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  • 151.
    Björnerfeldt, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Consequences of the Domestication of Man’s Best Friend, The Dog2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The dog was the first animal to be domesticated and the process started at least 15 000 years ago. Today it is the most morphologically diverse mammal, with a huge variation in size and shape. Dogs have always been useful to humans in several ways, from being a food source, hunting companion, guard, social companion and lately also a model for scientific research.

    This thesis describes some of the changes that have occurred in the dog’s genome, both during the domestication process and later through breed creation. To give a more comprehensive view, three genetic systems were studied: maternally inherited mitochondrial DNA, paternally inherited Y chromosome and biparental autosomal chromosomes. I also sequenced complete mitochondrial genomes to view the effect new living conditions might have had on dogs’ genes after domestication. Finally, knowledge of the genetic structure in purebred dogs was used to test analytic methods usable in other species or in natural populations where little information is available.

    The domestication process appears to have caused a relaxation of the selective constraint in the mitochondrial genome, leading to a faster rate of accumulation of nonsynonymous changes in the mitochondrial genes. Later, the process of breed creation resulted in genetically separated breed groups. Breeds are a result from an unequal contribution of males and females with only a few popular sires contributing and a larger amount of dams. However, modern breeder preferences might lead to disruptive selective forces within breeds, which can result in additional fragmentation of breeds. The increase in linkage disequilibrium that this represents increases the value of purebred dogs as model organisms for the identification and mapping of diseases and traits. Purebred dogs’ potential for these kinds of studies will probably increase the more we know about the dog’s genome.

    List of papers
    1. Relaxation of selective constraint on dog mitochondrial DNA following domestication
    Open this publication in new window or tab >>Relaxation of selective constraint on dog mitochondrial DNA following domestication
    2006 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 16, no 8, p. 990-994Article in journal (Refereed) Published
    Abstract [en]

    The domestication of dogs caused a dramatic change in their way of life compared with that of their ancestor, the gray wolf. We hypothesize that this new life style changed the selective forces that acted upon the species, which in turn had an effect on the dog's genome. We sequenced the complete mitochondrial DNA genome in 14 dogs, six wolves, and three coyotes. Here we show that dogs have accumulated nonsynonymous changes in mitochondrial genes at a faster rate than wolves, leading to elevated levels of variation in their proteins. This suggests that a major consequence of domestication in dogs was a general relaxation of selective constraint on their mitochondrial genome. If this change also affected other parts of the dog genome, it could have facilitated the generation of novel functional genetic diversity. This diversity could thus have contributed raw material upon which artificial selection has shaped modern breeds and may therefore be an important source of the extreme phenotypic variation present in modern-day dogs.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95703 (URN)10.1101/gr.5117706 (DOI)000239441400005 ()16809672 (PubMedID)
    Available from: 2007-04-12 Created: 2007-04-12 Last updated: 2017-12-14Bibliographically approved
    2. Unequal contribution of sexes in the origin of dog breeds
    Open this publication in new window or tab >>Unequal contribution of sexes in the origin of dog breeds
    Show others...
    2006 (English)In: Genetics, ISSN 0016-6731, Vol. 172, no 2, p. 1121–1128-Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95704 (URN)
    Available from: 2007-04-12 Created: 2007-04-12 Last updated: 2009-03-31Bibliographically approved
    3. Disruptive selection within dog breeds
    Open this publication in new window or tab >>Disruptive selection within dog breeds
    (English)Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-95705 (URN)
    Available from: 2007-04-12 Created: 2007-04-12 Last updated: 2009-03-31Bibliographically approved
    4. Estimation of recent gene flow in metapopulations: using poodles as a model organism
    Open this publication in new window or tab >>Estimation of recent gene flow in metapopulations: using poodles as a model organism
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95706 (URN)
    Available from: 2007-04-12 Created: 2007-04-12 Last updated: 2010-01-14Bibliographically approved
    5. Evaluation of methods for single hair DNA amplification
    Open this publication in new window or tab >>Evaluation of methods for single hair DNA amplification
    2007 (English)In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, no 4, p. 977-981Article in journal (Refereed) Published
    Abstract [en]

    Because of the low amount of DNA in single hairs, it may be difficult to obtain reliable genotypes for forensic and conservation genetics studies. We therefore compared different methods for reliably genotyping single hair samples. Our results indicate that preliminary whole genome amplification can increase the likelihood of successfully genotyping a single hair compared to other commonly used protocols. The difference between the methods is small for single locus comparisons, but it becomes more important in multi-locus comparisons. The economic and time costs of the whole genome amplification may prevent its large-scale use in non-invasive monitoring programs. Nevertheless, it may be a very useful approach for the analysis of especially valuable samples.

    Keywords
    Chelex, Dropout, GenomiPhi, Noninvasive monitoring, Whole genome amplification
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95707 (URN)10.1007/s10592-006-9220-z (DOI)000248300300019 ()
    Available from: 2007-04-12 Created: 2007-04-12 Last updated: 2017-12-14Bibliographically approved
  • 152.
    Björnerfeldt, Susanne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hailer, Frank
    Nord, Maria
    Vilà, Carles
    Disruptive selection within dog breedsArticle in journal (Refereed)
  • 153.
    Björnerfeldt, Susanne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hailer, Frank
    Vilà, Carles
    Estimation of recent gene flow in metapopulations: using poodles as a model organismManuscript (Other (popular science, discussion, etc.))
  • 154.
    Björnerfeldt, Susanne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Evaluation of methods for single hair DNA amplification2007In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, no 4, p. 977-981Article in journal (Refereed)
    Abstract [en]

    Because of the low amount of DNA in single hairs, it may be difficult to obtain reliable genotypes for forensic and conservation genetics studies. We therefore compared different methods for reliably genotyping single hair samples. Our results indicate that preliminary whole genome amplification can increase the likelihood of successfully genotyping a single hair compared to other commonly used protocols. The difference between the methods is small for single locus comparisons, but it becomes more important in multi-locus comparisons. The economic and time costs of the whole genome amplification may prevent its large-scale use in non-invasive monitoring programs. Nevertheless, it may be a very useful approach for the analysis of especially valuable samples.

  • 155.
    Björnerfeldt, Susanne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Webster, Matthew T.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Relaxation of selective constraint on dog mitochondrial DNA following domestication2006In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 16, no 8, p. 990-994Article in journal (Refereed)
    Abstract [en]

    The domestication of dogs caused a dramatic change in their way of life compared with that of their ancestor, the gray wolf. We hypothesize that this new life style changed the selective forces that acted upon the species, which in turn had an effect on the dog's genome. We sequenced the complete mitochondrial DNA genome in 14 dogs, six wolves, and three coyotes. Here we show that dogs have accumulated nonsynonymous changes in mitochondrial genes at a faster rate than wolves, leading to elevated levels of variation in their proteins. This suggests that a major consequence of domestication in dogs was a general relaxation of selective constraint on their mitochondrial genome. If this change also affected other parts of the dog genome, it could have facilitated the generation of novel functional genetic diversity. This diversity could thus have contributed raw material upon which artificial selection has shaped modern breeds and may therefore be an important source of the extreme phenotypic variation present in modern-day dogs.

  • 156.
    Bodare, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conservation Genetics and Speciation in Asian Forest Trees2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Tropical forests are important because they are the home of millions of species at the same time as they perform ecosystem services and provide food, cash income and raw materials for the people living there. The present thesis elucidates questions relevant to the conservation of selected forest trees as it adds to the knowledge in the phylogeny, population structure, genetic diversity and adaptation in these species.

    We investigated the genetic diversity and speciation of four spruce species around the Qinghai-Tibetan Plateau (QTP), Western China, and one from Taiwan. Nucleotide diversity was low in P. schrenkiana and the Taiwanese P. morrisonicola but higher in P. likiangensis, P. purpurea and P. wilsonii. This can be explained by the population bottlenecks that were detected in the two former species by coalescent-based analysis. The phylogenetic relationships between the five species were difficult to interpret, possibly because other Asian spruce species might have been involved. However, all species are distinct except P. purpurea, which likely has a hybrid origin. 

    The rate of bud set and expression of the FTL2 gene in response to photoperiod in the southernmost growing spruce species, P. morrisonicola, was studied. We found that in this species, although growing near the equator, bud set appears to be induced mainly by a shortening of photoperiod, similarly to its more northerly growing spruce relatives. In addition, seedlings originating from mother trees growing at higher elevations showed a trend towards earlier bud set than seedlings originating from mother trees at lower altitudes.

    We also studied the population structure and genetic diversity in the endemic white cedar (Dysoxylum malabaricum) in the Western Ghats, India. Overall, no increase in inbreeding that could be related to human activities could be detected. Populations appear to have maintained genetic diversity and gene flow in spite of forest fragmentation over the distribution range. However, there is a severe lack of juveniles and young adults in several populations that needs to be further addressed. Finally, we recommend conservation units based on population structure.

    List of papers
    1. 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
    2. Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)
    Open this publication in new window or tab >>Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)
    2013 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, p. 3320-3333Article in journal (Refereed) Published
    Abstract [en]

    Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long-term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3–0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false-positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4–8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.

    National Category
    Natural Sciences Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-198100 (URN)10.1002/ece3.698 (DOI)000324932600011 ()
    Note

    De två (2) första författarna delar förstaförfattarskapet.

    Available from: 2013-04-09 Created: 2013-04-09 Last updated: 2017-12-06Bibliographically approved
    3. Photoperiodic control of bud set and FTL2 expression in a tropical spruce species  (Picea morrisonicola)
    Open this publication in new window or tab >>Photoperiodic control of bud set and FTL2 expression in a tropical spruce species  (Picea morrisonicola)
    (English)Manuscript (preprint) (Other academic)
    National Category
    Natural Sciences
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-198107 (URN)
    Available from: 2013-04-09 Created: 2013-04-09 Last updated: 2013-08-30
    4. Genetic structure and demographic history of the endangered tree species, Dysoxylum  malabaricum (Meliaceae) in Western Ghats, India: Implications for conservation in a  biodiversity hotspot
    Open this publication in new window or tab >>Genetic structure and demographic history of the endangered tree species, Dysoxylum  malabaricum (Meliaceae) in Western Ghats, India: Implications for conservation in a  biodiversity hotspot
    Show others...
    2013 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, p. 3233-3248Article in journal (Other academic) Published
    Abstract [en]

    The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylummalabaricum (white cedar) is an economically important tree species, endemic to theWestern Ghats, India, one of the world's eight most important biodiversity hotspots. As D.malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-widegenetic structure of twelve D.malabaricum populations was evaluated to assess the impact ofhuman activities on genetic diversity and infer the species' evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (F-IS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred beforethe last glacial maximum. Finally we discussed the implications of these results, in particularthe presence of a clear pattern of historical genetic subdivision, on conservation policies.

    National Category
    Natural Sciences
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-198109 (URN)10.1002/ece3.669 (DOI)000324932600004 ()
    Note

    De två (2) första författarna delar förstaförfattarskapet.

    Available from: 2013-04-09 Created: 2013-04-09 Last updated: 2017-12-06Bibliographically approved
    5. Landscape and fine-scale genetic structure of white cedar (Dysoxylum malabaricum) in disturbed forest patches of the Western Ghats, India
    Open this publication in new window or tab >>Landscape and fine-scale genetic structure of white cedar (Dysoxylum malabaricum) in disturbed forest patches of the Western Ghats, India
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    Conservation genetics, Dysoxylum malabaricum, fragmentation, land use, spatial genetic structure, Western Ghats
    National Category
    Natural Sciences
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-198700 (URN)
    Funder
    Sida - Swedish International Development Cooperation Agency
    Available from: 2013-04-23 Created: 2013-04-23 Last updated: 2013-08-30
  • 157.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. 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.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Photoperiodic control of bud set and FTL2 expression in a tropical spruce species  (Picea morrisonicola)Manuscript (preprint) (Other academic)
  • 158.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ravikanth, G
    Ashoka Trust for Research in Ecology and the Environment.
    Sascha A, Ismail
    Department of Environmental Systems Science, ETH Zürich.
    Kumara Patel, Mohana
    University of Agricultural Sciences, Bangalore .
    Spanu, Ilaria
    Plant Genetics Institute National Research Council.
    Vasudeva, R
    Dharwad College of Forestry, Campus Karnataka .
    Uma Shaanker, R
    Ashoka Trust for Research in Ecology and the Environment.
    Vendramin, Giovanni Giuseppe
    5Plant Genetics Institute National Research Council.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Landscape and fine-scale genetic structure of white cedar (Dysoxylum malabaricum) in disturbed forest patches of the Western Ghats, IndiaManuscript (preprint) (Other academic)
  • 159.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Yang, J-C
    Taiwan Forestry Research Institute.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)2013In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, p. 3320-3333Article in journal (Refereed)
    Abstract [en]

    Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long-term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3–0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false-positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4–8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.

  • 160. Bolmgren, Kjell
    et al.
    Oxelman, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Generic limits in Rhamnus L. s.l. (Rhamnaceae) inferred from nuclear and chloroplast DNA sequence phylogenies2004In: TAXON, ISSN 0040-0262, Vol. 53, no 2, p. 383-390Article in journal (Refereed)
  • 161. Bond, Brian C
    et al.
    Virley, David J
    Cairns, Nigel J
    Hunter, A Jackie
    Moore, Gary B T
    Moss, Stephen J
    Mudge, Anne W
    Walsh, Frank S
    Jazin, Elena
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Preece, Paul
    The quantification of gene expression in an animal model of brain ischaemia using TaqMan real-time RT-PCR.2002In: Brain Res Mol Brain Res, ISSN 0169-328X, Vol. 106, no 1-2, p. 101-16Article in journal (Other scientific)
  • 162.
    Borge, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genetics and the Origin of Two Flycatcher Species2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, different genetic tools are used to investigate pre- and postzygotic barriers to gene exchange and their role in speciation in the pied flycatcher (Ficedula hypoleuca) and the collared flycatcher (F. albicollis). This species complex consists of four genetically distinct clades that apparently diverged in allopatry (I). Sequencing of introns from autosomal and Z-linked genes from the two species reveals signs of selection on the Z-chromosome. Sexual selection acting on Z-linked genes might explain this pattern (II). By using large-scale genotyping of single nucleotide polymorphisms (SNPs), introgression is observed at autosomal- but not Z-linked loci, mostly from the pied- to the collared flycatcher. Male plumage characters and genes involved in hybrid fitness are largely mapped to the Z-chromosome (III). By studying mate choice of female hybrids I show that there is a link between female preferences and the Z chromosome (IV). The rate of introgression in island versus clinal hybrid zones is consistent with regional differences in hybrid fertility. Asymmetric gene flow from allopatry on the islands may oppose reinforcement, leading to introgression and a partial breakdown of postzygotic isolation. Adaptive introgression may explain the high rate of introgression observed at one of the genetic markers (V). For late breeding female collared flycatchers it appears to be adaptive to use pied flycatchers as social fathers but conspecific males as genetic fathers. Additionally, females in mixed species pairs may reduce hybridization costs by producing an excess of male hybrid offspring that are more fertile than females (VI).

    In conclusion, the Z-chromosome appears to play a major role in flycatcher speciation. Sexual selection and reinforcement are important mechanisms in the divergence of these birds. However, gene flow from allopatry, introgression of adaptive genes and adaptive hetrospecific pairing by late breeding collared flycatcher females may work in the opposite direction.

    List of papers
    1. Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers
    Open this publication in new window or tab >>Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers
    Show others...
    2001 In: Molecular Ecology, Vol. 10, p. 737-749Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91245 (URN)
    Available from: 2004-01-07 Created: 2004-01-07Bibliographically approved
    2. Recurrent selective sweeps on the Z chromosome characterize the evolutionary history of two closely related flycatcher species (Ficedula hypoleuca and F. albicollis)
    Open this publication in new window or tab >>Recurrent selective sweeps on the Z chromosome characterize the evolutionary history of two closely related flycatcher species (Ficedula hypoleuca and F. albicollis)
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-91246 (URN)
    Available from: 2004-01-07 Created: 2004-01-07 Last updated: 2010-01-13Bibliographically approved
    3. Sex chromosome evolution and speciation in Ficedula flycatchers
    Open this publication in new window or tab >>Sex chromosome evolution and speciation in Ficedula flycatchers
    Show others...
    2003 In: Proceedings of the Royal Society of London: Biological Sciences, Vol. 270, p. 53-59Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91247 (URN)
    Available from: 2004-01-07 Created: 2004-01-07 Last updated: 2012-02-29
    4. Paternally determined species recognition in female flycathcer hybrids
    Open this publication in new window or tab >>Paternally determined species recognition in female flycathcer hybrids
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-91248 (URN)
    Available from: 2004-01-07 Created: 2004-01-07 Last updated: 2010-01-13Bibliographically approved
    5. Rate of introgression in island versus clinal hybrid zones of Ficedula flycatchers are consistent with regional differences in hybrid fertility
    Open this publication in new window or tab >>Rate of introgression in island versus clinal hybrid zones of Ficedula flycatchers are consistent with regional differences in hybrid fertility
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-91249 (URN)
    Available from: 2004-01-07 Created: 2004-01-07 Last updated: 2012-02-29
    6. Hybridization and adaptive mate choice in flycatchers
    Open this publication in new window or tab >>Hybridization and adaptive mate choice in flycatchers
    Show others...
    2001 In: Nature, Vol. 411, p. 45-50Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91250 (URN)
    Available from: 2004-01-07 Created: 2004-01-07Bibliographically approved
  • 163. Borge, Thomas
    et al.
    Webster, Matthew T
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Andersson, Gunilla
    Saetre, Glenn-Peter
    Contrasting patterns of polymorphism and divergence on the Z chromosome and autosomes in two Ficedula flycatcher species2005In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 171, no 4, p. 1861-1873Article in journal (Refereed)
    Abstract [en]

    In geographic areas where pied and collared flycatchers (Ficedula hypoleuca and F. albicollis) breed in sympatry, hybridization occurs, leading to gene flow (introgression) between the two recently diverged species. Notably, while such introgression is observable at autosomal loci it is apparently absent at the Z chromosome, suggesting an important role for genes on the Z chromosome in creating reproductive isolation during speciation. To further understand the role of Z-linked loci in the formation of new species, we studied genetic variation of the two species from regions where they live in allopatry. We analyzed patterns of polymorphism and divergence in introns from 9 Z-linked and 23 autosomal genes in pied and collared flycatcher males. Average variation on the Z chromosome is greatly reduced compared to neutral expectations based on autosomal diversity in both species. We also observe significant heterogeneity between patterns of polymorphism and divergence at Z-linked loci and a relative absence of polymorphisms that are shared by the two species on the Z chromosome compared to the autosomes. We suggest that these observations may indicate the action of recurrent selective sweeps on the Z chromosome during the evolution of the two species, which may be caused by sexual selection acting on Z-linked genes. Alternatively, reduced variation on the Z chromosome could result from substantially higher levels of introgression at autosomal than at Z-linked loci or from a complex demographic history, such as a population bottleneck.

  • 164.
    Boussau, Bastien
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Computational inference of scenarios for alpha-proteobacterial genome evolution2004In: Proceedings of the national academy of sciences USA, ISSN 1091-6490, Vol. 101, no 26, p. 9722-9727Article in journal (Refereed)
  • 165.
    Boussau, Bastien
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Karlberg, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Frank, Carolin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Legault, Boris-Antoine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Computational inference of scenarios for alpha-proteobecterial genome evolution2004In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 101, no 26, p. 9722-9727Article in journal (Refereed)
    Abstract [en]

    The alpha-proteobacteria, from which mitochondria are thought to have originated, display a 10-fold genome size variation and provide an excellent model system for studies of genome size evolution in bacteria. Here, we use computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree. Our study reveals massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches separating intracellular bacteria of animals and humans. Alterations in gene numbers have mostly affected functional categories associated with regulation, transport, and small-molecule metabolism, many of which are encoded by paralogous gene families located on auxiliary chromosomes. The results suggest that the alpha-proteobacterial ancestor contained 3,000-5,000 genes and was a free-living, aerobic, and motile bacterium with pili and surface proteins for host cell and environmental interactions. Approximately one third of the ancestral gene set has no homologs among the eukaryotes. More than 40% of the genes without eukaryotic counterparts encode proteins that are conserved among the alpha-proteobacteria but for which no function has yet been identified. These genes that never made it into the eukaryotes but are widely distributed in bacteria may represent bacterial drug targets and should be prime candidates for future functional characterization.

  • 166.
    Bousseau, Bastien
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Karlberg, E. Olof
    Frank, A. Carolin
    Legault, Boris
    Andersson, Siv G.E.
    Inferring the α-proteobacterial ancestorIn: Proc Natl Acad Sci USAArticle in journal (Refereed)
  • 167.
    Brandström, Miakel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias2008In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 18, no 6, p. 881-887Article in journal (Refereed)
    Abstract [en]

    Studies of microsatellites evolution based on marker data almost inherently suffer from an ascertainment bias because there is selection for the most mutable and polymorphic loci during marker development. To circumvent this bias we took advantage of whole-genome shotgun sequence data from three unrelated chicken individuals that, when aligned to the genome reference sequence, give sequence information on two chromosomes from about one-fourth (375,000) of all microsatellite loci containing di- through pentanucleotide repeat motifs in the chicken genome. Polymorphism is seen at loci with as few as five repeat units, and the proportion of dimorphic loci then increases to 50% for sequences with similar to 10 repeat units, to reach a maximum of 75%-80% for sequences with 15 or more repeat units. For any given repeat length, polymorphism increases with decreasing GC content of repeat motifs for dinucleotides, nonhairpin-forming trinucleotides, and tetranucleotides. For trinucleotide repeats which are likely to form hairpin structures, polymorphism increases with increasing GC content, indicating that the relative stability of hairpins affects the rate of replication slippage. For any given repeat length, polymorphism is significantly lower for imperfect compared to perfect repeats and repeat interruptions occur in >15% of loci. However, interruptions are not randomly distributed within repeat arrays but are preferentially located toward the ends. There is negative correlation between microsatellite abundance and single nucleotide polymorphism ( SNP) density, providing large-scale genomic support for the hypothesis that equilibrium microsatellite distributions are governed by a balance between rate of replication slippage and rate of point mutation.

  • 168.
    Brandström, Mikael
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Bioinformatic Analysis of Mutation and Selection in the Vertebrate Non-coding Genome2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The majority of the vertebrate genome sequence is not coding for proteins. In recent years, the evolution of this noncoding fraction of the genome has gained interest. These studies have been greatly facilitated by the availability of full genome sequences. The aim of this thesis is to study evolution of the noncoding vertebrate genome through bioinformatic analysis of large-scale genomic datasets.

    In a first analysis we addressed the use of conservation of sequence between highly diverged genomes to infer function. We provided evidence for a turnover of the patterns of negative selection. Hence, measures of constraint based on comparisons of diverged genomes might underestimate the functional proportion of the genome.

    In the following analyses we focused on length variation as found in small-scale insertion and deletion (indel) polymorphisms and microsatellites. For indels in chicken, replication slippage is a likely mutation mechanism, as a large proportion of the indels are parts of tandem-duplicates. Using a set of microsatellite polymorphisms in chicken, where we avoid ascertainment bias, we showed that polymorphism is positively correlated with microsatellite length and AT-content. Furthermore, interruptions in the microsatellite sequence decrease the levels of polymorphism.

    We also analysed the association between microsatellite polymorphism and recombination in the human genome. Here we found increased levels of microsatellite polymorphism in human recombination hotspots and also similar increases in the frequencies of single nucleotide polymorphisms (SNPs) and indels. This points towards natural selection shaping the levels of variation. Alternatively, recombination is mutagenic for all three kinds of polymorphisms.

    Finally, I present the program ILAPlot. It is a tool for visualisation, exploration and data extraction based on BLAST.

    Our combined results highlight the intricate connections between evolutionary phenomena. It also emphasises the importance of length variability in genome evolution, as well as the gradual difference between indels and microsatellites.

    List of papers
    1. Evidence for turnover of functional noncoding DNA in mammalian genome evolution
    Open this publication in new window or tab >>Evidence for turnover of functional noncoding DNA in mammalian genome evolution
    2004 In: Genomics, ISSN 0888-7543, Vol. 84, no 5, p. 806-813Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-96267 (URN)
    Available from: 2007-10-08 Created: 2007-10-08Bibliographically approved
    2. The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: A high frequency of deletions in tandem duplicates
    Open this publication in new window or tab >>The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: A high frequency of deletions in tandem duplicates
    2007 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 176, no 3, p. 1691-1701Article in journal (Refereed) Published
    Abstract [en]

    It is increasingly recognized that insertions and deletions(indels) are an important source of genetic as well as phenotypicdivergence and diversity. We analyzed length polymorphisms identifiedthrough partial (0.25x) shotgun sequencing of three breeds ofdomestic chicken made by the International Chicken PolymorphismMap Consortium. A data set of 140,484 short indel polymorphismsin unique DNA was identified after filtering for microsatellitestructures. There was a significant excess of tandem duplicatesat indel sites, with deletions of a duplicate motif outnumberingthe generation of duplicates through insertion. Indel densitywas lower in microchromosomes than in macrochromosomes, in theZ chromosome than in autosomes, and in 100 bp of upstream sequence,5'-UTR, and first introns than in intergenic DNA and in otherintrons. Indel density was highly correlated with single nucleotidepolymorphism (SNP) density. The mean density of indels in pairwisesequence comparisons was 1.9 x 10–4 indel events/bp, 5%the density of SNPs segregating in the chicken genome. The greatmajority of indels involved a limited number of nucleotides(median 1 bp), with A-rich motifs being overrepresented at indelsites. The overrepresentation of deletions at tandem duplicatesindicates that replication slippage in duplicate sequences isa common mechanism behind indel mutation. The correlation betweenindel and SNP density indicates common effects of mutation and/orselection on the occurrence of indels and point mutations.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96268 (URN)10.1534/genetics.107.070805 (DOI)000248416300026 ()17507681 (PubMedID)
    Available from: 2007-10-08 Created: 2007-10-08 Last updated: 2018-02-22Bibliographically approved
    3. Microsatellite polymorphism is elevated in human recombination hotspots
    Open this publication in new window or tab >>Microsatellite polymorphism is elevated in human recombination hotspots
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-96269 (URN)
    Available from: 2007-10-08 Created: 2007-10-08 Last updated: 2010-01-13Bibliographically approved
    4. A genome-wide analysis of microsatellite polymorphism circumventing the ascertainment bias
    Open this publication in new window or tab >>A genome-wide analysis of microsatellite polymorphism circumventing the ascertainment bias
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-96270 (URN)
    Available from: 2007-10-08 Created: 2007-10-08 Last updated: 2010-01-13Bibliographically approved
    5. ILAPlot: An interactive local alignment plotting tool
    Open this publication in new window or tab >>ILAPlot: An interactive local alignment plotting tool
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-96271 (URN)
    Available from: 2007-10-08 Created: 2007-10-08 Last updated: 2010-01-13Bibliographically approved
  • 169.
    Brandström, Mikael
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    ILAPlot: An interactive local alignment plotting toolManuscript (Other academic)
  • 170.
    Brandström, Mikael
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    ILAPlot: An interactive local alignment plotting toolManuscript (Other academic)
  • 171.
    Brandström, Mikael
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Bagshaw, Andrew T
    Gemmell, Neil
    Ellegren, Hans
    Microsatellite polymorphism is elevated in human recombination hotspotsManuscript (Other academic)
  • 172.
    Brandström, Mikael
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Bagshaw, Andrew T
    Gemmell, Neil J
    Ellegren, Hans
    Microsatellite polymorphism is elevated in human recombination hotspotsManuscript (Other academic)
  • 173.
    Brandström, Mikael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Bagshaw, Andrew T.
    Gemmell, Neil J.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    The relationship between microsatellite polymorphism and recombination hot spots in the human genome2008In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 25, no 12, p. 2579-2587Article in journal (Refereed)
    Abstract [en]

    Although previous studies have failed to detect an association between microsatellite polymorphism and broadscale recombination rates in the human genome, there are several possible reasons why such a relationship could exist. For instance, there might be a direct link if recombination is mutagenic to microsatellite sequences or if polymorphic microsatellites act as recombination signals. Alternatively, recombination could exert an indirect effect by uncoupling of natural selection at linked loci, promoting polymorphism. As recombination is concentrated in narrow hotspot regions in the human genome, we investigated the relationship between microsatellite polymorphism and recombination hot spots. By using data from a common allele frequency database, we found several polymorphism estimates to be similar for hot spots and the genomic average. However, this is likely explained by an ascertainment bias because markers with high polymorphism information content are usually selected for genotyping in human populations and pedigrees. In contrast, by using an unbiased set of shotgun sequence data, we found an excess of microsatellite polymorphism in recombination hot spots of 14%. However, when other genomic variables are taken into account in a generalized model and using wavelet analysis, the effect is no longer detectable and the only firm predictor of microsatellite polymorphism is the incidence of SNPs and indels. One possible neutral explanation to these observations is that there is a common denominator affecting the local rate of mutation in unique as well as in repetitive DNA, for example, base composition.

  • 174.
    Brandström, Mikael
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Ellegren, Hans
    A genome-wide analysis of microsatellite polymorphism circumventing the ascertainment biasManuscript (Other academic)
  • 175.
    Brandström, Mikael
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Ellegren, Hans
    A genome-wide analysis of microsatellite polymorphism circumventing the ascertainment biasManuscript (Other academic)
  • 176.
    Brandström, Mikael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: A high frequency of deletions in tandem duplicates2007In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 176, no 3, p. 1691-1701Article in journal (Refereed)
    Abstract [en]

    It is increasingly recognized that insertions and deletions(indels) are an important source of genetic as well as phenotypicdivergence and diversity. We analyzed length polymorphisms identifiedthrough partial (0.25x) shotgun sequencing of three breeds ofdomestic chicken made by the International Chicken PolymorphismMap Consortium. A data set of 140,484 short indel polymorphismsin unique DNA was identified after filtering for microsatellitestructures. There was a significant excess of tandem duplicatesat indel sites, with deletions of a duplicate motif outnumberingthe generation of duplicates through insertion. Indel densitywas lower in microchromosomes than in macrochromosomes, in theZ chromosome than in autosomes, and in 100 bp of upstream sequence,5'-UTR, and first introns than in intergenic DNA and in otherintrons. Indel density was highly correlated with single nucleotidepolymorphism (SNP) density. The mean density of indels in pairwisesequence comparisons was 1.9 x 10–4 indel events/bp, 5%the density of SNPs segregating in the chicken genome. The greatmajority of indels involved a limited number of nucleotides(median 1 bp), with A-rich motifs being overrepresented at indelsites. The overrepresentation of deletions at tandem duplicatesindicates that replication slippage in duplicate sequences isa common mechanism behind indel mutation. The correlation betweenindel and SNP density indicates common effects of mutation and/orselection on the occurrence of indels and point mutations.

  • 177.
    Bremdal, K T
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Seddon, J M
    MHC promoter polymorphism in grey wolves and domestic dogs.2006In: Tissue Antigens, no 67, p. 466-Article in journal (Refereed)
  • 178.
    Bremer, Kåre
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Bremer, Birgitta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Introduction to phylogeny and systematics of flowering plants2003 (ed. Ny utg.)Book (Other academic)
  • 179.
    Bremer, Kåre
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Fries, Else-Marie
    Bremer, Birgitta
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification2004In: Systematic Biology, Vol. 53, no 3, p. 496-505Article in journal (Refereed)
  • 180.
    Brg, Lars M
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Fluctuating selection, egg banks and population genetic structure in cyclically parthenogenetic species.2005In: Hydrobiologia, Vol. 549, p. 287-295Article in journal (Refereed)
  • 181.
    Brindefalk, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Mitochondrial and Eukaryotic Origins: A Phylogenetic Perspective2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Mitochondria are eukaryotic cellular organelles responsible for power-generation, believed to have come into existence by an endo-symbiontic event where a bacterial cell was incorporated by an un-specified "proto-eukaryote". Phylogenetic analysis have shown that the mitochondrial ancestor was most related to present-day alpha-proteobacteria, although the exact nature of the mitochondrial progenitor remains disputed.

    In this work, I have used phylogenetic and other methods to investigate the identity of the organism giving rise to mitochondria, by analysing the evolutionary history of select proteins, the events where they have been transfered to the eukaryotic nucleus, and the time-point of mitochondrial establishment. In addition, a search for mitochondrially related organisms in the ocean metagenome was performed, in the hope that something more related to the mitochondrial progenitor than anything previously identified could be found.

    Previous analysis have shown that a large fraction of mitochondrial proteins does indeed trace their descent to the alpha-proteobacteria, but I found that the amino-acyl tRNA-synthetases display more general bacterial descent, making it likely that these proteins are of a different origin from the mitochondria themselves.

    While the synthetases are encoded on the nuclear genome, most mitochondria still posses most of the tRNA on their own genomes. In the cases where the tRNA has been lost from the mitochondrial genome, I found that the probability of loss correspond to the evolutionary history of their synthetase.

    The ocean metagenome represents an order of magnitude more data than previously available, making it suitable for improving the analyses dealing with mitochondrial placement. This large of amount of data was utilised to improve the phylogenetic analyses, showing that previous works might have suffered from artefacts inflating the support for placement of mitochondria with a specific alpha-proteobacterial group.

    Eukaryotic/mitochondrial radiation was shown to be as old, or older, than radiation of extant alpha-proteobacteria, casting doubt on previous analysis identifying a specific alpha-proteobacterial group as the mitochondrial ancestor.

    List of papers
    1. Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases
    Open this publication in new window or tab >>Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases
    Show others...
    2007 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 24, no 3, p. 743-756Article in journal (Refereed) Published
    Abstract [en]

    Many theories favor a fusion of 2 prokaryotic genomes for the origin of the Eukaryotes, but there are disagreements on the origin, timing, and cellular structures of the cells involved. Equally controversial is the source of the nuclear genes for mitochondrial proteins, although the α-proteobacterial contribution to the mitochondrial genome is well established. Phylogenetic inferences show that the nuclearly encoded mitochondrial aminoacyl-tRNA synthetases (aaRSs) occupy a position in the tree that is not close to any of the currently sequenced α-proteobacterial genomes, despite cohesive and remarkably well-resolved α-proteobacterial clades in 12 of the 20 trees. Two or more α-proteobacterial clusters were observed in 8 cases, indicative of differential loss of paralogous genes or horizontal gene transfer. Replacement and retargeting events within the nuclear genomes of the Eukaryotes was indicated in 10 trees, 4 of which also show split α-proteobacterial groups. A majority of the mitochondrial aaRSs originate from within the bacterial domain, but none specifically from the α-Proteobacteria. For some aaRS, the endosymbiotic origin may have been erased by ongoing gene replacements on the bacterial as well as the eukaryotic side. For others that accurately resolve the α-proteobacterial divergence patterns, the lack of affiliation with mitochondria is more surprising. We hypothesize that the ancestral eukaryotic gene pool hosted primordial "bacterial-like" genes, to which a limited set of α-proteobacterial genes, mostly coding for components of the respiratory chain complexes, were added and selectively maintained.

    Keywords
    Aminoacyl-tRNA synthetase, Mitochondria, Phylogeny
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-14983 (URN)10.1093/molbev/msl202 (DOI)000244662000013 ()17182897 (PubMedID)
    Available from: 2008-02-01 Created: 2008-02-01 Last updated: 2017-12-11Bibliographically approved
    2. Lost and Found at Sea: a Phylomentagenomic Exploration of Mitochondrial Affiliations with Oceanic Bacteria.
    Open this publication in new window or tab >>Lost and Found at Sea: a Phylomentagenomic Exploration of Mitochondrial Affiliations with Oceanic Bacteria.
    Show others...
    (English)Manuscript (Other academic)
    Abstract [en]

     

    Background

    According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from a free-living bacterium related to present-day alpha-proteobacteria. Recent studies have identified two lineages as the closest mitochondrial relatives among bacteria with sequenced genomes; the Rickettsiales, a lineage comprising obligate intracellular pathogens, and Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the upper surface waters of the global oceans.

     

    Principal Findings

    Here, we present a phylogenetic study incorporating metagenomic data of mitochondrial genes for aerobic respiration that includes sequence data from the Global Ocean Sampling (GOS) Expedition, thereby increasing the sampling of alpha-proteobacterial sequences available for analysis greatly. Phylogenetic analysis of these expanded datasets including oceanic sequences that had been pruned down in numbers but still maintained the full genetic diversity present failed to show an increased support for a specific mitochondrial affiliation to any alpha-proteobacterial group, although concatenated datasets of different genes gave good support for conflicting mitochondrial placement. We utilized a jack-knifing method to randomly sample sequences from the GOS dataset and examined how the inclusion of such sequences influenced the support for mitochondrial affiliation in trees inferred from proteins in aerobic respiration. No evidence of an increased support for a specific mitochondrial placement in the alpha-proteobacterial tree in the jack-knifing analysis was obtained. A systematic search for sequences affiliated with mitochondria in the GOS dataset suggests the existence of previously unidentified clades of deeply diverging alpha-proteobacteria, with an unclear affiliation.

     

    Conclusions/Significance

    Our findings have several important implications. First, they support an early divergence of the mitochondrial ancestor from the alpha-proteobacterial lineage, possibly pre-dating the radiation of alpha-proteobacterial species with sequenced genomes. Second, they reject the hypothesis that the system for aerobic respiration in mitochondria is affiliated with the SAR11 clade. Third, they indicate horizontal transfer of genes for respiratory chain proteins in bacteria adapted to the upper surface waters of the oceans. Fourth, they show the presence of oceanic sequences for respiratory chain proteins that diverge as deeply as mitochondria in the alpha-proteobacterial phylogeny, possibly indicating a previously unidentified alpha-proteobacterial group at a basal position of the alpha-proteobacterial tree, underscoring the importance of expanding studies on mitochondrial origins beyond those of cultivated and intracellular bacteria. Finally, our study outlines a new methodology, phylometagenomics, which provides guidance on how to incorporate metagenome data into a phylogenetic framework for inferences of early evolutionary events.

     

    National Category
    Biochemistry and Molecular Biology
    Research subject
    Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-100841 (URN)
    Available from: 2009-04-08 Created: 2009-04-08 Last updated: 2010-01-14
    3. Mitochondrial and alpha-proteobacterial time of divergence - a question of antecedence
    Open this publication in new window or tab >>Mitochondrial and alpha-proteobacterial time of divergence - a question of antecedence
    (English)Manuscript (Other academic)
    Abstract [en]

    Mitochondria are believed to have originated by the incorporation of an alpha-proteobacterium into an un-defined "proto-eukaryote", although the exact nature of the two participants in this endo-symbiotic event is not known. Attempts to place the endo-symbiont with a specific group of extant alpha-proteobacteria has in most cases identified the Rickettsiales as the sister-group to mitochondria, although recent work has shown that this could be due to methodological artefacts and that the mitochondria should instead be considered a sister-clade to alphaproteobacteria. Equally uncertain is the time at which this endo-symbiotic event took place, and if it coincides with the event that gave rise to the eukaryotes themselves. In this work we attempt to use molecular dating methods to compare the time-point of mitochondrial divergence to the time-point of divergence of the alpha-proteobacteria, under the two hypothetical topologies mentioned. We show that if mitochondria are considered as a sister-clade to the alpha-proteobacteria, mitochondria likely diverged prior to the radiation of extant alpha-proteobacteria, and that the alpha-proteobacterial clade itself might be significantly younger than shown in previous analyses.

    National Category
    Biochemistry and Molecular Biology
    Research subject
    Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-100845 (URN)
    Available from: 2009-04-08 Created: 2009-04-08 Last updated: 2010-01-14
    4. Loss of Mitochondrial tRNA Genes Correlates with Loss of Genes for Aminoacyl-tRNA Synthetases
    Open this publication in new window or tab >>Loss of Mitochondrial tRNA Genes Correlates with Loss of Genes for Aminoacyl-tRNA Synthetases
    (English)Manuscript (Other academic)
    Abstract [en]

    Most mitochondrial genomes encode their own tRNAs, whereas the mitochondrial aminoacyl-tRNA synthetases (aaRS) are encoded by the nuclear genome. It has been suggested that the loss of mitochondrial tRNA genes from the mitocchondrial genome correlates with the sequence similarity between bacterial and eukaryotic aaRSs, in that aaRSs that are similar across the two domains can easily shift between charging mitochondrial and cytosolic tRNAs (Schneider 2001). However, recent work has shown that mitochondrial and cytosolic aaRSs have complex evolutionary histories and are not always of bacterial and eukaryotic origin, respectively (Brindefalk et al. 2007). We repeated the analysis performed by Schneider using all available mitochondrial genomes as of December 2006 and found that the loss of mitochondrial tRNA genes correlates with replacements of the genes for the corresponding aaRS. Our observations provide new insights into the co-evolution of mitochondrial tRNAs and their charging enzymes.

    National Category
    Biochemistry and Molecular Biology
    Research subject
    Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-100844 (URN)
    Available from: 2009-04-08 Created: 2009-04-08 Last updated: 2010-01-14
  • 182.
    Brindefalk, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Loss of Mitochondrial tRNA Genes Correlates with Loss of Genes for Aminoacyl-tRNA SynthetasesManuscript (Other academic)
    Abstract [en]

    Most mitochondrial genomes encode their own tRNAs, whereas the mitochondrial aminoacyl-tRNA synthetases (aaRS) are encoded by the nuclear genome. It has been suggested that the loss of mitochondrial tRNA genes from the mitocchondrial genome correlates with the sequence similarity between bacterial and eukaryotic aaRSs, in that aaRSs that are similar across the two domains can easily shift between charging mitochondrial and cytosolic tRNAs (Schneider 2001). However, recent work has shown that mitochondrial and cytosolic aaRSs have complex evolutionary histories and are not always of bacterial and eukaryotic origin, respectively (Brindefalk et al. 2007). We repeated the analysis performed by Schneider using all available mitochondrial genomes as of December 2006 and found that the loss of mitochondrial tRNA genes correlates with replacements of the genes for the corresponding aaRS. Our observations provide new insights into the co-evolution of mitochondrial tRNAs and their charging enzymes.

  • 183.
    Brindefalk, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Ettema, Thijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Viklund, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Tholleson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Lost and Found at Sea: a Phylomentagenomic Exploration of Mitochondrial Affiliations with Oceanic Bacteria.Manuscript (Other academic)
    Abstract [en]

     

    Background

    According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from a free-living bacterium related to present-day alpha-proteobacteria. Recent studies have identified two lineages as the closest mitochondrial relatives among bacteria with sequenced genomes; the Rickettsiales, a lineage comprising obligate intracellular pathogens, and Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the upper surface waters of the global oceans.

     

    Principal Findings

    Here, we present a phylogenetic study incorporating metagenomic data of mitochondrial genes for aerobic respiration that includes sequence data from the Global Ocean Sampling (GOS) Expedition, thereby increasing the sampling of alpha-proteobacterial sequences available for analysis greatly. Phylogenetic analysis of these expanded datasets including oceanic sequences that had been pruned down in numbers but still maintained the full genetic diversity present failed to show an increased support for a specific mitochondrial affiliation to any alpha-proteobacterial group, although concatenated datasets of different genes gave good support for conflicting mitochondrial placement. We utilized a jack-knifing method to randomly sample sequences from the GOS dataset and examined how the inclusion of such sequences influenced the support for mitochondrial affiliation in trees inferred from proteins in aerobic respiration. No evidence of an increased support for a specific mitochondrial placement in the alpha-proteobacterial tree in the jack-knifing analysis was obtained. A systematic search for sequences affiliated with mitochondria in the GOS dataset suggests the existence of previously unidentified clades of deeply diverging alpha-proteobacteria, with an unclear affiliation.

     

    Conclusions/Significance

    Our findings have several important implications. First, they support an early divergence of the mitochondrial ancestor from the alpha-proteobacterial lineage, possibly pre-dating the radiation of alpha-proteobacterial species with sequenced genomes. Second, they reject the hypothesis that the system for aerobic respiration in mitochondria is affiliated with the SAR11 clade. Third, they indicate horizontal transfer of genes for respiratory chain proteins in bacteria adapted to the upper surface waters of the oceans. Fourth, they show the presence of oceanic sequences for respiratory chain proteins that diverge as deeply as mitochondria in the alpha-proteobacterial phylogeny, possibly indicating a previously unidentified alpha-proteobacterial group at a basal position of the alpha-proteobacterial tree, underscoring the importance of expanding studies on mitochondrial origins beyond those of cultivated and intracellular bacteria. Finally, our study outlines a new methodology, phylometagenomics, which provides guidance on how to incorporate metagenome data into a phylogenetic framework for inferences of early evolutionary events.

     

  • 184.
    Brindefalk, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Tholleson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Mitochondrial and alpha-proteobacterial time of divergence - a question of antecedenceManuscript (Other academic)
    Abstract [en]

    Mitochondria are believed to have originated by the incorporation of an alpha-proteobacterium into an un-defined "proto-eukaryote", although the exact nature of the two participants in this endo-symbiotic event is not known. Attempts to place the endo-symbiont with a specific group of extant alpha-proteobacteria has in most cases identified the Rickettsiales as the sister-group to mitochondria, although recent work has shown that this could be due to methodological artefacts and that the mitochondria should instead be considered a sister-clade to alphaproteobacteria. Equally uncertain is the time at which this endo-symbiotic event took place, and if it coincides with the event that gave rise to the eukaryotes themselves. In this work we attempt to use molecular dating methods to compare the time-point of mitochondrial divergence to the time-point of divergence of the alpha-proteobacteria, under the two hypothetical topologies mentioned. We show that if mitochondria are considered as a sister-clade to the alpha-proteobacteria, mitochondria likely diverged prior to the radiation of extant alpha-proteobacteria, and that the alpha-proteobacterial clade itself might be significantly younger than shown in previous analyses.

  • 185.
    Brindefalk, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Viklund, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Larsson, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Thollesson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv G.E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases2007In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 24, no 3, p. 743-756Article in journal (Refereed)
    Abstract [en]

    Many theories favor a fusion of 2 prokaryotic genomes for the origin of the Eukaryotes, but there are disagreements on the origin, timing, and cellular structures of the cells involved. Equally controversial is the source of the nuclear genes for mitochondrial proteins, although the α-proteobacterial contribution to the mitochondrial genome is well established. Phylogenetic inferences show that the nuclearly encoded mitochondrial aminoacyl-tRNA synthetases (aaRSs) occupy a position in the tree that is not close to any of the currently sequenced α-proteobacterial genomes, despite cohesive and remarkably well-resolved α-proteobacterial clades in 12 of the 20 trees. Two or more α-proteobacterial clusters were observed in 8 cases, indicative of differential loss of paralogous genes or horizontal gene transfer. Replacement and retargeting events within the nuclear genomes of the Eukaryotes was indicated in 10 trees, 4 of which also show split α-proteobacterial groups. A majority of the mitochondrial aaRSs originate from within the bacterial domain, but none specifically from the α-Proteobacteria. For some aaRS, the endosymbiotic origin may have been erased by ongoing gene replacements on the bacterial as well as the eukaryotic side. For others that accurately resolve the α-proteobacterial divergence patterns, the lack of affiliation with mitochondria is more surprising. We hypothesize that the ancestral eukaryotic gene pool hosted primordial "bacterial-like" genes, to which a limited set of α-proteobacterial genes, mostly coding for components of the respiratory chain complexes, were added and selectively maintained.

  • 186. Britton, Tom
    et al.
    Anderson, Cajsa Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Jaquet, David
    Lundqvist, Samuel
    Bremer, Kåre
    Estimating divergence times in large phylogenetic trees2007In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 5, p. 741-752Article in journal (Refereed)
    Abstract [en]

    A new method, PATHd8, for estimating ultrametric trees from trees with edge (branch) lengths proportional to the number of substitutions is proposed. The method allows for an arbitrary number of reference nodes for time calibration, each defined either as absolute age, minimum age, or maximum age, and the tree need not be fully resolved. The method is based on estimating node ages by mean path lengths from the node to the leaves but correcting for deviations from a molecular clock suggested by reference nodes. As opposed to most existing methods allowing substitution rate variation, the new method smoothes substitution rates locally, rather than simultaneously over the whole tree, thus allowing for analysis of very large trees. The performance of PATHd8 is compared with other frequently used methods for estimating divergence times. In analyses of three separate data sets, PATHd8 gives similar divergence times to other methods, the largest difference being between crown group ages, where unconstrained nodes get younger ages when analyzed with PATHd8. Overall, chronograms obtained from other methods appear smoother, whereas PATHd8 preserves more of the heterogeneity seen in the original edge lengths. Divergence times are most evenly spread over the chronograms obtained from the Bayesian implementation and the clock-based Langley-Fitch method, and these two methods produce very similar ages for most nodes. Evaluations of PATHd8 using simulated data suggest that PATHd8 is slightly less precise compared with penalized likelihood, but it gives more sensible answers for extreme data sets. A clear advantage with PATHd8 is that it is more or less instantaneous even with trees having several thousand leaves, whereas other programs often run into problems when analyzing trees with hundreds of leaves. PATHd8 is implemented in freely available software.

  • 187.
    Britton, Tom
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Svennblad, Bodil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Erixon, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Bayesian support is larger than bootstrap support in phylogenetic inference: a mathematical argument.2007In: Mathematical Medicine and Biology, ISSN 1477-8599, E-ISSN 1477-8602, Vol. 24, no 4, p. 401-411Article in journal (Refereed)
    Abstract [en]

    In phylogenetic inference, the support of an estimated phylogenetic tree topology and its interior branches is usually measured either with non-parametric bootstrap support (BS) values or with Bayesian posterior probabilities (BPPs). Extensive empirical evidence indicates that BPP values are systematically larger than BS when measured on the same data set, but there are no theoretical results supporting such a systematic difference. In the present note, we give a heuristic mathematical argument supporting the empirically observed phenomenon. The argument uses properties of the marginal and profile likelihoods of the normal distribution. The heuristic arguments are supported in a simulation study evaluating different steps in the argument.

  • 188.
    Brohede, J.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Arnheim, N.
    Ellegren, H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Single molecule analysis of the hypermutable tetranucleotide rpeat locus D21S1245 through sperm genotyping:: A heterogeneous pattern of mutation but no clear male age effect.2004In: Molecular Biology and Evolution, no 21, p. 58-64Article in journal (Refereed)
  • 189. Brouns, Stan J. J.
    et al.
    Ettema, Thijs J. G.
    Stedman, Kenneth M.
    Walther, Jasper
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Smidt, Hauke
    Snijders, Ambrosius P. L.
    Young, Mark
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Wright, Phillip C.
    Siebers, Bettina
    van der Oost, John
    The hyperthermophilic archaeon Sulfolobus: from exploration to exploitation2005In: Geothermal Biology and Geochemistry in Yellowstone National Park: Proceeding of the Thermal Biology Institute Workshop, Yellowstone National Park, WY / [ed] William Inskeep and Timothy McDermott, Bozeman, MT: Montana State University Publications , 2005, p. 261-276Conference paper (Refereed)
  • 190. Brouns, Stan J. J.
    et al.
    Walther, Jasper
    Snijders, Ambrosius P. L.
    van de Werken, Harmen J. G.
    Willemen, Hanneke L. D. M.
    Worm, Petra
    de Vos, Marjon G. J.
    Andersson, Anders
    Lundgren, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Mazon, Hortense F. M.
    van den Heuvel, Robert H. H.
    Nilsson, Peter
    Salmon, Laurent
    de Vos, Willem M.
    Wright, Phillip C.
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    van der Oost, John
    Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment2006In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 281, no 37, p. 27378-27388Article in journal (Refereed)
    Abstract [en]

    The pentose metabolism of Archaea is largely unknown. Here, we have employed an integrated genomics approach including DNA microarray and proteomics analyses to elucidate the catabolic pathway for D-arabinose in Sulfolobus solfataricus. During growth on this sugar, a small set of genes appeared to be differentially expressed compared with growth on D-glucose. These genes were heterologously overexpressed in Escherichia coli, and the recombinant proteins were purified and biochemically studied. This showed that D-arabinose is oxidized to 2-oxoglutarate by the consecutive action of a number of previously uncharacterized enzymes, including a D-arabinose dehydrogenase, a D-arabinonate dehydratase, a novel 2-keto-3-deoxy-D-arabinonate dehydratase, and a 2,5-dioxopentanoate dehydrogenase. Promoter analysis of these genes revealed a palindromic sequence upstream of the TATA box, which is likely to be involved in their concerted transcriptional control. Integration of the obtained biochemical data with genomic context analysis strongly suggests the occurrence of pentose oxidation pathways in both Archaea and Bacteria, and predicts the involvement of additional enzyme components. Moreover, it revealed striking genetic similarities between the catabolic pathways for pentoses, hexaric acids, and hydroxyproline degradation, which support the theory of metabolic pathway genesis by enzyme recruitment.

  • 191. Brysting, A. K.
    et al.
    Oxelman, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Scheen, A.-C.
    Brochmann, Christian
    Tracking the origin and evolution of a group of high polyploid Cerastium species - (Caryophyllaceae) using non-coding regions of the RNA polymerase genes.2005Conference paper (Other scientific)
  • 192. Brysting, Anne K.
    et al.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Huber, Katharina T.
    Moulton, Vincent
    Brochmann, Christian
    Untangling complex histories of genome mergings in high polyploids2007In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 3, p. 467-476Article in journal (Refereed)
    Abstract [en]

    Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated network-like histories, and the evolutionary history of many plant groups cannot be adequately represented by phylogenetic trees because of such reticulate events. The history of complex genome mergings within a high-polyploid species complex in the genus Cerastium (Caryophyllaceae) is here untangled by the use of a network algorithm and noncoding sequences of a low-copy number gene. The resulting network illustrates how hybridization and polyploidization have acted as key evolutionary processes in creating a plant group where high-level allopolyploids clearly outnumber extant parental genomes.

  • 193. Buckley, Michael
    et al.
    Anderung, Cecilia
    Penkman, Kirsty
    Raney, Brian J.
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Thomas-Oates, Jane
    Collins, Matthew J.
    Comparing the survival of osteocalcin and mtDNA in archaeological bone from four European sites 2008In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 35, no 6, p. 1756-1764Article in journal (Refereed)
    Abstract [en]

    The small mineral-binding bone protein, osteocalcin, has been applied in a number of studies on ancient bone due to predictions of its long-term stability. However, the intact protein has not been shown to survive in ancient bone devoid of DNA, which is a much more phylogenetically informative biomolecule. In this investigation, the survival of osteocalcin is directly compared to the amplification of mtDNA in a set of 34 archaeological samples from four sites throughout Europe. We also present unpublished osteocalcin sequences of seven mammalian species in addition to the 19 published sequences to highlight phylogenetic limitations of this protein. The results indicate that the intact osteocalcin molecule survives less in archaeological samples than mtDNA and is more subject to the temperature of the archaeological site. Amino acid analyses show the persistence of the dominant protein collagen in samples that failed both osteocalcin and mtDNA analyses. The implications these findings present for biomolecular species identification in archaeological and palaeontological material are that, although proteins do survive beyond ancient DNA, osteocalcin does not appear to be the most ideal target

  • 194. Burger, J.
    et al.
    Rosendahl, W.
    Loriell, O.
    Hemmer, H.
    Eriksson, T.
    Götherström, A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Hiller, J.
    Coillins, M.
    Wess, T.
    Alt, K.W.
    Molecular phylogeny of the extinct cave lion Pathera leo spelaea.2004In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, no 30, p. 841-849Article in journal (Refereed)
  • 195. Cafferty, Steve
    et al.
    Oxelman, Bengt
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Proposal to reject the name Silene polyphylla L. 1753 (Caryophyllaceae)2001In: Taxon, ISSN 0040-0262, Vol. 50, no 3, p. 923-924Article in journal (Refereed)
  • 196. Cajal, Yolanda
    et al.
    Berg, Otto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Jain, Mahendra K.
    Origins of delays in monolayer kinetics: Phospholipase A2 paradigm2004In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 43, no 28, p. 9256-9264Article in journal (Refereed)
    Abstract [en]

    The interfacial kinetic paradigm is adopted to model the kinetic behavior of pig pancreatic phospholipase A2 (PLA2) at the monolayer interface. A short delay of about a minute to the onset of the steady state is observed under all monolayer reaction progress conditions, including the PLA2-catalyzed hydrolysis of didecanoylphosphatidyl-choline (PC10) and -glycerol (PG10) monolayers as analyzed in this paper. This delay is independent of enzyme concentration and surface pressure and is attributed to the equilibration time by stationary diffusion of the enzyme added to the stirred subphase to the monolayer through the intervening unstirred aqueous layer. The longer delays of up to several hours, seen with the PC10 monolayers at >15 mN/m, are influenced by surface pressure as well as enzyme concentration. Virtually all features of the monolayer reaction progress are consistent with the assumption that the product accumulates in the substrate monolayer, although the products alone do not spread as a compressible monolayer. These results rule out models that invoke slow “activation” of PLA2 on the monolayer. The observed steady-state rate on monolayers after the delays is <1% of the rate observed with micellar or vesicles substrates of comparable substrate. Together these results suggest that the monolayer steady-state rate includes contributions from steps other than those of the interfacial turnover cycle. Additional considerations that provide understanding of the pre-steady-state behaviors and other nonideal effects at the surface are also discussed.

  • 197.
    Canbäck, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Tamas, Ivica
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    A phylogenomic study of endosymbiotic bacteria2004In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 21, no 6, p. 1110-1122Article in journal (Refereed)
    Abstract [en]

    Endosymbiotic bacteria of aphids, Buchnera aphidicola, and tsetse flies, Wigglesworthia glossinidia, are descendents of free-living γ-Proteobacteria. The acceleration of sequence evolution in the endosymbiont genomes is here estimated from a phylogenomic analysis of the γ-Proteobacteria. The tree topologies associated with the most highly conserved genes suggest that the endosymbionts form a sister group with Escherichia coli, Salmonella sp., and Yersinia pestis. Our results indicate that deviant tree topologies result from high substitution rates and biased nucleotide patterns, rather than from lateral gene transfer, as previously suggested. A reinvestigation of the relative rate increase in the endosymbiont genomes reveals variability among genes that correlate with host-associated metabolic dependencies. The conclusion is that host-level selection has retarded both the loss of genes and the acceleration of sequence evolution in endocellular symbionts.

  • 198.
    Carlsbecker, Annelie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. fysiologisk botanik.
    Helariutta, Y
    Phloem and xylem specification: pieces of the puzzle emerge2005In: Current Opinion in Plant Biology, Vol. 8, no 5, p. 512-517Article in journal (Refereed)
    Abstract [en]

    The plant vascular system is composed of two tissue types, xylem and phloem, which originate from the vascular meristem, the procambium. Recently, several regulatory mechanisms that control the specification of these two tissue types have been uncovered. These include the asymmetric patterning of xylem and phloem in the vascular bundle by the class III HD-ZIP and KANADI genes, the tissue-type-specific control of vascular cell proliferation by brassinosteroids and class III HD-ZIP genes, the regulation of vascular tissue identity by the MYB-like transcription factor APL, and inductive signalling during xylem differentiation by xylogen. These findings define an emerging developmental framework for the control of vascular tissue specification.

  • 199.
    Carlsbecker, Annelie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Lee, Ji-Young
    Roberts, Christina J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Dettmer, Jan
    Lehesranta, Satu
    Zhou, Jing
    Lindgren, Ove
    Moreno-Risueno, Miguel A.
    Vatén, Anne
    Thitamadee, Siripong
    Campilho, Ana
    Sebastian, Jose
    Bowman, John L.
    Helariutta, Yka
    Benfey, Philip N.
    Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate2010In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 465, no 7296, p. 316-321Article in journal (Refereed)
    Abstract [en]

    A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and MIR166b. Endodermally produced microRNA165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage-dependent manner.

  • 200.
    Carlsbecker, Annelie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany. Fysiologisk botanik.
    Tandre, Karolina
    Johansson, Urban
    Englund, Marie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany. Fysiologisk botanik.
    Engström, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany. Fysiologisk botanik.
    The MADS-box gene DAL1 is a potential mediator of the juvenile-to-adult transition in Norway spruce (Picea abies)2004In: The Plant Journal, Vol. 40, p. 546-557Article in journal (Refereed)
    Abstract [en]

    Progression through the plant life cycle involves changes in many essential features, most notably in the capacity to reproduce. The transition from juvenile vegetative and non-reproductive to an adult reproductive phase is gradual and can take many years; in the conifer Norway spruce, Picea abiea, typically 20-25 years. We present a detailed analysis of the activities of three regulatory genes with potential roles in the transition in Norway spruce: DAL1, a MADS-box gene related to the AGL6 group of genes from angiosperms, and the two LEAFY-related genes PaLFY and PaNLY. DAL1 activity is initiated in the shoots of juvenile trees at an age of 3-5 years, and then increases with age, whereas both LFY genes are active throughout the juvenile phase. The activity of DAL1 further shows a spatial pattern along the stem of the tree that parallels a similar gradient in physiolpoical and morphological features associated with maturation to the adult phase. Constitutive expression of DAL1 in transgenic Arabidopsis plants caused a dramatic attenuation of both juvenile and adult growth phases;flowers forming immediately after the embryogenic phase of development in severely affected plants. Taken together, our resulsts support the notion that DAL1 may have a regulatory role in the juvenile-to-adult transition in Norway spruce.

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