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  • 251.
    de Boer, Hugo J.
    et al.
    Avd f systematisk botanik. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Thulin, Mats
    Avd f systematisk botanik. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Lectotypification of Callicocca ipecacuanha Brot. and neotypification of Cephaelis acuminata H.Karst., with reference to the drug ipecac2005In: Taxon, ISSN 0040-0262, Vol. 54, no 4, p. 1080-1082Article in journal (Refereed)
  • 252.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Vongsombath, Chanda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Pålsson, Katinka
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Björk, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Jaenson, Thomas G. T.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Botanical Repellents and Pesticides Traditionally Used Against Hematophagous Invertebrates in Lao People's Democratic Republic: A Comparative Study of Plants Used in 66 Villages2010In: Journal of medical entomology, ISSN 0022-2585, E-ISSN 1938-2928, Vol. 47, no 3, p. 400-414Article in journal (Refereed)
    Abstract [en]

    Hematophagous parasites such as leeches, ticks, mites, lice, bedbugs, mosquitoes, and myiasis-producing fly larvae are common health problems in Lao People's Democratic Republic. Several arthropod-borne infections, e.g., malaria, dengue fever, and Japanese encephalitis, are endemic there. Effective vector control methods including the use of pesticides, insecticide-treated bed nets, and synthetic and plant-based repellents are important means of control against such invertebrates and the pathogens they may transmit or directly cause. In this study, we documented traditional knowledge on plants that are used to repel or kill hematophagous arthropods, including mosquitoes, bedbugs, human lice, mites and ticks, fly larvae, and blood-sucking leeches. Structured interviews were carried out in 66 villages comprising 17 ethnic groups, covering a range of cultures, throughout Lao People's Democratic Republic. A total of 92 plant species was recorded as traditional repellents (including plants for pesticidal usages) in 123 different plant-ectoparasite combinations. The number and species of plants, and animal taxa repelled (or killed) per plant species differed per region, village, and ethnic group. Traditional use was confirmed in the scientific literature for 74 of these plant species, and for an additional 13 species using literature on closely related species. The use of botanical repellents and pesticides from many plant species is common and widespread in the Lao countryside. In the future, the identification of the active components in certain plants to develop more optimal, inexpensive repellents, insecticides, acaricides, or antileech compounds as alternatives to synthetic repellents/pesticides against blood-feeding insects, ticks, mites, and leeches is warranted.

  • 253.
    de Boer, Hugo
    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. systematisk botanik.
    Wieringa, Jan
    Thulin, Mats
    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. systematisk botanik.
    Lectotypification of Callicocca ipecacuanha Brot. and neotypification of Cephaelis acuminata H.Karst., with reference to the drug Ipecac2005In: abstracts XVII International Botanical Congress: Vienna, Austria, Europe 17-23 July 2005, 2005Conference paper (Other (popular scientific, debate etc.))
    Abstract [en]

    The main pharmacopoeias cite the roots of Cephaelis ipecacuanha (syn. Callicocca ipecacuanha Brot.) together with the roots of Cephaelis acuminata H.Karst. are the sources of the crude drug ipecac (European Pharmacopoeia, 2002, 2004; United States Pharmacopeia, 2004; British Pharmacopoeia, 2003; Japanese Pharmacopoeia, 2001). Ipecac is an important emetic and expectorant used in case of poisoning, mainly in children. However, C. acuminata does not occur in botanical literature, except in connection with the original description, and this falls entirely within the variation of the widespread and variable Cephaelis ipecacuanha. Callicocca ipecacuanha was described from Brazil, but no type specimen has been found and the name is here lectotypified with an illustration from the protologue. For Cephaelis acuminata, described from Colombia, no original material is extant, and a recent specimen from Colombia is here selected to serve as neotype.

  • 254. Dearborn, Donald C.
    et al.
    Hailer, Frank
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Fleischer, Robert C.
    Microsatellite Primers for Relatedness and Population Structure in Great Frigatebirds (Pelecaniformes: Fregatidae)2008In: Molecular Ecology Resources, ISSN 1755-098X, Vol. 8, no 6, p. 1399-1401Article in journal (Refereed)
    Abstract [en]

    Eighteen moderately polymorphic microsatellite loci were isolated and characterized for great frigatebirds Fregata minor. Polymorphism for the 12 dinucleotide and six tetranucleotide markers was assessed in 23 birds from a Hawaii population. Allelic diversity ranged from two to 12 (mean 5.9), with observed heterozygosity from 0.304 to 0.956 (mean 0.637). Three loci showed homozygote excess, possibly due to null alleles. One additional pair of loci exhibited strong gametic disequilibrium. Thus, at least 14 loci will be useful for studies of relatedness and population structure

  • 255. DeGiorgio, Michael
    et al.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Rosenberg, Noah A.
    Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 38, p. 16057-16062Article in journal (Refereed)
    Abstract [en]

    Studies of worldwide human variation have discovered three trends in summary statistics as a function of increasing geographic distance from East Africa: a decrease in heterozygosity, an increase in linkage disequilibrium (LD), and a decrease in the slope of the ancestral allele frequency spectrum. Forward simulations of unlinked loci have shown that the decline in heterozygosity can be described by a serial founder model, in which populations migrate outward from Africa through a process where each of a series of populations is formed from a subset of the previous population in the outward expansion. Here, we extend this approach by developing a retrospective coalescent-based serial founder model that incorporates linked loci. Our model both recovers the observed decline in heterozygosity with increasing distance from Africa and produces the patterns observed in LD and the ancestral allele frequency spectrum. Surprisingly, although migration between neighboring populations and limited admixture between modern and archaic humans can be accommodated in the model while continuing to explain the three trends, a competing model in which a wave of outward modern human migration expands into a series of preexisting archaic populations produces nearly opposite patterns to those observed in the data. We conclude by developing a simpler model to illustrate that the feature that permits the serial founder model but not the archaic persistence model to explain the three trends observed with increasing distance from Africa is its incorporation of a cumulative effect of genetic drift as humans colonized the world.

  • 256. Dehio, Michaela
    et al.
    Quebatte, Maxime
    Basler, A.
    Toller, I.
    Raddatz, G.
    Tropel, D.
    Lindroos, Hillevi Lina
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Andersson, Siv G. E.
    Dehio, Christoph
    The Expression Profile of Bartonella during Human Cell Infections Reveals the Adaptability of Two-Component System RegulonsManuscript (Other academic)
  • 257.
    den Tex, Robert-Jan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Maldonado, Jesus E.
    Thorington, Richard
    Leonard, Jennifer A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Nuclear copies of mitochondrial genes: another problem for ancient DNA2010In: Genetica, ISSN 0016-6707, E-ISSN 1573-6857, Vol. 138, no 9-10, p. 979-984Article in journal (Refereed)
    Abstract [en]

    The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.

  • 258. Deng, Xin
    et al.
    Phillips, Jonathan
    Bräutigam, Anne
    Engström, Peter
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik.
    Johannesson, Henrik
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik.
    Ouwerkerk, Pieter. B.F.
    Ruberti, Ida
    Salinas, Julio
    Vera, Pablo
    Iannacone, Rina
    Meijer, Annemarie H.
    Bartels, Dorothea
    A homeodomain leucine zipper gene from Craterostigma plantagineum regulates abscisic acid responsive gene expression and physiological responses.2006In: Plant Molecular Biology, Vol. 61, p. 469-489Article in journal (Other (popular scientific, debate etc.))
  • 259. Denk, A.G.
    et al.
    Gautschi, B.
    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.
    Carter, K.
    Kempenaers, B.
    Seven polymorphic microsatellite loci for paternity assessment in the mallard (Anas platyrhynchos)2004In: Molecular Ecology Notes, no 4, p. 506-508Article in journal (Refereed)
  • 260. Denk, Thomas
    et al.
    Oh, Il-Chan
    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.
    Phylogeny of Schisandraceae based on morphological data: evidence from modern plants and the fossil record2005In: Plant Systematics and Evolution, Vol. 256, p. 113-145Article in journal (Refereed)
  • 261. Dorazi, Robert
    et al.
    Götz, Dorothee
    Munro, Stacey
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    White, Malcolm F.
    Equal rates of repair of DNA photoproducts in transcribed and non-transcribed strands in Sulfolobus solfataricus2007In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 63, no 2, p. 521-529Article in journal (Refereed)
    Abstract [en]

    The nucleotide excision repair (NER) pathway removes bulky lesions such as photoproducts from DNA. In both bacteria and eukarya, lesions located in transcribed strands are repaired significantly faster than those located in non-transcribed strands due to damage signalling by stalled RNA polymerase molecules: a phenomenon known as transcription-coupled repair (TCR). TCR requires a mechanism for coupling the detection of stalled RNA polymerase molecules to the NER pathway, provided in bacteria by the Mfd protein. In the third domain of life, archaea, the pathway of NER is not well defined, there are no Mfd homologues and the existence of TCR has not been investigated. In this report we looked at rates of removal of photoproducts in three different operons of the crenarchaeon Sulfolobus solfataricus following UV irradiation. We found no evidence for significantly faster repair in the transcribed strands of these three operons. The rate of global genome repair in S. solfataricus is relatively rapid, and this may obviate the requirement for a specialized TCR pathway. Significantly faster repair kinetics were observed in the presence of visible light, consistent with the presence of a gene for photolyase in the genome of S. solfataricus.

  • 262.
    Dowling, Damian K.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Friberg, Urban
    Lindell, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Evolutionary implications of non-neutral mitochondrial genetic variation2008In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 23, no 10, p. 546-554Article, review/survey (Refereed)
    Abstract [en]

    Sequence variation in mitochondrial DNA (mtDNA) was traditionally considered to be selectively neutral. However, an accumulating body of evidence indicates that this assumption is invalid. Furthermore, recent advances indicate that mtDNA polymorphism can be maintained within populations via selection on the joint mitochondrial-nuclear genotype. Here, we review the latest findings that show mitochondrial and cytoplasmic genetic variation for life-history traits and fitness. We highlight the key importance of the mitochondrial-nuclear interaction as a unit of selection and discuss the consequences of mitochondrially encoded fitness effects on several key evolutionary processes. Our goal is to draw attention to the profound, yet neglected, influence of the mitochondrial genome on the fields of ecology and evolution.

  • 263. Durka, A.G.
    et al.
    Bossdorf, O
    Gautschi, B.
    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.
    Isolation and characterization of microsatellite loci in the invasive Alliaria petiolata (Brassicaceae).2004In: Molecular Ecology Notes, no 4, p. 173-715Article in journal (Refereed)
  • 264.
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Proposal to conserve the name Silene linearis Decne. against Silene linearis Sweet (Caryophyllaceae)Manuscript (Other (popular science, discussion, etc.))
  • 265.
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Systematics in Sileneae (Caryophyllaceae) – Taxonomy and Phylogenetic patterns2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The focus for the first part of the thesis is on the systematics of species belonging to Silene subgenus Silene. Phylogenetic relationships are inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ITS, intron of the RPB2 gene) genomes. Silene section Rigidulae is shown to be non-monophyletic in its previous circumscription, but instead consisting of six separate clades, each correlated to the geographical distribution of the included species. The taxonomic consequences for each clade are discussed. One of the clades is recognized as a new section and described as Silene sect. Arenosae sect. nov. The morphological descriptions of the species are formalized using a novel implementation of the Prometheus Description Model. Two proposals are included in the thesis, one to reject the name Silene polyphylla L., which is a senior synonym to S. portensis L. Silene linearis Decne. is proposed for conservation against the rarely used S. linearis Sweet.

    Silene antirrhina, a weedy American annual, is strongly supported as sister to the Hawaiian endemic species of Silene, suggesting an American origin for these. Two of the endemics have evolved woodiness after introduction to Hawaii.

    In the second part of the thesis we use four nuclear DNA regions, (introns from RPA2, RPB2, RPD2a, RPD2b), and the chloroplast psbE-petG spacer. A framework is developed to evaluate different phylogenetic explanations for conflicting gene trees, where divergence times are used to discriminate among inter- and intralineage processes. The incongruences observed regarding the relationships among the three major lineages of Heliosperma are best explained by homoploid hybridization. The pattern regarding the origin of Heliosperma itself is more complicated and is likely to include several reticulate events. Two lineages have probably been involved in the origin of Heliosperma, one leading to Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.

    List of papers
    1. A re-evaluation of Silene sect. Rigidulae (Caryophyllaceae) based on multiple gene phylogenies
    Open this publication in new window or tab >>A re-evaluation of Silene sect. Rigidulae (Caryophyllaceae) based on multiple gene phylogenies
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95247 (URN)
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2010-01-14Bibliographically approved
    2. Proposal to reject the name Silene polyphylla L. 1753 (Caryophyllaceae)
    Open this publication in new window or tab >>Proposal to reject the name Silene polyphylla L. 1753 (Caryophyllaceae)
    2001 (English)In: Taxon, ISSN 0040-0262, Vol. 50, no 3, p. 923-924Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95248 (URN)
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2009-04-02Bibliographically approved
    3. A taxonomic revision of Silene sect. Arenosae sect. nov. (Caryophyllaceae)
    Open this publication in new window or tab >>A taxonomic revision of Silene sect. Arenosae sect. nov. (Caryophyllaceae)
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95249 (URN)
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2010-01-14Bibliographically approved
    4. Proposal to conserve the name Silene linearis Decne. against Silene linearis Sweet (Caryophyllaceae)
    Open this publication in new window or tab >>Proposal to conserve the name Silene linearis Decne. against Silene linearis Sweet (Caryophyllaceae)
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95250 (URN)
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2010-01-14Bibliographically approved
    5. The Origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae)
    Open this publication in new window or tab >>The Origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae)
    Show others...
    2007 (English)In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 94, no 2, p. 210-218Article in journal (Refereed) Published
    Abstract [en]

    The Hawaiian endemic Silene are a small group of woody or semiwoody representatives from a large, predominantly herbaceous, species-rich genus. We here investigated the origin and number of introductions of the endemic Hawaiian Silene based on phylogenetic relationships inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ribosomal internal transcribed sequences, ITS, and intron 23 of the RPB2 gene) genomes. Silene antirrhina, a widespread weedy American annual, is strongly supported as sister to a monophyletic group consisting of the Hawaiian Silene, indicating a single colonization event. There are no obvious morphological similarities between S. antirrhina and any of the species of Hawaiian Silene. Our results suggest an American origin for the Hawaiian endemics because that would require only a single trans-ocean dispersal. Two of the Hawaiian endemics (S. struthioloides and S. hawaiiensis) that form a subclade in the analyses have evolved woodiness after introduction to the Hawaiian Islands. Our results contribute to other recent results based on molecular phylogenetics that emphasize the American continent as a source area for the Hawaiian flora and support a striking morphological radiation and evolution of woodiness from a single introduction to the archipelago.

    Keywords
    Caryophyllaceae, Hawaiian Silene, ITS, phylogeny, RPB2, rps16, Silene antirrhina, woodiness
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95251 (URN)10.3732/ajb.94.2.210 (DOI)000244241800008 ()
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2017-12-14Bibliographically approved
    6. Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae) – a multigene phylogenetic approach  with  Relative Dating
    Open this publication in new window or tab >>Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae) – a multigene phylogenetic approach  with  Relative Dating
    2009 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 58, no 3, p. 328-345Article in journal (Refereed) Published
    Abstract [en]

    We used four potentially unlinked nuclear DNA regions from the gene   family encoding the second largest subunit of the RNA polymerases, as   well as the psbE-petG spacer and the rps16 intron from the chloroplast   genome, to evaluate the origin of and relationships within Heliosperma   (Sileneae, Caryophyllaceae). Relative dates of divergence times are   used to discriminate between hybridization and gene duplication/loss as   alternative explanations for topological conflicts between gene trees.   The observed incongruent relationships among the three major lineages   of Heliosperma are better explained by homoploid hybridization than by   gene duplication/losses because species branching events exceed gene   coalescence times under biologically reasonable population sizes and   generation times, making lineage sorting an unlikely explanation. The  origin of Heliosperma is complex and the gene trees likely reflect both reticulate evolution and sorting events. At least two lineages have   been involved in the origin of Heliosperma, one most closely related to   the ancestor of Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.

    Keywords
    BEAST, homoploid hybridization, incongruence, lineage sorting, PATHd8, r8s, relative dating, RPA2, RPB2, RPD2
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95252 (URN)10.1093/sysbio/syp030 (DOI)000270004400004 ()
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2017-12-14Bibliographically approved
  • 266.
    Eggens, Frida
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    A re-evaluation of Silene sect. Rigidulae (Caryophyllaceae) based on multiple gene phylogeniesManuscript (Other (popular science, discussion, etc.))
  • 267.
    Eggens, Frida
    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. Systematisk botanik.
    Popp, Magnus
    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. Systematisk botanik.
    Nepokreoff, Molly
    Wagner, Warren L.
    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. Systematisk botanik.
    The Origin of the Hawaiian endemic Silene species2005In: Abstracts - XVII International Botanical Congress: Vienna, Austria, 2005Conference paper (Other scientific)
    Abstract [en]

    Geographically, one could expect an Asian origin for species from the Hawaiian Islands. Despite this, a number of Hawaiian taxa have been shown to have their closest relatives on the North American continent. The seven species of Silene endemic to Hawaii were placed in a section with two Japanese Silene in the latest global revision of the genus. They were thought to be the result of two colonizations, one for the shrubby species and one for the remaining herbaceous ones. Our results, based on DNA sequences from the plastid genome, ITS, and the nuclear low copy number gene RPB2 of five of the seven species (representing both of the putative colonizations) instead strongly indicate a close relationship between the endemic Hawaiian species and the North American species S. antirrhina, which is sister to a monophyletic group of the Hawaiian Silene, indicating a single colonization event. S. antirrhina is a diploid North American species that is not related to other native North American Silene, of which the majority are polyploid and belong to other clades. There is no obvious morphological support for the relationship between the Hawaiian Silene and S. antirrhina.

  • 268.
    Eggens, Frida
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Popp, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Nepokroeff, Molly
    Wagner, Warren L.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    The Origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae)2007In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 94, no 2, p. 210-218Article in journal (Refereed)
    Abstract [en]

    The Hawaiian endemic Silene are a small group of woody or semiwoody representatives from a large, predominantly herbaceous, species-rich genus. We here investigated the origin and number of introductions of the endemic Hawaiian Silene based on phylogenetic relationships inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ribosomal internal transcribed sequences, ITS, and intron 23 of the RPB2 gene) genomes. Silene antirrhina, a widespread weedy American annual, is strongly supported as sister to a monophyletic group consisting of the Hawaiian Silene, indicating a single colonization event. There are no obvious morphological similarities between S. antirrhina and any of the species of Hawaiian Silene. Our results suggest an American origin for the Hawaiian endemics because that would require only a single trans-ocean dispersal. Two of the Hawaiian endemics (S. struthioloides and S. hawaiiensis) that form a subclade in the analyses have evolved woodiness after introduction to the Hawaiian Islands. Our results contribute to other recent results based on molecular phylogenetics that emphasize the American continent as a source area for the Hawaiian flora and support a striking morphological radiation and evolution of woodiness from a single introduction to the archipelago.

  • 269.
    Eggens, Frida
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Thollesson, Mikael
    Oxelman, Bengt
    A taxonomic revision of Silene sect. Arenosae sect. nov. (Caryophyllaceae)Manuscript (Other (popular science, discussion, etc.))
  • 270.
    Ekenäs, Catarina
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Phylogenies and Secondary Chemistry in Arnica (Asteraceae)2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The genus Arnica (Asteraceae) was investigated for phylogenetic relationships and sesquiterpene lactone (STL) content with the aims to trace the evolutionary history of the genus and to investigate possible congruencies between DNA sequence data, secondary chemistry, and biological activity.

    Complex evolutionary patterns in Arnica are evident from phylogenetic analyses of chloroplast regions (the rpl16 and rps16 introns and the psbA–trnH, ycf4–cemA, and trnT–L spacers), nuclear ribosomal regions (the internal and external transcribed spacers) and the nuclear low-copy DNA region coding for the second largest subunit of RNA polymerase II (RPB2) between exons 17 and 23. Polymorphism was detected in nuclear ribosomal and low-copy regions, likely caused by polyploidy and agamospermy. Lineage sorting and/or hybridization is a possible explanation for incongruencies between topologies of the different DNA regions. None of the five subgenera in Arnica constitute a monophyletic group according to any of our analyses.

    Sesquiterpene lactone profiles were compared to nuclear ribosomal DNA data using phylogenetic inference and principal component analysis for 33 accessions of 16 species. Clusters supported by both STL chemistry and ribosomal DNA sequence data consist of multiple accessions of the same species (e.g. A montana and A. longifolia), indicating that these species are well defined both genetically and chemically, based on our sampling. Support for subspecies classification of A. chamissonis and A. parryi was found in chemical data. For the first time STLs are reported from subtribe Madiinae, sister to Arniciinae.

    Anti-inflammatory properties, as measured by inhibition of human neutrophil elastase release from neutrophils and inhibition of the binding of transcription factor NF-κB to DNA, were investigated for extracts of 12 Arnica species. Arnica montana, A. chamissonis and A. longifolia accessions show high inhibitory effects in both bioassays. Generally, species with a more diverse STL chemistry also possess the strongest inhibitory activity in the bioassays.

    List of papers
    1. A molecular phylogenetic study of Arnica (Asteraceae): Low chloroplast DNA variation and problematic subgeneric classification
    Open this publication in new window or tab >>A molecular phylogenetic study of Arnica (Asteraceae): Low chloroplast DNA variation and problematic subgeneric classification
    2007 (English)In: Systematic Botany, ISSN 0363-6445, E-ISSN 1548-2324, Vol. 32, no 4, p. 917-928Article in journal (Refereed) Published
    Abstract [en]

    DNA sequences from five chloroplast DNA regions (the rpl16 and rps16 introns and the psbA-trnH, ycf4-cemA, and trnT-L spacers), and the nuclear ribosomal internal and external transcribed spacer (ITS and ETS) regions, were analyzed using maximum parsimony and Bayesian methods to explore the putatively complicated history of the mainly North American genus Arnica. The chloroplast regions were found to contain minimal variation in Arnica. Of 3710 nucleotides, only 119 were variable and 45 informative. However, combined with the ribosomal DNA data, the analysis yielded a number of well-supported clades. Strong support for the monophyly of Arnica was found in both the separate and combined analyses but none of the five currently recognized subgenera was resolved as monophyletic in any of the analyses. Arnica (Whitneya) dealbata and A. mallotopus (Mallotopus japonicus), two species that were previously placed outside Arnica, were confidently confirmed as members of the genus. The analyses revealed that A. nevadensis (subg. Austromontana) is most closely related to A. dealbata and that A. mallotopus forms a strongly supported clade with A. unalaschcensis (subg. Andropurpurea). Earlier biogeographical hypotheses that suggested an arctic origin and southward spread of the genus are not supported by our analyses. Hybridization, homoplasy, and rapid evolution are possible explanations for conflicts between the chloroplast and nuclear ribosomal data sets and for low support of the deeper nodes.

    Keywords
    Arnica, Asteraceae, chloroplast, Compositae, dealbata, ETS, ITS, mallotopus, phylogeny
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96739 (URN)000251559200020 ()
    Available from: 2008-02-21 Created: 2008-02-21 Last updated: 2017-12-14
    2. Secondary chemistry and ribosomal DNA data congruencies in Arnica (Asteraceae)
    Open this publication in new window or tab >>Secondary chemistry and ribosomal DNA data congruencies in Arnica (Asteraceae)
    Show others...
    2009 (English)In: Cladistics, ISSN 0748-3007, E-ISSN 1096-0031, Vol. 25, no 1, p. 78-92Article in journal (Refereed) Published
    Abstract [en]

    To investigate possible congruencies between DNA sequence data and secondary chemistry, we compared nuclear ribosomal DNA (nrDNA) sequence data, sesquiterpene lactone (STL) contents, and cytometric data from 35 accessions of 16 Arnica (Asteraceae) species and two outgroup taxa (Layia hieracioides and Madia sativa), using phylogenetic inference and principal component analysis (PCA). Several groups supporting multiple accessions of the same species (of A. montana, A. longifolia, A. gracilis, and A. chamissonis) are congruent between the phylogenetic trees based on nrDNA and STL data. Sesquiterpene lactone profiles were found to be highly consistent within multiple samples of A. montana and A. longifolia respectively. Moreover, sesquiterpene lactone data support subspecies classifications of A. chamissonis and A. parryi, with additional support from DNA sequence data and cytometric data. Morphology, STL data (PCA), cytometric data and DNA sequence data suggest a hybrid origin of one accession (A. gracilis × longifolia). In A. gracilis, A. latifolia, and Layia hieracioides, previously not investigated for STLs, we found large amounts of xanthalongin derivatives. This is the first time STLs have been reported from subtribe Madiinae.

    National Category
    Pharmaceutical Sciences Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96740 (URN)10.1111/j.1096-0031.2008.00244.x (DOI)000262636700004 ()
    Available from: 2008-02-21 Created: 2008-02-21 Last updated: 2018-01-13Bibliographically approved
    3. Anti-inflammatory activity of extracts from Arnica (Asteraceae) species assessed by inhibition of NF-κB and release of human neutrophil elastase
    Open this publication in new window or tab >>Anti-inflammatory activity of extracts from Arnica (Asteraceae) species assessed by inhibition of NF-κB and release of human neutrophil elastase
    Show others...
    In: Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-96741 (URN)
    Available from: 2008-02-21 Created: 2008-02-21 Last updated: 2012-11-06
    4. RPB2 phylogeny in Arnica (Asteraceae) reveals multiple d-paralogues
    Open this publication in new window or tab >>RPB2 phylogeny in Arnica (Asteraceae) reveals multiple d-paralogues
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-96742 (URN)
    Available from: 2008-02-21 Created: 2008-02-21 Last updated: 2010-01-13Bibliographically approved
  • 271.
    Ekenäs, Catarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Baldwin, Bruce G.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    A molecular phylogenetic study of Arnica (Asteraceae): Low chloroplast DNA variation and problematic subgeneric classification2007In: Systematic Botany, ISSN 0363-6445, E-ISSN 1548-2324, Vol. 32, no 4, p. 917-928Article in journal (Refereed)
    Abstract [en]

    DNA sequences from five chloroplast DNA regions (the rpl16 and rps16 introns and the psbA-trnH, ycf4-cemA, and trnT-L spacers), and the nuclear ribosomal internal and external transcribed spacer (ITS and ETS) regions, were analyzed using maximum parsimony and Bayesian methods to explore the putatively complicated history of the mainly North American genus Arnica. The chloroplast regions were found to contain minimal variation in Arnica. Of 3710 nucleotides, only 119 were variable and 45 informative. However, combined with the ribosomal DNA data, the analysis yielded a number of well-supported clades. Strong support for the monophyly of Arnica was found in both the separate and combined analyses but none of the five currently recognized subgenera was resolved as monophyletic in any of the analyses. Arnica (Whitneya) dealbata and A. mallotopus (Mallotopus japonicus), two species that were previously placed outside Arnica, were confidently confirmed as members of the genus. The analyses revealed that A. nevadensis (subg. Austromontana) is most closely related to A. dealbata and that A. mallotopus forms a strongly supported clade with A. unalaschcensis (subg. Andropurpurea). Earlier biogeographical hypotheses that suggested an arctic origin and southward spread of the genus are not supported by our analyses. Hybridization, homoplasy, and rapid evolution are possible explanations for conflicts between the chloroplast and nuclear ribosomal data sets and for low support of the deeper nodes.

  • 272.
    Ekenäs, Catarina
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Heidari, Nahid
    Andreasen, Katarina
    RPB2 phylogeny in Arnica (Asteraceae) reveals multiple d-paraloguesManuscript (Other academic)
  • 273.
    Ekenäs, Catarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Zebrowska, Anna
    Schuler, Barbara
    Vrede, Tobias
    Andreasen, Katarina
    Backlund, Anders
    Merfort, Irmgard
    Bohlin, Lars
    Anti-inflammatory activity of extracts from Arnica (Asteraceae) species assessed by inhibition of NF-κB and release of human neutrophil elastaseIn: Article in journal (Refereed)
  • 274.
    Ekenäs, Catarina
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Zebrowska, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Schuler, Barbara
    Vrede, Tobias
    Department of Ecology and Environmental Science, Umeå University, Sweden .
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Merfort, Irmgard
    Albert-Ludwigs- Universität, Freiburg, Germany.
    Bohlin, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Screening for Anti-Inflammatory Activity of 12 Arnica (Asteraceae) Species Assessed by Inhibition of NF-κB and Release of Human Neutrophil Elastase2008In: Planta Medica, ISSN 0032-0943, E-ISSN 1439-0221, Vol. 74, no 15, p. 1789-1794Article in journal (Refereed)
    Abstract [en]

    Several species in the genus Arnica have been used in traditional medicine to treat inflammatory-related disorders. Extracts of twelve Arnica species and two species closely related to Arnica (Layia hieracioides and Madia sativa) were investigated for inhibition of human neutrophil elastase release and inhibition of transcription factor NF-κB. Statistical analyses reveal significant differences in inhibitory capacities between extracts. Sesquiterpene lactones of the helenanolide type, of which some are known inhibitors of human neutrophil elastase release and NF-κB, are present in large amounts in the very active extracts of A. montana and A. chamissonis. Furthermore, A. longifolia, which has previously not been investigated, shows a high activity similar to that of A. montana and A. chamissonis in both bioassays. Sesquiterpene lactones of the xanthalongin type are present in large amounts in A. longifolia and other active extracts and would be interesting to evaluate further.

  • 275. Eklund, D. Magnus
    et al.
    Svensson, Emma M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Kost, Benedikt
    Physcomitrella patens: a model to investigate the role of RAC/ROP GTPase signalling in tip growth2010In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 61, no 7, p. 1917-1937Article, review/survey (Refereed)
    Abstract [en]

    Polarized cell expansion plays an important role in plant morphogenesis. Tip growth is a dramatic form of this process, which is widely used as a model to study its regulation by RAC/ROP GTPase signalling. During the dominant haploid phase of its life cycle, the moss Physcomitrella patens contains different types of cells that expand by tip growth. Physcomitrella is a highly attractive experimental system because its genome has been sequenced, and transgene integration by homologous recombination occurs in this plant at frequencies allowing effective gene targeting. Furthermore, together with the vascular spikemoss Selaginella moellendorffii, whose genome has also been sequenced, the non-vascular moss Physcomitrella provides an evolutionary link between green algae and angiosperms. BLAST searches established that the Physcomitrella and Selaginella genomes encode not only putative RAC/ROP GTPases, but also homologues of all known regulators of polarized RAC/ROP signalling, as well as of key effectors acting in signalling cascades downstream of RAC/ROP activity. Nucleotide sequence relationships within seven different families of Physcomitrella, Selaginella, Arabidopsis thaliana and Nicotiana tabacum (tobacco) genes with distinct functions in RAC/ROP signalling were characterized based on extensive maximum likelihood and Neighbor-Joining analyses. The results of these analyses are interpreted in the light of current knowledge concerning expression patterns and molecular functions of RAC/ROP signalling proteins in angiosperms. A key aim of this study is to facilitate the use of Physcomitrella as a model to investigate the molecular control of tip growth in plants.

  • 276. Eklund, Julie A.
    et al.
    Thomas, Mark G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Assessing the effects of conservation treatments on short sequences of DNA in vitro2010In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 37, no 11, p. 2831-2841Article in journal (Refereed)
    Abstract [en]

    Little is known about what effects conservation treatments used to preserve human and animal hard and soft tissues have on DNA preservation. We have developed a method to assess quantitatively the extent of lesions or strand breakage caused by conservation treatments on short sequences of DNA in vitro. The method developed enables the determination of the percentage of DNA preserved following exposure to a conservation treatment solution relative to control samples, thereby allowing the direct comparison of treatments based upon their preserving/damaging effects on a DNA sequence. Forty-three chemicals commonly used in the preparation and/or conservation of human and/or animal remains were examined. We found that the majority were damaging, in particular and as expected, acidic treatments and treatments carried out at elevated temperatures. A few, primarily organic solvents, were not damaging. The approach we have adopted can be applied to screen other treatments either used in the past or for future conservation applications as they are developed to assess their effects on DNA. How these results should be interpreted in terms of conservation and sampling is also discussed.

  • 277.
    Elf, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Paulsson, Johan
    Berg, Otto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Mesoscopic kinetics and its applications in protein synthesis2005In: Systems Biology: Definitions and Perspectives / [ed] Lila Alberghina and H.V. Westerhoff, Heidelberg: Springer-Verlag GmbH , 2005, p. 95-118Chapter in book (Other academic)
    Abstract [en]

    Molecular biology emerged through unification of genetics and nucleic acid chemistry that took place with the discovery of the double helix (Watson and Crick 1953). Accordingly, molecular biology could be defined as the sum of all techniques used to perform genetic experiments by manipulating DNA. One consequence of the development of these techniques is large-scale sequencing of genomes from an ever increasing number of organisms. However, it became clear from this development that genetic information per se is not enough to grasp the most interesting functional and evolutionary aspects of cells and multi-cellular organisms. In fact, understanding how genotype leads to phenotype depends on concepts and techniques from areas that so far have been largely alien to molecular biological research, like physics, mathematics, and engineering. From the bits and pieces from these and other scientific fields new tools must be generated to make possible an understanding of the dynamic, adapting, and developing living systems that somehow take shape from the instructions given by their genomes. The growing total of these tools and their integration in experimental and theoretical approaches to understand complex biological processes in ways previously out of reach could be a way to define systems biology, in analogy with the above definition of molecular biology.

  • 278.
    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.
    DNA löser brott med djur.2004In: Kriminalteknik, no 3, p. 10-11Article in journal (Other (popular scientific, debate etc.))
  • 279.
    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.
    Genetisk forskning visar på den framgångsrike hingsten.2004In: Miljöforskning: (FORMAS), Vol. 2, no 22-24Article in journal (Other (popular scientific, debate etc.))
  • 280.
    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.
    Microsatellites: simple sequences with complex evolution.2004In: Nature Reviews Genetics, no 5, p. 435-445Article in journal (Refereed)
  • 281.
    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.
    Vad är en människa?2004In: Forsking och framsteg, no 4, p. 16-Article in journal (Other (popular scientific, debate etc.))
  • 282.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Characteristics, causes and evolutionary consequences of male-biased mutation2007In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 274, no 1606, p. 1-10Article, review/survey (Refereed)
    Abstract [en]

    Mutation has traditionally been considered a random process, but this paradigm is challenged by recent evidence of divergence rate heterogeneity in different genomic regions. One facet of mutation rate variation is the propensity for genetic change to correlate with the number of germ cell divisions, reflecting the replication-dependent origin of many mutations. Haldane was the first to connect this association of replication and mutation to the difference in the number of cell divisions in oogenesis (low) and spermatogenesis (usually high), and the resulting sex difference in the rate of mutation. The concept of male-biased mutation has been thoroughly analysed in recent years using an evolutionary approach, in which sequence divergence of autosomes and/or sex chromosomes are compared to allow inference about the relative contribution of mothers and fathers in the accumulation of mutations. For instance, assuming that a neutral sequence is analysed, that rate heterogeneity owing to other factors is cancelled out by the investigation of many loci and that the effect of ancestral polymorphism is properly taken into account, the male-to-female mutation rate ratio, αm, can be solved from the observed difference in rate of X and Y chromosome divergence. The male mutation bias is positively correlated with the relative excess of cell divisions in the male compared to the female germ line, as evidenced by a generation time effect: in mammals, αm is estimated at approximately 4–6 in primates, approximately 3 in carnivores and approximately 2 in small rodents. Another life-history correlate is sexual selection: when there is intense sperm competition among males, increased sperm production will be associated with a larger number of mitotic cell divisions in spermatogenesis and hence an increase in αm. Male-biased mutation has implications for important aspects of evolutionary biology such as mate choice in relation to mutation load, sexual selection and the maintenance of genetic diversity despite strong directional selection, the tendency for a disproportionate large role of the X (Z) chromosome in post-zygotic isolation, and the evolution of sex.

  • 283.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Comparative genomics and the study of evolution by natural selection2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 21, p. 4586-4596Article, review/survey (Refereed)
    Abstract [en]

    Genomics profoundly affects most areas of biology, including ecology and evolutionary biology. By examining genome sequences from multiple species, comparative genomics offers new insight into genome evolution and the way natural selection moulds DNA sequence evolution. Functional divergence, as manifested in the accumulation of nonsynonymous substitutions in protein-coding genes, differs among lineages in a manner seemingly related to population size. For example, the ratio of nonsynonymous to synonymous substitution (d(N)/d(S)) is higher in apes than in rodents, compatible with Ohta's nearly neutral theory of molecular evolution, which suggests that the fixation of slightly deleterious mutations contributes to protein evolution at an extent negatively correlated with effective population size. While this supports the idea that functional evolution is not necessarily adaptive, comparative genomics is uncovering a role for positive Darwinian selection in 10-40% of all genes in different lineages, estimates that are likely to increase when the addition of more genomes gives increased power. Again, population size seems to matter also in this context, with a higher proportion of fixed amino acid changes representing advantageous mutations in large populations. Genes that are particularly prone to be driven by positive selection include those involved with reproduction, immune response, sensory perception and apoptosis. Genetic innovations are also frequently obtained by the gain or loss of complete gene sequences. Moreover, it is increasingly realized, from comparative genomics, that purifying selection conserves much more than just the protein-coding part of the genome, and this points at an important role for regulatory elements in trait evolution. Finally, genome sequencing using outbred or multiple individuals has provided a wealth of polymorphism data that gives information on population history, demography and marker evolution.

  • 284.
    Ellegren, Hans
    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.
    Evolution: Natural selection in the evolution of humans and chimps.2005In: Curren Biology, no 22, p. R919-922Article in journal (Refereed)
  • 285.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Evolutionary stasis: the stable chromosomes of birds2010In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 25, no 5, p. 283-291Article in journal (Refereed)
    Abstract [en]

    Evolution at the molecular level is manifested in a variety of types of change in DNA sequences, including changes in the structure and organisation of chromosomes. However, in birds chromosomal evolution occurs at an unusually slow rate and recent whole-genome comparisons have shown that many chromosomes have remained more or less intact during avian evolution. Here I discuss progress in the development of genetic maps of natural bird populations, which has revealed that the evolutionary stasis of chromosomes often extends to conservation of gene order. The evolutionary stability of bird chromosomes, which might relate to a low frequency of transposable elements, will facilitate the transfer of genomic information from model to non-model organisms and might have a connection to the rarity of postzygotic incompatibilities observed in birds.

  • 286.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Platypus genome suggests a recent origin for the human X.2008In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 18, no 13, p. R557-R559Article in journal (Refereed)
  • 287.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Sequencing goes 454 and takes large-scale genomics into the wild2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 7, p. 1629-1631Article in journal (Refereed)
    Abstract [en]

    Sometimes, science takes a big leap forward. This is often due to new technology that allows the study of questions previously difficult or even impossible to address. An example of this is provided in this issue (Vera et al. 2008) by the first large-scale attempt toward genome sequencing of an ecologically important model, based on the new '454-sequencing technology'. Using this new technology, the protein-coding sequences of the Glanville fritillary butterfly genome have now been largely characterized.

  • 288.
    Ellegren, Hans
    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.
    The avian genome uncovered.2005In: Trends in Ecology and Evolution, no 20, p. 180-186Article in journal (Refereed)
  • 289.
    Ellegren, Hans
    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.
    The dog has its day.2005In: Nature, no 438, p. 745-746Article in journal (Refereed)
  • 290.
    Ellegren, Hans
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hultin-Rosenberg, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Brunström, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology.
    Dencker, Lennart
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Kultima, Kim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Scholz, Birger
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Faced with inequality: chicken do not have a general dosage compensation of sex-linked genes2007In: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 5, no 1, p. 40-Article in journal (Refereed)
    Abstract [en]

    Background: The contrasting dose of sex chromosomes in males and females potentially introduces a large-scale imbalance in levels of gene expression between sexes, and between sex chromosomes and autosomes. In many organisms, dosage compensation has thus evolved to equalize sex-linked gene expression in males and females. In mammals this is achieved by X chromosome inactivation and in flies and worms by up- or down-regulation of X-linked expression, respectively. While otherwise widespread in systems with heteromorphic sex chromosomes, the case of dosage compensation in birds (males ZZ, females ZW) remains an unsolved enigma. Results: Here, we use a microarray approach to show that male chicken embryos generally express higher levels of Z-linked genes than female birds, both in soma and in gonads. The distribution of male-to-female fold-change values for Z chromosome genes is wide and has a mean of 1.4-1.6, which is consistent with absence of dosage compensation and sex-specific feedback regulation of gene expression at individual loci. Intriguingly, without global dosage compensation, the female chicken has significantly lower expression levels of Z-linked compared to autosomal genes, which is not the case in male birds. Conclusion: The pronounced sex difference in gene expression is likely to contribute to sexual dimorphism among birds, and potentially has implication to avian sex determination. Importantly, this report, together with a recent study of sex-biased expression in somatic tissue of chicken, demonstrates the first example of an organism with a lack of global dosage compensation, providing an unexpected case of a viable system with large-scale imbalance in gene expression between sexes.

  • 291.
    Ellegren, Hans
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Parsch, John
    The evolution of sex-biased genes and sex-biased gene expression2007In: Nature reviews genetics, ISSN 1471-0056, E-ISSN 1471-0064, Vol. 8, no 9, p. 689-698Article, review/survey (Refereed)
    Abstract [en]

    Differences between males and females in the optimal phenotype that is favoured by selection can be resolved by the evolution of differential gene expression in the two sexes. Microarray experiments have shown that such sex-biased gene expression is widespread across organisms and genomes. Sex-biased genes show unusually rapid sequence evolution, are often labile in their pattern of expression, and are non-randomly distributed in the genome. Here we discuss the characteristics and expression of sex-biased genes, and the selective forces that shape this previously unappreciated source of phenotypic diversity. Sex-biased gene expression has implications beyond just evolutionary biology, including for medical genetics.

  • 292.
    Ellegren, Hans
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Sheldon, Ben C.
    Genetic basis of fitness differences in natural populations2008In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 452, no 7184, p. 169-175Article, review/survey (Refereed)
    Abstract [en]

    Genomics profoundly influences current biology. One of many exciting consequences of this revolution is the potential for identifying and studying the genetic basis of those traits affecting fitness that are key to natural selection. Recent studies using a multitude of genomic approaches have established such genotype - phenotype relationships in natural populations, giving new insight into the genetic architecture of quantitative variation. In parallel, an emerging understanding of the quantitative genetics of fitness variation in the wild means that we are poised to see a synthesis of ecological and molecular approaches in evolutionary biology.

  • 293.
    Elmhalli, Fawzeia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Pålsson, Katinka
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Örberg, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Environmental Toxicology.
    Jaenson, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Acaricidal effects of Corymbia citriodora oil containing para-menthane-3,8-diol against nymphs of Ixodes ricinus (Acari: Ixodidae)2009In: Experimental & applied acarology, ISSN 0168-8162, E-ISSN 1572-9702, Vol. 48, no 3, p. 251-262Article in journal (Refereed)
    Abstract [en]

    The toxicity of para-menthane-3,8-diol (PMD), the main arthropod-repellent compound in the oil of the lemon eucalyptus, Corymbia citriodora, was evaluated against nymphs of Ixodes ricinus using five methods (A-E) of a contact toxicity bioassay. Mortality rates were estimated by recording numbers of dead nymphs at 30 min intervals during the first 5 h after the start of exposure and at longer intervals thereafter. The mortality rate increased with increasing concentration of PMD and duration of exposure with a distinct effect after 3.5 h. From the results obtained by methods A, C and E, the LC(50) range was 0.035-0.037 mg PMD/cm(2) and the LC(95) range was 0.095-0.097 mg PMD/cm(2) at 4 h of exposure; the LT(50) range was 2.1-2.8 h and the LT(95) range was 3.9-4.2 h at 0.1 mg PMD/cm(2). To determine the duration of toxic activity of PMD, different concentrations (0.002, 0.01, 0.1 mg PMD/cm(2)) were tested and mortality was recorded at each concentration after 1 h; thereafter new ticks were tested. This test revealed that the lethal activity of PMD remained for 24 h but appeared absent after 48 h. The overall results show that PMD is toxic to nymphs of I. ricinus and may be useful for tick control.

  • 294.
    Emilsson, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Detection of Differentially Expressed Genes in Alzheimer's Disease: Regulator of G-protein Signalling 4: A Novel Mediator of APP Processing2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Alzheimer’s disease is a neurodegenerative disease characterised by progressive memory deterioration and cognitive impairment. Pathological hallmarks are extracellular senile plaques, neurofibrillary tangles and neuron loss. Senile plaques are produced through altered processing of the membrane-bound protein APP. Different neurotransmitter signal transduction pathways have been implicated in the formation or development of Alzheimer’s pathologies, but the molecular mechanisms behind these changes are not well known.

    The overall aims of this thesis were to identify novel genes with differential expression in Alzheimer’s disease and to investigate mechanisms initiating these changes and their relationship to the disease. A real-time RT-PCR strategy was developed to enable detection of small mRNA changes in human brain autopsy samples. This approach was first used to investigate levels of expression of a candidate gene (MAO), and later employed to verify gene expression differences detected by cDNA microarray analysis. Of several genes verified as differentially expressed in the patients, ITPKB (Inositol 1,4,5-trisphosphate 3-kinase B) and RGS4 (Regulator of G-protein signalling 4) presented the largest expression differences in Alzheimer’s cases compared to control samples. Several splice variants of RGS4 showed similar down-regulation levels and one rare haplotype was associated with decreased RGS4 expression. Functional studies in SH-SY5Y cell cultures overexpressing RGS4 showed that it is likely that RGS4 affects APP processing by regulating PRKC expression levels.

    The combined expression of RGS4 and ITPKB is for the first time presented in this thesis as genes with altered mRNA levels in Alzheimer’s disease. These two genes are implicated in the same signalling pathway that modifies calcium levels in the cell. Furthermore, the fact that RGS4 affects APP processing suggests that RGS4 is involved in the development of senile plaques. This motivates further functional studies of this gene and suggests that RGS4 may become a new potential drug target for Alzheimer’s disease.

    List of papers
    1. High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies
    Open this publication in new window or tab >>High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies
    2000 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 10, no 8, p. 1219-29Article in journal (Refereed) Published
    Abstract [en]

    Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. Comparison of the relative mRNA levels between two groups of samples with different time postmortem revealed unchanged relative expression levels for most genes. Only CYP26A1 mRNA levels showed a significant decrease with prolonged time postmortem (p = 0.00004). Also, there was a general decrease in measured mRNA levels for all genes in autopsies compared to biopsies; however, on comparing mRNA levels after adjusting with reference genes, no significant differences were found between mRNA levels in autopsies and biopsies. This observation indicates that studies of postmortem material can be performed to reveal the relative in vivo mRNA levels of genes. Power calculations were done to determine the number of individuals necessary to detect differences in mRNA levels of 1.5-fold to tenfold using the strategy described here. This analysis showed that samples from at least 50 individuals per group, patients and controls, are required for high-resolution ( approximately twofold changes) differential expression screenings in the human brain. Experiments done on ten individuals per group will result in a resolution of approximately fivefold changes in expression levels. In general, the sensitivity and resolution of any differential expression study will depend on the sample size used and the between-individual variability of the genes analyzed.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-90900 (URN)10.1101/gr.10.8.1219 (DOI)10958640 (PubMedID)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2017-12-14Bibliographically approved
    2. Increased monoamine oxidase messenger RNA expression levels in frontal cortex of Alzheimer's disease patients
    Open this publication in new window or tab >>Increased monoamine oxidase messenger RNA expression levels in frontal cortex of Alzheimer's disease patients
    Show others...
    2002 (English)In: Neuroscience Letters, ISSN 0304-3940, E-ISSN 1872-7972, Vol. 326, no 1, p. 56-60.Article in journal (Refereed) Published
    Abstract [en]

    Alzheimer's disease (AD) is a neurodegenerative disorder and the most common cause of dementia in the industrialised world. The two monoamine oxidase (MAO) enzymes, monoamine oxidase A (MAOA) and monoamine oxidase B (MAOB), are important in the metabolism of monoamine neurotransmitters. AD and ageing have been shown to increase enzyme activity for both MAOA and MAOB. An increase (rather than decrease) of enzyme activity is a rare event in a disease that results in a decrease in the number of cells in the brain. The mechanism, transcriptional or post-transcriptional, responsible for the increase in protein activity, is not known. In this study, we investigate for the first time the messenger RNA (mRNA) expression levels of both MAOA and MAOB in 246 cortical brain samples obtained at autopsy from 62 AD patients and 61 normal controls. We found a significant increase in mRNA levels for both MAOA (P=0.001) and MAOB (P=0.002) in disease brain tissue. This indicates that both MAO enzymes might be important in the progression of AD.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-93406 (URN)0.1016/S0304-3940(02)00307-5 (DOI)
    Available from: 2005-09-08 Created: 2005-09-08 Last updated: 2017-12-14Bibliographically approved
    3. Alzheimer’s disease: mRNA expression profiles of multiple patients show alterations of genes involved with calcium signalling
    Open this publication in new window or tab >>Alzheimer’s disease: mRNA expression profiles of multiple patients show alterations of genes involved with calcium signalling
    2006 (English)In: Neurobiology of Disease, ISSN 0969-9961, E-ISSN 1095-953X, Vol. 21, no 3, p. 618-625Article in journal (Refereed) Published
    Abstract [en]

    We combined global and high-resolution strategies to find genes with altered mRNA expression levels in one of the largest collection of brain autopsies from Alzheimer's patients and controls ever studied. Our global analysis involved microarray hybridizations of large pools of samples obtained from 114 individuals, using two independent sets of microarrays. Ten genes selected from the microarray experiments were quantified on each individual separately using real-time RT-PCR. This high-resolution analysis accounted for systematic differences in age, postmortem interval, brain pH, and reference gene expression, and it estimated the effect of disease on mRNA levels, on top of the effect of all other variables. Differential expression was confirmed for eight out of ten genes. Among them, Type B inositol 1,4,5-trisphosphate 3-kinase (ITPKB), and regulator of G protein signaling 4 (RGS4) showed highly altered expression levels in patients (P values < 0.0001). Our results point towards increased inositol triphospate (IP3)-mediated calcium signaling in Alzheimer's disease.

    Keywords
    Aged, Aged; 80 and over, Alzheimer Disease/*genetics, Calcium Signaling/*genetics, Female, Gene Expression, Gene Expression Profiling, Humans, In Situ Hybridization, Male, Middle Aged, Oligonucleotide Array Sequence Analysis, RNA; Messenger/analysis, Reverse Transcriptase Polymerase Chain Reaction
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-93407 (URN)10.1016/j.nbd.2005.09.004 (DOI)16257224 (PubMedID)
    Available from: 2005-09-08 Created: 2005-09-08 Last updated: 2017-12-14Bibliographically approved
    4. Low mRNA levels of RGS4 splice variants in Alzheimer’s disease and association between a rare haplotype and decreased mRNA expression
    Open this publication in new window or tab >>Low mRNA levels of RGS4 splice variants in Alzheimer’s disease and association between a rare haplotype and decreased mRNA expression
    2006 (English)In: Synapse, ISSN 0887-4476, E-ISSN 1098-2396, Vol. 59, no 3, p. 173-176Article in journal (Refereed) Published
    Abstract [en]

    Regulator of G-protein signaling 4 (RGS4) showed decreased mRNAlevels in Alzheimer’s disease in a large collection of human brain autopsies from prefrontalcortex. The expression levels of three RGS4 splice variants were examined inthe same samples, and the association between RGS4 gene expression and/or the diseasewith single nucleotide polymorphisms located in this gene was explored. We showthat all splice variants are down-regulated in patients. We also demonstrate that onerare haplotype (ATAG) is associated with decreased mRNA levels in both cases andcontrols. Our results suggest that an altered regulation in transcription initiation maybe an important mechanism for low RGS4 protein levels in Alzeimer’s disease.

    Keywords
    neurodegeneration, RGS splice variants, SNP, real-time RT-PCR
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-93408 (URN)10.1002/SYN.20226 (DOI)16358332 (PubMedID)
    Available from: 2005-09-08 Created: 2005-09-08 Last updated: 2017-12-14Bibliographically approved
    5. RGS4: A novel mediator of APP processing
    Open this publication in new window or tab >>RGS4: A novel mediator of APP processing
    Show others...
    (English)Manuscript (Other academic)
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-93409 (URN)
    Available from: 2005-09-08 Created: 2005-09-08 Last updated: 2010-02-11Bibliographically approved
  • 295.
    Emilsson, Lina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Nilsson, Tatjana
    Cedazo-Minguez, Angel
    Benedikz, Eirikur
    Jazin, Elena
    RGS4: A novel mediator of APP processingManuscript (Other academic)
  • 296.
    Emilsson, Lina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Balciuniene, Jorune
    Castensson, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Cairns, Nigel
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Increased monoamine oxidase messenger RNA expression levels in frontal cortex of Alzheimer's disease patients2002In: Neuroscience Letters, ISSN 0304-3940, E-ISSN 1872-7972, Vol. 326, no 1, p. 56-60.Article in journal (Refereed)
    Abstract [en]

    Alzheimer's disease (AD) is a neurodegenerative disorder and the most common cause of dementia in the industrialised world. The two monoamine oxidase (MAO) enzymes, monoamine oxidase A (MAOA) and monoamine oxidase B (MAOB), are important in the metabolism of monoamine neurotransmitters. AD and ageing have been shown to increase enzyme activity for both MAOA and MAOB. An increase (rather than decrease) of enzyme activity is a rare event in a disease that results in a decrease in the number of cells in the brain. The mechanism, transcriptional or post-transcriptional, responsible for the increase in protein activity, is not known. In this study, we investigate for the first time the messenger RNA (mRNA) expression levels of both MAOA and MAOB in 246 cortical brain samples obtained at autopsy from 62 AD patients and 61 normal controls. We found a significant increase in mRNA levels for both MAOA (P=0.001) and MAOB (P=0.002) in disease brain tissue. This indicates that both MAO enzymes might be important in the progression of AD.

  • 297. Engen, Steinar
    et al.
    Ringsby, Thor Harald
    Saether, Bernt-Erik
    Lande, Russell
    Jensen, Henrik
    Lillegård, Magnar
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Effective size of fluctuating populations with two sexes and overlapping generations2007In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 61, no 8, p. 1873-1885Article in journal (Refereed)
    Abstract [en]

    We derive formulas that can be applied to estimate the effective population size N(e) for organisms with two sexes reproducing once a year and having constant adult mean vital rates independent of age. Temporal fluctuations in population size are generated by demographic and environmental stochasticity. For populations with even sex ratio at birth, no deterministic population growth and identical mean vital rates for both sexes, the key parameter determining N(e) is simply the mean value of the demographic variance for males and females considered separately. In this case Crow and Kimura's generalization of Wright's formula for N(e) with two sexes, in terms of the effective population sizes for each sex, is applicable even for fluctuating populations with different stochasticity in vital rates for males and females. If the mean vital rates are different for the sexes then a simple linear combination of the demographic variances determines N(e), further extending Wright's formula. For long-lived species an expression is derived for N(e) involving the generation times for both sexes. In the general case with nonzero population growth and uneven sex ratio of newborns, we use the model to investigate numerically the effects of different population parameters on N(e). We also estimate the ratio of effective to actual population size in six populations of house sparrows on islands off the coast of northern Norway. This ratio showed large interisland variation because of demographic differences among the populations. Finally, we calculate how N(e) in a growing house sparrow population will change over time.

  • 298.
    Engström, The REGIA Consortium, Peter
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik.
    REGIA, an EU project on functional genomics of transcription factors from Arabidopsis thaliana2002In: Comparartive and Functional Genomics, Vol. 3, p. 102-108Article, book review (Other (popular scientific, debate etc.))
  • 299. Ericson, Per G. P.
    et al.
    Anderson, Cajsa Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Britton, Tom
    Elzanowski, Andrzej
    Johansson, Ulf S.
    Källersjö, Mari
    Ohlson, Jan I.
    Parsons, Thomas J.
    Zuccon, Dario
    Mayr, Gerald
    Diversification of Neoaves through time: Integration of molecular sequence data and fossils2006In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, no 4, p. 543-547Article in journal (Refereed)
    Abstract [en]

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

  • 300. Ericson, Per G. P.
    et al.
    Anderson, Cajsa Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Mayr, Gerald
    Hangin’ on to our rocks ’n clocks: a reply to Brown et al.2007In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 3, no 3, p. 260-261Article in journal (Refereed)
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