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  • 151.
    Berg, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computer Systems. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Efficient and Flexible Characterization of Data Locality through Native Execution Sampling2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Data locality is central to modern computer designs. The widening gap between processor speed and memory latency has introduced the need for a deep hierarchy of caches. Thus, the performance of an application is to a large extent dependent on the amount of data locality the caches can exploit. Some data locality comes naturally from the way most programs are written and the way their data is allocated in the memory. Compilers further try to create data locality by loop transformations and optimized data layout. Different ways of writing a program and/or laying out its data may improve an application’s locality even more. However, it is far from obvious how such a locality optimization can be achieved, especially since the optimizing compiler may have left the optimization job half done. Thus, efficient tools are needed to guide the software developers on their quest for data locality.

    The main contribution of this dissertation is a sample-based novel method for analyzing the data locality of an application. Very sparse data is collected during a single execution of the studied application. The sparse sampling adds a minimum overhead to the execution time, which enables complex applications running realistic data sets to be studied. The architecturalindependent information collected during the execution is fed to a mathematical cache model for predicting the cache miss ratio. The sparsely-collected data can be used to characterize the application’s data locality in respect to almost any possible cache hierarchy, such as complicated multiprocessor memory systems with multilevel cache hierarchies. Any combination of cache size, cache line size and degree of sharing can be modeled. Each new modeled design point takes only a fraction of a second to evaluate, even though the application from which the sampled data was collected may have executed for hours. This makes the tool not just usable for software developers, but also for hardware developers who need to evaluate a huge memory-system design space.

    We also discuss different ways of presenting data-locality information to a programmer in an intuitive and easily interpreted way. Some of the locality metrics we introduce utilize the flexibility of our algorithm and its ability to vary different cache parameters for one run. The dissertation also presents several prototype implementations of tools for profiling the memory system.

    List of papers
    1. SIP: Performance Tuning through Source Code Interdependence
    Open this publication in new window or tab >>SIP: Performance Tuning through Source Code Interdependence
    2002 In: Proceedings of the 8th International Euro-Par ConferenceArticle in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93582 (URN)
    Available from: 2005-10-19 Created: 2005-10-19Bibliographically approved
    2. StatCache: A Probabilistic Approach to Efficient and Accurate Data Locality Analysis
    Open this publication in new window or tab >>StatCache: A Probabilistic Approach to Efficient and Accurate Data Locality Analysis
    2004 In: Proceedings of the 2004 IEEE International Symposium on Performance Analysis of Systems and SoftwareArticle in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93583 (URN)
    Available from: 2005-10-19 Created: 2005-10-19Bibliographically approved
    3. Fast Data-Locality Profiling of Native Execution
    Open this publication in new window or tab >>Fast Data-Locality Profiling of Native Execution
    2005 (English)In: ACM SIGMETRICS Performance Evaluation Review, ISSN 0163-5999, Vol. 33, no 1, p. 169-180Article in journal (Refereed) Published
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-93584 (URN)10.1145/1071690.1064232 (DOI)
    Available from: 2005-10-19 Created: 2005-10-19 Last updated: 2018-01-13Bibliographically approved
    4. A Statistical Multiprocessor Cache Model
    Open this publication in new window or tab >>A Statistical Multiprocessor Cache Model
    2006 (English)In: Proc. International Symposium on Performance Analysis of Systems and Software: ISPASS 2006, Piscataway, NJ: IEEE , 2006, p. 89-99Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Piscataway, NJ: IEEE, 2006
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-93585 (URN)10.1109/ISPASS.2006.1620793 (DOI)1-4244-0186-0 (ISBN)
    Available from: 2005-10-19 Created: 2005-10-19 Last updated: 2018-01-13Bibliographically approved
  • 152.
    Berg, Jens
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Stable and High-Order Finite Difference Methods for Multiphysics Flow Problems2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Partial differential equations (PDEs) are used to model various phenomena in nature and society, ranging from the motion of fluids and electromagnetic waves to the stock market and traffic jams. There are many methods for numerically approximating solutions to PDEs. Some of the most commonly used ones are the finite volume method, the finite element method, and the finite difference method. All methods have their strengths and weaknesses, and it is the problem at hand that determines which method that is suitable. In this thesis, we focus on the finite difference method which is conceptually easy to understand, has high-order accuracy, and can be efficiently implemented in computer software.

    We use the finite difference method on summation-by-parts (SBP) form, together with a weak implementation of the boundary conditions called the simultaneous approximation term (SAT). Together, SBP and SAT provide a technique for overcoming most of the drawbacks of the finite difference method. The SBP-SAT technique can be used to derive energy stable schemes for any linearly well-posed initial boundary value problem. The stability is not restricted by the order of accuracy, as long as the numerical scheme can be written in SBP form. The weak boundary conditions can be extended to interfaces which are used either in domain decomposition for geometric flexibility, or for coupling of different physics models.

    The contributions in this thesis are twofold. The first part, papers I-IV, develops stable boundary and interface procedures for computational fluid dynamics problems, in particular for problems related to the Navier-Stokes equations and conjugate heat transfer. The second part, papers V-VI, utilizes duality to construct numerical schemes which are not only energy stable, but also dual consistent. Dual consistency alone ensures superconvergence of linear integral functionals from the solutions of SBP-SAT discretizations. By simultaneously considering well-posedness of the primal and dual problems, new advanced boundary conditions can be derived. The new duality based boundary conditions are imposed by SATs, which by construction of the continuous boundary conditions ensure energy stability, dual consistency, and functional superconvergence of the SBP-SAT schemes.

    List of papers
    1. A stable and high-order accurate conjugate heat transfer problem
    Open this publication in new window or tab >>A stable and high-order accurate conjugate heat transfer problem
    2010 (English)In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 229, p. 5440-5456Article in journal (Refereed) Published
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-122740 (URN)10.1016/j.jcp.2010.04.010 (DOI)000279139200010 ()
    Available from: 2010-04-13 Created: 2010-04-17 Last updated: 2018-01-12Bibliographically approved
    2. Spectral analysis of the continuous and discretized heat and advection equation on single and multiple domains
    Open this publication in new window or tab >>Spectral analysis of the continuous and discretized heat and advection equation on single and multiple domains
    2012 (English)In: Applied Numerical Mathematics, ISSN 0168-9274, E-ISSN 1873-5460, Vol. 62, p. 1620-1638Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-177315 (URN)10.1016/j.apnum.2012.05.002 (DOI)000309027700002 ()
    Available from: 2012-05-15 Created: 2012-07-08 Last updated: 2017-12-07Bibliographically approved
    3. Stable Robin solid wall boundary conditions for the Navier-Stokes equations
    Open this publication in new window or tab >>Stable Robin solid wall boundary conditions for the Navier-Stokes equations
    2011 (English)In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 230, p. 7519-7532Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-156456 (URN)10.1016/j.jcp.2011.06.027 (DOI)000294979400027 ()
    Available from: 2011-07-05 Created: 2011-07-23 Last updated: 2017-12-08Bibliographically approved
    4. Conjugate heat transfer for the unsteady compressible Navier–Stokes equations using a multi-block coupling
    Open this publication in new window or tab >>Conjugate heat transfer for the unsteady compressible Navier–Stokes equations using a multi-block coupling
    2013 (English)In: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 72, p. 20-29Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-187192 (URN)10.1016/j.compfluid.2012.11.018 (DOI)000314442900002 ()
    Available from: 2012-12-19 Created: 2012-12-04 Last updated: 2017-12-07Bibliographically approved
    5. Superconvergent functional output for time-dependent problems using finite differences on summation-by-parts form
    Open this publication in new window or tab >>Superconvergent functional output for time-dependent problems using finite differences on summation-by-parts form
    2012 (English)In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 231, p. 6846-6860Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-177320 (URN)10.1016/j.jcp.2012.06.032 (DOI)000307299400014 ()
    Available from: 2012-07-05 Created: 2012-07-08 Last updated: 2017-12-07Bibliographically approved
    6. On the impact of boundary conditions on dual consistent finite difference discretizations
    Open this publication in new window or tab >>On the impact of boundary conditions on dual consistent finite difference discretizations
    2013 (English)In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 236, p. 41-55Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-187194 (URN)10.1016/j.jcp.2012.11.019 (DOI)000314801500005 ()
    Available from: 2012-12-12 Created: 2012-12-04 Last updated: 2017-12-07Bibliographically approved
  • 153.
    Berg, Sylvia E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences. Nordic Volcanological Center, Institute of Earth Sciences, University of Iceland.
    Silicic Magma Genesis in Basalt-dominated Oceanic Settings: Examples from Iceland and the Canary Islands2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The origin of silicic magma in basalt-dominated oceanic settings is fundamental to our understanding of magmatic processes and formation of the earliest continental crust. Particularly significant is magma-crust interaction that can modify the composition of magma and the dynamics of volcanism. This thesis investigates silicic magma genesis on different scales in two ocean island settings. First, volcanic products from a series of voluminous Neogene silicic centres in northeast Iceland are investigated using rock and mineral geochemistry, U-Pb geochronology, and oxygen isotope analysis. Second, interfacial processes of magma-crust interaction are investigated using geochemistry and 3D X-ray computed microtomography on crustal xenoliths from the 2011-12 El Hierro eruption, Canary Islands.

    The results from northeast Iceland constrain a rapid outburst of silicic magmatism driven by a flare of the Iceland plume and/or by formation of a new rift zone, causing large volume injection of basaltic magma into hydrated basaltic crust. This promoted crustal recycling by partial melting of the hydrothermally altered Icelandic crust, thereby producing mixed-origin silicic melt pockets that reflect the heterogeneous nature of the crustal protolith with respect to oxygen isotopes. In particular, a previously unrecognised high-δ18O end-member on Iceland was documented, which implies potentially complex multi-component assimilation histories for magmas ascending through the Icelandic crust. Common geochemical traits between Icelandic and Hadean zircon populations strengthen the concept of Iceland as an analogue for early Earth, implying that crustal recycling in emergent rifts was pivotal in generating Earth’s earliest continental silicic crust.

    Crustal xenoliths from the El Hierro 2011-2012 eruption underline the role of partial melting and assimilation of pre-island sedimentary layers in the early shield-building phase of ocean islands. This phenomenon may contribute to the formation of evolved magmas, and importantly, the release of volatiles from the xenoliths may be sufficient to increase the volatile load of the magma and temporarily alter the character and intensity of an eruption.

    This thesis sheds new light on the generation of silicic magma in basalt-dominated oceanic settings and emphasises the relevance of magma-crust interaction for magma evolution, silicic crust formation, and eruption style from early Earth to present.

    List of papers
    1. Iceland's best kept secret
    Open this publication in new window or tab >>Iceland's best kept secret
    Show others...
    2014 (English)In: Geology Today, ISSN 0266-6979, E-ISSN 1365-2451, Vol. 30, no 2, p. 54-60Article in journal (Refereed) Published
    Abstract [en]

    The ‘forgotten fjords’ and ‘deserted inlets’ of NE-Iceland, in the region between Borgarfjörður Eystri and Loðmundarfjörður, are not only prominent because of their pristine landscape, their alleged elfin settlements, and the puffins that breed in the harbour, but also for their magnificent geology. From a geological point of view, the area may hold Iceland's best kept geological secret. The greater Borgarfjörður Eystri area hosts mountain chains that consist of voluminous and colourful silicic rocks that are concentrated within a surprisingly small area (Fig. 1), and that represent the second-most voluminous occurrence of silicic rocks in the whole of Iceland. In particular, the presence of unusually large volumes of ignimbrite sheets documents extremely violent eruptions during the Neogene, which is atypical for this geotectonic setting. As a group of geoscientists from Uppsala University (Sweden) and the Nordic Volcanological Center (NordVulk, Iceland) we set out to explore this remote place, with the aim of collecting material that may allow us to unravel the petrogenesis of these large volumes of silicic rocks. This effort could provide an answer to a long-standing petrological dilemma; the question of how silicic continental crust is initially created. Here we document on our geological journey, our field strategy, and describe our field work in the remote valleys of NE-Iceland.

    National Category
    Geosciences, Multidisciplinary
    Research subject
    Earth Science with specialization in Mineral Chemistry, Petrology and Tectonics
    Identifiers
    urn:nbn:se:uu:diva-213020 (URN)DOI: 10.1111/gto.12042 (DOI)
    Available from: 2013-12-17 Created: 2013-12-17 Last updated: 2017-12-06
    2. Rapid generation of high-silica magmas in basalt-dominated rift settings
    Open this publication in new window or tab >>Rapid generation of high-silica magmas in basalt-dominated rift settings
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Geology Geochemistry
    Research subject
    Mineral Chemistry, Petrology and Tectonics
    Identifiers
    urn:nbn:se:uu:diva-272262 (URN)
    Available from: 2016-01-13 Created: 2016-01-13 Last updated: 2016-02-19
    3. Zircons from northeast Iceland analogous to those from early Earth
    Open this publication in new window or tab >>Zircons from northeast Iceland analogous to those from early Earth
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Geochemistry
    Identifiers
    urn:nbn:se:uu:diva-272264 (URN)
    Available from: 2016-01-13 Created: 2016-01-13 Last updated: 2016-02-19
    4. Origin of high whole-rock δ18O values in rhyolites from northeast Iceland
    Open this publication in new window or tab >>Origin of high whole-rock δ18O values in rhyolites from northeast Iceland
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Geochemistry
    Identifiers
    urn:nbn:se:uu:diva-272315 (URN)
    Available from: 2016-01-13 Created: 2016-01-13 Last updated: 2016-02-19
    5. Floating stones off El Hierro, Canary Islands: xenoliths of pre-island sedimentary origin in the early products of the October 2011 eruption
    Open this publication in new window or tab >>Floating stones off El Hierro, Canary Islands: xenoliths of pre-island sedimentary origin in the early products of the October 2011 eruption
    Show others...
    2012 (English)In: Solid Earth, ISSN 1869-9510, E-ISSN 1869-9529, Vol. 3, no 1, p. 97-110Article in journal (Refereed) Published
    Abstract [en]

    A submarine eruption started off the south coast of El Hierro, Canary Islands, on 10 October 2011 and continues at the time of this writing (February 2012). In the first days of the event, peculiar eruption products were found floating on the sea surface, drifting for long distances from the eruption site. These specimens, which have in the meantime been termed "restingolites" (after the close-by village of La Restinga), appeared as black volcanic "bombs" that exhibit cores of white and porous pumice-like material. Since their brief appearance, the nature and origin of these "floating stones" has been vigorously debated among researchers, with important implications for the interpretation of the hazard potential of the ongoing eruption. The "restingolites" have been proposed to be either (i) juvenile high-silica magma (e. g. rhyolite), (ii) remelted magmatic material (trachyte), (iii) altered volcanic rock, or (iv) reheated hyaloclastites or zeolite from the submarine slopes of El Hierro. Here, we provide evidence that supports yet a different conclusion. We have analysed the textures and compositions of representative "restingolites" and compared the results to previous work on similar rocks found in the Canary Islands. Based on their high-silica content, the lack of igneous trace element signatures, the presence of remnant quartz crystals, jasper fragments and carbonate as well as wollastonite (derived from thermal overprint of carbonate) and their relatively high oxygen isotope values, we conclude that "restingolites" are in fact xenoliths from pre-island sedimentary layers that were picked up and heated by the ascending magma, causing them to partially melt and vesiculate. As they are closely resembling pumice in appearance, but are xenolithic in origin, we refer to these rocks as "xeno-pumice". The El Hierro xeno-pumices hence represent messengers from depth that help us to understand the interaction between ascending magma and crustal lithologies beneath the Canary Islands as well as in similar Atlantic islands that rest on sediment-covered ocean crust (e. g. Cape Verdes, Azores). The occurrence of "restingolites" indicates that crustal recycling is a relevant process in ocean islands, too, but does not herald the arrival of potentially explosive high-silica magma in the active plumbing system beneath El Hierro.

    Place, publisher, year, edition, pages
    Copernicus Publications, 2012
    National Category
    Geology Geochemistry
    Identifiers
    urn:nbn:se:uu:diva-171483 (URN)10.5194/se-3-97-2012 (DOI)000309884400008 ()
    Funder
    Swedish Research Council
    Note

    Correction in Solid Earth. Vol. 3(2) p. 189. DOI: 10.5194/se-3-189-2012

    Available from: 2012-03-19 Created: 2012-03-19 Last updated: 2019-10-03Bibliographically approved
    6. Heterogeneous vesiculation of 2011 El Hierro xeno-pumice revealed by X-ray computed microtomography
    Open this publication in new window or tab >>Heterogeneous vesiculation of 2011 El Hierro xeno-pumice revealed by X-ray computed microtomography
    Show others...
    2016 (English)In: Bulletin of Volcanology, ISSN 0258-8900, E-ISSN 1432-0819, Vol. 78, no 12, article id 85Article in journal (Refereed) Published
    Abstract [en]

    During the first week of the 2011 El Hierro submarine eruption, abundant light-coloured pumiceous, high-silica volcanic bombs coated in dark basanite were found floating on the sea. The composition of the light-coloured frothy material ('xeno-pumice') is akin to that of sedimentary rocks from the region, but the textures resemble felsic magmatic pumice, leaving their exact mode of formation unclear. To help decipher their origin, we investigated representative El Hierro xeno-pumice samples using X-ray computed microtomography for their internal vesicle shapes, volumes, and bulk porosity, as well as for the spatial arrangement and size distributions of vesicles in three dimensions (3D). We find a wide range of vesicle morphologies, which are especially variable around small fragments of rock contained in the xeno-pumice samples. Notably, these rock fragments are almost exclusively of sedimentary origin, and we therefore interpret them as relicts an the original sedimentary ocean crust protolith(s). The irregular vesiculation textures observed probably resulted from pulsatory release of volatiles from multiple sources during xeno-pumice formation, most likely by successive release of pore water and mineral water during incremental heating and decompression of the sedimentary protoliths.

    Keywords
    El Hierro, Xeno-pumice, X-CT imaging, Vesicle morphologies, Vesicle size distribution, Heterogeneous vesiculation, Sedimentary ocean crust
    National Category
    Geology
    Identifiers
    urn:nbn:se:uu:diva-272316 (URN)10.1007/s00445-016-1080-x (DOI)000394130700001 ()
    Funder
    The Royal Swedish Academy of SciencesSwedish Research Council
    Note

    The manuscript version of this article was used under the name "Heterogeneous vesiculation of 2011 El Hierro xeno-pumice revealed by synchrotron μ-CT" in the following thesis: Silicic Magma Genesis in Basalt-dominated Oceanic Settings: Examples from Iceland and the Canary Islands http://uu.diva-portal.org/smash/record.jsf?pid=diva2:893923

    Available from: 2016-01-13 Created: 2016-01-13 Last updated: 2017-11-30Bibliographically approved
    7. Hur bildades kontinenterna?
    Open this publication in new window or tab >>Hur bildades kontinenterna?
    2014 (Swedish)In: Geologiskt Forum, ISSN 1104-4721, Vol. 84, p. 12-13Article in journal (Other (popular science, discussion, etc.)) Published
    Place, publisher, year, edition, pages
    Jönköping: Geologiska Föreningen, 2014
    National Category
    Geology
    Identifiers
    urn:nbn:se:uu:diva-272317 (URN)
    Available from: 2016-01-13 Created: 2016-01-13 Last updated: 2016-02-19
  • 154.
    Berga Quintana, Mercè
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Assembly Mechanisms in Aquatic Bacterial Communities: The Role of Disturbances, Dispersal and History2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Environmental conditions, biotic interactions, dispersal and history have been suggested to be important processes influencing the spatial distribution of organisms and thus to affect community assembly. Understanding how these processes influence community assembly is important, particularly because community diversity and composition are suggested to be relevant for ecosystem functioning. Moreover, bacteria are strongly contributing to nutrient and carbon cycle. Bacteria are highly abundant and ubiquitous, and thus it is relevant to study how they are assembled. This thesis aims to gain insight on the role of these processes on aquatic bacterial community assembly, diversity and functioning. The studies included in this thesis involve transplant and microcosm experiments performed in the lab as well as manipulation experiments and field surveys in a natural rock pool systems. Bacterial community composition was addressed by analysis of 16S rRNA gene and community functioning by measuring bacterial production, community respiration and the ability to use different carbon substrates. This thesis highlights that species sorting is a very important assembly mechanism for bacterial communities, but also finds that other processes such as dispersal and history contribute to the patterns observed. Dispersal caused rescuing effects compensating for losses of diversity; at the same time it increased the similarity between communities. Moreover, bacteria have shown a high level of functional plasticity when colonizing a new locality. Interestingly, past environmental conditions explained the structure of bacterial communities better than present-day environmental conditions. Disturbances and biotic interactions are also important in the assembly of communities. Disturbance caused temporary shifts in bacterial function and changes in composition, the magnitude of which depended on the intensity and the frequency of the disturbance. However, natural aquatic bacterial communities showed quite high resilience capacities. Competition can shift the proportion of generalists and specialists species whereas predation or trophic interactions have been found to decrease diversity and to modify the importance of stochasticity. Both caused alterations of community functioning. Finally, this thesis shows that the diversity-functioning relationship is context dependent. Further research should be directed to understanding the intensity and direction of changes in composition and how this affects the functionality of bacterial communities

    List of papers
    1. Effects of Disturbance Intensity and Frequency on Bacterial Community Composition and Function
    Open this publication in new window or tab >>Effects of Disturbance Intensity and Frequency on Bacterial Community Composition and Function
    2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 5, p. e36959-Article in journal (Refereed) Published
    Abstract [en]

    Disturbances influence community structure and ecosystem functioning. Bacteria are key players in ecosystems and it is therefore crucial to understand the effect of disturbances on bacterial communities and how they respond to them, both compositionally and functionally. The main aim of this study was to test the effect of differences in disturbance strength on bacterial communities. For this, we implemented two independent short-term experiments with dialysis bags containing natural bacterial communities, which were transplanted between ambient and 'disturbed' incubation tanks, manipulating either the intensity or the frequency of a salinity disturbance. We followed changes in community composition by terminal restriction fragment analysis (T-RFLP) and measured various community functions (bacterial production, carbon substrate utilization profiles and rates) directly after and after a short period of recovery under ambient conditions. Increases in disturbance strength resulted in gradually stronger changes in bacterial community composition and functions. In the disturbance intensity experiment, the sensitivity to the disturbance and the ability of recovery differed between different functions. In the disturbance frequency experiment, effects on the different functions were more consistent and recovery was not observed. Moreover, in case of the intensity experiment, there was also a time lag in the responses of community composition and functions, with functional responses being faster than compositional ones. To summarize, our study shows that disturbance strength has the potential to change the functional performance and composition of bacterial communities. It further highlights that the overall effects, rates of recovery and the degree of congruence in the response patterns of community composition and functioning along disturbance gradients depend on the type of function and the character of the disturbance.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-177625 (URN)10.1371/journal.pone.0036959 (DOI)000305339400046 ()
    Available from: 2012-07-18 Created: 2012-07-17 Last updated: 2017-12-07Bibliographically approved
    2. Testing responses of bacterial communities to environmental change using whole ecosystem manipulation experiments
    Open this publication in new window or tab >>Testing responses of bacterial communities to environmental change using whole ecosystem manipulation experiments
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology Microbiology
    Identifiers
    urn:nbn:se:uu:diva-207179 (URN)
    Available from: 2013-09-10 Created: 2013-09-10 Last updated: 2014-05-08
    3. Mechanisms determining the fate of dispersed bacterial communities in new environments
    Open this publication in new window or tab >>Mechanisms determining the fate of dispersed bacterial communities in new environments
    2013 (English)In: ISME Journal, ISSN 1751-7362, Vol. 7, no 1, p. 61-71Article in journal (Refereed) Published
    Abstract [en]

    Recent work has shown that dispersal has an important role in shaping microbial communities. However, little is known about how dispersed bacteria cope with new environmental conditions and how they compete with local resident communities. To test this, we implemented two full-factorial transplant experiments with bacterial communities originating from two sources (freshwater or saline water), which were incubated, separately or in mixes, under both environmental conditions. Thus, we were able to separately test for the effects of the new environment with and without interactions with local communities. We determined community composition using 454-pyrosequencing of bacterial 16S rRNA to specifically target the active fraction of the communities, and measured several functional parameters. In absence of a local resident community, the net functional response was mainly affected by the environmental conditions, suggesting successful functional adaptation to the new environmental conditions. Community composition was influenced both by the source and the incubation environment, suggesting simultaneous effects of species sorting and functional plasticity. In presence of a local resident community, functional parameters were higher compared with those expected from proportional mixes of the unmixed communities in three out of four cases. This was accompanied by an increase in the relative abundance of generalists, suggesting that competitive interactions among local and immigrant taxa could explain the observed functional overachievement. In summary, our results suggest that environmental filtering, functional plasticity and competition are all important mechanisms influencing the fate of dispersed communities.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-192014 (URN)10.1038/ismej.2012.80 (DOI)000313236000006 ()
    Available from: 2013-01-24 Created: 2013-01-15 Last updated: 2014-01-23Bibliographically approved
    4. The spatial structure of bacterial communities is influenced by historical environmental conditions
    Open this publication in new window or tab >>The spatial structure of bacterial communities is influenced by historical environmental conditions
    2014 (English)In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 95, no 5, p. 1134-1140Article in journal (Refereed) Published
    Abstract [en]

    The spatial structure of ecological communities, including that of bacteria, is often influenced by species sorting by contemporary environmental conditions. Moreover, historical processes, i.e., ecological and evolutionary events that have occurred at some point in the past, such as dispersal limitation, drift, priority effects, or selection by past environmental conditions, can be important, but are generally investigated much less. Here, we conducted a field study using 16 rock pools, where we specifically compared the importance of past vs. contemporary environmental conditions for bacterial community structure by correlating present differences in bacterial community composition among pools to environmental conditions measured on the same day, as well as to those measured 2, 4, 6, and 8 d earlier. The results prove that selection by past environmental conditions exists, since we were able to show that bacterial communities are, to a greater extent, an imprint of past compared to contemporary environmental conditions. We suggest that this is the result of a combination of different mechanisms, including priority effects that cause rapid adaptation to new environmental conditions of taxa that have been initially selected by past environmental conditions, and slower rates of turnover in community composition compared to environmental conditions.

    National Category
    Ecology Microbiology
    Identifiers
    urn:nbn:se:uu:diva-207181 (URN)10.1890/13-1300.1 (DOI)000336740500003 ()
    Available from: 2013-09-10 Created: 2013-09-10 Last updated: 2017-12-06Bibliographically approved
    5. Effects of predation and dispersal on the diversity an functioning of bacterial metacommunities
    Open this publication in new window or tab >>Effects of predation and dispersal on the diversity an functioning of bacterial metacommunities
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology Microbiology
    Identifiers
    urn:nbn:se:uu:diva-207177 (URN)
    Available from: 2013-09-10 Created: 2013-09-10 Last updated: 2014-01-23
  • 155.
    Bergek, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Population divergence at small spatial scales: – theoretical and empirical investigations in perch2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Genetically structured populations arise when gene flow between groups of individuals is hindered by geographical, behavioural or temporal barriers. The identification of such groups is important for understanding evolution and has large implications for conservation concern. The field of population subdivision has received a lot of interest throughout the years and gained empirical support from a number of species. However, very little is known about population structure at small spatial scales, especially in a highly mobile species such as fish. The main object for my thesis was to further investigate population differentiation, explicitly at small spatial scales in the Eurasian perch. My results show that in this species, genetic differentiation occurs, even at very small spatial scales, both within lakes and in the Baltic Sea. Additionally, the differentiation can be stable over years and thus have a large impact in the evolution of adaptation to different environments. I also found barriers to gene flow that overlapped with the largest change in spring temperature, suggesting a temporal difference in spawning. Morphological differences were found at these small scales as well which indicates that a difference in food resources might be an underlying cause of change. My thesis work shows that the aquatic environment might not be as homogenous as widely thought and that there could be barriers or adaptations to different environments that hinder the fish from genetic panmixia. Slight patterns of isolation by distance (IBD) were found in the Baltic Sea, implying that the distance (i.e. currents) effect the level of differentiation via drifting of larvae and/or small fish. However, I have also theoretically investigated the IBD model of and seen that it is no longer correct when differences in population sizes are introduced. The pattern of IBD can mean high levels of gene flow or no gene flow at all, solely dependent on population size differences and fluctuations. My thesis has resulted in new and important findings regarding the existence and cause of genetic differentiation at very small spatial scales and thus added new knowledge into the field of evolution and speciation. In addition, my results also give insights into the contemporary state of the Eurasian perch and future evolutionary potential.

    List of papers
    1. Cryptic barriers to dispersal within a lake allow genetic differentiation of Eurasian perch
    Open this publication in new window or tab >>Cryptic barriers to dispersal within a lake allow genetic differentiation of Eurasian perch
    2007 (English)In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 61, no 8, p. 2035-2041Article in journal (Refereed) Published
    Abstract [en]

    Gene flow between coexisting or nearby populations normally prevents genetic divergence and local adaptation. Despite this, there are an increasing number of reports of sympatric sister taxa, indicating potential divergence and speciation in the face of gene flow. A large number of such reported cases involve lake-dwelling fish, which are expected to run into few physical barriers to dispersal within their aquatic habitat. However, such cases may not necessarily reflect sympatric speciation if cryptic dispersal barriers are common in lakes and other aquatic systems. In this study, we examined genetic differentiation in perch (Perca fluviatilis L.) from nine locations in a single, small lake (24 km(2)), using microsatellites. We detected significant genetic differentiation in all but two pairwise comparisons. These patterns were not consistent with divergence by distance or the existence of kin groups. Instead, they suggest that cryptic barriers to dispersal exist within the lake, allowing small-scale genetic divergence. Such an observation suggests that allopatric (or parapatric) divergence may be possible, even in small, apparently homogenous environments such as lakes. This has important consequences for how we currently view evidence from nature for sympatric speciation.

    Place, publisher, year, edition, pages
    Oxford: Wiley-Blackwell, 2007
    Keywords
    Allopatric speciation, Geographic reproductive barriers, Microsatellites, Perca fluviatilis L., Small-scale genetic divergence, sympatric speciation
    National Category
    Biological Sciences
    Research subject
    Animal Ecology
    Identifiers
    urn:nbn:se:uu:diva-107227 (URN)10.1111/j.1558-5646.2007.00163.x (DOI)000248600300022 ()
    Available from: 2009-07-30 Created: 2009-07-30 Last updated: 2017-12-13Bibliographically approved
    2. Spatiotemporal analysis shows stable genetic differentiation and barriers to dispersal in the Eurasian perch (Perca fluviatilis L.)
    Open this publication in new window or tab >>Spatiotemporal analysis shows stable genetic differentiation and barriers to dispersal in the Eurasian perch (Perca fluviatilis L.)
    2009 (English)In: Evolutionary Ecology Research, ISSN 1522-0613, E-ISSN 1937-3791, Vol. 11, no 5, p. 827-840Article in journal (Refereed) Published
    Abstract [en]

    Background: Recently, unexpected or cryptic barriers to gene flow causing genetic discontinuities have been found in a number of animal taxa, even in apparently highly connected areas such as aquatic environments. 

    Goal: Investigate the temporal stability of previously documented microgeographic genetic structure in a fish.

    Organism: Eurasian perch (Perca fluviatilis L.)

    Method: We sampled four locations over a period of 2 years. We used six microsatellites to investigate population differentiation. We compared within-year to between-year differentiation.

    Results: The significant genetic differentiation found between locations in 2004 was still present in 2006. The strongest barriers to gene flow in the lake were consistent over both sampling periods. Furthermore, temporal differentiation existed within each site between the years. Populations of perch appear to cluster in different patches in the lake that harbour genetically differentiated groups of fish. Hence, limited migration and barriers to dispersal can persist over time, even at a very small geographical scale and in an open aquatic environment.

    Place, publisher, year, edition, pages
    Tucson: Evolutionary Ecology Ltd., 2009
    Keywords
    Barriers to gene flow, Microsatellites, Perca fluviatilis L, Small-scale genetic divergence, Spatiotemporal stability
    National Category
    Biological Sciences
    Research subject
    Animal Ecology
    Identifiers
    urn:nbn:se:uu:diva-107228 (URN)000269674500009 ()
    Available from: 2009-07-30 Created: 2009-07-30 Last updated: 2018-05-31Bibliographically approved
    3. Genetic and morphological divergence reveals local subdivision of perch (Perca fluviatilis L.)
    Open this publication in new window or tab >>Genetic and morphological divergence reveals local subdivision of perch (Perca fluviatilis L.)
    2009 (English)In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 96, no 4, p. 746-758Article in journal (Refereed) Published
    Abstract [en]

    The level of gene flow is an important factor influencing genetic differentiation between populations. Typically, geographic distance is considered to be the major factor limiting dispersal and should thus only influence the degree of genetic divergence at larger spatial scales. However, recent studies have revealed the possibility for small-scale genetic differentiation, suggesting that the spatial scale considered is pivotal for finding patterns of isolation by distance. To address this question, genetic and morphological differentiation were studied at two spatial scales (range 2–13 km and range 300 m to 2 km) in the perch (Perca fluviatilis L.) from the east coast archipelago of Sweden, using seven microsatellite loci and geometric morphometrics. We found highly significant genetic differentiation between sampled locations at both scales. At the larger spatial scale, the distance not affecting the level of divergence. At the small scale, however, we found subtle patterns of isolation by distance. In addition, we also found morphological divergence between locations, congruent with a spatial separation at a microgeographic scale, most likely due to phenotypic plasticity. The present study highlights the importance of geographical scale and indicates that there might be a disparity between the dispersal capacity of a species and the actual movement of genes. Thus, how we view the environment and possible barriers to dispersal might have great implications for our ability to fully understand the evolution of genetic differentiation, local adaptation, and, in the end, speciation.

    Place, publisher, year, edition, pages
    Wiley-Blackwell, 2009
    Keywords
    Differentiation, Dispersal, Gene flow, Isolation by distance, Microsatellites, Morphometrics
    National Category
    Biological Sciences
    Research subject
    Animal Ecology
    Identifiers
    urn:nbn:se:uu:diva-107229 (URN)10.1111/j.1095-8312.2008.01149.x (DOI)000264730400004 ()
    Available from: 2009-07-30 Created: 2009-07-30 Last updated: 2017-12-13Bibliographically approved
    4. Population differentiation in perch Perca fluviatilis: environmental effects on gene flow?
    Open this publication in new window or tab >>Population differentiation in perch Perca fluviatilis: environmental effects on gene flow?