| 1. |
- Davies, Thomas G., et al.
(författare)
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Open data and digital morphology.
- 2017
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 284:1852, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.
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| 2. |
- Cunningham, J. A., et al.
(författare)
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Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils.
- 2012
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Ingår i: Proceedings of the Royal Society of London. B. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 279:1734, s. 1857-1864
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Tidskriftsartikel (refereegranskat)abstract
- The Ediacaran Doushantuo biota has yielded fossils interpreted as eukaryotic organisms, either animal embryos or eukaryotes basal or distantly related to Metazoa. However, the fossils have been interpreted alternatively as giant sulphur bacteria similar to the extant Thiomargarita. To test this hypothesis, living and decayed Thiomargarita were compared with Doushantuo fossils and experimental taphonomic pathways were compared with modern embryos. In the fossils, as in eukaryotic cells, subcellular structures are distributed throughout cell volume; in Thiomargarita, a central vacuole encompasses approximately 98 per cent cell volume. Key features of the fossils, including putative lipid vesicles and nuclei, complex envelope ornament, and ornate outer vesicles are incompatible with living and decay morphologies observed in Thiomargarita. Microbial taphonomy of Thiomargarita also differed from that of embryos. Embryo tissues can be consumed and replaced by bacteria, forming a replica composed of a threedimensional biofilm, a stable fabric for potential fossilization. Vacuolated Thiomargarita cells collapse easily and do not provide an internal substrate for bacteria. The findings do not support the hypothesis that giant sulphur bacteria are an appropriate interpretative model for the embryo-like Doushantuo fossils. However, sulphur bacteria may have mediated fossil mineralization and may provide a potential bacterial analogue for other macroscopic Precambrian remains.
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| 3. |
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| 4. |
- Bengtson, Per, et al.
(författare)
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Links between methanotroph community composition and CH(4) oxidation in a pine forest soil
- 2009
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 70:3, s. 356-366
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Tidskriftsartikel (refereegranskat)abstract
- The main gap in our knowledge about what determines the rate of CH(4) oxidation in forest soils is the biology of the microorganisms involved, the identity of which remains unclear. In this study, we used stable-isotope probing (SIP) following (13)CH(4) incorporation into phospholipid fatty acids (PLFAs) and DNA/RNA, and sequencing of methane mono-oxygenase (pmoA) genes, to identify the influence of variation in community composition on CH(4) oxidation rates. The rates of (13)C incorporation into PLFAs differed between horizons, with low (13)C incorporation in the organic soil and relatively high (13)C incorporation into the two mineral horizons. The microbial community composition of the methanotrophs incorporating the (13)C label also differed between horizons, and statistical analyses suggested that the methanotroph community composition was a major cause of variation in CH(4) oxidation rates. Both PLFA and pmoA-based data indicated that CH(4) oxidizers in this soil belong to the uncultivated 'upland soil cluster alpha'. CH(4) oxidation potential exhibited the opposite pattern to (13)C incorporation, suggesting that CH(4) oxidation potential assays may correlate poorly with in situ oxidation rates. The DNA/RNA-SIP assay was not successful, most likely due to insufficient (13)C-incorporation into DNA/RNA. The limitations of the technique are briefly discussed.
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| 5. |
- Callier, Myriam D., et al.
(författare)
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Attraction and repulsion of mobile wild organisms to finfish and shellfish aquaculture: A review
- 2018
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Ingår i: Reviews in Aquaculture. - : Wiley. - 1753-5123 .- 1753-5131. ; 10:4, s. 924-949
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Tidskriftsartikel (refereegranskat)abstract
- © 2017 Wiley Publishing Asia Pty Ltd. Knowledge of aquaculture-environment interactions is essential for the development of a sustainable aquaculture industry and efficient marine spatial planning. The effects of fish and shellfish farming on sessile wild populations, particularly infauna, have been studied intensively. Mobile fauna, including crustaceans, fish, birds and marine mammals, also interact with aquaculture operations, but the interactions are more complex and these animals may be attracted to (attraction) or show an aversion to (repulsion) farm operations with various degrees of effects. This review outlines the main mechanisms and effects of attraction and repulsion of wild animals to/from marine finfish cage and bivalve aquaculture, with a focus on effects on fisheries-related species. Effects considered in this review include those related to the provision of physical structure (farm infrastructure acting as fish aggregating devices (FADs) or artificial reefs (ARs), the provision of food (e.g. farmed animals, waste feed and faeces, fouling organisms associated with farm structures) and some farm activities (e.g. boating, cleaning). The reviews show that the distribution of mobile organisms associated with farming structures varies over various spatial (vertical and horizontal) and temporal scales (season, feeding time, day/night period). Attraction/repulsion mechanisms have a variety of direct and indirect effects on wild organisms at the level of individuals and populations and may have implication for the management of fisheries species and the ecosystem in the context of marine spatial planning. This review revealed considerable uncertainties regarding the long-term and ecosystem-wide consequences of these interactions. The use of modelling may help better understand consequences, but long-term studies are necessary to better elucidate effects.
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| 6. |
- Cunningham, J.A., et al.
(författare)
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Distinguishing geology from biology in the Ediacaran Doushantuo biota relaxes constraints on the timing of the origin of bilaterians.
- 2012
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Ingår i: Proceedings of the Royal Society. B. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 279:1737, s. 2369-2376
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Tidskriftsartikel (refereegranskat)abstract
- The Ediacaran Doushantuo biota has yielded fossils that include the oldest widely accepted record of the animal evolutionary lineage, as well as specimens with alleged bilaterian affinity. However, these systematic interpretations are contingent on the presence of key biological structures that have been reinterpreted by some workers as artefacts of diagenetic mineralization. On the basis of chemistry and crystallographic fabric, we characterize and discriminate phases of mineralization that reflect: (i) replication of original biological structure, and (ii) void-filling diagenetic mineralization. The results indicate that all fossils from the Doushantuo assemblage preserve a complex me´lange of mineral phases, even where subcellular anatomy appears to be preserved. The findings allow these phases to be distinguished in more controversial fossils, facilitating a critical re-evaluation of the Doushantuo fossil assemblage and its implications as an archive of Ediacaran animal diversity. We find that putative subcellular structures exhibit fabrics consistent with preservation of original morphology. Cells in later developmental stages are not in original configuration and are therefore uninformative concerning gastrulation. Key structures used to identify Doushantuo bilaterians can be dismissed as late diagenetic artefacts. Therefore, when diagenetic mineralization is considered, there is no convincing evidence for bilaterians in the Doushantuo assemblage.
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| 7. |
- Donoghue, Philip C. J., et al.
(författare)
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Synchrotron X-ray tomographic microscopy of fossil embryos
- 2006
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Ingår i: Nature. - 0028-0836. ; 442:7103, s. 601-718
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Tidskriftsartikel (refereegranskat)abstract
- Fossilized embryos from the late Neoproterozoic and earliest Phanerozoic have caused much excitement because they preserve the earliest stages of embryology of animals that represent the initial diversification of metazoans1, 2, 3, 4. However, the potential of this material has not been fully realized because of reliance on traditional, non-destructive methods that allow analysis of exposed surfaces only1, 2,3, 4, and destructive methods that preserve only a single two-dimensional view of the interior of the specimen5, 6. Here, we have applied synchrotron-radiation X-ray tomographic microscopy (SRXTM)7, obtaining complete three-dimensional recordings at submicrometre resolution. The embryos are preserved by early diagenetic impregnation and encrustation with calcium phosphate, and differences in X-ray attenuation provide information about the distribution of these two diagenetic phases. Three-dimensional visualization of blastomere arrangement and diagenetic cement in cleavage embryos resolves outstanding questions about their nature, including the identity of the columnar blastomeres. The anterior and posterior anatomy of embryos of the bilaterian worm-like Markuelia confirms its position as a scalidophoran, providing new insights into body-plan assembly among constituent phyla. The structure of the developing germ band in another bilaterian, Pseudooides, indicates a unique mode of germ-band development. SRXTM provides a method of non-invasive analysis that rivals the resolution achieved even by destructive methods, probing the very limits of fossilization and providing insight into embryology during the emergence of metazoan phyla.
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| 8. |
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| 9. |
- Murdock, Duncan J.E., et al.
(författare)
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Evaluating scenarios for the evolutionary assembly of the brachiopod body plan.
- 2014
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Ingår i: Evolution & Development. - : Wiley. - 1520-541X .- 1525-142X. ; 16:1, s. 13-24
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Tidskriftsartikel (refereegranskat)abstract
- The fossil faunas of the Cambrian provide the only direct insight into the assembly of animal body plans. However, for many animal groups, their early fossil record is linked to disarticulated remains, interpretation of which is problematic since they possess few characters from which their affinity to phyla can be established and, indeed, few characters at all. One such group is the tommotiids, which has been interpreted, on the basis of skeletal anatomy, as a paraphyletic assemblage uniting brachiopods and phoronids, through the acquisition and subsequent modification, or loss, of an imbricated set of dorsal phosphatic sclerites. Here we present a reexamination of the fossil evidence uniting the tommotiids and brachiopods, supplemented with new anatomical data from synchrotron radiation X-ray tomographic microscopy of key tommotiid taxa. The characters used to support the complex hypothesis of character evolution in the brachiopod stem lineage relies on scleritome reconstructions and inferred mode of life which themselves rely on brachiopods being chosen as the interpretative model. We advocate a more conservative interpretation of the affinity of these fossils, based a priori on their intrinsic properties, rather than the modern analogue in whose light they have been interpreted.
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| 10. |
- Murdock, Duncan J.E., et al.
(författare)
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Ontogeny and microstructure of the enigmatic Cambrian tommotiid Sunnaginia Missarzhevsky 1969.
- 2012
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Ingår i: Palaeontology. - : Wiley. - 0031-0239. ; 55:3, s. 661-676
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Tidskriftsartikel (refereegranskat)abstract
- The tommotiids are a significant component of the earliest skeletal animal remains in the fossil record, occurring in large numbers in the Lower Cambrian. Sclerites of the tommotiid genus Sunnaginia have been implicated as integral to hypotheses regarding the evolution of the brachiopod body plan, with a morphology intermediate between the unspecialized sclerites of the tubular Eccentrotheca and the specialized sclerites of the tannuolinids. Abundant Sunnaginia ?imbricata sclerites, of a broad ontogenetic spectrum, were recovered from the Comley Limestone, Lower Cambrian (Stages 3–4), Shropshire, UK and compared to Sunnaginia imbricata from the Aldan River, Siberia (uppermost Tommotian). New microstructural data, collected using synchrotron radiation X-ray tomographic microscopy, reveal a unique microstructure for Sunnaginia ?imbricata sclerites among the tommotiids; interlamellar cavities spanned by a series of continuous pillars, giving a colonnaded appearance contrasting to that of S. imbricata. These data refute the inclusion of Eccentrotheca within the Sunnaginiidae and highlight the need for a revision of suprageneric classification of the tommotiids. Rather, structural similarities between Sunnaginia sclerites and those of the tannuolinids suggest a close affinity to this group. Recent phylogenetic hypotheses place the tannuolinids as stem-linguliform brachiopods, with Paterimitra plus the paterinid (and possibly rhynchonelliform) brachiopods as their sister group. Our new data therefore resolve Sunnaginia as close to the node defining crown-Brachiopoda. However, the characters supporting this phylogenetic scheme cannot be consistently applied to all taxa, nor do they define a series of nested clades. We therefore suggest that a more thorough phylogenetic analysis is required in the light of the data presented here and other recent descriptions.
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