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- Alström, Per, et al.
(författare)
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Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae.
- 2011
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 58:3, s. 513-26
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Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of most of the species in the avian passerine family Locustellidae is inferred using a Bayesian species tree approach (Bayesian Estimation of Species Trees, BEST), as well as a traditional Bayesian gene tree method (MrBayes), based on a dataset comprising one mitochondrial and four nuclear loci. The trees inferred by the different methods agree fairly well in topology, although in a few cases there are marked differences. Some of these discrepancies might be due to convergence problems for BEST (despite up to 1×10(9) iterations). The phylogeny strongly disagrees with the current taxonomy at the generic level, and we propose a revised classification that recognizes four instead of seven genera. These results emphasize the well known but still often neglected problem of basing classifications on non-cladistic evaluations of morphological characters. An analysis of an extended mitochondrial dataset with multiple individuals from most species, including many subspecies, suggest that several taxa presently treated as subspecies or as monotypic species as well as a few taxa recognized as separate species are in need of further taxonomic work.
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| 2. |
- Alström, Per, et al.
(författare)
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Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset.
- 2011
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 352-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The avian family Cettiidae, including the genera Cettia, Urosphena, Tesia, Abroscopus and Tickellia and Orthotomus cucullatus, has recently been proposed based on analysis of a small number of loci and species. The close relationship of most of these taxa was unexpected, and called for a comprehensive study based on multiple loci and dense taxon sampling. In the present study, we infer the relationships of all except one of the species in this family using one mitochondrial and three nuclear loci. We use traditional gene tree methods (Bayesian inference, maximum likelihood bootstrapping, parsimony bootstrapping), as well as a recently developed Bayesian species tree approach (*BEAST) that accounts for lineage sorting processes that might produce discordance between gene trees. We also analyse mitochondrial DNA for a larger sample, comprising multiple individuals and a large number of subspecies of polytypic species.RESULTS: There are many topological incongruences among the single-locus trees, although none of these is strongly supported. The multi-locus tree inferred using concatenated sequences and the species tree agree well with each other, and are overall well resolved and well supported by the data. The main discrepancy between these trees concerns the most basal split. Both methods infer the genus Cettia to be highly non-monophyletic, as it is scattered across the entire family tree. Deep intraspecific divergences are revealed, and one or two species and one subspecies are inferred to be non-monophyletic (differences between methods).CONCLUSIONS: The molecular phylogeny presented here is strongly inconsistent with the traditional, morphology-based classification. The remarkably high degree of non-monophyly in the genus Cettia is likely to be one of the most extraordinary examples of misconceived relationships in an avian genus. The phylogeny suggests instances of parallel evolution, as well as highly unequal rates of morphological divergence in different lineages. This complex morphological evolution apparently misled earlier taxonomists. These results underscore the well-known but still often neglected problem of basing classifications on overall morphological similarity. Based on the molecular data, a revised taxonomy is proposed. Although the traditional and species tree methods inferred much the same tree in the present study, the assumption by species tree methods that all species are monophyletic is a limitation in these methods, as some currently recognized species might have more complex histories.
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| 3. |
- Andersson, Ki, et al.
(författare)
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Sabertoothed carnivores and the killing of large prey
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:10, s. e24971-
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Tidskriftsartikel (refereegranskat)abstract
- Sabre-like canines clearly have the potential to inflict grievous wounds leading to massive blood loss and rapid death. Hypotheses concerning sabretooth killing modes include attack to soft parts such as the belly or throat, where biting deep is essential to generate strikes reaching major blood vessels. Sabretoothed carnivorans are widely interpreted as hunters of larger and more powerful prey than that of their present-day nonsabretoothed relatives. However, the precise functional advantage of the sabretooth bite, particularly in relation to prey size, is unknown. Here, we present a new point-to-point bite model and show that, for sabretooths, depth of the killing bite decreases dramatically with increasing prey size. The extended gape of sabretooths only results in considerable increase in bite depth when biting into prey with a radius of less than ~10 cm. For sabretooths, this size-reversed functional advantage suggests predation on species within a similar size range to those attacked by present-day carnivorans, rather than “megaherbivores” as previously believed. The development of the sabretooth condition appears to represent a shift in function and killing behaviour, rather than one in predator-prey relations. Furthermore, our results demonstrate how sabretoothed carnivorans are likely to have evolved along a functionally continuous trajectory: beginning as an extension of a jaw-powered killing bite, as adopted by present-day pantherine cats, followed by neck-powered biting and thereafter shifting to neck-powered shear-biting. We anticipate this new insight to be a starting point for detailed study of the evolution of pathways that encompass extreme specialisation, for example, understanding how neck-powered biting shifts into shear-biting and its significance for predator-prey interactions. We also expect that our model for point-to-point biting and bite depth estimations will yield new insights into the behaviours of a broad range of extinct predators including therocephalians (gorgonopsian + cynodont, sabretoothed mammal-like reptiles), sauropterygians (marine reptiles) and theropod dinosaurs.
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| 4. |
- Bengtson, Stefan, 1947-
(författare)
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Presentation of the 2010 Charles Schuchert Award of the Paleontological Society to Philip C. J. Donoghue.
- 2011
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Ingår i: Journal of Paleontology. - 0022-3360 .- 1937-2337. ; 85:5, s. 1015-
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Tidskriftsartikel (refereegranskat)abstract
- LADIES AND gentlemen, friends and colleagues, the winner of the 2010 Charles Schuchert Award is Professor Philip Donoghue of the University of Bristol. In the natural progression of our personal lives, the transition from young snot to old fart is so gradual that one tends not to recognize it, least of all in oneself. Most of us— those further along in their careers— have passed through the stage of young, promising paleontologist to become middleaged promising paleontologists. Not so Phil Donoghue. I first met him when he was a graduate student at the University of Leicester. We got into a discussion about the nature of conodonts and certain pet ideas of mine that I had published. Phil did not agree with me so he went down in my book as a young snot. Soon thereafter, he published a ground-breaking, paradigm-changing paper, together with Peter Forey and Dick Aldridge, on the phylogenetic position of conodonts. Now, I realized that it was I who was the old fart. Phil had demonstrated that he had skipped the young-and-promising stage. He was, and is, young and delivering. Most people who start working on conodonts tend to remain with them. There is something about that mouth apparatus and the way in which it grabs hold of you. But Phil quickly tore himself loose from its grip. He quickly demonstrated an unquenchable zeal in attacking central issues in evolutionary paleontology, such as the origin of microstructures in teeth, the origin of teeth in jaws, the origin of jaws in vertebrates, the origin of vertebrates among animals, the origin of animals in the biosphere, and so on. I fear he will not stop until he has solved the question of the origin of life, the universe, and everything else. The breadth of questions he has already addressed is one aspect of Phil’s work. The diversity of tools he brings to bear on them is another. There is a lot of grinding powder under his fingernails, and lots of devo in his evo. After a sabbatical at the University of Bath, where he seems to have broken every rule of the Sabbath, he came out as a full-fledged molecular biologist, with RNA libraries at his fingertips. He is at the forefront in marrying data from living organisms with that from fossil taxa in phylogenetic analyses. Recently, he came out in defense of the paraphyletic stem group with arguments such that I have high hopes for his post-Schuchert development. Yes, paraphyletic groups are much more interesting than the monophyletic dead-ends called clades, although Phil of course refuses to call them groups. When Phil and some colleagues published a paper in Nature on the Cambrian fossil embryo Markuelia (again showing me wrong on a central issue), it caught the eye of Marco Stampanoni, a physicist who works at the Swiss Light Source (SLS) synchrotron near Zu¨ rich, in Switzerland. Marco had been developing methods of X-ray microtomography, using SLS beamlines. He contacted Phil with a proposal to collaborate, and Phil contacted me. Now, our collaboration based on this revolutionary technique, with Phil at the forefront, has opened our eyes to a huge amount of information to which we did not have access only a few years ago. Taphonomy is like the weather, people speak about it, but few do anything about it. But if you neglect it, you are in deep peril. Phil is much more concerned about taphonomy than most colleagues I know, and he does something about it. He started a project with embryologist Rudy Raff to determine how bacteria go about decomposing embryos in ways such that they are upgraded to exquisite fossils. He is engaging many colleagues, post-docs and students in the investigation of these processes and their end results. As a result, we are gaining insight into how bacteria can invade, devour and faithfully replicate intracellular features, and how different populations of bacteria play different roles in the process. An intriguing observation has emerged from Phil’s taphonomic work with Mark Purnell. Taphonomic degradation tends to bring about a stemward slippage of taxa in their apparent phylogenetic relationships, on account of sequential disappearance of preserved apomorphies. The general significance of this observation has still to be tested, but its potential importance for the phylogenetic analysis of fossils is obvious. Phil is leading an amazingly diverse and successful program in paleontology at the University of Bristol, permeated by his holistic approach and addressing everything from organismbased paleontology to molecular biology. Molecular, organismic, orgiastic paleontology—that’s the realm of Phil Donoghue. Mr. President, please hand the Schuchert Award for 2010 over to Phil. He thoroughly deserves it.
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| 5. |
- Bengtson, Stefan, 1947-
(författare)
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Presentation of the 2010 Paleontological Society Medal to Bruce Runnegar.
- 2011
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Ingår i: Journal of Paleontology. - 0022-3360 .- 1937-2337. ; 85:5, s. 1012-
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Tidskriftsartikel (refereegranskat)abstract
- Ladies and gentlemen, friends and colleagues, the 2010 Paleontological Society Medal is awarded to Professor Bruce Runnegar of the University of California at Los Angeles. Preparing for this presentation, I got hold of a list of Bruce’s invited lectures, given during the past ten years. There are 86 titles on almost as many subjects. I will mention what these presentations were about, so you can get an impression of this Renaissance mind: Carbon isotopes and ocean evolution; Precambrian–Cambrian stratigraphy; Molecular evolution and the fossil record; Ediacaran organisms; Life on Mars; Oxygen and metazoan evolution; Orbital dynamics of the Earth–Moon system; Snowball Earth; Multiplated mollusks; Mass-independent fractionation of sulfur; Biomineralization; The Cambrian Explosion; Geobiology in the Archean; Cross-calibration of geological and astronomical time scales; Origins of biological complexity; Astrobiology of the Earth; Astrobiology of everything else; The Acraman impact of the Ediacaran; Biosignatures in ancient rocks; Microbial metabolism in the Early Archean. Now, most people can waffle about almost anything. A good teacher can read up on such topics and deliver useful lectures on them to students. But, as you will know if you are the least bit familiar with Bruce’s work, these are nearly all topics in fields where he has made startlingly innovative and pioneering contributions. Some would say that his most important contributions are missing from this list, such as molecular paleobiology, for example, or—if you prefer more tangible fossils—the systematics and evolution of Cambrian and Permian mollusks. But what is represented on the list is sufficient to document several brilliant careers in science: Bruce broke new ground in understanding the biomineralization processes of early mollusks by working with natural phosphatic replicas of the now vanished crystals of various species of calcium carbonate. He published a seminal set of papers on the evolution of the earliest mollusks, together with his longtime friend John Pojeta. And, as a leader of the astrobiology movement, Bruce has not only inspired everyone to start looking at life in a universal context, he has also brought his visions to life as Director of NASA’s Astrobiology Institute. It was in this context that Bruce was formally transformed from a U.S.-based Aussie to a full-fledged Australian– American (which is, I think, the politically correct term). In reference to molecular paleontology, I have some personal recollections. Bruce and I both have backgrounds as editors of paleontological journals. Bruce founded and for several years edited the successful Australasian journal Alcheringa, which is still going strong. Some of my first interactions with Bruce occurred in the 1970s, when he submitted manuscripts to Lethaia, of which I was an editor. One of my early forays was to question the number of authors of one of these manuscripts. I knew that no less than five authors of a single paper was excessive and confronted Bruce with this. It may have been the first time I really annoyed him, as he politely told me not to forget to turn my brain on, next time I wrote to him. Well, recently I saw an article in Nature with 230 authors, at which point it finally became clear to me that Bruce was ahead of his time. But back in those times I was a wee bit miffed, so when Bruce sent me a manuscript in which he estimated geological ages of major animal lineages using molecular clock techniques, I knew I could get my revenge. I sent the paper out for review by the sharpest molecular biologists of the day, smugly expecting to receive patronizing comments about paleontologists who should stick to their snail shells rather than pretending to be real scientists. No such luck. The reviews that came in were extravagant in their praise of the paper. Published in 1982, it predated by almost 15 years the avalanche of contributions that later came out on this topic. As usual, Bruce was ahead of the pack, but when others reached the spot where he had stood 15 years earlier, he wasn’t there anymore. Discrepancies between molecular and fossil data for a while seemed insurmountable, not to mention the discrepancies between different sets of molecular data and different sorts of analyses. But Bruce had inspired a bright set of younger biologists and paleontologists to refine their calculations. When the dust settled, one of those with whom Bruce had shared his spark, Kevin Peterson, was able to show that there is no significant conflict between the dates provided by fossils and by molecules. But I mentioned molecular paleontology. In 1986, Bruce published a seminal paper with just that title. In it he expressed his credo, thus: ‘‘palaeontologists should use all available sources of information to understand the evolution of life and its effect on the planet.’’ These are not empty words; they present a formidable challenge. Like all splendid visions, they stake out a direction rather than a goal. That it is possible to pursue this vision we see from the example set by this year’s Schuchert Award winner, Phil Donoghue, who together with Kevin Peterson and Roger Summons wrote a stimulating twenty-first century follow-up to Bruce’s earlier paper. But the foremost example is Bruce Runnegar himself. Here is a taste of the way in which his productive mind works. In 1982, Bruce used the anatomy and hypothesized physiology of the Ediacaran fossil Dickinsonia to estimate constraints for ambient oxygen levels in the Ediacaran atmosphere. This paper is much cited, and geochemists are only now catching up with him, developing geochemical proxies to test the hypothesis that a rising oxygen level was a trigger for the Cambrian Explosion, or, as Bruce so aptly put it, that one ‘‘ingredient, as in most explosives, may well have been a strong oxidising agent.’’ Finally, consider another example. In 1998, Bruce published a cladistic analysis of glaciogenic sediments, testing and corroborating the hypothesis that there were only two major Neoproterozoic glaciations, a result that still seems to stand. Who but Bruce would have thought of such a preposterous idea, using cladistics to resolve a stratigraphical conundrum? Bruce Runnegar has, over the years, formed collegial bonds with many scientists. The many younger people inspired by him include Phil Donoghue, now standing on Bruce’s shoulders. Bruce himself has stood on the shoulders of other giants, as he is quick to acknowledge. But, like Sir Isaac Newton, he has no reason to be bashful about his success, and I don’t think he is. The Paleontological Society Medal was really made for Bruce Runnegar, so please, Mr. President, give it to him!
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| 10. |
- Cawood, P. A., et al.
(författare)
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Orogenesis without collision : Stabilizing the Terra Australis accretionary orogen, eastern Australia
- 2011
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Ingår i: Geological Society of America Bulletin. - 0016-7606 .- 1943-2674. ; 123:11-12, s. 2240-2255
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Tidskriftsartikel (refereegranskat)abstract
- The Neoproterozoic to end-Paleozoic Terra Australis orogen extended along the Gondwana margin of the paleo–Pacific Ocean, and it now provides a detailed record of orogenic activity and continental stabilization within an ongoing convergent, accretionary plate margin. New geochronological data from end-Paleozoic plutonic and volcanic rocks associated with the Gondwanide orogeny in the New England region of eastern Australia, integrated with information on the nature and timing of associated sedimentation, deformation, and metamorphism, allow resolution of a high-fidelity record of orogenesis.At the end of the Carboniferous, around 305 Ma, convergent margin magmatism, which had been active along the western margin of the New England region, terminated and was followed by a short pulse of regional compressional deformation and metamorphism, marking the commencement of the Tablelands phase of Gondwanide orogenesis. Deformation was almost immediately followed by the onset of clastic sedimentation and local calc-alkaline volcanism, dated at 293 Ma, in the extensional Barnard Basin. Emplacement of the two New England S-type granitic suites, the Bundarra and the Hillgrove suites, along with localized high-temperature, low-pressure metamorphism, was essentially contemporaneous, ranging in age from 296 to 288 Ma, and overlapped in time with I-type magmatism and the switch from regional compression to extension and Barnard Basin rifting.The Hunter-Bowen phase of the Gondwanide orogeny commenced with contractional deformation, resulting in termination of sedimentation in the Barnard Basin and regional deformation and metamorphism across New England and into the Sydney and Gunnedah basins to the west at around 265–260 Ma. Contractional loading of the Sydney and Gunnedah basins resulted in their conversion from extensional to foreland basins, which received ongoing pulses of sediment from the New England orogenic welt until 230 Ma. The Hunter-Bowen phase was associated with widespread I-type plutonism and volcanic activity in New England that ceased around 230 Ma, marking the termination of Gondwanide orogenesis.Orogenesis occurred in an evolving convergent plate-margin setting. S- and I-type magmatic activity ranging in age from ca. 300 to 230 Ma represents a stepping out of arc magmatism from the western margin of New England (prior to 305 Ma) into the preexisting arc-trench gap. There is no evidence that deformation was related to the collision of the convergent margin with a major lithospheric mass, and the widespread development of extensional basins in the eastern third of Australia in the Early Permian indicates control by phenomena acting on a continental scale, probably changing plate kinematics associated with the amalgamation of Pangea.
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