| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
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| 3. |
- Bazzi, Mohamad
(författare)
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100 million years of shark macroevolution : A morphometric dive into tooth shape diversity
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Few vertebrate clades exhibit the evolutionary longevity and versatility of sharks, which constitute nearly half of all current chondrichthyan biodiversity and represent an ecological diversity of mid-to-apex trophic-level predators in both marine and freshwater environments. The rich fossil record of shark teeth from Mesozoic and Cenozoic rocks also makes the group amenable to large-scale quantitative analyses. This thesis reconstructs the morphological tooth disparity of dominant lamniform (Mackerel sharks) and carcharhiniform (Ground sharks) clades over the last 100 million years. The relative diversity of these major lineages is strongly skewed, with lamniforms, including the famous White shark, making up less than 3% of the total species richness, whereas carcharhiniforms, such as Tiger sharks, comprise over 290 described species. Paradoxically, this long-recognized disproportionate representation was reversed in the distant geological past. Indeed, the fossil record shows that lamniforms accounted for nearly all of the documented shark diversity during the final stages of the Late Cretaceous — the terminal time interval of the ‘Age of Dinosaurs’, which ended 66 million years ago. The causes of this radical diversity turnover are debated, with recent research suggesting that competition and/or climate change drove major shifts in shark evolution. Perhaps more surprisingly, most analyses of diversity dynamics of sharks centre largely on taxonomic data, thus omitting more direct proxies of ecology, such as morphological diversity, or disparity. To mitigate this shortfall, I adopt a Procrustes framework combined with phylogenetic comparative and multivariate statistics to shed light on the deep-time morphological evolution of sharks. My work indicates that the end-Cretaceous mass extinction initiated a sustained evolutionary turnover in ecological dominance between lamniforms and carcharhiniforms. More specifically, the morphospace of these clades, indicate a selective extinction at the K/Pg Boundary affecting ‘large-bodied’ anacoracid lamniform sharks, whereas triakid carcharhiniforms proliferated in the extinction aftermath, perhaps as a response to new prey sources. Overall, my thesis suggests that the modern shark assemblages are the synergistic result of feeding ecology (including dietary niche breadth) and environmental shifts in global sea levels and temperature acting over the last 100 million years.
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| 4. |
- Blom, Henning, et al.
(författare)
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Devonian vertebrates from East Greenland : a review of faunal composition and distribution
- 2007
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Ingår i: Geodiversitas. - 1280-9659 .- 1638-9395. ; 29:1, s. 119-141
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Forskningsöversikt (refereegranskat)abstract
- The Devonian vertebrate faunas of East Greenland are reviewed and their distribution discussed for the first time in the light of the most recently published stratigraphical framework for the area. The predominantly Middle and Upper Devonian continental sediments have yielded representatives of most major groups of early fossil vertebrates, including heterostracans, placoderms, acanthodians, chondrichthyans, actinopterygians, lungfishes, porolepiforms, "osteolepiforms" and tetrapods, but to date, no single publication has treated them all in their stratigraphical context. We therefore attempt to place them into the most recent, formalised lithostratigraphy, providing improved resolution for their stratigraphical distribution, as a basis for comparing East Greenland with other Devonian faunal successions worldwide. The review highlights the fact that many problems of stratigraphical correlation and dating of the East Greenland Devonian deposits remain to be resolved by further fieldwork. Several assemblages ranging from Givetian to Famennian in age can be distinguished, that correspond to older superceded subdivisional nomenclature. A possible Frasnian fauna has been recognised for the first time, adding details to an otherwise poorly dated part of the succession. Typical Devonian taxa such as Holoptychius Agassiz, 1839 and Groenlandaspis Heintz, 1932 have apparently been recorded in an otherwise unique position above the Devonian-Carboniferous boundary in the upper part of the succession. New specimens of rare elements of the fauna including an unknown arthrodire placoderm, a putative chondrichthyan spine and a patch of possibly regurgitated acanthodian spines, are illustrated for the first time.
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| 5. |
- Byrne, Hannah
(författare)
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Novel approaches to the environments and ecosystems of the fish-tetrapod transition
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The fish-tetrapod transition is one of the most important evolutionary events in Earth’s history, giving rise to terrestrial vertebrates around 390 million years ago. It set the stage for a series of evolutionary events that ultimately resulted in modern-day terrestrial vertebrates including ourselves. The fish-tetrapod transition occurred during the Middle Palaeozoic and although it has been the subject of intense study over the last century, many questions remain unanswered. In this thesis, novel techniques were used to help elucidate certain aspects of the fish-tetrapod transition. The first project sought to use numerical tidal simulations to test the premise of a hypothesis that large tides occurred during the Middle Palaeozoic and acted as a driver for the evolution of lungs and limbs. The simulations produced for the Late Silurian-Late Devonian revealed unusually large tides during the Late Silurian, thus the origin of lungs, supporting the hypothesis that deoxygenated tidal pools could have been the setting for this evolutionary step. The following three projects used propagation phase-contrast synchrotron microtomography (PPC-SRμCT) to analyse new tetrapod material from the terminal Famennian (latest Devonian) and coprolite material from the earliest Tournaisian of Greenland (earliest Carboniferous), spanning a mass extinction event (the Hangenberg crisis) believed to have impacted early tetrapod diversity. Spectacular data sets were generated using this technique, with analysis of the tetrapod material revealing the presence of new taxa, making East Greenland home to the greatest known diversity of tetrapods in the world during the Devonian. Synchrotron scanning allowed for the accurate determination of coprolite morphotypes from a post-Hangenberg crisis lake deposit, revealing greater diversity among the coprolites compared with vertebrate body fossil taxa and thus demonstrating that the fauna contained additional taxa not captured by the body fossil record. Most of the large coprolites are non-spiral and were probably produced by a large aquatic tetrapod. One large coprolite is spiral and is postulated to have been produced by a chondrichthyan. Virtual reconstructions of several coprolites were generated using the scan data. The largest coprolites were full of actinopterygian and acanthodian remains, showing that the probable tetrapod was a proficient aquatic predator. Another large coprolite contained remains of two new body fossil taxa; an actinopterygian and small tetrapod. The coprolite data challenge our initial interpretation of a low-diversity lake fauna, revealing instead a complex ecosystem immediately after a major mass extinction event. Tetrapods and chondrichthyans appear to have been the apex predators in this ecosystem. This thesis demonstrates the capabilities of two novel analytical techniques, tidal simulation and synchrotron microtomography, to uncover previously inaccessible information about the fish-tetrapod transition and its environmental-ecological context.
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| 6. |
- Castiello, Marco, et al.
(författare)
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Endocranial morphology of the petalichthyid placoderm Ellopetalichthys scheii from the Middle Devonian of Arctic Canada, with remarks on the inner ear and neck joint morphology of placoderms
- 2021
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Ingår i: Canadian journal of earth sciences (Print). - : CANADIAN SCIENCE PUBLISHING. - 0008-4077 .- 1480-3313. ; 58:1, s. 93-104
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Tidskriftsartikel (refereegranskat)abstract
- Petalichthyid and "acanthothoracid" placoderms have taken pivotal positions in the debate on placoderm- and, by extension, jawed vertebrate - relationships owing to perceived similarities with certain jawless vertebrates. Neurocranial characters are integral to current hypotheses of early gnathostome relationships. Here, we describe the three-dimensionally preserved neurocranial anatomy of the petalichthyid placoderm Ellopetalichthys scheii (Kiaer, 1915), from the Middle Devonian (early Eifelian) of Ellesmere Island, Canada. Using X-ray computed microtomography, we generated three-dimensional reconstructions of the endocranial surfaces, orbital walls, and cranial endocavity. These reconstructions verify the absence of a crus commune of the skeletal labyrinth and the complex shape of the petalichthyid endolympathic duct. Details of the craniothoracic joint and occipital musculature fossae help resolve the problematic comparative anatomy of the occipital surface of petalichthyids. These new data highlight similarities with arthrodire placoderms, consistent with older hypotheses of a sister-group relationship between petalichthyids and that clade.
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| 7. |
- Davesne, Donald, et al.
(författare)
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Fossilized cell structures identify an ancient origin for the teleost whole-genome duplication
- 2021
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 118:30
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Tidskriftsartikel (refereegranskat)abstract
- Teleost fishes comprise one-half of all vertebrate species and possess a duplicated genome. This whole-genome duplication (WGD) occurred on the teleost stem lineage in an ancient common ancestor of all living teleosts and is hypothesized as a trigger of their exceptional evolutionary radiation. Genomic and phylogenetic data indicate that WGD occurred in the Mesozoic after the divergence of teleosts from their closest living relatives but before the origin of the extant teleost groups. However, these approaches cannot pinpoint WGD among the many extinct groups that populate this 50- to 100-million-y lineage, preventing tests of the evolutionary effects of WGD. We infer patterns of genome size evolution in fossil stem-group teleosts using high-resolution synchrotron X-ray tomography to measure the bone cell volumes, which correlate with genome size in living species. Our findings indicate that WGD occurred very early on the teleost stem lineage and that all extinct stem-group teleosts known so far possessed duplicated genomes. WGD therefore predates both the origin of proposed key innovations of the teleost skeleton and the onset of substantial morphological diversification in the clade. Moreover, the early occurrence of WGD allowed considerable time for postduplication reorganization prior to the origin of the teleost crown group. This suggests at most an indirect link between WGD and evolutionary success, with broad implications for the relationship between genomic architecture and large-scale evolutionary patterns in the vertebrate Tree of Life.
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| 8. |
- 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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| 9. |
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| 10. |
- Friedman, Matt, et al.
(författare)
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A new actinopterygian from the Famennian of East Greenland and the interrelationships of Devonian ray-finned fishes
- 2006
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Ingår i: Journal of Paleontology. - 0022-3360 .- 1937-2337. ; 80:6, s. 1186-1204
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Forskningsöversikt (refereegranskat)abstract
- A new actinopterygian, Cuneognathus gardineri new genus and species, is described from the Devonian (Famennian) Obrutschew Bjerg Formation of East Greenland on the basis of multiple incomplete specimens. Cuneognathus most closely resembles Limnomis from the Famennian Catskill Formation of Pennsylvania, and, like that taxon, is known exclusively from freshwater deposits. A cladistic analysis with an ingroup of 13 actinopterygians and an outgroup of five sarcopterygians explores the relationships between the new genus and some of its better-known Devonian contemporaries, and recovers the same four topologies regardless of the implementation of limited character ordering. Cheirolepis is resolved as the most basal of well-known Devonian actinopterygians, consistent with a majority of previous studies. A novel sister-group relationship between Howqualepis and Tegeolepis is found in all trees. Disagreement between the most parsimonious cladograms is concentrated in a clade whose members are often informally referred to as 'stegotrachelids.' Cuneognathus and Limnomis are resolved as sister taxa within this large radiation along with the pairings of Moythomasia dugaringa plus M. nitida and Krasnoyarichtkys plus Stegotrachelus. The arrangement of taxa is conserved when the enigmatic Dialipina is added to the analysis, although the reconstructed position of that genus above both Cheirolepis and Osorioichthys seems improbable. Our scheme of relationships suggests that actinopterygians invaded freshwater environments at least four times during the Devonian, while age constraints indicate that many of the cladogenic events between ingroup taxa included in this study occurred during or before the Givetian.
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