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  • 251.
    Butler, Aodhán D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Garwood, Russell
    The University of Manchester, School of Earth Atmospheric and Environmental Sciences.
    Streng, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Lowe, Tristan
    The Manchester X-Ray Imaging Facility, School of Materials, The University of Manchester.
    Holmer, Lars E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    X-ray microtomography of the tommotiid Micrina reveals cellular and ultrastructural preservation, confirming a tommotiid stem-linguliform affinityManuscript (preprint) (Other academic)
  • 252.
    Butler, Aodhán D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Streng, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Holmer, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Babcock, Loren
    Lund.
    Exceptionally-preserved Mickwitzia from the Indian Springs Lagerstätte.In: Journal of Paleontology, ISSN 0022-3360, E-ISSN 1937-2337Article in journal (Other academic)
    Abstract [en]

    A new assemblage of the early Cambrian stem group brachiopod Mickwitzia is described from the Indian Springs Lagerstätte possessing exceptionally preserved mantle setae. Critical analysis of shell structure and mantle setae from these specimens with those from additional sites with variable diagenetic history reveals the extent of taphonomic alteration and further sheds light on the phylogenetic position of the mickwitziids. A morphometric approach to shell outline and growth landmarks within these specimens reveals a clear species level discriminant signal of Nevada Mickwitzia in comparison to M. monlifera from Sweden. Detailed electron micrographs allow revision of the genus diagnosis for Mickwitzia based on presence of inward pointing phosphatic cones and tangential setae bearing tubes. We also conclude the inward pointing cone structures are not consistent with setal bearing structures as previously thought, but rather represent an endopunctae-like structure. A tommotiid-like shell architecture and presence of acrotretid columns in the dorsal juvenile shell of M. cf. occidens further strengthens the proposed close relationship between stem-group brachiopods and tommotiids.

  • 253.
    Bäckström, Disa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Exploring the diversity and evolution of giant viruses in deep sea sediments using genome-resolved metagenomics2018Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Viruses are the most abundant biological entities on this planet, which is impressive considering that they are completely dependent on their hosts for reproduction. Recently the idea of what viruses are has changed dramatically, with the discovery of giant viruses that belong to the Nucleocytoplasmic Large DNA Viruses (NCLDV), such as Mimiviridae, Marseilleviridae, and the proposed families Pandoraviruses, and Pithoviruses. Not only are some of these viruses as large as bacteria in size, their genomes also exceed the size of some prokaryotic genomes. The evolutionary path to viral giganticism is not yet fully understood, and several opposing theories have been proposed. The more examples of giant viruses we have to study, the clearer the picture becomes. The rate of discovery, however, is limited by the low capacity of culturing. In an effort to contribute through culture-independent methods, I used genome-resolved metagenomics to retrieve genomes of 23 new members of the NCLDV from deep sea sediment samples that were taken near Loki’s Castle hydrothermal vent field. This method has previously been used to study uncultured Bacteria and Archaea, but few successful cases of metagenomic binning of NCLDV have been documented. New methods for refinement and quality control of the binned genomes were developed, combining reads profiling with differential coverage binning, and composition-based cleaning of potentially contaminating sequences. The binned genomes represent several novel clades of NCLDV, the most noteworthy ones distantly related to Pithoviruses and Marseilleviridae, and greatly expand their overall diversity. Phylogenetic analysis of their genome content supports the independent evolution of viral giganticism from smaller viruses. Continued use of metagenomics to explore the presence of NCLDV in environmental samples will lead to new insights into their diversity, evolution, and biology.

    List of papers
    1. Novel virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism
    Open this publication in new window or tab >>Novel virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism
    Show others...
    (English)In: Article in journal (Refereed) Submitted
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-362611 (URN)
    Available from: 2018-10-11 Created: 2018-10-11 Last updated: 2018-10-14Bibliographically approved
  • 254.
    Bäckström, Disa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Yutin, Natalya
    Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD, USA.
    Jorgensen, Steffen L.
    Univ Bergen, Ctr Geobiol, Dept Biol, Bergen, Norway.
    Dharamshi, Jennah
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Homa, Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zaremba-Niedzwiedzka, Katarzyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Royal Netherlands Inst Sea Res, NIOZ, Dept Marine Microbiol & Biogeochem, Yerseke, Netherlands; Univ Utrecht, Den Burg, Netherlands.
    Wolf, Yuri I.
    Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD, USA.
    Koonin, Eugene V.
    Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD, USA.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism2019In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 2, article id e02497-18Article in journal (Refereed)
    Abstract [en]

    The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, “Megavirales”) include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki’s Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki’s Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae. Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.

    Importance: Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.

  • 255.
    Bäckström, Disa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Yutin, Natalya
    National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA.
    Jørgensen, Steffen L.
    Department of Biology, Centre for Geobiology, University of Bergen, N -5020 Bergen, Norway.
    Dharamshi, Jennah
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Homa, Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zaremba-Niedzwiedzka, Katarzyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wolf, Yuri I.
    National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA.
    Koonin, Eugene V.
    National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Novel virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantismIn: Article in journal (Refereed)
  • 256.
    Campbell, Charles
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The effects of winter stress on Sphagnum specieswith contrasting macro- and microdistributions2019In: Journal of Bryology, ISSN 0373-6687, E-ISSN 1743-2820, Vol. 41, no 3, p. 205-217Article in journal (Refereed)
    Abstract [en]

    Introduction: Sphagnum L. forms much of the ground cover in northern peatlands. Different species show affinities for bioclimatic regions in Europe (oceanic/continental; northern/southern) and species-specific tolerance of winter conditions can be a factor explaining their distribution.

    Methods: We focussed on low temperature in a series of experiments and tested (1) the innate ability of a selection of Sphagnum species to tolerate low temperature in relation to their micro-topographic (wetness) and geographical (climate) distribution; (2) the rate of cold tolerance acquisition; and (3) the ability of species to survive a range of low temperature once cold hardened.

    Key results: Our experiments showed that maximal PSII efficiency (Fv/Fm, chlorophyll fluorescence), growth rates and survival were all negatively affected by sub-zero temperatures. Environmental conditions associated with the onset of winter (colder nights and shorter days) triggered the acquisition of cold tolerance in Sphagnum.

    Conclusions: The results were not unequivocal, but species associated with colder climates were generally more tolerant of sub-zero conditions. Species associated with the wettest and driest ends of the wetness gradient were more consistent in their responses than those in between, with wetter-dwelling species being less sensitive to sub-zero temperature than species found in drier microhabitats. Overall, our results suggest that adaptation to winter conditions contribute to the current distribution patterns of Sphagnum species.

     

  • 257. Campbell-Staton, Shane C
    et al.
    Goodman, Rachel M
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Edwards, Scott V
    Losos, Jonathan B
    Kolbe, Jason J
    Out of Florida: mtDNA reveals patterns of migration and Pleistocene range expansion of the Green Anole lizard (Anolis carolinensis).2012In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 2, no 9Article in journal (Refereed)
    Abstract [en]

    Anolis carolinensis is an emerging model species and the sole member of its genus native to the United States. Considerable morphological and physiological variation has been described in the species, and the recent sequencing of its genome makes it an attractive system for studies of genome variation. To inform future studies of molecular and phenotypic variation within A. carolinensis, a rigorous account of intraspecific population structure and relatedness is needed. Here, we present the most extensive phylogeographic study of this species to date. Phylogenetic analyses of mitochondrial DNA sequence data support the previous hypothesis of a western Cuban origin of the species. We found five well-supported, geographically distinct mitochondrial haplotype clades throughout the southeastern United States. Most Florida populations fall into one of three divergent clades, whereas the vast majority of populations outside Florida belong to a single, shallowly diverged clade. Genetic boundaries do not correspond to major rivers, but may reflect effects of Pleistocene glaciation events and the Appalachian Mountains on migration and expansion of the species. Phylogeographic signal should be examined using nuclear loci to complement these findings.

  • 258.
    Campione, Nicolas E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Postcranial Anatomy of Edmontosaurus regalis (Hadrosauridae) from the Horseshoe Canyon Formation, Alberta, Canada2014In: Hadrosaurs: Proceedings of the International Hadrosaur Symposium / [ed] David A. Ebert, David C. Evans, Indiana University Press, 2014, p. 208-244Chapter in book (Refereed)
  • 259.
    Campione, Nicolas E.
    et al.
    Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
    Brink, Kirstin S.
    University of Toronto.
    Freedman, Elizabeth A.
    Montana State University.
    McGarrity, Christopher T.
    University of Toronto.
    Evans, David C,
    Royal Ontario Museum.
    Glishades ericksoni’, an indeterminate juvenile hadrosaurid from the Two Medicine Formation of Montana: implications for hadrosauroid diversity in the latest Cretaceous (Campanian-Maastrichtian) of western North America2013In: Palaeobiodiversity and Palaeoenvironments, ISSN 1867-1594, Vol. 93, no 1, p. 65-75Article in journal (Refereed)
    Abstract [en]

    Glishades ericksoni was named on the basis of partial paired premaxillae collected from the Late Campanian Two Medicine Formation of Montana, and was described as a non-hadrosaurid hadrosauroid. This interpretation of G. ericksoni has significant implications for hadrosauroid diversity and distribution because it represents the first occurrence of a non-hadrosaurid hadrosauroid in the Late Campanian of North America, and therefore implies either a prolonged period of sympatry between these forms and hadrosaurids or a biotic interchange with Asia. Given its small size, and therefore potential juvenile status, the taxonomic identity of G. ericksoni is re-evaluated here. Comparison with similarly-sized, taxonomically determinate, and coeval hadrosaurid specimens from the Two Medicine Formation (ProsaurolophusGryposaurus, andMaiasaura) suggest that the combination of characters used to distinguish G. ericksoni as a non-hadrosaurid hadrosauroid are more widely distributed or individually variable in hadrosaurids, or can be explained as the result of ontogenetic variation. In particular, the unique combination of characters used to diagnose G. ericksoni is also found in juvenile individuals of Prosaurolophus,Gryposaurus, and Maiasaura. Inclusion of juveniles of these taxa, scored on the basis of comparable anatomy, in the original phylogenetic analysis recovers the juvenile hadrosaurid specimens outside Hadrosauridae. Consequently, G. ericksoni cannot be confidently differentiated from a juvenile saurolophine, which are common in the upper and middle sections of the Two Medicine Formation, and is thus considered a nomen dubium. Given their absence in well-sampled Late Campanian and Maastrichtian deposits, non-hadrosaurid hadrosauroids appear to have been completely replaced by hadrosaurids in western North America by the Late Campanian.

  • 260. Campione, Nicolas E.
    et al.
    Evans, David C.
    Royal Ontario Museum.
    A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods2012In: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 10, p. 60-Article in journal (Refereed)
    Abstract [en]

    Background

    Body size is intimately related to the physiology and ecology of an organism. Therefore, accurate and consistent body mass estimates are essential for inferring numerous aspects of paleobiology in extinct taxa, and investigating large-scale evolutionary and ecological patterns in the history of life. Scaling relationships between skeletal measurements and body mass in birds and mammals are commonly used to predict body mass in extinct members of these crown clades, but the applicability of these models for predicting mass in more distantly related stem taxa, such as non-avian dinosaurs and non-mammalian synapsids, has been criticized on biomechanical grounds. Here we test the major criticisms of scaling methods for estimating body mass using an extensive dataset of mammalian and non-avian reptilian species derived from individual skeletons with live weights.

    Results

    Significant differences in the limb scaling of mammals and reptiles are noted in comparisons of limb proportions and limb length to body mass. Remarkably, however, the relationship between proximal (stylopodial) limb bone circumference and body mass is highly conserved in extant terrestrial mammals and reptiles, in spite of their disparate limb postures, gaits, and phylogenetic histories. As a result, we are able to conclusively reject the main criticisms of scaling methods that question the applicability of a universal scaling equation for estimating body mass in distantly related taxa.

    Conclusions

    The conserved nature of the relationship between stylopodial circumference and body mass suggests that the minimum diaphyseal circumference of the major weight-bearing bones is only weakly influenced by the varied forces exerted on the limbs (that is, compression or torsion) and most strongly related to the mass of the animal. Our results, therefore, provide a much-needed, robust, phylogenetically corrected framework for accurate and consistent estimation of body mass in extinct terrestrial quadrupeds, which is important for a wide range of paleobiological studies (including growth rates, metabolism, and energetics) and meta-analyses of body size evolution.

  • 261.
    Campione, Nicolas E.
    et al.
    Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
    Evans, David C.
    Royal Ontario Museum.
    Cranial Growth and Variation in Edmontosaurs (Dinosauria: Hadrosauridae): Implications for Latest Cretaceous Megaherbivore Diversity in North America2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 9, p. e25186-Article in journal (Refereed)
    Abstract [en]

    The well-sampled Late Cretaceous fossil record of North America remains the only high-resolution dataset for evaluating patterns of dinosaur diversity leading up to the terminal Cretaceous extinction event. Hadrosaurine hadrosaurids (Dinosauria: Ornithopoda) closely related to Edmontosaurus are among the most common megaherbivores in latest Campanian and Maastrichtian deposits of western North America. However, interpretations of edmontosaur species richness and biostratigraphy have been in constant flux for almost three decades, although the clade is generally thought to have undergone a radiation in the late Maastrichtian. We address the issue of edmontosaur diversity for the first time using rigorous morphometric analyses of virtually all known complete edmontosaur skulls. Results suggest only two valid species, Edmontosaurus regalis from the late Campanian, and E. annectens from the late Maastrichtian, with previously named taxa, including the controversial Anatotitan copei, erected on hypothesized transitional morphologies associated with ontogenetic size increase and allometric growth. A revision of North American hadrosaurid taxa suggests a decrease in both hadrosaurid diversity and disparity from the early to late Maastrichtian, a pattern likely also present in ceratopsid dinosaurs. A decline in the disparity of dominant megaherbivores in the latest Maastrichtian interval supports the hypothesis that dinosaur diversity decreased immediately preceding the end Cretaceous extinction event.

  • 262.
    Campione, Nicolas E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Evans, David C.
    Brown, Caleb M.
    Carrano, Matthew T.
    Body mass estimation in non-avian bipeds using a theoretical conversion to quadruped stylopodial proportions2014In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 5, no 9, p. 913-923Article in journal (Refereed)
    Abstract [en]

    Body mass is strongly related to both physiological and ecological properties of living organisms. As a result, generating robust, broadly applicable models for estimating body mass in the fossil record provides the opportunity to reconstruct palaeobiology and investigate evolutionary ecology on a large temporal scale. A recent study provided strong evidence that the minimum circumference of stylopodial elements (humerus and femur) is conservatively associated with body mass in living quadrupeds. Unfortunately, this model is not directly applicable to extinct bipeds, such as non-avian dinosaurs. This study presents a new equation that mathematically corrects the quadruped equation for use in bipeds. It is derived from the systemic difference in the circumference-to-area scaling relationship of two circles (hypothetical quadruped) and one circle (hypothetical biped), which represent the cross-section of the main weight-bearing limb bones. When applied to a newly constructed data set of femoral circumferences and body masses in living birds, the new equation reveals errors that are significantly lower than other published equations, but significantly higher than the error inherent in the avian data set. Such errors, however, are expected given the unique overall femoral circumference-body mass scaling relationship found in birds. Body mass estimates for a sample of bipedal dinosaurs using the new model are consistent with recent estimates based on volumetric life reconstructions, but, in contrast, this equation is simpler to use, with the concomitant potential to provide a wider set of body mass estimates for extinct bipeds. Although it is evident that no one estimation model is flawless, the combined use of the corrected quadrupedal equations and the previously published quadrupedal equation offer a consistent approach with which to estimate body masses in both quadrupeds and bipeds. These models have implications for conducting large-scale macroevolutionary analyses of body size throughout the evolutionary history of terrestrial vertebrates, and, in particular, across major changes in body plan, such as the evolution of bipedality in archosaurs and quadrupedality in dinosaurs.

  • 263.
    Campione, Nicolas E.
    et al.
    Carleton University , Ottawa , Canada.
    Holmes, Robert
    University of Alberta.
    The anatomy and homologies of the ceratopsid syncervical2006In: Journal of Vertebrate Paleontology, ISSN 0272-4634, E-ISSN 1937-2809, Vol. 26, no 4, p. 1014-1017Article in journal (Refereed)
  • 264.
    Campione, Nicolas E.
    et al.
    University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, Canada.
    Reisz, Robert R.
    University of Toronto Mississauga.
    Morphology and evolutionary significance of the atlas-axis complex in varanopid synapsids2011In: Acta Palaeontologica Polonica, ISSN 0567-7920, E-ISSN 1732-2421, Vol. 56, no 4, p. 739-748Article in journal (Refereed)
    Abstract [en]

    The atlas−axis complex has been described in few Palaeozoic taxa, with little effort being placed on examining variation of this structure within a small clade. Most varanopids, members of a clade of gracile synapsid predators, have well preserved atlas−axes permitting detailed descriptions and examination of morphological variation. This study indicates that the size of the transverse processes on the axis and the shape of the axial neural spine vary among members of this clade. In particular, the small mycterosaurine varanopids possess small transverse processes that point posteroventrally, and the axial spine is dorsoventrally short, with a flattened dorsal margin in lateral view. The larger varanodontine varanopids have large transverse processes with a broad base, and a much taller axial spine with a rounded dorsal margin in lateral view. Based on outgroup comparisons, the morphology exhibited by the transverse processes is interpreted as derived in varanodontines, whereas the morphology of the axial spine is derived in mycterosaurines. The axial spine anatomy of Middle Permian South African varanopids is reviewed and our interpretation is consistent with the hypothesis that at least two varanopid taxa are present in South Africa, a region overwhelmingly dominated by therapsid synapsids and parareptiles.

  • 265.
    Campione, Nicolas E.
    et al.
    University of Toronto at Mississauga, Mississauga, Ontario, Canada.
    Reisz, Robert R.
    University of Toronto Mississauga.
    Varanops brevirostris (Eupelycosauria: Varanopidae) from the Lower Permian of Texas, with discussion of varanopid morphology and interrelationships2010In: Journal of Vertebrate Paleontology, ISSN 0272-4634, E-ISSN 1937-2809, Vol. 30, no 3, p. 724-746Article in journal (Refereed)
    Abstract [en]

    A comprehensive revision of Varanops brevirostris on the basis of a large, well-preserved specimen from a new Lower Permian locality in Texas provides valuable new anatomical information and additional autapomorphies for this varanopid synapsid taxon. These include the loss of the postorbital boss, the presence of a smooth transition between the dorsal and lateral surfaces of the postorbital, hypertrophied basipterygoid processes, the presence of deep, elongate lateral neural spine excavations, posterior dorsal vertebrae with dorsally tapered neural spines, and a deep groove proximal to the femoral fourth trochanter. Furthermore, this specimen is the first fully developed adult specimen of Varanops, and it preserves the most complete lower jaw of the taxon. A revised phylogenetic analysis places V. brevirostris as the sister taxon to the Varanodon-Watongia clade. A stratocladistic analysis assessing varanopid relationships by incorporating a stratigraphic character into the analysis recovers the same topology among varanodontines, but an alternate topology between mycterosaurines and Elliotsmithia longiceps.

  • 266.
    Camus, M. Florencia
    et al.
    Monash Univ, Sch Biol Sci, Clayton, Vic 3800, Australia..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Morrow, Edward H.
    Univ Sussex, Sch Life Sci, Brighton BN1 9QG, E Sussex, England..
    Dowling, Damian K.
    Monash Univ, Sch Biol Sci, Clayton, Vic 3800, Australia..
    Single Nucleotides in the mtDNA Sequence Modify Mitochondrial Molecular Function and Are Associated with Sex-Specific Effects on Fertility and Aging2015In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 25, no 20, p. 2717-2722Article in journal (Refereed)
    Abstract [en]

    Mitochondria underpin energy conversion in eukaryotes. Their small genomes have been the subject of increasing attention, and there is evidence that mitochondrial genetic variation can affect evolutionary trajectories and shape the expression of life-history traits considered to be key human health indicators [1, 2]. However, it is not understood how genetic variation across a diminutive genome, which in most species harbors only about a dozen protein-coding genes, can exert broad-scale effects on the organisnnal phenotype [2, 3]. Such effects are particularly puzzling given that the mitochondrial genes involved are under strong evolutionary constraint and that mitochondrial gene expression is highly conserved across diverse taxa [4]. We used replicated genetic lines in the fruit fly, Drosophila melanogaster, each characterized by a distinct and naturally occurring mitochondrial haplotype placed alongside an isogenic nuclear background. We demonstrate that sequence variation within the mitochondria! DNA (mtDNA) affects both the copy number of mitochondrial genomes and patterns of gene expression across key mitochondrial protein-coding genes. In several cases, haplotype-mediated patterns of gene expression were gene-specific, even for genes from within the same transcriptional units. This invokes post-transcriptional processing of RNA in the regulation of mitochondrial genetic effects on organismal phenotypes. Notably, the haplotype-mediated effects on gene expression could be traced backward to the level of individual nucleotides and forward to sex-specific effects on fertility and longevity. Our study thus elucidates how small-scale sequence changes in the mitochondrial genome can achieve broad-scale regulation of health-related phenotypes and even contribute to sex-related differences in longevity.

  • 267. Cao, Jun
    et al.
    Schneeberger, Korbinian
    Ossowski, Stephan
    Günther, Torsten
    Bender, Sebastian
    Fitz, Joffrey
    Koenig, Daniel
    Lanz, Christa
    Stegle, Oliver
    Lippert, Christoph
    Wang, Xi
    Ott, Felix
    Müller, Jonas
    Alonso-Blanco, Carlos
    Borgwardt, Karsten
    Schmid, Karl J
    Weigel, Detlef
    Whole-genome sequencing of multiple Arabidopsis thaliana populations.2011In: Nature genetics, ISSN 1546-1718, Vol. 43, no 10, p. 956-63Article in journal (Refereed)
    Abstract [en]

    The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations.

  • 268.
    Carreira, Bruno M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Lisbon, cE3c, Fac Ciencias, Bloco C2, P-1749016 Lisbon, Portugal;Univ South Bohemia, Fac Sci, Dept Ecosyst Biol & Soil & Water Res Infrastruct, Branisovska 1760, Ceske Budejovice 37005, Czech Republic.
    Segurado, Pedro
    Univ Lisbon, Ctr Estudos Florestais, Inst Super Agron, P-1349017 Lisbon, Portugal.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rebelo, Rui
    Univ Lisbon, cE3c, Fac Ciencias, Bloco C2, P-1749016 Lisbon, Portugal.
    Heat waves trigger swift changes in the diet and life-history of a freshwater snail2020In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 847, no 4, p. 999-1011Article in journal (Refereed)
    Abstract [en]

    Extreme climatic events, such as heat waves, may induce changes in nutrient acquisition by omnivorous ectotherms. Likely modulated by the intensity, frequency and duration of these events, dietary shifts during heat waves may threaten the stability of freshwaters. We investigated the effects of heat wave duration on diet assimilation and life-history traits of the freshwater gastropod Radix balthica. We compared the magnitude of the effects of a short (1 week) and a long heat wave (7 weeks) on the assimilation of animal- and plant-based diets, measuring performance in terms of growth rate and reproduction. We hypothesized that heat waves should increase the proportion of plant material assimilated on the mixed diet and change the performance of snails on the animal and plant-based diets. Both heat waves increased the assimilation of plant material on the mixed diet and growth rate, with minor negative effects on reproduction. However, responses were disproportional to heat wave duration, as the short heat wave elicited swift and relatively stronger responses. Our findings showcase the role of phenotypic plasticity in aiding ectotherms to cope with increased thermal stress and acclimate. Temporarily changing the strength of trophic interactions, heat waves may alter community dynamics in freshwater habitats.

  • 269.
    Carter, Mauricio J.
    et al.
    Universidad de Chile, Centro Nacional del Medio Ambiente; Universidad Andres Bello, Facultad de Ecología y Recursos Naturales, Departamento de Ecología.
    Lind, Martin I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Dennis, Stuart R.
    Eawag, Department of Aquatic Ecology.
    Hentley, William
    University of Sheffield, Department of Animal and Plant Sciences.
    Beckerman, Andrew P.
    University of Sheffield, Department of Animal and Plant Sciences.
    Evolution of a predator-induced, nonlinear reaction norm2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1861, article id 20170859Article in journal (Refereed)
    Abstract [en]

    Inducible, anti-predator traits are a classic example of phenotypic plasticity. Their evolutionary dynamics depend on their genetic basis, the historical pattern of predation risk that populations have experienced and current selection gradients. When populations experience predators with contrasting hunting strategies and size preferences, theory suggests contrasting micro-evolutionary responses to selection. Daphnia pulex is an ideal species to explore the microevolutionary response of anti-predator traits because they face heterogeneous predation regimes, sometimes experiencing only invertebrate midge predators and other times experiencing vertebrate fish and invertebrate midge predators. We explored plausible patterns of adaptive evolution of a predator-induced morphological reaction norm. We combined estimates of selection gradients that characterize the various habitats that D. pulex experiences with detail on the quantitative genetic architecture of inducible morphological defences. Our data reveal a fine scale description of daphnid defensive reaction norms, and a strong covariance between the sensitivity to cues and the maximum response to cues. By analysing the response of the reaction norm to plausible, predator-specific selection gradients, we show how in the context of this covariance, micro-evolution may be more uniform than predicted from size-selective predation theory. Our results show how covariance between the sensitivity to cues and the maximum response to cues for morphological defence can shape the evolutionary trajectory of predator-induced defences in D. pulex.

  • 270.
    Caruso, Christina M.
    et al.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada.
    Eisen, Katherine E.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada; Cornell Univ, Dept Ecol & Evolutionary Biol, Ithaca, NY, USA.
    Martin, Ryan A.
    Case Western Reserve Univ, Dept Biol, Cleveland, OH, USA.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    A meta-analysis of the agents of selection on floral traits2019In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 73, no 1, p. 4-14Article in journal (Refereed)
    Abstract [en]

    Floral traits are hypothesized to evolve primarily in response to selection by pollinators. However, selection can also be mediated by other environmental factors. To understand the relative importance of pollinator-mediated selection and its variation among trait and pollinator types, we analyzed directional selection gradients on floral traits from experiments that manipulated the environment to identify agents of selection. Pollinator-mediated selection was stronger than selection by other biotic factors (e.g., herbivores), but similar in strength to selection by abiotic factors (e.g., soil water), providing partial support for the hypothesis that floral traits evolve primarily in response to pollinators. Pollinator-mediated selection was stronger on pollination efficiency traits than on other trait types, as expected if efficiency traits affect fitness via interactions with pollinators, but other trait types also affect fitness via other environmental factors. In addition to varying among trait types, pollinator-mediated selection varied among pollinator taxa: selection was stronger when bees, long-tongued flies, or birds were the primary visitors than when the primary visitors were Lepidoptera or multiple animal taxa. Finally, reducing pollinator access to flowers had a relatively small effect on selection on floral traits, suggesting that anthropogenic declines in pollinator populations would initially have modest effects on floral evolution.

  • 271.
    Caruso, Christina M.
    et al.
    Univ Guelph, Dept Integrat Biol..
    Martin, Ryan A.
    Case Western Reserve Univ, Dept Biol..
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Morrissey, Michael B.
    Univ St Andrews, Sch Biol..
    Wade, Michael J.
    Indiana Univ, Dept Biol..
    Augustine, Kate E.
    Univ N Carolina, Dept Biol..
    Carlson, Stephanie M.
    Univ Calif Berkeley, Dept Environm Sci Policy & Management..
    MacColl, Andrew D. C.
    Univ Nottingham, Sch Life Sci..
    Siepielski, Adam M.
    Univ Arkansas, Dept Biol Sci..
    Kingsolver, Joel G.
    Univ N Carolina, Dept Biol..
    What Are the Environmental Determinants of Phenotypic Selection?: A Meta-analysis of Experimental Studies2017In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 190, no 3, p. 363-376Article in journal (Refereed)
    Abstract [en]

    Although many selection estimates have been published, the environmental factors that cause selection to vary in space and time have rarely been identified. One way to identify these factors is by experimentally manipulating the environment and measuring selection in each treatment. We compiled and analyzed selection estimates from experimental studies. First, we tested whether the effect of manipulating the environment on selection gradients depends on taxon, trait type, or fitness component. We found that the effect of manipulating the environment was larger when selection was measured on life-history traits or via survival. Second, we tested two predictions about the environmental factors that cause variation in selection. We found support for the prediction that variation in selection is more likely to be caused by environmental factors that have a large effect on mean fitness but not for the prediction that variation is more likely to be caused by biotic factors. Third, we compared selection gradients from experimental and observational studies. We found that selection varied more among treatments in experimental studies than among spatial and temporal replicates in observational studies, suggesting that experimental studies can detect relationships between environmental factors and selection that would not be apparent in observational studies.

  • 272. Casewell, Nicholas R
    et al.
    Petras, Daniel
    Card, Daren C
    Suranse, Vivek
    Mychajliw, Alexis M
    Richards, David
    Koludarov, Ivan
    Albulescu, Laura-Oana
    Slagboom, Julien
    Hempel, Benjamin-Florian
    Ngum, Neville M
    Kennerley, Rosalind J
    Brocca, Jorge L
    Whiteley, Gareth
    Harrison, Robert A
    Bolton, Fiona M S
    Debono, Jordan
    Vonk, Freek J
    Alföldi, Jessica
    Johnson, Jeremy
    Karlsson, Elinor K
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
    Mellor, Ian R
    Süssmuth, Roderich D
    Fry, Bryan G
    Kuruppu, Sanjaya
    Hodgson, Wayne C
    Kool, Jeroen
    Castoe, Todd A
    Barnes, Ian
    Sunagar, Kartik
    Undheim, Eivind A B
    Turvey, Samuel T
    Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals.2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 51, p. 25745-25755Article in journal (Refereed)
    Abstract [en]

    Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions.

  • 273.
    Catalan, Ana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, D-82152 Planegg Martinsried, Germany.
    Briscoe, Adriana D.
    Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92697 USA.
    Hohna, Sebastian
    Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, D-82152 Planegg Martinsried, Germany;Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92697 USA;Ludwig Maximilians Univ Munchen, Dept Earth & Environm Sci Paleontol & Geobiol, D-80333 Munich, Germany;Ludwig Maximilians Univ Munchen, GeoBio Ctr, D-80333 Munich, Germany.
    Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Heliconius Butterflies2019In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 213, no 2, p. 581-594Article in journal (Refereed)
    Abstract [en]

    Investigating gene expression evolution over micro- and macroevolutionary timescales will expand our understanding of the role of gene expression in adaptation and speciation. In this study, we characterized the evolutionary forces acting on gene expression levels in eye and brain tissue of five Heliconius butterflies with divergence times of similar to 5-12 MYA. We developed and applied Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to identify genes whose expression levels are evolving through drift, stabilizing selection, or a lineage-specific shift. We found that 81% of the genes evolve under genetic drift. When testing for branch-specific shifts in gene expression, we detected 368 (16%) shift events. Genes showing a shift toward upregulation have significantly lower gene expression variance than those genes showing a shift leading toward downregulation. We hypothesize that directional selection is acting in shifts causing upregulation, since transcription is costly. We further uncovered through simulations that parameter estimation of OU models is biased when using small phylogenies and only becomes reliable with phylogenies having >= 50 taxa. Therefore, we developed a new statistical test based on BM to identify highly conserved genes (i.e., evolving under strong stabilizing selection), which comprised 3% of the orthoclusters. In conclusion, we found that drift is the dominant evolutionary force driving gene expression evolution in eye and brain tissue in Heliconius. Nevertheless, the higher proportion of genes evolving under directional than under stabilizing selection might reflect species-specific selective pressures on vision and the brain that are necessary to fulfill species-specific requirements. Characterization of gene expression patterns across species - and the evolutionary forces driving them - can reveal processes that have remained conserved across species, as well as those that have changed in a species- specific manner...

  • 274.
    Cauchard, Laure
    et al.
    Univ Montreal, Dept Sci Biol, Montreal, PQ, Canada.
    Angers, Bernard
    Univ Montreal, Dept Sci Biol, Montreal, PQ, Canada.
    Boogert, Neeltje J.
    Univ Exeter, Ctr Ecol & Conservat, Penryn, England.
    Lenarth, Melissa
    Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland.
    Bize, Pierre
    Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland;Univ Aberdeen, Inst Biol & Environm Sci, Aberdeen, Scotland.
    Doligez, Blandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Lyon 1, Dept Biometry & Evolutionary Biol, CNRS, Villeurbanne, France.
    An Experimental Test of a Causal Link between Problem-Solving Performance and Reproductive Success in Wild Great Tits2017In: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 5, article id 107Article in journal (Refereed)
    Abstract [en]

    Recent studies have uncovered relationships between measures of various cognitive performances and proxies of fitness such as reproductive success in non-human animals. However, to better understand the evolution of cognition in the wild, we still have to determine the causality of these relationships and the underlying mechanisms. The cognitive ability of an individual may directly influence its ability to raise many and/or high quality young through for example its provisioning ability. Conversely, large and/or high quality broods may lead to high parental motivation to solve problems related to their care. To answer this question, we manipulated reproductive success through brood size and measured subsequent problem-solving performance in wild great tit parents. Our results show that brood size manipulation did not affect the probability to solve the task. Moreover, solver pairs fledged more young than non-solver pairs independently of brood size treatment in one of the two experimental years and they showed higher nestling provisioning rate in both years. Overall, it shows that problem-solving performance was not driven by motivation and suggest that problem-solvers may achieve higher fledging success through higher provisioning rates. Our study constitutes a first key step toward a mechanistic understanding of the consequences of innovation ability for individual fitness in the wild.

  • 275.
    Cenci, Ugo
    et al.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.
    Sibbald, Shannon J.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.
    Curtis, Bruce A.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.
    Kamikawa, Ryoma
    Kyoto Univ, Grad Sch Human & Environm Studies, Kyoto, Kyoto 6068501, Japan.
    Eme, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.
    Moog, Daniel
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada;Philipps Univ Marburg, Cell Biol Lab, Karl von Frisch Str 8, D-35043 Marburg, Germany.
    Henrissat, Bernard
    Univ Aix Marseille, CNRS, AFMB, 163 Ave Luminy, F-13288 Marseille, France;INRA, USC AFMB 1408, F-13288 Marseille, France;King Abdulaziz Univ, Dept Biol Sci, Jeddah 21589, Saudi Arabia.
    Marechal, Eric
    Univ Grenoble Alpes, Lab Physiol Cellulaire & Vegetale, CNRS, CEA,INRA,Inst Biosci & Biotechnol Grenoble,CEA Gr, 17 Rue Martyrs, F-38000 Grenoble, France.
    Chabi, Malika
    Univ Lille 1, UMR 8576, Unite Glycobiol Struct & Fonct, F-59650 Villeneuve Dascq, France.
    Djemiel, Christophe
    Univ Lille 1, UMR 8576, Unite Glycobiol Struct & Fonct, F-59650 Villeneuve Dascq, France.
    Roger, Andrew J.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada;Canadian Inst Adv Res, Program Integrated Microbial Biodivers, Toronto, ON, Canada.
    Kim, Eunsoo
    Amer Museum Nat Hist, Div Invertebrate Zool, Cent Pk West & 79 St, New York, NY 10024 USA;Amer Museum Nat Hist, Sackler Inst Comparat Genom, Cent Pk West & 79 St, New York, NY 10024 USA.
    Archibald, John M.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada;Canadian Inst Adv Res, Program Integrated Microbial Biodivers, Toronto, ON, Canada.
    Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids2018In: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 16, article id 137Article in journal (Refereed)
    Abstract [en]

    Background: The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cyanobacterium (primary endosymbiosis) or indirectly by engulfing a photosynthetic eukaryote (secondary or tertiary endosymbiosis). The timing and frequency of secondary endosymbiosis during eukaryotic evolution is currently unclear but may be resolved in part by studying cryptomonads, a group of single-celled eukaryotes comprised of both photosynthetic and non-photosynthetic species. While cryptomonads such as Guillardia theta harbor a red algal-derived plastid of secondary endosymbiotic origin, members of the sister group Goniomonadea lack plastids. Here, we present the genome of Goniomonas avonlea-the first for any goniomonad-to address whether Goniomonadea are ancestrally non-photosynthetic or whether they lost a plastid secondarily. Results: We sequenced the nuclear and mitochondrial genomes of Goniomonas avonlea and carried out a comparative analysis of Go. avonlea, Gu. theta, and other cryptomonads. The Go. avonlea genome assembly is similar to 92 Mbp in size, with 33,470 predicted protein-coding genes. Interestingly, some metabolic pathways (e.g., fatty acid biosynthesis) predicted to occur in the plastid and periplastidal compartment of Gu. theta appear to operate in the cytoplasm of Go. avonlea, suggesting that metabolic redundancies were generated during the course of secondary plastid integration. Other cytosolic pathways found in Go. avonlea are not found in Gu. theta, suggesting secondary loss in Gu. theta and other plastid-bearing cryptomonads. Phylogenetic analyses revealed no evidence for algal endosymbiont-derived genes in the Go. avonlea genome. Phylogenomic analyses point to a specific relationship between Cryptista (to which cryptomonads belong) and Archaeplastida. Conclusion: We found no convincing genomic or phylogenomic evidence that Go. avonlea evolved from a secondary red algal plastid-bearing ancestor, consistent with goniomonads being ancestrally non-photosynthetic eukaryotes. The Go. avonlea genome sheds light on the physiology of heterotrophic cryptomonads and serves as an important reference point for studying the metabolic "rewiring" that took place during secondary plastid integration in the ancestor of modern-day Cryptophyceae.

  • 276. Chapman, T
    et al.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Bangham, J
    Rowe, L
    Response to Eberhard and Cordero, and Cordoba-Aguilar and Contreras-Garduno: sexual conflict and female choice2003In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 18, no 9, p. 440-441Article in journal (Refereed)
  • 277. Chapman, T
    et al.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Bangham, J
    Rowe, L
    Sexual conflict2003In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 18, no 1, p. 41-47, article id PII S0169-5347(02)00004-6Article in journal (Refereed)
  • 278.
    Chapron, Guillaume
    et al.
    Swedish University of Agricultural Sciences, Department of Ecology, Grimsö Wildlife Research Station, Riddarhyttan, Sweden.
    Epstein, Yaffa
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Law, Department of Law.
    Trouwborst, Arie
    Tilburg University, Department of European and International Law, Tilburg, The Netherlands.
    Vicente López-Bao, José
    Oviedo University, Research Unit of Biodiversity (UO/CSIC/PA), Mieres, Spain.
    Bolster Legal Boundaries to Stay within Planetary Boundaries2017In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 1, no 3, article id UNSP 0086Article in journal (Refereed)
    Abstract [en]

    The mounting threats posed to the global environment by harmful human activities cannot be averted without effective legislation controlling those activities. However, the environmental laws designed for this purpose are themselves under global attack. Because it is binding and enforceable, legislation is a unique and essential instrument in the overall effort to keep humanity’s impacts on the planet from transgressing critical thresholds. For instance, biodiversity laws do so by designating and protecting natural areas and controlling the exploitation of wildlife populations. Yet, due to short-term economic and other interests, such laws face constant pressures aimed at weakening their regulating impact on human activities. 

    This new study reveals and illustrates the staggering number and diversity of tactics used to weaken biodiversity legislation across the globe. This ‘taxonomy of tactics’ encompasses dozens of categories, ranging from the creative re-definition of terms to the ‘fast-tracking’ of environmentally harmful projects, and from limiting concerned citizens’ access to court, to the silent or even express refusal of appointed authorities to enforce biodiversity laws.

    Whereas the predicament of the planet’s wild fauna and flora would have been even worse without the legal protection they have received so far, the onslaught against biodiversity laws has prevented these from fully performing their assigned function. The global acceleration of wildlife population declines bears witness to this. To stem the tide, strategic approaches are needed to anticipate and counter attacks on biodiversity legislation; to make the most of existing laws, including in court if need be; and to develop new or improved laws where necessary.

  • 279.
    Chapurlat, Elodie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Evolutionary Ecology of Floral Traits in Fragrant Orchids2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Why are flowers so diverse? Much of floral evolution is thought to be driven by pollinator-mediated selection. However, the connection between macroevolutionary patterns of floral diversity and microevolutionary processes remains poorly understood. In this thesis, I have used the fragrant orchids Gymnadenia conopsea s.s. and Gymnadenia densiflora to investigate the role of pollinators as agents of selection on floral traits and to test whether they cause spatial variation in selection. I addressed the following questions (1) Is there divergent selection on flowering phenology and floral traits between these two closely related species? (2) What is the contribution of pollinators relative to other selective agents to selection on phenology, visual display, floral scent and spur length? (3) Do diurnal and nocturnal pollinators mediate different selection patterns? (4) Does spatial variation in pollinator communities cause spatial variation in selection?

    A phenotypic selection study in G. conopsea s.s. and G. densiflora indicated that divergent selection on flowering time contributes to the maintenance of phenological differentiation between the two species. Hand-pollination experiments combined with selection analysis showed that while pollinators were the main selective agent on spur length, their contribution to selection on phenology, visual display and floral scent was more variable and sometimes opposed by non-pollinator mediated selection. Selection analyses combined with a selective exclusion experiment showed that diurnal and nocturnal pollinators exerted different selection patterns on floral traits. Hand-pollination experiments also demonstrated that variation in pollinator-mediated selection largely explained spatial variation in net selection on phenology, visual display and spur length among four populations. A study of floral scent emission of G. conopsea s.s. in the field coupled with a growth-chamber experiment revealed genetically-based variation in floral scent consistent with a scenario where spatial variation in relative importance of nocturnal and diurnal pollinators has resulted in the evolution of different scent emission rhythms.

    Taken together, the results support the hypothesis that pollinators cause spatial variation in selection on floral traits. They also highlight the importance of experimentally identifying sources of selection to reveal conflicting and reinforcing selection by multiple agents and thus advance our understanding of the evolutionary ecology of floral traits.

    List of papers
    1. Divergent selection on flowering phenology but not on floral morphology between two closely related orchids
    Open this publication in new window or tab >>Divergent selection on flowering phenology but not on floral morphology between two closely related orchids
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-358245 (URN)
    Available from: 2018-08-26 Created: 2018-08-26 Last updated: 2018-08-26
    2. Spatial variation in pollinator-mediated selection on phenology, floral display and spur length in the orchid Gymnadenia conopsea
    Open this publication in new window or tab >>Spatial variation in pollinator-mediated selection on phenology, floral display and spur length in the orchid Gymnadenia conopsea
    2015 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, no 4, p. 1264-1275Article in journal (Refereed) Published
    Abstract [en]

    Spatial variation in plant-pollinator interactions may cause variation in pollinator-mediated selection on floral traits, but to establish this link conclusively experimental studies are needed. We quantified pollinator-mediated selection on flowering phenology and morphology in four populations of the fragrant orchid Gymnadenia conopsea, and compared selection mediated by diurnal and nocturnal pollinators in two of the populations. Variation in pollinator-mediated selection explained most of the among-population variation in the strength of directional and correlational selection. Pollinators mediated correlational selection on pairs of display traits, and on one display trait and spur length, a trait affecting pollination efficiency. Only nocturnal pollinators selected for longer spurs, and mediated stronger selection on the number of flowers compared with diurnal pollinators in one population. The two types of pollinators caused correlational selection on different pairs of traits and selected for different combinations of spur length and number of flowers. The results demonstrate that spatial variation in interactions with pollinators may result in differences in directional and correlational selection on floral traits in a plant with a semi-generalized pollination system, and suggest that differences in the relative importance of diurnal and nocturnal pollinators can cause variation in selection.

    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-275786 (URN)10.1111/nph.13555 (DOI)000365393000025 ()
    Funder
    Swedish Research CouncilSwedish Research Council Formas
    Available from: 2016-02-06 Created: 2016-02-06 Last updated: 2018-08-26Bibliographically approved
    3. Diel pattern of floral scent emission matches the relative importance of diurnal and nocturnal pollinators in populations of Gymnadenia conopsea
    Open this publication in new window or tab >>Diel pattern of floral scent emission matches the relative importance of diurnal and nocturnal pollinators in populations of Gymnadenia conopsea
    Show others...
    2018 (English)In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 121, p. 711-721Article in journal (Refereed) Published
    Abstract [en]

    Background and Aims

    Floral scent is considered an integral component of pollination syndromes, and its composition and timing of emission are thus expected to match the main pollinator type and time of activity. While floral scent differences among plant species with different pollination systems can be striking, studies on intraspecific variation are sparse, which limits our understanding of the role of pollinators in driving scent divergence.

    Methods

    Here, we used dynamic headspace sampling to quantify floral scent emission and composition during the day and at night in the natural habitat of six Scandinavian populations of the fragrant orchid Gymnadenia conopsea. We tested whether diel scent emission and composition match pollinator type by comparing four populations in southern Sweden, where nocturnal pollinators are more important for plant reproductive success than are diurnal pollinators, with two populations in central Norway, where the opposite is true. To determine to what extent scent patterns quantified in the field reflected plasticity, we also measured scent emission in a common growth chamber environment.

    Key Results

    Both scent composition and emission rates differed markedly between day and night, but only the latter varied significantly among populations. The increase in scent emission rate at night was considerably stronger in the Swedish populations compared with the Norwegian populations. These patterns persisted when plants were transferred to a common environment, suggesting a genetic underpinning of the scent variation.

    Conclusions

    The results are consistent with a scenario where spatial variation in relative importance of nocturnal and diurnal pollinators has resulted in selection for different scent emission rhythms. Our study highlights the importance of adding a characterization of diel variation of scent emission rates to comparative studies of floral scent, which so far have often focused on scent composition only.

    Keywords
    diel variation, diurnal and nocturnal pollination, floral evolution, floral scent, geographic variation, Gymnadenia conopsea (fragrant orchid), plasticity, population differentiation, scent emission rate, scent rhythm, semi-generalkized pollination, spatial variation
    National Category
    Evolutionary Biology Ecology
    Identifiers
    urn:nbn:se:uu:diva-358243 (URN)10.1093/aob/mcx203 (DOI)000427884200015 ()29360931 (PubMedID)
    Funder
    Swedish Research Council FormasSwedish Research Council
    Available from: 2018-08-26 Created: 2018-08-26 Last updated: 2019-06-28Bibliographically approved
    4. Conflicting selection on floral scent in the fragrant orchid Gymnadenia conopsea s.s.
    Open this publication in new window or tab >>Conflicting selection on floral scent in the fragrant orchid Gymnadenia conopsea s.s.
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-358247 (URN)
    Available from: 2018-08-26 Created: 2018-08-26 Last updated: 2018-08-26
  • 280.
    Chapurlat, Elodie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Anderson, Joseph
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Lund University.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conflicting selection on floral scent in the fragrant orchid Gymnadenia conopsea s.s.Manuscript (preprint) (Other academic)
  • 281.
    Chapurlat, Elodie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Anderson, Joseph
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Diel pattern of floral scent emission matches the relative importance of diurnal and nocturnal pollinators in populations of Gymnadenia conopsea2018In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 121, p. 711-721Article in journal (Refereed)
    Abstract [en]

    Background and Aims

    Floral scent is considered an integral component of pollination syndromes, and its composition and timing of emission are thus expected to match the main pollinator type and time of activity. While floral scent differences among plant species with different pollination systems can be striking, studies on intraspecific variation are sparse, which limits our understanding of the role of pollinators in driving scent divergence.

    Methods

    Here, we used dynamic headspace sampling to quantify floral scent emission and composition during the day and at night in the natural habitat of six Scandinavian populations of the fragrant orchid Gymnadenia conopsea. We tested whether diel scent emission and composition match pollinator type by comparing four populations in southern Sweden, where nocturnal pollinators are more important for plant reproductive success than are diurnal pollinators, with two populations in central Norway, where the opposite is true. To determine to what extent scent patterns quantified in the field reflected plasticity, we also measured scent emission in a common growth chamber environment.

    Key Results

    Both scent composition and emission rates differed markedly between day and night, but only the latter varied significantly among populations. The increase in scent emission rate at night was considerably stronger in the Swedish populations compared with the Norwegian populations. These patterns persisted when plants were transferred to a common environment, suggesting a genetic underpinning of the scent variation.

    Conclusions

    The results are consistent with a scenario where spatial variation in relative importance of nocturnal and diurnal pollinators has resulted in selection for different scent emission rhythms. Our study highlights the importance of adding a characterization of diel variation of scent emission rates to comparative studies of floral scent, which so far have often focused on scent composition only.

  • 282.
    Chapurlat, Elodie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Le Roncé, Iris
    Ecole Normale Supérieure de Lyon.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Divergent selection on flowering phenology but not on floral morphology between two closely related orchidsManuscript (preprint) (Other academic)
  • 283.
    Chapurlat, Elodie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Anderson, Joseph
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Lund Univ, Dept Biol, SE-22362 Lund, Sweden.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conflicting selection on floral scent emission in the orchid Gymnadenia conopsea2019In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 222, no 4, p. 2009-2022Article in journal (Refereed)
    Abstract [en]

    Floral scent is a crucial trait for pollinator attraction. Yet only a handful of studies have estimated selection on scent in natural populations and no study has quantified the relative importance of pollinators and other agents of selection. In the fragrant orchid Gymnadenia conopsea, we used electroantennographic data to identify floral scent compounds detected by local pollinators and quantified pollinator-mediated selection on emission rates of 10 target compounds as well as on flowering start, visual display and spur length. Nocturnal pollinators contributed more to reproductive success than diurnal pollinators, but there was significant pollinator-mediated selection on both diurnal and nocturnal scent emission. Pollinators selected for increased emission of two compounds and reduced emission of two other compounds, none of which were major constituents of the total bouquet. In three cases, pollinator-mediated selection was opposed by nonpollinator-mediated selection, leading to weaker or no detectable net selection. Our study demonstrates that minor scent compounds can be targets of selection, that pollinators do not necessarily favour stronger scent signalling, and that some scent compounds are subject to conflicting selection from pollinators and other agents of selection. Hence, including floral scent traits into selection analysis is important for understanding the mechanisms behind floral evolution.

  • 284.
    Cheeke, Tanya E.
    et al.
    Swedish Univ Agr Sci, Uppsala Bioctr, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden.;Indiana Univ, Dept Biol, 1001 E Third St, Bloomington, IN 47405 USA..
    Phillips, Richard P.
    Indiana Univ, Dept Biol, 1001 E Third St, Bloomington, IN 47405 USA..
    Brzostek, Edward R.
    West Virginia Univ, Dept Biol, 53 Campus Dr, Morgantown, WV 26506 USA..
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bever, James D.
    Indiana Univ, Dept Biol, 1001 E Third St, Bloomington, IN 47405 USA.;Univ Kansas, Dept Ecol & Evolutionary Biol, 2041 Haworth Hall,1200 Sunnyside Ave, Lawrence, KS 66045 USA..
    Fransson, Petra
    Swedish Univ Agr Sci, Uppsala Bioctr, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden..
    Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, no 1, p. 432-442Article in journal (Refereed)
    Abstract [en]

    While it is well established that plants associating with arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi cycle carbon (C) and nutrients in distinct ways, we have a limited understanding of whether varying abundance of ECM and AM plants in a stand can provide integrative proxies for key biogeochemical processes. We explored linkages between the relative abundance of AM and ECM trees and microbial functioning in three hardwood forests in southern Indiana, USA. Across each site's 'mycorrhizal gradient', we measured fungal biomass, fungal : bacterial (F : B) ratios, extracellular enzyme activities, soil carbon : nitrogen ratio, and soil pH over a growing season. We show that the percentage of AM or ECM trees in a plot promotes microbial communities that both reflect and determine the C to nutrient balance in soil. Soils dominated by ECM trees had higher F : B ratios and more standing fungal biomass than AM stands. Enzyme stoichiometry in ECM soils shifted to higher investment in extracellular enzymes needed for nitrogen and phosphorus acquisition than in C-acquisition enzymes, relative to AM soils. Our results suggest that knowledge of mycorrhizal dominance at the stand or landscape scale may provide a unifying framework for linking plant and microbial community dynamics, and predicting their effects on ecological function.

  • 285.
    Chen, Dong Lei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tafforeau, Paul
    Estonian Marine Institute, University of Tartu.
    Märss, Tiiu
    Estonian Marine Institute, University of Tartu.
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Development of cyclic shedding teeth from semi-shedding teeth: the inner dental arcade of the stem osteichthyan Lophosteus 2017In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 4, no 5, article id 161084Article in journal (Refereed)
    Abstract [en]

    The numerous cushion-shaped tooth-bearing plates attributed to the stem-group osteichthyan Lophosteus superbus, which are argued here to represent the ancient form of inner dental arcade, display a unique and presumably primitive way of tooth shedding by basal hard tissue resorption. They carry regularly spaced, recumbent, gently recurved teeth arranged in transverse tooth files that diverge towards the lingual margin of the cushion. Three-dimensional (3D) reconstruction from propagation phase contrast synchrotron microtomography (PPC-SRμCT) reveals remnants of the first-generation teeth embedded in the basal plate that have never been discerned in any taxa. These teeth were shed by semi-basal resorption with the periphery of their bases retained as dentine rings. The rings are highly overlapped, which evidences tooth shedding prior to adding the next first-generation tooth. Later teeth at the same sites underwent cyclical replacing and shedding through basal resorption, producing stacks of buried resorption surfaces separated by bone of attachment. The number and spatial arrangement of resorption surfaces elucidates that basal resorption of replacement teeth had taken place at the older tooth sites before the addition of the youngest first-generation teeth at the lingual margin. Thus the replacement tooth buds cannot have been generated by a single permanent dental lamina, but must have arisen either from successional dental laminae associated with the predecessor teeth, or directly from the dental epithelium of these teeth. The virtual histological dissection of these Late Silurian microfossils broadens our understanding of the development of the gnathostome dental systems and the acquisition of the osteichthyan-type of tooth replacement. 

  • 286.
    Chen, Donglei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Squamation in Andreolepis from the late Silurian of Sweden2010Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The origin of osteichthyans (bony fishes and tetrapods) dates back to the Late Silurian, but theearly evolution of osteichthyans is poorly understood. Andreolepis is one of the oldest knownosteichthyans, but exclusively documented by detached and fragmented dermal microremains.Nevertheless, Andreolepis has unequivocally been attributed to the osteichthyan stem group.A variety of isolated scales of Andreolepis from Gotland, Sweden provides a large dataset,which would potentially improve our understanding of the acquisition of the osteichthyanbody plan. In the present study, various forms of Andreolepis scales were classified into tenmorphotypes by landmark-based geometric morphometrics. Based on comparative anatomyand functional morphology, each morphotype was assigned to a specific area of the body anda squamation model of Andreolepis was established. In this model, scales are allocated toanterior-mid lateral flank scales, posterior lateral flank scales, caudal peduncle scales, pectoralpeduncle scales, dorsal flank scales, dorsal fulcral scales, caudal fulcral scales, ventral flankscales, medioventral scales and cranial scales.

  • 287.
    Chen, Donglei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The Origin of Tooth Replacement: Three-dimensional Synchrotron Histology Visualizes the Dental Development of Silurian Stem Osteichthyans2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Mechanisms of tooth replacement distribute incongruently among extant gnathostomes (jawed vertebrates): a permanent tooth-generating dental lamina exists in chondrichthyans (cartilaginous fish) and tetrapods but not teleosts, whereas tooth shedding by basal hard tissue resorption occurs in tetrapods and teleosts but not chondrichthyans. Theories about the evolution of tooth development have been biased towards the chondrichthyan conveyor-belt replacement, since there has been no fossil evidence for the origin of osteichthyan (bony fish and tetrapods) tooth replacement until now. 3D virtual dissections with submicron-scale resolution, based on propagation phase contrast synchrotron microtomography (PPC-SRµCT), reveal the growth history of the dentitions of Andreolepis and Lophosteus, 423-Myr-old Silurian stem osteichthyans close to the common ancestor of tetrapods and teleosts. Their marginal jawbones and “tooth cushions” (possible homologues of coronoids) shed teeth by in situ cyclic basal resorption, the earliest examples of osteichthyan-style tooth replacement. The replacement cycles were site-autonomic, and occurred in broad irregular multi-row tooth fields, including at sites separated from the margin of the bone by intervening teeth, showing that the production of replacement teeth did not occur in a single deep dental lamina, but in pockets associated with each tooth, as in many teleosts. It suggests that the functionally and anatomically similar laminae of chondrichthyans and tetrapods are convergent. The marginal jaw bones of both genera carry an initial non-shedding dentition arranged in alternate transverse files, labial to the shedding tooth field, overgrown by later dermal ornament and probably not belonging to the oral domain, but bearing in vivo biting damage showing that they functioned as teeth. The most lingual of these odontodes have been resorbed apically and are overlain by shedding teeth. The first-generation teeth on the tooth cushions display basal resorption in Andreolepis, but semi-basal resorption in Lophosteus. The latter leaves a basal dentine ring from each tooth, implying only odontoclasts are involved in the semi-basal resorption, which is probably the first step towards evolving a site-specific resorption. The polarized displacement of each generation of resorption surfaces reflects the fact that the cyclic replacement, as well as the sequential addition of tooth sites, is closely related to bone growth. Resorption surfaces and growth arrest surfaces also record the life history and the replacement rate. These data provide unique insights into the origin of osteichthyan tooth replacement.

    List of papers
    1. The stem osteichthyan Andreolepis and the origin of tooth replacement
    Open this publication in new window or tab >>The stem osteichthyan Andreolepis and the origin of tooth replacement
    Show others...
    2016 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 539, no 7628, p. 237-+Article in journal (Refereed) Published
    Abstract [en]

    The teeth of gnathostomes (jawed vertebrates) show rigidly patterned, unidirectional replacement that may or may not be associated with a shedding mechanism. These mechanisms, which are critical for the maintenance of the dentition, are incongruently distributed among extant gnathostomes. Although a permanent tooth-generating dental lamina is present in all chondrichthyans, many tetrapods and some teleosts, it is absent in the non-teleost actinopterygians. Tooth-shedding by basal hard tissue resorption occurs in most osteichthyans (including tetrapods) but not in chondrichthyans. Here we report a three-dimensional virtual dissection of the dentition of a 424-million-year-old stem osteichthyan, Andreolepis hedei, using propagation phase-contrast synchrotron microtomography, with a reconstruction of its growth history. Andreolepis, close to the common ancestor of all extant osteichthyans, shed its teeth by basal resorption but probably lacked a permanent dental lamina. This is the earliest documented instance of resorptive tooth shedding and may represent the primitive osteichthyan mode of tooth replacement.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-310754 (URN)10.1038/nature19812 (DOI)000387318500034 ()27750278 (PubMedID)
    Funder
    EU, European Research Council, 233111Knut and Alice Wallenberg Foundation
    Available from: 2016-12-20 Created: 2016-12-19 Last updated: 2017-11-29Bibliographically approved
    2. Development of cyclic shedding teeth from semi-shedding teeth: the inner dental arcade of the stem osteichthyan Lophosteus 
    Open this publication in new window or tab >>Development of cyclic shedding teeth from semi-shedding teeth: the inner dental arcade of the stem osteichthyan Lophosteus 
    Show others...
    2017 (English)In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 4, no 5, article id 161084Article in journal (Refereed) Published
    Abstract [en]

    The numerous cushion-shaped tooth-bearing plates attributed to the stem-group osteichthyan Lophosteus superbus, which are argued here to represent the ancient form of inner dental arcade, display a unique and presumably primitive way of tooth shedding by basal hard tissue resorption. They carry regularly spaced, recumbent, gently recurved teeth arranged in transverse tooth files that diverge towards the lingual margin of the cushion. Three-dimensional (3D) reconstruction from propagation phase contrast synchrotron microtomography (PPC-SRμCT) reveals remnants of the first-generation teeth embedded in the basal plate that have never been discerned in any taxa. These teeth were shed by semi-basal resorption with the periphery of their bases retained as dentine rings. The rings are highly overlapped, which evidences tooth shedding prior to adding the next first-generation tooth. Later teeth at the same sites underwent cyclical replacing and shedding through basal resorption, producing stacks of buried resorption surfaces separated by bone of attachment. The number and spatial arrangement of resorption surfaces elucidates that basal resorption of replacement teeth had taken place at the older tooth sites before the addition of the youngest first-generation teeth at the lingual margin. Thus the replacement tooth buds cannot have been generated by a single permanent dental lamina, but must have arisen either from successional dental laminae associated with the predecessor teeth, or directly from the dental epithelium of these teeth. The virtual histological dissection of these Late Silurian microfossils broadens our understanding of the development of the gnathostome dental systems and the acquisition of the osteichthyan-type of tooth replacement. 

    Place, publisher, year, edition, pages
    ROYAL SOC, 2017
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-315882 (URN)10.1098/rsos.161084 (DOI)000402541800020 ()28573003 (PubMedID)
    Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2017-08-02Bibliographically approved
    3. Microstructures of the most primitive form of inner dental arcade and life history of the Silurian stem osteichthyan Andreolepis.
    Open this publication in new window or tab >>Microstructures of the most primitive form of inner dental arcade and life history of the Silurian stem osteichthyan Andreolepis.
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-315883 (URN)
    Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2017-02-22
    4. The marginal dentition of Lophosteus superbus Pander 1856, a Late Silurian stem osteichthyan from Estonia.
    Open this publication in new window or tab >>The marginal dentition of Lophosteus superbus Pander 1856, a Late Silurian stem osteichthyan from Estonia.
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-315884 (URN)
    Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2017-02-22
  • 288.
    Chen, Donglei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The marginal dentition of Lophosteus superbus Pander 1856, a Late Silurian stem osteichthyan from Estonia.Manuscript (preprint) (Other academic)
  • 289.
    Chen, Donglei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tafforeau, Paul
    European Synchrotron Radiation Facility.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Microstructures of the most primitive form of inner dental arcade and life history of the Silurian stem osteichthyan Andreolepis.Manuscript (preprint) (Other academic)
  • 290.
    Chen, Donglei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. European Synchrotron Radiat Facil, 6 Rue Jules Horowitz, F-38043 Grenoble, France..
    Tafforeau, Paul
    European Synchrotron Radiat Facil, 6 Rue Jules Horowitz, F-38043 Grenoble, France..
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The stem osteichthyan Andreolepis and the origin of tooth replacement2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 539, no 7628, p. 237-+Article in journal (Refereed)
    Abstract [en]

    The teeth of gnathostomes (jawed vertebrates) show rigidly patterned, unidirectional replacement that may or may not be associated with a shedding mechanism. These mechanisms, which are critical for the maintenance of the dentition, are incongruently distributed among extant gnathostomes. Although a permanent tooth-generating dental lamina is present in all chondrichthyans, many tetrapods and some teleosts, it is absent in the non-teleost actinopterygians. Tooth-shedding by basal hard tissue resorption occurs in most osteichthyans (including tetrapods) but not in chondrichthyans. Here we report a three-dimensional virtual dissection of the dentition of a 424-million-year-old stem osteichthyan, Andreolepis hedei, using propagation phase-contrast synchrotron microtomography, with a reconstruction of its growth history. Andreolepis, close to the common ancestor of all extant osteichthyans, shed its teeth by basal resorption but probably lacked a permanent dental lamina. This is the earliest documented instance of resorptive tooth shedding and may represent the primitive osteichthyan mode of tooth replacement.

  • 291.
    Chen, Donglei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Janvier, Philippe
    Département Histoire de la Terre, Muséum National d'Histoire Naturelle,.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Scale morphology and squamation of the Late Silurian osteichthyan Andreolepis from Gotland, Sweden2012In: Historical Biology, ISSN 0891-2963, E-ISSN 1029-2381, Vol. 24, no 4, p. 411-423Article in journal (Refereed)
    Abstract [en]

    The origin of osteichthyans (bony fishes and tetrapods) dates back to the Late Silurian, but the early evolution of the group is poorly understood. Andreolepis is one of the oldest known osteichthyans, but exclusively documented by detached and fragmentary dermal microremains. A large data-set of Andreolepis scales from the Silurian of Gotland has been used to explore the scale morphology on different parts of the body. Landmark-based geometric morphometrics together with comparative anatomy and functional morphology has allowed 10 morphotypes to be identified and incorporated into a squamation model, in which scales are allocated to anterior-mid lateral flank scales, posterior lateral flank scales, caudal peduncle scales, pectoral peduncle scales, dorsal flank scales, dorsal fulcral scales, caudal fulcral scales, ventral flank scales, medioventral scales and cranial scales. The scale morphology and squamation pattern ofAndreolepis may be primitive for the Osteichthyes and thus informative about the acquisition of the osteichthyan body plan.

  • 292.
    Chen, Hwei -Yen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Spagopoulou, Foteini
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Maklakov, Alexei A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Evolution of male age-specific reproduction under differential risks and causes of death: males pay the cost of high female fitness2016In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 29, no 4, p. 848-856Article in journal (Refereed)
    Abstract [en]

    Classic theories of ageing evolution predict that increased extrinsic mortality due to an environmental hazard selects for increased early reproduction, rapid ageing and short intrinsic lifespan. Conversely, emerging theory maintains that when ageing increases susceptibility to an environmental hazard, increased mortality due to this hazard can select against ageing in physiological condition and prolong intrinsic lifespan. However, evolution of slow ageing under high-condition-dependent mortality is expected to result from reallocation of resources to different traits and such reallocation may be hampered by sex-specific trade-offs. Because same life-history trait values often have different fitness consequences in males and females, sexually antagonistic selection can preserve genetic variance for lifespan and ageing. We previously showed that increased condition-dependent mortality caused by heat shock leads to evolution of long-life, decelerated late-life mortality in both sexes and increased female fecundity in the nematode, Caenorhabditis remanei. Here, we used these cryopreserved lines to show that males evolving under heat shock suffered from reduced early-life and net reproduction, while mortality rate had no effect. Our results suggest that heat-shock resistance and associated long-life trade-off with male, but not female, reproduction and therefore sexually antagonistic selection contributes to maintenance of genetic variation for lifespan and fitness in this population.

  • 293.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conifer Evolution, from Demography and Local Adaptation to Evolutionary Rates: Examples from the Picea genus2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Evolutionary process can be inferred at three different levels: the species level, the population level and the molecular level. In this thesis, I applied approaches at these three levels and aimed to get a comprehensive picture of conifer evolution, from speciation and demography to geographic variation and local adaptation, and then to the molecular evolution of proteins and small regulatory RNAs.

    Spruce species have been observed to possess a large number of trans-species shared polymorphisms. Using an “Isolation with migration” model, we found that the large effective population size of spruce retained these shared polymorphisms, inheriting them from the common ancestor. Post-divergence gene flow only existed between Picea abies and P. glauca, and between P. wilsonii and P. schrenkiana. The combination of Tajima’s D and Fay & Wu’s H at most of loci suggested an ancient and severe bottleneck for most species except P. breweriana.

    Furthermore, I investigated the effect of local selection in two parallel clines, which is one of the major forces that can cause divergence or even speciation. The timing of bud set and growth cessation was found correlated with latitude in populations of P. abies and P. obovata. Using allele frequency spectrum analyses we identified three genes under local selection in both species including two circadian-clock genes GI and PRR7, and one photoperiodic gene FTL2. This indicated that parallel evolution could occur through groups of genes within related pathways. Clinal variation at expression level provided stronger evidence of selection in FTL2, which has previously been associated with bud set in P. abies.

    Finally we focused on the molecular evolution of mRNA and small regulatory RNAs in P. abies. With the help of Next-Generation sequencing, we have achieved in spruce the first de novel assembly of the needle transcriptome and a preliminary characterization of sRNA populations. Along with features common in plants, spruce also exhibited novelties in many aspects including lower substitution rate and protein evolutionary rate, dominance of 21-nt sRNA, and a large proportion of TIR-NBS-LRR genes as sRNA sources and targets.

    List of papers
    1. New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict
    Open this publication in new window or tab >>New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict
    2010 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 104, no 1, p. 3-14Article in journal (Refereed) Published
    Abstract [en]

    In all, 10 nuclear loci were re-sequenced in four spruce species. Three of the species are boreal species with very large natural ranges: Picea mariana and P. glauca are North American, and P. abies, is Eurasian. The fourth species, P. breweriana, is a Tertiary relict from Northern California, with a very small natural range. Although the boreal species population sizes have fluctuated through the Ice Ages, P. breweriana is believed to have had a rather stable population size through the Quaternary. Indeed, the average Tajima’s D was close to zero in this species and negative in the three boreal ones. Reflecting differences in current population sizes, nucleotide diversity was an order of magnitude lower in P. breweriana than in the boreal species. This is in contrast to the similar and high levels of heterozygosity observed in previous studies at allozyme loci across species. As the species have very different histories and effective population sizes, selection at allozyme loci rather than demography appears to be a better explanation for this discrepancy. Parameters of Isolation-with-Migration (IM) models were also estimated for pairs of species. Shared polymorphisms were extensive and fixed polymorphisms few. Divergence times were much shorter than those previously reported. There was also evidence of historical gene flow between P. abies and P. glauca. The latter was more closely related to P. abies than to its sympatric relative P. mariana. This last result suggests that North American and Eurasian species might have been geographically much closer in the recent past than they are today.

    Keywords
    picea; nucleotide diversity; divergence time; migration; speciation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-119939 (URN)10.1038/hdy.2009.88 (DOI)000272794600002 ()
    Available from: 2010-03-03 Created: 2010-03-03 Last updated: 2017-12-12Bibliographically approved
    2. Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    Open this publication in new window or tab >>Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    Show others...
    2010 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 27, no 5, p. 1001-1014Article in journal (Refereed) Published
    Abstract [en]

    Nucleotide variation at 12 to 16 nuclear loci was studied in three spruce species from the Qinghai-Tibetan Plateau (QTP), Picea likiangensis, P. wilsonii and P. purpurea, and one species from the Tian Shan mountain range, P. schrenkiana. Silent nucleotide diversity was limited in P. schrenkiana and high in the three species from the QTP, with values higher than in boreal spruce species, despite their much more restricted distributions compared to that of the boreal species. In contrast to European boreal species that have experienced severe bottlenecks in the past, coalescent-based analysis suggests that DNA polymorphism in the species from the QTP and adjacent areas is compatible with the standard neutral model (P. likiangensis, P. wilsonii, P. schrenkiana) or with population growth (P. purpurea). In order to test if P. purpurea is a diploid hybrid of P. likiangensis and P. wilsonii, we used a combination of approaches, including model based inference of population structure, Isolation-with-Migration models and recent theoretical results on the effect of introgression on the geographic distribution of diversity. In contrast to the three other species, each of which was predominantly assigned to a single cluster in the Structure analysis, P. purpurea individuals were scattered over the three main clusters and not, as we had expected, confined to the P. likiangensis and P. wilsonii clusters. Furthermore the contribution of P. schrenkiana was by far the largest one. In agreement with this, the divergence between P. purpurea and P. schrenkiana was lower than the divergence of either P. likiangensis or P. wilsonii from P. schrenkiana. These results, together with previous ones showing that P. purpurea and P. wilsonii share the same haplotypes at both chloroplast and mitochondrial markers, suggest that P. purpurea has a complex origin, possibly involving additional species.

    Keywords
    Picea, Qinghai Tibetan Plateau, effective population size, divergence time, introgression, speciation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121399 (URN)10.1093/molbev/msp301 (DOI)000276994800004 ()20031927 (PubMedID)
    Available from: 2010-03-23 Created: 2010-03-23 Last updated: 2017-12-12Bibliographically approved
    3. Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)
    Open this publication in new window or tab >>Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)
    Show others...
    2012 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 191, no 3, p. 865-881Article in journal (Refereed) Published
    Abstract [en]

    Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (F(ST) = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to F(ST). The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.

    Keywords
    clinal variation, photoperiodic pathway, Norway spruce, FT genes
    National Category
    Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-177467 (URN)10.1534/genetics.112.140749 (DOI)000308999900015 ()22542968 (PubMedID)
    Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2017-12-07Bibliographically approved
    4. Clinal variation in allele frequency at photoperiodic genes in Siberian spruce: an example of convergent evolution?
    Open this publication in new window or tab >>Clinal variation in allele frequency at photoperiodic genes in Siberian spruce: an example of convergent evolution?
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology Genetics
    Research subject
    Biology with specialization in Evolutionary Functional Genomics; Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-177474 (URN)
    Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2013-01-22
    5. Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms compared to angiosperms
    Open this publication in new window or tab >>Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms compared to angiosperms
    Show others...
    2012 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 13, p. 589-Article in journal (Other academic) Published
    Abstract [en]

    Background: A detailed knowledge about which genes are expressed in which tissues and at which developmental stage is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now give both a snap-shot of the transcribed part of a species genome and simultaneously estimate levels of gene expression.

    Results: mRNA from actively growing needles of Norway spruce (Picea abies) was sequenced using next generation sequencing technology. In total, close to 70 million fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw data. A de novo assembly of these reads were, together with publicly available expressed sequence tag (EST) data from Norway spruce, used to create a reference transcriptome. Of the 38,419 PUTs (putative unique transcripts) longer than 150 bp in this reference assembly, 59% show similarity to ESTs from other spruce species and of the remaining PUTs, 3,704 show similarity to protein sequences from other plant species, leaving 4,167 PUTs with limited similarity to currently available plant proteins. By predicting coding frames and comparing not only the Norway spruce PUTs, but also PUTs from the close relatives Picea glauca and Picea sitchensis to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous and non-synonymous divergence among conifer species. In addition, we detected close to 15,000 SNPs of high quality and estimated gene expression difference between samples collected during dark and light conditions.

    Conclusions: Our study yielded a large number of single nucleotide polymorphisms as well as estimates of gene expression on transcriptome scale. In agreement with a recent study we find that the synonymous substitution rate per year (0.6 × 10-09 and 1.1 × 10-09) is an order of magnitude smaller than values reported for angiosperm herbs, but if one takes generation time in to account, most of this difference disappear. The estimates of the non-synonymous over the synonymous divergence (dN/dS ratio) reported here is in general much lower than 1 and only a few genes showed a ratio larger than 1.

    National Category
    Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-177479 (URN)10.1186/1471-2164-13-589 (DOI)000314646900001 ()
    Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2017-12-07Bibliographically approved
    6. Major difference in short RNA populations among plants - the results of interaction with pathogen?
    Open this publication in new window or tab >>Major difference in short RNA populations among plants - the results of interaction with pathogen?
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Small RNA (sRNA) including miRNA and siRNA are important in the regulation of diverse biological processes. Comparative studies of sRNA from plants have mainly focused on miRNA even though this group in most cases is just a mere fraction of the total sRNA diversity. In the present study we report results from an in-depth analysis of the sRNA population from the conifer Picea abies and compared the results to those of a range of species from the plant kingdom. The vast majority of sRNA in P. abies was 21 nucleotides long siRNA, of which a large fraction originate from degradation of transcribed sequences related to TIR-NBS-LRR (Toll/Interleukin-1-Nucleotide Binding Site-Leucine Rich Repeats) type resistance genes. Over 90% of all genes predicted to contain either a TIR or an NBS domain showed evidence of siRNA degradation. Data further suggests that those phased siRNA are initiated from miRNA guided cleavage, often by an abundant 22 nt miRNA. Comparative analysis over a range of divergent plant species revealed a large variation between species in the abundance of this phenomenon. The process seemed to be virtually absent in several species, including Arabidopsis thaliana, Oryza sativa and non-vascular plants, while particularly high frequencies were observed in Vitis vinifera and Populus thrichocarpa. This divergent pattern between species might reflect a mechanism to limit runaway transcription of these genes in species with rapidly expanding NBS-LRR gene families. Alternatively it might reflect variation in a counter-counter defence mechanism partly affected by differences in life history traits, e.g. perennial versus annual life cycles. A major difference between annuals and perennials, affecting the evolution of resistance, is that perennials will with almost certainty encounter many different pathogens before reproduction, and that the long generation times confers problems in matching the evolutionary rates of the pathogens.

    National Category
    Evolutionary Biology Genetics
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-177475 (URN)
    Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2013-06-27
  • 294.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ma, Xiaofei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Zaina, Giusi
    Morgante, Michele
    Bousquet, Jean
    Eckert, Andrew
    Wegrzyn, Jill
    Neale, David
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)2012In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 191, no 3, p. 865-881Article in journal (Refereed)
    Abstract [en]

    Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (F(ST) = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to F(ST). The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.

  • 295.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tsuda, Yoshiaki
    CNR, Plant Genetics Institute, Sesto Fiorentino, Firenze, Italy.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Semerikov, Vladimir
    Institute of Plant and Animal Ecology, Ural Division of the Russian Academy of Sciences.
    Vendramin, Giovanni
    CNR, Plant Genetics Institute, Sesto Fiorentino, Firenze, Italy.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Clinal variation in allele frequency at photoperiodic genes in Siberian spruce: an example of convergent evolution?Manuscript (preprint) (Other academic)
  • 296.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tsuda, Yoshiaki
    CNR, Plant Genetics Institute, Sesto Fiorentino, Firenze, Italy.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Xu, Nannan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Semerikov, Vladimir
    Institute of Plant and Animal Ecology, Ural Division of the Russian Academy of Sciences.
    Vendramin, Giovanni
    CNR, Plant Genetics Institute, Sesto Fiorentino, Firenze, Italy.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Clinal variation in allele frequency and gene expression at photoperiodic and circadian genes in Siberian spruce: an example of parallel evolution?Manuscript (preprint) (Other academic)
  • 297.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Uebbing, Severin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gyllenstrand, Niclas
    Department of Plant Biology and Forest Genetics, Swedish University of Agriculture Science.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms compared to angiosperms2012In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 13, p. 589-Article in journal (Other academic)
    Abstract [en]

    Background: A detailed knowledge about which genes are expressed in which tissues and at which developmental stage is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now give both a snap-shot of the transcribed part of a species genome and simultaneously estimate levels of gene expression.

    Results: mRNA from actively growing needles of Norway spruce (Picea abies) was sequenced using next generation sequencing technology. In total, close to 70 million fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw data. A de novo assembly of these reads were, together with publicly available expressed sequence tag (EST) data from Norway spruce, used to create a reference transcriptome. Of the 38,419 PUTs (putative unique transcripts) longer than 150 bp in this reference assembly, 59% show similarity to ESTs from other spruce species and of the remaining PUTs, 3,704 show similarity to protein sequences from other plant species, leaving 4,167 PUTs with limited similarity to currently available plant proteins. By predicting coding frames and comparing not only the Norway spruce PUTs, but also PUTs from the close relatives Picea glauca and Picea sitchensis to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous and non-synonymous divergence among conifer species. In addition, we detected close to 15,000 SNPs of high quality and estimated gene expression difference between samples collected during dark and light conditions.

    Conclusions: Our study yielded a large number of single nucleotide polymorphisms as well as estimates of gene expression on transcriptome scale. In agreement with a recent study we find that the synonymous substitution rate per year (0.6 × 10-09 and 1.1 × 10-09) is an order of magnitude smaller than values reported for angiosperm herbs, but if one takes generation time in to account, most of this difference disappear. The estimates of the non-synonymous over the synonymous divergence (dN/dS ratio) reported here is in general much lower than 1 and only a few genes showed a ratio larger than 1.

  • 298. Chen, Yu-Chia
    et al.
    Harrison, Peter W.
    Kotrschal, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kolm, Niclas
    Mank, Judith E.
    Panula, Pertti
    Expression change in Angiopoietin-1 underlies change in relative brain size in fish2015In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1810, article id 20150872Article in journal (Refereed)
    Abstract [en]

    Brain size varies substantially across the animal kingdom and is often associated with cognitive ability; however, the genetic architecture underpinning natural variation in these key traits is virtually unknown. In order to identify the genetic architecture and loci underlying variation in brain size, we analysed both coding sequence and expression for all the loci expressed in the telencephalon in replicate populations of guppies (Poecilia reticulata) artificially selected for large and small relative brain size. A single gene, Angiopoietin-1 (Ang-1), a regulator of angiogenesis and suspected driver of neural development, was differentially expressed between large-and small-brain populations. Zebra fish (Danio rerio) morphants showed that mild knock down of Ang-1 produces a small-brained phenotype that could be rescued with Ang-1 mRNA. Translation inhibition of Ang-1 resulted in smaller brains in larvae and increased expression of Notch-1, which regulates differentiation of neural stem cells. In situ analysis of newborn large-and small-brained guppies revealed matching expression patterns of Ang-1 and Notch-1 to those observed in zebrafish larvae. Taken together, our results suggest that the genetic architecture affecting brain size in our population may be surprisingly simple, and Ang-1 may be a potentially important locus in the evolution of vertebrate brain size and cognitive ability.

  • 299.
    Cheng, George
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Uncovering the genetic organisation of Claroideoglomus candidum2019Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Arbuscular mycorrhizal (AM) fungi are hypothesized to have been key players in facilitating thetransition from aquatic to terrestrial plants and continue to benefit plants through their symbioticassociation after 450 million years. These fungi form mycelia that can contain hundreds of nucleiwithin one aseptate cytoplasm, which leads to the ongoing debate on whether thesemultinucleated fungi are homokaryotic or heterokaryotic. Not only is there evidence to supportthe hypothesis of the nuclei as genetically identical, but also the other hypothesis of divergentnuclei within a single strain. There has been no evidence of sexual reproduction, howeverspecialized genomic regions specific to meiosis and a putative mating-type (MAT) locus haverecently been identified and may help answer the ongoing debate between homokaryosis andheterokaryosis.

    In this study I applied de novo genome assembly and annotation of 24 individual nuclei from asingle spore of Claroideoglomus candidum. The full length of the de novo genome assembly was87.6 Mb with 17,542 genes. Estimated polymorphism between the nuclei was very low. Iidentified the MAT locus in C. candidum, using a previously sequenced MAT locus fromanother congeneric species. Only one of the MAT locus alleles was found in the examined spore.The evidence points towards homokaryosis as the genetic organization of Claroideoglomuscandidum.

  • 300. Childs, Liam H
    et al.
    Witucka-Wall, Hanna
    Günther, Torsten
    Sulpice, Ronan
    Korff, Maria V
    Stitt, Mark
    Walther, Dirk
    Schmid, Karl J
    Altmann, Thomas
    Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana.2010In: BMC genomics, ISSN 1471-2164, Vol. 11, p. 188-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Single Feature Polymorphism (SFP) detection via genomic DNA hybridization to Arabidopsis Tiling 1.0 Arrays for the detection of selective sweeps, and identification of associations between sweep regions and growth-related metabolic traits.

    RESULTS: A total of 1,072,557 high-quality SFPs were detected and indications for 3,943 deletions and 1,007 duplications were obtained. A significantly lower than expected SFP frequency was observed in protein-, rRNA-, and tRNA-coding regions and in non-repetitive intergenic regions, while pseudogenes, transposons, and non-coding RNA genes are enriched with SFPs. Gene families involved in plant defence or in signalling were identified as highly polymorphic, while several other families including transcription factors are depleted of SFPs. 198 significant associations between metabolic genes and 9 metabolic and growth-related phenotypic traits were detected with annotation hinting at the nature of the relationship. Five significant selective sweep regions were also detected of which one associated significantly with a metabolic trait.

    CONCLUSIONS: We generated a high density polymorphism map for 54 A. thaliana accessions that highlights the variability of resistance genes across geographic ranges and used it to identify selective sweeps and associations between metabolic genes and metabolic phenotypes. Several associations show a clear biological relationship, while many remain requiring further investigation.

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