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  • 1. Alerstam, Thomas
    et al.
    Rosén, Mikael
    Bäckman, Johan
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Hellgren, Olof
    Flight speeds among bird species: allometric and phylogenetic effects.2007Inngår i: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 5, nr 8, s. e197-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Flight speed is expected to increase with mass and wing loading among flying animals and aircraft for fundamental aerodynamic reasons. Assuming geometrical and dynamical similarity, cruising flight speed is predicted to vary as (body mass)(1/6) and (wing loading)(1/2) among bird species. To test these scaling rules and the general importance of mass and wing loading for bird flight speeds, we used tracking radar to measure flapping flight speeds of individuals or flocks of migrating birds visually identified to species as well as their altitude and winds at the altitudes where the birds were flying. Equivalent airspeeds (airspeeds corrected to sea level air density, Ue) of 138 species, ranging 0.01-10 kg in mass, were analysed in relation to biometry and phylogeny. Scaling exponents in relation to mass and wing loading were significantly smaller than predicted (about 0.12 and 0.32, respectively, with similar results for analyses based on species and independent phylogenetic contrasts). These low scaling exponents may be the result of evolutionary restrictions on bird flight-speed range, counteracting too slow flight speeds among species with low wing loading and too fast speeds among species with high wing loading. This compression of speed range is partly attained through geometric differences, with aspect ratio showing a positive relationship with body mass and wing loading, but additional factors are required to fully explain the small scaling exponent of Ue in relation to wing loading. Furthermore, mass and wing loading accounted for only a limited proportion of the variation in Ue. Phylogeny was a powerful factor, in combination with wing loading, to account for the variation in Ue. These results demonstrate that functional flight adaptations and constraints associated with different evolutionary lineages have an important influence on cruising flapping flight speed that goes beyond the general aerodynamic scaling effects of mass and wing loading.

  • 2. Aliabadian, Mansour
    et al.
    Kaboli, Mohammad
    Foerschler, Marc I.
    Nijman, Vincent
    Chamani, Atefeh
    Tillier, Annie
    Prodon, Roger
    Pasquet, Eric
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Zuccon, Dario
    Erratum to: Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae) (vol 65, pg 35, 2012)2012Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, nr 3, s. 1017-1019Artikkel i tidsskrift (Fagfellevurdert)
  • 3. Aliabadian, Mansour
    et al.
    Kaboli, Mohammad
    Förschler, Marc I
    Nijman, Vincent
    Chamani, Atefeh
    Tillier, Annie
    Prodon, Roger
    Pasquet, Eric
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Zuccon, Dario
    Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae).2012Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, nr 1, s. 35-45Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Open-habitat chats (genera Myrmecocichla, Cercomela, Oenanthe and relative) are a morphologically and ecologically cohesive group of genera with unclear phylogenetic relationships. They are distributed mostly in open, arid and/or rocky habitats of Africa and Eurasia. Here, we present the most comprehensive molecular phylogenetic analysis of this group to date, with a complete taxon sampling at the species level. The analysis, based on a multilocus dataset including three mitochondrial and three nuclear loci, allows us to elucidate the phylogenetic relationships and test the traditional generic limits. All genera are non-monophyletic, suggesting extensive convergence on similar plumage patterns in unrelated species. While the colour pattern appear to be a poor predictor of the phylogenetic relationships, some of the ecological and behavioural traits agree relatively well with the major clades. Following our results, we also propose a revised generic classification for the whole group.

  • 4. Alstrom, Per
    et al.
    Olsson, Urban
    Rasmussen, Pamela C.
    Yao, Cheng-Te
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Sundberg, Per
    Morphological, vocal and genetic divergence in the Cettia acanthizoides complex (Aves: Cettiidae)2007Inngår i: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 149, nr 3, s. 437-452Artikkel i tidsskrift (Fagfellevurdert)
  • 5. Alström, Per
    et al.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Olsson, Urban
    Sundberg, Per
    Phylogeny and classification of the avian superfamily Sylvioidea.2006Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 38, nr 2, s. 381-97Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sylvioidea is one of the three superfamilies recognized within the largest avian radiation, the parvorder Passerida. In the present study, which is the first taxon-dense analysis of the Sylvioidea based on sequence data (nuclear myoglobin intron II and mitochondrial cytochrome b gene), we investigate the interrelationships among the four "sylvioid" clades found by previous workers, as well as the relationships within the largest of these clades. The nuclear and mitochondrial loci estimate basically the same phylogeny, with minor differences in resolution. The trees based on myoglobin and the combined data identify a strongly supported clade that includes the taxa previously allocated to Sylvioidea, except for Sitta (nuthatches), Certhia (treecreepers), Parus (tits), Remiz (penduline tits), Troglodytes and Campylorhynchus (wrens), Polioptila (gnatcatchers), and Regulus (crests/kinglets); this clade also comprises larks, which have previously been placed in the superfamily Passeroidea. We refer to this clade as Sylvioidea. This clade is further divided into 10 main, well-supported clades, which we suggest form the basis for a revised classification.

  • 6. Alström, Per
    et al.
    Fregin, Silke
    Norman, Janette A
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Christidis, Les
    Olsson, Urban
    Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae.2011Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 58, nr 3, s. 513-26Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    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.

  • 7. Alström, Per
    et al.
    Höhna, Sebastian
    Gelang, Magnus
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Olsson, Urban
    Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset.2011Inngår i: BMC evolutionary biology, ISSN 1471-2148, Vol. 11, s. 352-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    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.

  • 8. Batalha-Filho, Henrique
    et al.
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Fjeldså, Jon
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Silveira, Luis F
    Miyaki, Cristina Y
    Molecular systematics and evolution of the Synallaxis ruficapilla complex (Aves: Furnariidae) in the Atlantic Forest.2013Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 67, nr 1, s. 86-94Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Neotropical Synallaxis ruficapilla complex is endemic to the Atlantic Forest and is comprised of three species: S. ruficapilla, S. whitneyi, and S. infuscata. This group is closely related to the Synallaxis moesta complex that occurs in the Andes, Tepuis, and Guianan shield. Here we used mitochondrial and nuclear gene sequences to infer the phylogeny and the time of diversification of the S. ruficapilla and S. moesta complexes. We also included samples of an undescribed population of Synallaxis that resembles other populations of the S. ruficapilla complex. Our results showed that different geographical lineages within the S. ruficapilla complex are reciprocally monophyletic, but the northern form (S. infuscata) grouped with an Andean taxon. This suggests that at least two lineages of this group independently colonized the Atlantic Forest. Specimens of the undescribed population formed a monophyletic clade with deep divergence. Estimated diversification dates were within the late Pliocene to Pleistocene (2.75-0.16 million of years ago). This suggests that at this time there was a higher connectivity between habitats in the rugged landscapes of the circum-Amazonian bioregions. The observed Pleistocene diversification within the Atlantic Forest is congruent in space and time with studies of other co-distributed organisms, and may be associated with climate changes and tectonic activity during this period.

  • 9. Batalha-Filho, Henrique
    et al.
    Pessoa, Rodrigo O
    Fabre, Pierre-Henri
    Fjeldså, Jon
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Silveira, Luís F
    Miyaki, Cristina Y
    Phylogeny and historical biogeography of gnateaters (Passeriformes, Conopophagidae) in the South America forests.2014Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 79, s. 422-432Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We inferred the phylogenetic relationships, divergence time and biogeography of Conopophagidae (gnateaters) based on sequence data of mitochondrial genes (ND2, ND3 and cytb) and nuclear introns (TGFB2 and G3PDH) from 45 tissue samples (43 Conopophaga and 2 Pittasoma) representing all currently recognized species of the family and the majority of subspecies. Phylogenetic relationships were estimated by maximum likelihood and Bayesian inference. Divergence time estimates were obtained based on a Bayesian relaxed clock model. These chronograms were used to calculate diversification rates and reconstruct ancestral areas of the genus Conopophaga. The phylogenetic analyses support the reciprocal monophyly of the two genera, Conopophaga and Pittasoma. All species were monophyletic with the exception of C. lineata, as C. lineata cearae did not cluster with the other two C. lineata subspecies. Divergence time estimates for Conopophagidae suggested that diversification took place during the Neogene, and that the diversification rate within Conopophaga clade was highest in the late Miocene, followed by a slower diversification rate, suggesting a diversity-dependent pattern. Our analyses of the diversification of family Conopophagidae provided a scenario for evolution in Terra Firme forest across tropical South America. The spatio-temporal pattern suggests that Conopophaga originated in the Brazilian Shield and that a complex sequence of events possibly related to the Andean uplift and infilling of former sedimentation basins and erosion cycles shaped the current distribution and diversity of this genus.

  • 10.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Presentation of the 2010 Charles Schuchert Award of the Paleontological Society to Philip C. J. Donoghue.2011Inngår i: Journal of Paleontology, ISSN 0022-3360, E-ISSN 1937-2337, Journal of Paleontology, Vol. 85, nr 5, s. 1015-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    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.

  • 11.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Presentation of the 2010 Paleontological Society Medal to Bruce Runnegar.2011Inngår i: Journal of Paleontology, ISSN 0022-3360, E-ISSN 1937-2337, Journal of Paleontology, Vol. 85, nr 5, s. 1012-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    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!

  • 12.
    Bengtson, Stefan
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Rasmussen, Birger
    Curtin University.
    Ivarsson, Magnus
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Muhling, Janet
    Curtin University.
    Broman, Curt
    Stockholm University.
    Marone, Federica
    Stampanoni, Marco
    Bekker, Andrey
    University of California Riverside.
    Fungus-like mycelial fossils in 2.4-billion-year-old vesicular basalt.2017Inngår i: Nature Ecology & Evolution, ISSN 2397-334X, Vol. 1, nr 6, s. 1-6, artikkel-id 0141Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Fungi have recently been found to comprise a significant part of the deep biosphere in oceanic sediments and crustal rocks. Fossils occupying fractures and pores in Phanerozoic volcanics indicate that this habitat is at least 400 million years old, but its origin may be considerably older. A 2.4-billion-year-old basalt from the Palaeoproterozoic Ongeluk Formation in South Africa contains filamentous fossils in vesicles and fractures. The filaments form mycelium-like structures growing from a basal film attached to the internal rock surfaces. Filaments branch and anastomose, touch and entangle each other. They are indistinguishable from mycelial fossils found in similar deep-biosphere habitats in the Phanerozoic, where they are attributed to fungi on the basis of chemical and morphological similarities to living fungi. The Ongeluk fossils, however, are two to three times older than current age estimates of the fungal clade. Unless they represent an unknown branch of fungus-like organisms, the fossils imply that the fungal clade is considerably older than previously thought, and that fungal origin and early evolution may lie in the oceanic deep biosphere rather than on land. The Ongeluk discovery suggests that life has inhabited submarine volcanics for more than 2.4 billion years.

  • 13.
    Bengtson, Stefan
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Sallstedt, Therese
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Belivanova, Veneta
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Whitehouse, Martin
    Naturhistoriska riksmuseet, Enheten för geovetenskap.
    Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae2017Inngår i: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 15, nr 3, s. 1-38, artikkel-id e2000735Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as probable crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n. gen, n. sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and pit plugs. Another filamentous form, Denaricion mendax n. gen., n. sp., has coin-like cells reminiscent of those in large sulfur-oxidizing bacteria but much more recalcitrant than the liquid-vacuole-filled cells of the latter. There are also resemblances with oscillatoriacean cyanobacteria, although cell volumes in the latter are much smaller. The wider affinities of Denaricion are uncertain. Ramathallus lobatus n. gen., n. sp. is a lobate sessile alga with pseudoparenchymatous thallus, “cell fountains,” and apical growth, suggesting florideophycean affinity. If these inferences are correct, Rafatazmia and Ramathallus represent crown-group multicellular rhodophytes, antedating the oldest previously accepted red alga in the fossil record by about 400 million years.

  • 14.
    Bergsten, Johannes
    Naturhistoriska riksmuseet, Enheten för zoologi.
    A bee-fly's host, Facebook, and DNA Barcoding.2016Inngår i: Barcode Bulletin, Vol. 7, nr 2, s. 8-9Artikkel i tidsskrift (Annet (populærvitenskap, debatt, mm))
  • 15.
    Bergsten, Johannes
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Nilsson, Lars G R
    Bukontaite, Rasa
    Naturhistoriska riksmuseet, Enheten för zoologi. Stockholm University.
    Åkerjordfly, Agrotis exclamationis, identifierad som värdart för svävflugan Villa hottentotta med hjälp av DNA streckkodning (Diptera: Bombyliidae).2015Inngår i: Entomologisk Tidskrift, ISSN 0013-886X, Vol. 136, nr 4, s. 121-130Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this study we identify Agrotis exclamationis (Linnaeus, 1758) as a host species for the bee y Villa hottentotta (Linnaeus, 1758) in Sweden. Host use and speci city for bee y species are generally very poorly known, why the hatching of a bee y of the genus Villa from an unknown Noctuid pupa caught our attention. The parasitized Noctuid pupa was found in a garden in Staffanstorp, Skåne (Sweden), in May 2015 and kept in a jar to hatch. The bee y hatched in June leaving two empty exuviae in the jar. DNA was extracted sepa- rately from both excuviae to identify the y and the host using DNA Barcoding. A 600+ bp long sequence of the gene Cytochrome oxidase subunit 1 was sequenced for both samples and queried against the reference library BOLD (www.boldsystems.org). The Noctuid host pupa was unambiguously identi ed as the common Noctuid species Agrotis exclamationis. The sequence was identical to the most common haplotype over much of Europe. The bee y pupa was identi ed as Villa hottentotta, the most common Villa species in Sweden. This added a new Noctuid species to the list of known hosts for V. hottentotta which also includes several other Noctuid genera as well as a Geometrid moth. Belonging to the sand chamber group of bee ies where the female scatter the eggs on the ground while hovering, the active host-seeking rst instar planidium larvae bene ts from having a wide host range to potentially encounter in the substrate zone. 

  • 16.
    Bisang, Irene
    et al.
    Naturhistoriska riksmuseet, Enheten för botanik.
    Ehrlén, Johan
    Persson, Christin
    Hedenäs, Lars
    Naturhistoriska riksmuseet, Enheten för botanik.
    Family affiliation, sexratio and sporophyte frequency in unisexual mosses2014Inngår i: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 174, s. 163-172Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Patterns of sex expression and sex ratios are key features of the life histories of organisms. Bryophytes are the only haploid-dominant land plants. In contrast with seed plants, more than half of bryophyte species are dioecious, with rare sexual expression and sporophyte formation and a commonly female-biased sex ratio. We asked whether variation in sex expression, sex ratio and sporophyte frequency in ten dioecious pleurocarpous wetland mosses of two different families was best explained by assuming that character states  evolved: (1) in ancestors within the respective families or (2) at the species level as a response to recent habitat conditions. Lasso regression shrinkage identified relationships between family membership and sex ratio and sporophyte frequency, whereas environmental conditions were not correlated with any investigated reproductive trait. Sex ratio and sporophyte frequency were correlated with each other. Our results suggest that ancestry is more important than the current environment in explaining reproductive patterns at and above the species level in the studied wetland mosses, and that mechanisms controlling sex ratio and sporophyte frequency are phylogenetically conserved. Obviously, ancestry should be considered in the study of reproductive character state variation in plants.

  • 17.
    Bisang, Irene
    et al.
    Naturhistoriska riksmuseet, Enheten för botanik.
    Hedenäs, Lars
    Naturhistoriska riksmuseet, Enheten för botanik.
    Infraspecific sex ratio variation and its predictors in mosses – the case of the wetland moss Drepanocladus lycopodioides2015Inngår i: Botany 2015. Science and Plants for People. Abstracts. / [ed] Anonymous, 2015Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Sex ratio variation is a common but unexplained phenomenon of many species with chromosomal sex determination, including many bryophytes. Expressed sex ratio variation could be related to environmental conditions in a few mosses investigated to date. However, many bryophyte populations are non-fertile during their entire life cycle and intraspecific genetic sex ratio variation remains highly unexplored in natural populations. Drepanocladus lycopodioides, a pleurocarpous wetland moss with a distribution largely confined to Western Eurasia, rarely to occasionally forms sexual organs. It belongs to the majority of bryophytes that exhibits a female bias in expressed sex ratio. We applied a novel approach to sex individual shoots irrespective of their reproductive state using a specifically designed female-targeting molecular marker. We demonstrated that the bias in sex expression corresponds to a genetic female bias in the European adult population. Here, we investigated three regional populations of D. lycopodioides in its core distribution area. We asked whether haplotype diversity (H), sex expression (SE), genetic sex ratios, and sporophyte frequency varied within and among regions, whether these characteristics were related with each other, and / or to environmental parameters. Levels of H differed among regions and were positively related to habitat patch size. H was unequally partitioned between the sexes and was associated with estimated regional sporophyte frequency. Recorded plot-wise sporophyte frequency was generally very low in all regions. Overall genetic sex ratio was female-biased in all regions. Sex expression and genetic sex ratio varied strongly within regions (SE 0 –75%), with 27% of the plots lacking sex organs and 78% of the plots one-sexed, but differences among regions were non-significant. While no sex expression occurred in habitats deeper than 25cm, genetic sex ratio was not related to the measured environmental parameters.

  • 18.
    Bisang, Irene
    et al.
    Naturhistoriska riksmuseet, Enheten för botanik.
    Hedenäs, Lars
    Naturhistoriska riksmuseet, Enheten för botanik.
    Males Are Not Shy in the Wetland Moss Drepanocladus lycopodioides2013Inngår i: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 174, nr 5, s. 733-739Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Premise of research. Maintenance of dioecious and monoecious sexual systems at nearly equal frequencies, infrequent sexual expression, and distinctly female-skewed sex ratios among the dioecious species are reproductive characteristics of bryophytes, which are otherwise unusual among embryophytes. Most sex ratio assessments to date have relied on gametophytes forming sexual organs, and how these reflect genetic genders is largely unresolved.

    Methodology. For the European wetland moss Drepanocladus lycopodioides, we ask whether the adult expressed sex ratio is more strongly female biased than the “true” population sex ratio based on genetically male and female plants, i.e., whether males exhibit a lower sex expression rate than females (shy males). We assess expressed sex ratio on the basis of sex expression in individually scored herbarium specimens. We directly and on a large geographic scale assess nonexpressed sex ratio, for the second time in a moss, by sexing individual shoots from nonexpressing specimens using a molecular sex marker.

    Pivotal results. On the basis of the female and male frequencies in these two data sets and the overall proportion of expressing specimens, we estimate the European population sex ratio as 2.6 : 1 (female to male). All three sex ratios are significantly female skewed and do not significantly differ from each other, indicating that there is no gender difference in sex expression rates.

    Conclusions. These results and previous data for Drepanocladus trifarius show that males are not shy in the two wetland mosses of markedly different habitats.

  • 19.
    Bisang, Irene
    et al.
    Naturhistoriska riksmuseet, Enheten för botanik.
    Hedenäs, Lars
    Naturhistoriska riksmuseet, Enheten för botanik.
    Mass occurrence of springtails on a moss cushion – what are they doing?2015Inngår i: Melting Pot, Swedish Museum of Natural History, Abstracts: https://vega.nrm.se/vanstermenyn/forskningochsamlingar/meltingpot/2015.9654.html, 2015Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    The motile spermatozoids of bryophytes can swim up to a few centimetres. They require free water to fertilize the egg of the female organs, which sit on plants separate from the males in more than 50% of the species. When the sex organs are produced on different plants, this presents a serious obstacle to successful fertilization. The problems are overcome by a variety of mechanisms. Some of the more spectacular include spermatozoid transport up to at least several decimetres by water movement, by water drops spread from splash-cups surrounding the male organs up to two meters, by ejection up to15 centimetres into the air, or by having dwarf males that grow directly on the female plants. Here we report on another special kind of spermatozoid transfer that we came across during fieldwork in 2014, namely by micro-arthropods. Bryophyte fertilization mediated by animals was suggested more than a century ago, and was recently shown to occur in experimental settings. However, our observation is likely one of the first made directly in nature.

     

     

  • 20.
    Bukontaite, Rasa
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi. Stockholm University.
    Miller, Kelly
    University of New Mexico.
    Bergsten, Johannes
    Naturhistoriska riksmuseet, Enheten för zoologi.
    The utility of CAD in recovering Gondwanan vicariance events and the evolutionary history of Aciliini (Coleoptera: Dytiscidae).2014Inngår i: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 14, nr 5, s. 1-18Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background

    Aciliini presently includes 69 species of medium-sized water beetles distributed on all continents except Antarctica. The pattern of distribution with several genera confined to different continents of the Southern Hemisphere raises the yet untested hypothesis of a Gondwana vicariance origin. The monophyly of Aciliini has been questioned with regard to Eretini, and there are competing hypotheses about the intergeneric relationship in the tribe. This study is the first comprehensive phylogenetic analysis focused on the tribe Aciliini and it is based on eight gene fragments. The aims of the present study are: 1) to test the monophyly of Aciliini and clarify the position of the tribe Eretini and to resolve the relationship among genera within Aciliini, 2) to calibrate the divergence times within Aciliini and test different biogeographical scenarios, and 3) to evaluate the utility of the gene CAD for phylogenetic analysis in Dytiscidae.

    Results

    Our analyses confirm monophyly of Aciliini with Eretini as its sister group. Each of six genera which have multiple species are also supported as monophyletic. The origin of the tribe is firmly based in the Southern Hemisphere with the arrangement of Neotropical and Afrotropical taxa as the most basal clades suggesting a Gondwana vicariance origin. However, the uncertainty as to whether a fossil can be used as a stem-or crowngroup calibration point for Acilius influenced the result: as crowngroup calibration, the 95% HPD interval for the basal nodes included the geological age estimate for the Gondwana break-up, but as a stem group calibration the basal nodes were too young. Our study suggests CAD to be the most informative marker between 15 and 50 Ma. Notably, the 2000 bp CAD fragment analyzed alone fully resolved the tree with high support.

    Conclusions

    1) Molecular data confirmed Aciliini as a monophyletic group. 2) Bayesian optimizations of the biogeographical history are consistent with an influence of Gondwana break-up history, but were dependent on the calibration method. 3) The evaluation using a method of phylogenetic signal per base pair indicated Wnt and CAD as the most informative of our sampled genes.

  • 21. Cahill, James A
    et al.
    Stirling, Ian
    Kistler, Logan
    Salamzade, Rauf
    Ersmark, Erik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik. Stockholms Universitet.
    Fulton, Tara L
    Stiller, Mathias
    Green, Richard E
    Shapiro, Beth
    Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears.2015Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArtikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof, and Chichagof Islands (ABC Islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC Islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC Islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction. This article is protected by copyright. All rights reserved.

  • 22.
    Chris, Mays
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi. Monash University.
    Bevitt, Joseph
    Australian Nuclear Science and Technology Organisation, Research Office, Lucas Heights, Australia.
    Stilwell, Jeffrey
    School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria, Australia.
    Pushing the limits of neutron tomography in palaeontology: Three-dimensional modelling of in situ resin within fossil plants2017Inngår i: Palaeontologia Electronica, ISSN 1935-3952, E-ISSN 1094-8074, Vol. 20, nr 3, s. 1-12, artikkel-id 20.3.57AArtikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Computed tomography is an increasingly popular technique for the non-destructivestudy of fossils. Whilst the science of X-ray computed tomography (CT) has greatlymatured since its first fossil applications in the early 1980s, the applications and limitationsof neutron tomography (NT) remain relatively unexplored in palaeontology. Thesehighest resolution neutron tomographic scans in palaeontology to date were conductedon a specimen of Austrosequoia novae-zeelandiae (Ettingshausen) Mays and Cantrillrecovered from mid-Cretaceous (Cenomanian; ~100–94 Ma) strata of the ChathamIslands, eastern Zealandia. Previously, the species has been identified with in situ fossilresin (amber); the new neutron tomographic analyses demonstrated an anomalouslyhigh neutron attenuation signal for fossil resin. The resulting data provided astrong contrast between, and distinct three-dimensional representations of the: 1) fossilresin; 2) coalified plant matter; and 3) sedimentary matrix. These data facilitated ananatomical model of endogenous resin bodies within the cone axis and bract-scalecomplexes. The types and distributions of resin bodies support a close alliance withSequoia Endlicher (Cupressaceae), a group of conifers whose extant members areonly found in the Northern Hemisphere. This study demonstrates the feasibility of NTas a means to differentiate chemically distinct organic compounds within fossils.Herein, we make specific recommendations regarding: 1) the suitability of fossil preservationstyles for NT; 2) the conservation of organic specimens with hydrogenous consolidantsand adhesives; and 3) the application of emerging methods (e.g., neutronphase contrast) for further improvements when imaging fine-detailed anatomical structures.These findings demonstrate that we are still far from reaching the conceptuallimits of NT as a means of virtually extracting fossils, or imaging their internal anatomyeven when embedded within a rock matrix.

  • 23.
    Cunningham, John A.
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi. University of Bristol.
    Liu, Alexander G.
    University of Cambridge.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Donoghue, Philip C.J.
    University of Bristol.
    The origin of animals: Can molecular clocks and the fossil record be reconciled?2016Inngår i: Bioessays, ISSN 0265-9247, E-ISSN 1521-1878, Vol. 38, s. 1-12Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The evolutionary emergence of animals is one of the most significant episodes in the history of life, but its timing remains poorly constrained. Molecular clocks estimate that animals originated and began diversifying over 100 million years before the first definitive metazoan fossil evidence in the Cambrian. However, closer inspection reveals that clock estimates and the fossil record are less divergent than is often claimed. Modern clock analyses do not predict the presence of the crown-representatives of most animal phyla in the Neoproterozoic. Furthermore, despite challenges provided by incomplete preservation, a paucity of phylogenetically informative characters, and uncertain expectations of the anatomy of early animals, a number of Neoproterozoic fossils can reasonably be interpreted as metazoans. A considerable discrepancy remains, but much of this can be explained by the limited preservation potential of early metazoans and the difficulties associated with their identificationin the fossil record. Critical assessment of both recordsmay permitbetter resolutionof the tempo and mode of early animal evolution.

  • 24.
    Cunningham, John A.
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi. University of Bristol.
    Vargas, Kelly
    School of Earth Sciences, University of Bristol, Bristol.
    Yin, Zongjun
    State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Donoghue, Philip C.J.
    University of Bristol.
    The Weng’an Biota (Doushantuo Formation): an Ediacaran window on soft bodied and multicellular microorganisms.2017Inngår i: journal of the geological society, ISSN 2041-479X, Vol. 174, nr 5, s. 793-802Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Weng’an Biota is a fossil Konservat-Lagerstätte in South China that is approximately 570-600 million years old and provides an unparalleled snapshot of marine life during the interval in which molecular clocks estimate that animal clades were diversifying. It yields specimens that are three-dimensionally preserved in calcium phosphate with cellular and sometimes subcellular fidelity. The biota includes candidates for the oldest animals in the fossil record, including embryonic, larval and adult forms. We argue that, while the Weng’an Biota includes forms that could be animals, none can currently be assigned to this group with confidence. Nonetheless, the biota offers a rare and valuable window on the evolution of multicellular and soft-bodied organisms in the prelude to the Cambrian radiation.

  • 25.
    Cunningham, John
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Donoghue, Philip C.J.
    University of Bristol.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Distinguishing biology from geology in soft-tissue preservation.2014Inngår i: Reading and Writing of the Fossil Record: Preservational Pathways to Exceptional Fossilization / [ed] Marc Laflamme, James D. Schiffbauer, Simon A. F. Darroch, The Paleontological Society , 2014, s. 275-287Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    Knowledge of evolutionary history is based extensively on relatively rare fossils that preserve soft tissues. These fossils record a much greater proportion of anatomy than would be known solely from mineralized remains and provide key data for testing evolutionary hypotheses in deep time. Ironically, however, exceptionally preserved fossils are often among the most contentious because they are difficult to interpret. This is because their morphology has invariably been affected by the processes of decay and diagenesis, meaning that it is often difficult to distinguish preserved biology from artifacts introduced by these processes. Here we describe how a range of analytical techniques can be used to tease apart mineralization that preserves biological structures from unrelated geological mineralization phases. This approach involves using a series of X-ray, ion, electron and laser beam techniques to characterize the texture and chemistry of the different phases so that they can be differentiated in material that is difficult to interpret. This approach is demonstrated using a case study of its application to the study of fossils from the Ediacaran Doushantuo Biota.

  • 26.
    Cunningham, John
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Vargas, Kelly
    Liu, Pengju
    Belivanova, Veneta
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Marone, Federica
    Martínez-Pérez, Carlos
    Guizar-Sicairos, Manuel
    Holler, Mirko
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Donoghue, Philip C.J.
    Critical appraisal of tubular putative eumetazoans from the Ediacaran Weng’an Doushantuo biota2015Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, s. 1-9, artikkel-id 2151169Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecular clock analyses estimate that crown-group animals began diversifying hundreds of millions of years before the start of the Cambrian period. However, the fossil record has not yielded unequivocal evidence for animals during this interval. Some of the most promising candidates for Precambrian animals occur in theWeng’an biota of South China, including a suite of tubular fossils assigned to Sinocyclocyclicus, Ramitubus, Crassitubus and Quadratitubus, that have been interpreted as soft-bodied eumetazoans comparable to tabulate corals. Here, we present new insights into the anatomy, original composition and phylogenetic affinities of these taxa based on data from synchrotron radiation X-ray tomographic microscopy, ptychographic nanotomography, scanning electron microscopy and electron probe microanalysis. The patterns of deformation observed suggest that the cross walls of Sinocyclocyclicus and Quadratitubus were more rigid than those of Ramitubus and Crassitubus. Ramitubus and Crassitubus specimens preserve enigmatic cellular clusters at terminal positions in the tubes. Specimens of Sinocyclocyclicus and Ramitubus have biological features that might be cellular tissue or subcellular structures filling the spaces between the crosswalls. These observations are incompatible with a cnidarian interpretation, in which the spaces between cross walls are abandoned parts of the former living positions of the polyp. The affinity of the Weng’an tubular fossils may lie within the algae.

  • 27. Dalsätt, J
    et al.
    Zhou, Z
    Zhang, F
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Food remains in Confuciusornis sanctus suggest a fish diet.2006Inngår i: Die Naturwissenschaften, ISSN 0028-1042, E-ISSN 1432-1904, Vol. 93, nr 9, s. 444-6Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Despite hundreds of excellent fossils of Confuciusornis, the most abundant group of birds in the Early Cretaceous, 'Jehol Biota' in China, there is yet no indication of the food choice of these birds. Here, we describe fish remains preserved in the alimentary system of a specimen of Confuciusornis sanctus from the Jiufotang Formation. This find is about five million years younger than all previously published confuciusornithid birds from the Yixian Formation. Although it is unknown how common fish was in the diet of Confuciusornis, the find does not support previous hypotheses that it fed on plants or grain.

  • 28.
    Doguzhaeva, Larisa A.
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Weaver, Patricia G.
    North Carolina Museum of Natural Sciences.
    Ciampaglio, Charles N.
    Wright State University.
    A unique late Eocene coleoid cephalopod Mississaepia from Mississippi, USA: New data on cuttlebone structure, and their phylogenetic implications.2014Inngår i: Acta Palaeontologica Polonica, ISSN 0567-7920, E-ISSN 1732-2421, Vol. 59, nr 1, s. 147-162Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A new family, Mississaepiidae, from the Sepia–Spirula branch of decabrachian coleoids (Cephalopoda), is erected on the basis of the following, recently revealed, morphological, ultrastructural and chemical traits of the cuttlebone in the late Eocene Mississaepia, formerly referred to Belosaepiidae: (i) septa are semi−transparent, largely chitinous (as opposed to all other recorded cephalopods having non−transparent aragonitic septa); (ii) septa have a thin lamello−fibrillar nacreous covering (Sepia lacks nacre altogether, Spirula has fully lamello−fibrillar nacreous septa, ectochochleate cephalopods have columnar nacre in septa); (iii) a siphonal tube is present in early ontogeny (similar to siphonal tube development of the Danian Ceratisepia, and as opposed to complete lack of siphonal tube in Sepiaand siphonal tube development through its entire ontogeny in Spirula); (iv) the lamello−fibrillar nacreous ultrastructure of septal necks (similar to septal necks in Spirula); (v) a sub−hemispherical protoconch (as opposed to the spherical protoconchs of the Danian Ceratisepia and Recent Spirula); (vi) conotheca has ventro−lateral extension in early ontogenetic stages (as opposed to Sepia that has no ventro−lateral extention of the conotheca and to Spirula that retains fully−developed phragmocone throughout its entire ontogeny). Chitinous composition of septa in Mississaepia is deduced from (i) their visual similarity to the chitinous semi−transparent flange of Sepia, (ii) angular and rounded outlines and straight compressive failures of the partial septa and mural parts of septa similar to mechanically−damaged dry rigid chitinous flange of Sepia or a gladius of squid, and (iii) organics consistent with −chitin preserved in the shell. The family Mississaepiidae may represent a unknown lineage of the Sepia–Spirulabranch of coleoids, a conotheca lacking a nacreous layer being a common trait of the shell of this branch. However, Mississaepiidae is placed with reservation in Sepiida because of similarities between their gross shell morphology (a cuttlebone type of shell) and inorganic−organic composition. In Mississaepia, as in Sepia, the shell contains up to 6% of nitrogen by weight; phosphatised sheets within the dorsal shield may have been originally organic, like similar structures in Sepia; accumulations of pyrite in peripheral zones of aragonitic spherulites and in−between the spherulites of the dorsal shield may also indicate additional locations of organics in the shell of living animal.

  • 29.
    Doguzhaeva, Larisa A.
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Weis, Robert
    Musée national d’histoire naturelle, Luxembourg.
    Delsate, Dominique
    Musée national d’histoire naturelle, Luxembourg.
    Mariotti, Nino
    Università ‘La Sapienza’, Roma, Italy.
    Embryonic shell structure of Early–Middle Jurassic belemnites, and its significance for belemnite expansion and diversification in the Jurassic.2014Inngår i: Lethaia: an international journal of palaeontology and stratigraphy, ISSN 0024-1164, E-ISSN 1502-3931, Vol. 47, nr 1, s. 49-65Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Early Jurassic belemnites are of particular interest to the study of the evolution of skeletal morphology in Lower Carboniferous to the uppermost Cretaceous belemnoids, because they signal the beginning of a global Jurassic–Cretaceous expansion and diversification of belemnitids. We investigated potentially relevant, to this evolutionary pattern, shell features of Sinemurian–Bajocian Nannobelus, Parapassaloteuthis, Holcobelus and Pachybelemnopsis from the Paris Basin. Our analysis of morphological, ultrastructural and chemical traits of the earliest ontogenetic stages of the shell suggests that modified embryonic shell structure of Early–Middle Jurassic belemnites was a factor in their expansion and colonization of the pelagic zone and resulted in remarkable diversification of belemnites. Innovative traits of the embryonic shell of Sinemurian– Bajocian belemnites include: (1) an inorganic–organic primordial rostrum encapsulating the protoconch and the phragmocone, its non-biomineralized component, possibly chitin, is herein detected for the first time; (2) an organic rich closing membrane which was under formation. It was yet perforated and possessed a foramen; and (3) an organic rich pro-ostracum earlier documented in an embryonic shell of Pliensbachian Passaloteuthis. The inorganic–organic primordial rostrum tightly coating the protoconch and phragmocone supposedly enhanced protection, without increase in shell weight, of the Early Jurassic belemnites against explosion in deepwater environment. This may have increased the depth and temperature ranges of hatching eggs, accelerated the adaptation of hatchlings to a nektonic mode of life and promoted increasing diversity of belemnoids. This study supports the hypothesis that belemnite hatchlings were ‘a miniature of the adults’.

  • 30.
    Dong, Xi-ping
    et al.
    Peking University.
    Vargas, Kelly
    University of Bristol.
    Cunningham, John
    Naturhistoriska riksmuseet, Enheten för paleobiologi. University of Bristol.
    Zhang, Huaqiao
    Nanjing Institute of Geology and Palaeontology.
    Liu, Teng
    Peking University.
    Chen, Fang
    Peking University.
    Liu, Jianbo
    Peking University.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Donoghue, Philip C.J.
    Developmental biology of the early Cambrian cnidarian Olivooides.2016Inngår i: Palaeontology, ISSN 0031-0239, E-ISSN 1475-4983, Vol. 59, nr 3, s. 387-407Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Fossilized embryos afford direct insight into the pattern of development in extinct organisms, providing unique tests of hypotheses of developmental evolution based in comparative embryology. However, these fossils can only be effective in this role if their embryology and phylogenetic affinities are well constrained. We elucidate and interpret the development of Olivooides from embryonic and adult stages and use these data to discriminate among competing interpretations of their anatomy and affinity. The embryology of Olivooides is principally characterized by the development of an ornamented periderm that initially forms externally and is subsequently formed internally, released at the aperture, facilitating the direct development of the embryo into an adult theca. Internal anatomy is known only from embryonic stages, revealing two internal tissue layers, the innermost of which is developed into three transversally arranged walls that partly divide the lumen into an abapertural region, interpreted as the gut of a polyp, and an adapertural region that includes structures that resemble the peridermal teeth of coronate scyphozoans. The anatomy and pattern of development exhibited by Olivooides appears common to the other known genus of olivooid, Quadrapyrgites, which differs in its tetraradial, as opposed to pentaradial symmetry. We reject previous interpretations of the olivooids as cycloneuralians, principally on the grounds that they lack a through gut and introvert, in embryo and adult. Instead we consider the affinities of the olivooids among medusozoan cnidarians; our phylogenetic analysis supports their classification as totalgroup Coronata, within crown-Scyphozoa. Olivooides and Quadrapyrgites evidence a broader range of life history strategies and bodyplan symmetry than is otherwise commonly represented in extant Scyphozoa specifically, and Cnidaria more generally.

  • 31. Donoghue, Philip C.J.
    et al.
    Cunningham, John
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Dong, Xi-ping
    Peking University.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Embryology in deep time.2015Inngår i: Evolutionary Developmental Biology of Invertebrates 1 / [ed] Wanninger, Andreas, Wien: Springer Science+Business Media B.V., 2015, s. 45-63Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    For anyone who has cared for animal embryos, it beggars belief that these squishy cellular aggregates could be fossilised. Hence, with hindsight, it is possible to empathise with palaeontologists who found such fossils and, in their naming of Olivooides, Pseudooides, etc., drew attention to their likeness to animal eggs and embryos but without going so far as to propose such an interpretation. However, in 1994, Zhang Xi-guang and Brian Pratt described microscopic balls of calcium phosphate from Cambrian rocks of China, one or two of which preserved polygonal borders that resembled blastomeres on the surface of an early cleaving animal embryo. In retrospect, these fossils are far from remarkable, some of them may not be fossils at all, and it is not as if anyone ever conceived Cambrian animals as having lacked an embryology. But Zhang Xi-guang and Brian Pratt dared the scientific world, not least their fellow palaeontologists, to believe that the fragile embryonic stages of invertebrate animals could be fossilised, that there was a fossil record of animal embryology, that this record hailed from the interval of time in which animal body plans were first established, and that it had been awaiting discovery in the rocks, for want of looking. The proof of this concept came a few years later, when phosphatised Cambrian fossils from China and Siberia were shown to display indisputable features of animal embryonic morphologies. In the case of Olivooides, a series of developmental stages from cleavage to morphogenesis through hatching and juvenile growth could be tentatively identified; in Markuelia, the coiled-up body of an annulated worm-like animal could be clearly seen within its fertilisation envelope.

  • 32. Drovetski, Sergei V.
    et al.
    Zink, Robert M.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Fadeev, Igor V.
    A multilocus study of pine grosbeak phylogeography supports the pattern of greater intercontinental divergence in Holarctic boreal forest birds than in birds inhabiting other high-latitude habitats2010Inngår i: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 37, nr 4, s. 696-706Artikkel i tidsskrift (Fagfellevurdert)
  • 33.
    Dussex, Nicolas
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world’s most diverse penguin clade2018Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513Artikkel i tidsskrift (Fagfellevurdert)
  • 34.
    Dussex, Nicolas
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species2018Inngår i: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, nr 17Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Next- generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the populationstructure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS methodGenotyping-By- Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily ex -ploited by the 19th century commercial sealing industry and has since rapidly recolonized most of its former range from a few isolated colonies. Using 26,026 neutral single nucleotide polymorphisms (SNPs), we assessed genetic variationwithin and between NZFS colonies. We identified low levels of population differen-tiation across the species range (<1% of variation explained by regional differences)suggesting a state of near panmixia. Nonetheless, we observed subtle populationsubstructure between West Coast and Southern East Coast colonies and a weak, but significant (p = 0.01), isolation- by- distance pattern among the eight coloniesstudied. Furthermore, our demographic reconstructions supported severe bottle -necks with potential 10-fold and 250- fold declines in response to Polynesian and European hunting, respectively. Finally, we were able to assign individuals treatedas unknowns to their regions of origin with high confidence (96%) using our SNP data. Our results indicate that while it may be difficult to detect population structure in species that have experienced rapid recovery, next-generation markers and methods are powerful tools for resolving fine-scale structure and informing conservation and management efforts. 

  • 35. Ekman, Jan
    et al.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Out of Gondwanaland; the evolutionary history of cooperative breeding and social behaviour among crows, magpies, jays and allies.2006Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 273, nr 1590, s. 1117-25Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cooperative breeding is comparatively rare among birds in the mainly temperate and boreal Northern Hemisphere. Here we test if the distribution of breeding systems reflects a response to latitude by means of a phylogenetic analysis using correlates with geographical range among the corvids (crows, jays, magpies and allied groups). The corvids trace their ancestry to the predominantly cooperative 'Corvida' branch of oscine passerines from the Australo-Papuan region on the ancient Gondwanaland supercontinent, but we could not confirm the ancestral state of the breeding system within the family, while family cohesion may be ancestral. Initial diversification among pair-breeding taxa that are basal in the corvid phylogeny, represented by genera such as Pyrrhocorax and Dendrocitta, indicates that the corvid family in its current form could have evolved from pair-breeding ancestors only after they had escaped the Australo-Papuan shield. Within the family, cooperative breeding (alloparental care/family cohesion) is strongly correlated to latitude and its predominance in species maintaining a southerly distribution indicates a secondary evolution of cooperative breeding in the lineage leading away from the basal corvids. Multiple transitions show plasticity in the breeding system, indicating a response to latitude rather than evolutionary inertia. The evolutionary background to the loss of cooperative breeding among species with a northerly distribution is complex and differs between species, indicating a response to a variety of selection forces. Family cohesion where the offspring provide alloparental care is a main route to cooperatively breeding groups among corvids. Some corvid species lost only alloparental care, while maintaining coherent family groups. Other species lost family cohesion and, as a corollary, they also lost the behaviour where retained offspring provide alloparental care.

  • 36.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Current perspectives on the evolution of birds2008Inngår i: Contributions to zoology, ISSN 1383-4517, E-ISSN 1875-9866, Vol. 77, nr 2, s. 109-116Artikkel i tidsskrift (Fagfellevurdert)
  • 37.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Evolution of terrestrial birds in three continents: biogeography and parallel radiations2012Inngår i: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 39, nr 5, s. 813-824Artikkel i tidsskrift (Fagfellevurdert)
  • 38.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Anderson, Caisa Lisa
    Mayr, Gerald
    Hangin' on to our rocks 'n clocks: a reply to Brown et al2007Inngår i: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 3, nr 3, s. 260-261Artikkel i tidsskrift (Annet vitenskapelig)
  • 39.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Anderson, Cajsa L
    Britton, Tom
    Elzanowski, Andrzej
    Johansson, Ulf S
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Källersjö, Mari
    Ohlson, Jan I
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Parsons, Thomas J
    Zuccon, Dario
    Mayr, Gerald
    Diversification of Neoaves: integration of molecular sequence data and fossils.2006Inngår i: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, nr 4, s. 543-7Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.

  • 40.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Christidis, Les
    Cooper, Alan
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Jackson, Jennifer
    Johansson, Ulf S
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Norman, Janette A
    A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens.2002Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 269, nr 1488, s. 235-41Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Zoogeographic, palaeontological and biochemical data support a Southern Hemisphere origin for passerine birds, while accumulating molecular data suggest that most extant avian orders originated in the mid-Late Cretaceous. We obtained DNA sequence data from the nuclear c-myc and RAG-1 genes of the major passerine groups and here we demonstrate that the endemic New Zealand wrens (Acanthisittidae) are the sister taxon to all other extant passerines, supporting a Gondwanan origin and early radiation of passerines. We propose that (i) the acanthisittids were isolated when New Zealand separated from Gondwana (ca. 82-85 Myr ago), (ii) suboscines, in turn, were derived from an ancestral lineage that inhabited western Gondwana, and (iii) the ancestors of the oscines (songbirds) were subsequently isolated by the separation of Australia from Antarctica. The later spread of passerines into the Northern Hemisphere reflects the northward migration of these former Gondwanan elements.

  • 41.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Christidis, Les
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Norman, Janette A
    Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds.2002Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 25, nr 1, s. 53-62Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phylogenetic relationships of the lyrebirds are investigated using DNA sequence data. The aligned data matrix consists of 4027 bp obtained from three nuclear genes (c-myc, RAG-1 and myoglobin intron II) and two mitochondrial genes (cytochrome b and ND2). Both maximum-likelihood and parsimony analyses show that the lyrebirds unambiguously belong to the oscine radiation, and that they are the sister taxon to all other oscines. The results do not support the suggestion based on DNA-DNA hybridization data (Sibley and Ahlquist, 1990) that the treecreepers and bowerbirds are part of the lyrebird clade. Nevertheless, treecreepers and bowerbirds are sister taxa to all other oscines (except the lyrebirds) and may constitute a monophyletic group, although bootstrap support values for this clade are low. A major disagreement between the present analysis and that based on DNA-DNA hybridization data is that the Corvida (sensu Sibley and Ahlquist, 1990) and Passerida are not reciprocally monophyletic, as we find the latter group be nested within the Corvida. Also, the superfamilies Meliphagoidea and Corvoidea sensu, are not recovered as monophyletic in the present study. Within the oscine radiation, all taxa belonging to the earliest splits are confined to the Australo-Papuan region. This suggests strongly that the origins and early radiation of the oscines occurred in the southern supercontinent Gondwana. A new classification of the major groups of passerines is presented following from the results presented in the present study, as well as those published recently on analyses of sequence data from the nuclear c-myc and RAG-1 genes (Ericson et al., 2002; Irestedt et al., 2001).

  • 42.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Envall, Ida
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Norman, Janette A
    Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data.2003Inngår i: BMC evolutionary biology, ISSN 1471-2148, Vol. 3, s. 16-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    BACKGROUND: Phylogenetic hypotheses of higher-level relationships in the order Charadriiformes based on morphological data, partly disagree with those based on DNA-DNA hybridisation data. So far, these relationships have not been tested by analysis of DNA sequence data. Herein we utilize 1692 bp of aligned, nuclear DNA sequences obtained from 23 charadriiform species, representing 15 families. We also test earlier suggestions that bustards and sandgrouses may be nested with the charadriiforms. The data is analysed with methods based on the parsimony and maximum-likelihood criteria.

    RESULTS: Several novel phylogenetic relationships were recovered and strongly supported by the data, regardless of which method of analysis was employed. These include placing the gulls and allied groups as a sistergroup to the sandpiper-like birds, and not to the plover-like birds. The auks clearly belong to the clade with the gulls and allies, and are not basal to most other charadriiform birds as suggested in analyses of morphological data. Pluvialis, which has been supposed to belong to the plover family (Charadriidae), represents a basal branch that constitutes the sister taxon to a clade with plovers, oystercatchers and avocets. The thick-knees and sheathbills unexpectedly cluster together.

    CONCLUSION: The DNA sequence data contains a strong phylogenetic signal that results in a well-resolved phylogenetic tree with many strongly supported internodes. Taxonomically it is the most inclusive study of shorebird families that relies on nucleotide sequences. The presented phylogenetic hypothesis provides a solid framework for analyses of macroevolution of ecological, morphological and behavioural adaptations observed within the order Charadriiformes.

  • 43.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Johansson, Ulf S
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Evolution, biogeography, and patterns of diversification in passerine birds2003Inngår i: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 34, nr 1, s. 3-15Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper summarizes and discusses the many new insights into passerine evolution gained from an increased general interest in avian evolution among biologists, and particularly from the extensive use of DNA sequence data in phylogenetic reconstruction. The sister group relationship between the New Zealand rifleman and all other passerines, indicates the importance of the former southern supercontinent Gondwana in the earliest evolution of this group. Following the break-up of Gondwana, the ancestors of other major passerine groups became isolated in Australia (oscines), South America (New World suboscines), and possibly, the then connected Kerguelen Plateau/India/Madagascar tectonic plates (Old World suboscines). The oscines underwent a significant radiation in the Australo-Papuan region and only a few oscine lineages have spread further than to the nearby Southeast Asia. A remarkable exception is the ancestor to the vast Passerida radiation, which now comprises 35% of all bird species. This group obviously benefitted greatly from the increased diversity in plant seed size and morphology during the Tertiary. The lyrebirds (and possibly scrub-birds) constitute the sister group to all other oscines, which renders “Corvida” (sensu Sibley and Ahlquist 1990) paraphyletic. Sequence data suggests that Passerida, the other clade of oscines postulated based on the results of DNA–DNA hybridizations, is monophyletic, and that the rockfowl and rock-jumpers are the most basal members of this clade. The suboscines in the Old World (Eurylamides) and the New World (Tyrannides), respectively, are sister groups. A provisional, working classification of the passerines is presented based on the increased understanding of the major patterns of passerine evolution.

  • 44.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Jansén, Anna-Lee
    Stockholms universitet.
    Johansson, Ulf S
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Ekman, Jan
    Uppsala universitet.
    Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data2005Inngår i: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 36, nr 3, s. 222-234Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phylogenetic relationships were studied based on DNA sequences obtained from all recognized genera of the family Corvidae sensu stricto. The aligned data set consists 2589 bp obtained from one mitochondrial and two nuclear genes. Maximum parsimony, maximum-likelihood, and Bayesian inference analyses were used to estimate phylogenetic relationships. The analyses were done for each gene separately, as well as for all genes combined. An analysis of a taxonomically expanded data set of cytochrome b sequences was performed in order to infer the phylogenetic positions of six genera for which nuclear genes could not be obtained. Monophyly of the Corvidae is supported by all analyses, as well as by the occurrence of a deletion of 16 bp in the β-fibrinogen intron in all ingroup taxa. Temnurus and Pyrrhocorax are placed as the sister group to all other corvids, while Cissa and Urocissa appear as the next clade inside them. Further up in the tree, two larger and well-supported clades of genera were recovered by the analyses. One has an entirely New World distribution (the New World jays), while the other includes mostly Eurasian (and one African) taxa. Outside these two major clades are Cyanopica and Perisoreus whose phylogenetic positions could not be determined by the present data. A biogeographic analysis of our data suggests that the Corvidae underwent an initial radiation in Southeast Asia. This is consistent with the observation that almost all basal clades in the phylogenetic tree consist of species adapted to tropical and subtropical forest habitats.

  • 45.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Johansson, Ulf S
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data.2003Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 29, nr 1, s. 126-38Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Passerida is a monophyletic group of oscine passerines that includes almost 3500 species (about 36%) of all bird species in the world. The current understanding of higher-level relationships within Passerida is based on DNA-DNA hybridizations [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Our results are based on analyses of 3130 aligned nucleotide sequence data obtained from 48 ingroup and 13 outgroup genera. Three nuclear genes were sequenced: c-myc (498-510 bp), RAG-1 (930 bp), and myoglobin (693-722 bp), as well one mitochondrial gene; cytochrome b (879 bp). The data were analysed by parsimony, maximum-likelihood, and Bayesian inference. The African rockfowl and rockjumper are found to constitute the deepest branch within Passerida, but relationships among the other taxa are poorly resolved--only four major clades receive statistical support. One clade corresponds to Passeroidea of [C.G. Sibley, B.L. Monroe, Distribution and Taxonomy of Birds of the World, 1990, Yale University Press, New Haven, CT] and includes, e.g., flowerpeckers, sunbirds, accentors, weavers, estrilds, wagtails, finches, and sparrows. Starlings, mockingbirds, thrushes, Old World flycatchers, and dippers also group together in a clade corresponding to Muscicapoidea of Sibley and Monroe [op. cit.]. Monophyly of their Sylvioidea could not be corroborated--these taxa falls either into a clade with wrens, gnatcatchers, and nuthatches, or one with, e.g., warblers, bulbuls, babblers, and white-eyes. The tits, penduline tits, and waxwings belong to Passerida but have no close relatives among the taxa studied herein.

  • 46.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Klopfstein, Seraina
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Nguyen, Jacqueline MT
    Nylander, Johan A A
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Dating the diversification of the major lineages of Passeriformes (Aves)2014Inngår i: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 14, nr 8, s. 1-15Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% ofall living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the lateCretaceous. However, previous molecular dating studies have relied heavily on the geological split between NewZealand and Antarctica, assumed to have occurred 85–82 Mya, for calibrating the molecular clock and might thusbe circular in their argument.Results: This study provides a time-scale for the evolution of the major clades of passerines using seven nuclearmarkers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealandsplit from Antarctica 85–52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretationsof the New Zealand–Antarctica vicariance event influence our age estimates. Our results suggest that thediversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration forthe New Zealand–Antarctica vicariance event (85–52 Mya) dramatically increases the 95% credibility intervals andleads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genesanalyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines,which can be used as secondary calibration points in future molecular studies.Conclusions: Our analysis takes recent paleontological and geological findings into account and provides the bestestimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporalframework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, andadds to the growing support for a Cretaceous origin of Passeriformes.

  • 47.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Olson, Storrs L.
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Alvarenga, Herculano
    Fjeldsa, Jon
    Circumscription of a monophyletic family for the tapaculos (Aves: Rhinocryptidae)2010Inngår i: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 151, nr 2, s. 337-345Artikkel i tidsskrift (Fagfellevurdert)
  • 48.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Tyrberg, T.
    Kjellberg, A. S.
    Jonsson, L.
    Ullen, I.
    The earliest record of house sparrows (Passer domesticus) in northern Europe1997Inngår i: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 24, nr 2, s. 183-190Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Remains of the house sparrow (Passer domesticus) recovered from a late Bronze Age (1200-800 sc) settlement in central Sweden are described. The house sparrow is conspicuously rare in prehistoric Europe, and this record constitutes the earliest from the northern part. The find predates the introduction of domestic fowl (Gallus gallus) to Sweden, a species with which the house sparrow has been assumed to be spread simultaneously. Instead, it is here suggested that house sparrows most likely spread over Europe along with the horse Equus caballus. (C) 1997 Academic Press Limited

  • 49.
    Ericson, Per G P
    et al.
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Zuccon, Dario
    Ohlson, Jan I
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Johansson, Ulf S
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Alvarenga, Herculano
    Prum, Richard O
    Higher-level phylogeny and morphological evolution of tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannida).2006Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 40, nr 2, s. 471-83Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Despite increased understanding of higher-level relationships in passerine birds in the last 15 years, the taxonomic boundaries and phylogenetic interrelationships of the major groups of the Tyrannida (including the cotingas, manakins, tityrines, and tyrant flycatchers) remain unclear. Here, we present an analysis of DNA sequence data obtained from two nuclear exons, three introns, and one mitochondrial gene for 26 genera of Tyrannida and 6 tracheophone outgroups. The analysis resulted in well-supported hypotheses about the earliest evolution within Tyrannida. The Cotingidae, Pipridae, Tityrinae (sensu) [Prum, R.O., Rice, N.H., Mobley, J.A., Dimmick, W.W., 2000. A preliminary phylogenetic hypothesis for the cotingas (Cotingidae) based on mitochondrial DNA. Auk 117, 236-241], Tyrannidae, and the tyrannid subfamiles Tyranninae and Pipromorphinae (sensu) [Sibley, C.G., Monroe, B. L. Jr., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT] were all found to be reciprocally monophyletic (given the present taxon sampling). The Cotingidae and Pipridae form a clade that is the sister group to a well-supported clade including Oxyruncus, the Tityrinae, Piprites, and the Tyrannidae. Oxyruncus is the sister group to the Tityrinae, and Piprites is placed as the sister group to the Tyrannidae. The tyrannid subfamilies Tyranninae and Pipromorphinae are monophyletic sister taxa, but the relationships of Platyrinchus mystaceus to these two clades remains ambiguous. The presence of medial (=internal) cartilages in the syrinx is a synapomorphy for the Oxyruncus-Tityrinae-Piprites-Tyrannidae clade. Although morphological synapomorphies currently support the monophyly of both the Pipridae and the Cotingidae, convergences and/or reversals in morphological character states are common in Tyrannida. The relationship between Oxyruncus and the Tityrinae is congruent with additional syringeal synapomorphies and allozyme distance data. Accordingly, we propose the recognition the family Tityridae within the Tyrannida to include the genera Schiffornis, Laniisoma, Laniocera, Iodopleura, Xenopsaris, Pachyramphus, Tityra, and Oxyruncus.

  • 50. Ewen, John G
    et al.
    Flux, Ian
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Systematic affinities of two enigmatic New Zealand passerines of high conservation priority, the hihi or stitchbird Notiomystis cincta and the kokako Callaeas cinerea.2006Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 40, nr 1, s. 281-4Artikkel i tidsskrift (Fagfellevurdert)
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