and connected lakes; Group 3– Seven isolated and hypertrophic (TP = 163.2 ± 101.5 μg/L; TN = 1.55 ± 0.3 mg/L) lakes. Pre‐1950 palaeolimnological data for macrophytes and invertebrates for 5 lakes and a basin in the central lake most resembled extant lake communities of Group 1. However, palaeo‐records revealed that macrophytes and invertebrates subsequently converged towards those of Groups 2 and 3.
Main conclusions
Our study reveals that the central “mother” lake acts as a hub for preserving biodiversity via shared hydrological connectivity with satellite lakes and high zebra mussel abundances. These may buffer the impoverishing effects of eutrophication and sustain unexpectedly high biodiversity in the short term. Such protective buffering, however, cannot be relied upon indefinitely to conserve biodiversity.This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. The attached file is the published pdf.
© 2019 The Authors. Diversity and Distributions Published by John Wiley & Sons Ltd.NHM Repositor
Distinct Genetic Diversity of Oncomelania hupensis, Intermediate Host of Schistosoma japonicum in Mainland China as Revealed by ITS Sequences
Get PDFBackground
Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum, which causes schistosomiasis endemic in the Far East, and especially in mainland China. O. hupensis largely determines the parasite's geographical range. How O. hupensis's genetic diversity is distributed geographically in mainland China has never been well examined with DNA sequence data.
Methodology/Principal Findings
In this study we investigate the genetic variation among O. hupensis from different geographical origins using the combined complete internal transcribed spacer 1 (ITS1) and ITS2 regions of nuclear ribosomal DNA. 165 O. hupensis isolates were obtained in 29 localities from 7 provinces across mainland China: lake/marshland and hill regions in Anhui, Hubei, Hunan, Jiangxi and Jiangsu provinces, located along the middle and lower reaches of Yangtze River, and mountainous regions in Sichuan and Yunnan provinces. Phylogenetic and haplotype network analyses showed distinct genetic diversity and no shared haplotypes between populations from lake/marshland regions of the middle and lower reaches of the Yangtze River and populations from mountainous regions of Sichuan and Yunnan provinces. The genetic distance between these two groups is up to 0.81 based on Fst, and branch time was estimated as 2–6 Ma. As revealed in the phylogenetic tree, snails from Sichuan and Yunnan provinces were also clustered separately. Geographical separation appears to be an important factor accounting for the diversification of the two groups of O. hupensis in mainland China, and probably for the separate clades between snails from Sichuan and Yunnan provinces. In lake/marshland and hill regions along the middle and lower reaches of the Yangtze River, three clades were identified in the phylogenetic tree, but without any obvious clustering of snails from different provinces.
Conclusions
O. hupensis in mainland China may have considerable genetic diversity, and a more complex population structure than expected. It will be of significant importance to consider the genetic diversity of O. hupensis when assessing co-evolutionary interactions with S. japonicum.© 2010 Zhao et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published pdf.NHM Repositor
The Mitochondrial Genome of Toxocara canis
Get PDFToxocara canis (Ascaridida: Nematoda), which parasitizes (at the adult stage) the small intestine of canids, can be transmitted to a range of other mammals, including humans, and can cause the disease toxocariasis. Despite its significance as a pathogen, the genetics, epidemiology and biology of this parasite remain poorly understood. In addition, the zoonotic potential of related species of Toxocara, such as T. cati and T. malaysiensis, is not well known. Mitochondrial DNA is known to provide genetic markers for investigations in these areas, but complete mitochondrial genomic data have been lacking for T. canis and its congeners. In the present study, the mitochondrial genome of T. canis was amplified by long-range polymerase chain reaction (long PCR) and sequenced using a primer-walking strategy. This circular mitochondrial genome was 14162 bp and contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for secernentean nematodes, including Ascaris suum and Anisakis simplex (Ascaridida). The mitochondrial genome of T. canis provides genetic markers for studies into the systematics, population genetics and epidemiology of this zoonotic parasite and its congeners. Such markers can now be used in prospecting for cryptic species and for exploring host specificity and zoonotic potential, thus underpinning the prevention and control of toxocariasis in humans and other hosts.© 2008 Jex et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published pdf.NHM Repositor
Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics
Get PDFMitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags (‘barcodes’). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three ‘bait’ sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species ‘barcodes’ that currently use the cox1 gene only.© The Author(s) 2010. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
The attached file is the published pdf.NHM Repositor
Malacosporean myxozoans exploit a diversity of fish hosts
Get PDFMyxozoans are widespread and common endoparasites of fish with complex life cycles, infecting vertebrate and invertebrate hosts. There are two classes: Myxosporea and Malacosporea. To date about 2500 myxosporean species have been described. By comparison, there are only five described malacosporean species. Malacosporean development in the invertebrate hosts (freshwater bryozoans) has been relatively well studied but is poorly known in fish hosts. Our aim was to investigate the presence and development of malacosporeans infecting a diversity of fish from Brazil, Europe and the USA. We examined kidney from 256 fish belonging variously to the Salmonidae, Cyprinidae, Nemacheilidae, Esocidae, Percidae, Polyodontidae, Serrasalmidae, Cichlidae and Pimelodidae. Malacosporean infections were detected and identified by polymerase chain reaction and small subunit ribosomal DNA sequencing, and the presence of sporogonic stages was evaluated by ultrastructural examination. We found five malacosporean infections in populations of seven European fish species (brown trout, rainbow trout, white fish, dace, roach, gudgeon and stone loach). Ultrastructural analyses revealed sporogonic stages in kidney tubules of three fish species (brown trout, roach and stone loach), providing evidence that fish belonging to at least three families are true hosts. These results expand the range of fish hosts exploited by malacosporeans to complete their life cycle.The attached document is the authors’ submitted version of the journal article. You are advised to consult the publisher’s version if you wish to cite from it.NHM Repositor
The Anatomy of an Alkalic Porphyry Cu-Au System: Geology and Alteration at Northparkes Mines, New South Wales, Australia
No full textThe Late Ordovician-early Silurian (~455–435 Ma) Northparkes system is a group of silica-saturated, alkalic porphyry deposits and prospects that developed within the Macquarie island arc. The system is host to a spectacular and diverse range of rocks and alteration-mineralization textures that facilitate a detailed understanding of its evolution, in particular the nature and controls of porphyry-related propylitic alteration.
The first intrusive phase at Northparkes is a pre- to early-mineralization pluton that underlies all the deposits and varies in composition from a biotite quartz monzonite to alkali feldspar granite. Prior to total crystallization, this pluton was intruded by a more primitive quartz monzonite that marks the onset of a fertile fractionation series. Toward its upper levels, the quartz monzonite is porphyritic and locally rich in Cu sulfides. Subsequently, a complex series of synmineralization quartz monzonite porphyries was emplaced. The quartz monzonite porphyry intrusions have a distinct pipe-like morphology and are ubiquitously K-feldspar–altered with a crystal-crowded porphyritic texture. The textures of the quartz monzonite porphyries and common occurrence of porphyry-cemented contact breccias indicate they were forcibly emplaced and of relatively low viscosity. The quartz monzonite porphyries are therefore interpreted as crystal-bearing, silicate melt-aqueous fluid slurries that represent the conduits through which deep-seated magmatic-derived ore fluid was discharged into the shallow crust (1–2 km depth).
Each deposit is centered on a multiphase cluster of quartz monzonite porphyry intrusions that drove discrete hydrothermal systems. Initial fluid evolution was similar in all the deposits, with three major alteration facies developed as largely concentric zones around the quartz monzonite porphyry complexes. The innermost zone is host to Cu sulfide ore and dominated by K-feldspar alteration. This transitions outward through a shell of magnetite ± biotite alteration, with pyrite and minor chalcopyrite, to an outer halo of propylitic alteration. Generally, epidote, chlorite, and pyrite are abundant in the most deposit-proximal propylitic zone, with a decrease in the abundance of pyrite, and then epidote, with increasing distance away from deposit centers.
Propylitic alteration, particularly within relatively low permeability rocks, is fracture-controlled and a hierarchy of veins is observed. Veins of chlorite-quartz-pyrite ± calcite ± hematite ± epidote ± chalcopyrite (P1) appear to represent the principal fluid conduits. They are surrounded by pervasive and intense alteration halos with a distinct mineralogical zonation from vein-proximal chlorite-sericite (phengite) ± epidote ± pyrite, through hematite-sericite-chlorite ± epidote, ultimately to a vein-distal hematite-albite ± chlorite ± epidote assemblage. These P1 veins are surrounded by regions in which smaller epidote-chlorite ± calcite ± quartz ± pyrite veins (P2) are abundant, again with zoned alteration envelopes: vein-proximal chlorite-sericite (phengite) ± epidote ± pyrite grades out into an epidote-rich zone, which in turn transitions into vein-distal albite-hematite ± chlorite ± epidote. Areas of weakest propylitic alteration, distant from both P1 and P2 veins, are characterized by small epidote-only veinlets (P3) with albite-hematite halos. Mineralogical transitions across the propylitic zone are therefore repeated in the evolution from P1 to P3 veins, as well as in the halos around these veins. It is the overall vein abundance and overlap of associated alteration halos that controls the intensity and appearance of propylitic alteration in most rocks. Such scale invariance and spatial relationships strongly suggest the transition from P1 to P3 veins reflects a broadly decreasing outward flux of (magmatic-derived?) fluid that passed through the fracture network and progressively reacted with country rocks. Further support for this hypothesis comes from crosscutting relationships and Rb-Sr dating of epidote (returning an age of 450 ± 11 Ma), which demonstrate the bulk of propylitic alteration was coeval with mineralization and potassic alteration.
Late-stage fluid evolution at each deposit was unique. Much of the E48 orebody, and locally the GRP314 deposit, was overprinted by texturally destructive, white sericite-albite-quartz-alunite ± chlorite alteration. In the E26 deposit and in regions of the GRP314 deposit a series of quartz-anhydrite ± pyrite ± Cu sulfide veins with distinctive, vein-proximal, sericite-dominant alteration halos cuts the primary, deposit-concentric alteration facies. The vein-distal mineralogy of these alteration halos is controlled by their distance from deposit centers, changing from K-feldspar ± biotite in deposit-proximal veins to chlorite ± epidote-albite in depositdistal veins. Late-mineralization quartz monzonite porphyries at E26 and GRP314 also appear to be related to the generation of anhydrite-quartz ± sphalerite veins and a set of quartz-calcite-pyrite-sphalerite ± chalcopyrite ± galena veins. Postmineralization magmatic activity produced relatively primitive and barren monzonite porphyries and younger alkali basalt dikes.The attached document is the author(’s’) final accepted/submitted version of the journal article. You are advised to consult the publisher’s version if you wish to cite from it.NHM Repositor