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  • 51.
    Andreasen, K
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Systematisk botanik.
    "Huru skall då et skadeligit träd, en giftig præparation, och en obehaglig smak, kunna gifwa en hälsosam dryck?": Om kaffets (Coffea arabica) botanik och användning2004In: Växter i Linnés landskap, Swedish Science Press, Uppsala , 2004, p. 11-22Chapter in book (Other (popular scientific, debate etc.))
  • 52.
    Andreasen, Katarina
    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.
    Implications of molecular systematic analyses on the conservation of rare and threatened taxa: Contrasting examples from Malvaceae2005In: Conservation Genetics, Vol. 6, p. 399-412Article in journal (Refereed)
  • 53.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk botanik.
    Implications of molecular systematic analyses on the conservation of rare and threatened taxa: contrasting examples from Malvaceae2005In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 6, no 3, p. 399-412Article in journal (Refereed)
    Abstract [en]

    Systematic research provides essential evidence for setting conservation priorities for rare and endangered taxa. Phylogenetic analyses can identify cryptic, genetically distinct lineages as well as actively interbreeding, and hence, non-distinctive lineages earlier perceived as separate taxa. A major aim of this study was to identify genetically distinct, rare lineages within two Malvaceae sister-genera, Sidalcea and Eremalche. The focus was two taxon-pairs each consisting of one rare and one more common taxon. The results demonstrate that even within two closely related genera, with a large number of rare taxa, molecular phylogenetic analyses can reveal contrasting degrees of evolutionary divergence and thus contrasting conservation implications for threatened taxa. Contrary to expectations, the substitution rate in the nuclear ribosomal transcribed spacers for annualEremalche did not correspond to the faster evolutionary rate of annuals – compared to perennials – detected earlier within Sidalcea. Branch lengths in the (annual) Eremalche clade were shorter than those of annual members of Sidalcea. The phylogenetic analyses showed that the rare and endangered S. keckii and E. kernensis each are most closely related to a common species that has been regarded as insufficiently distinct to warrant separate taxonomic status. An additional aim of the study was to test the utility of the Phylogenetic Diversity (PD) measure to formalize the procedure of prioritizing conservation efforts. The measure demonstrated S. keckii (but not E. kernensis) to be genetically distinct from its closest relative and a good candidate for conservation. The PD measure was earlier used for assessing conservation priorities for areas, but proved useful to more objectively suggest conservation priorities among threatened taxa. Because this measure is calculated directly from the data, it retains more character information and gives a better representation of genetic diversity than other measures relying on tree topologies.

  • 54.
    Andreasen, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Manktelow, Mariette
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Razafimandimbison, Sylvain G.
    Successful DNA amplification of a more than 200-year-old herbarium specimen: recovering genetic material from the Linnaean era2009In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 58, no 3, p. 959-962Article in journal (Refereed)
    Abstract [en]

    The limit for successful DNA extraction was tested by amplification and sequencing of an over 200-year-old herbarium specimen collected by Adam Afzelius, a student of Carl Linnaeus. We amplified and sequenced a 800-bp region between 16S ribosomal DNA and the 3' part of the trnI gene (16S-trnI) in the chloroplast genome of Phaulopsis talbotii S. Moore (Acanthaceae). To test the replicability and to control for contamination the procedure was performed in sealed vials and with negative PCR controls. The procedure was also repeated in a separate laboratory. In addition, the chloroplast rpl16 intron was successfully amplified and sequenced and the rps16 intron amplified. Sequences of taxa closely related to Acanthaceae were found to be most similar to the produced sequences. The results Suggest that molecular investigations of other 18th century botanical collections are feasible and that molecular methods could be employed for comparative studies to extant plant collections. An important application would be to identify descendants or clones of Linnaean lectotypes by comparing DNA from these with potentially remnant plants from Linnaeus' cultivations.

  • 55.
    Antal, Taras
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik.
    Lindblad, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik.
    Production of H2 by sulphur-deprived cells of the unicellular cyanobacteria Gloeocapsa alpicola and Synechocystis sp. PCC 6803 during dark incubation with methane or a various extracellular pH2005In: Journal of Applied Microbiology, Vol. 98, p. 114-120Article in journal (Refereed)
    Abstract [en]

    Aims: To examine sulphur (S) deprivation in combination with the presence of methane (CH4) and changes in extracellular pH as a method to enhance in situ hydrogen (H2) generation during fermentation in the unicellular non-diazotrophic cyanobacteria Gloeocapsa alpicola and Synechocystis PCC 6803.

    Methods and Results: The level of H2 production, measured using a gas chromatography, was determined in S-deprived cells of G. alpicola and Synechocystis PCC 6803 during fermentation. Starvation on S enhanced the rate of H2 production by more than fourfold in both strains. S-deprived cyanobacteria were able to maintain maximum rate of H2 production during at least 8 h of fermentaion representing the entire dark period of a day. Increased H2 production was observed during dark anoxic incubation with a gas phase of 100% CH4 (up to four times) at lower pH of the medium (5.0-5.5)

    Conclusions: S-deprivation in combination with CH4, added or maybe produced by another micro-organisms, and the changes in the pH of the media can be used to further increase the specific capacity of unicellular non-N2-fixing cyanobacteria to produce H2 during fermentaion with the overall aim of applying it for outdoor photobiological H2 production.

    Significance and Impact of the Studies: S-deprivation with respect to H2 production is well studied in the green algae Chlamydomonas reinhardtii while its application for H2 production of cyanobacteria is novel. Similarly, the stimulation of H2 generation in the presence of CH4 opens up new possibilities to increase the H2 production. Natural gas enriched with H2 seems to be a perspective fuel and may be an intermediate step on the pathway to the exploitation of pure biohydrogen.

  • 56.
    Antal, T.K.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. fysiologisk botanik.
    Oliveira, P.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. fysiologisk botanik.
    Lindblad, P.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. fysiologisk botanik.
    The bidirectional hydrogenase in the cyanobacterium Synechocystis sp. strain PCC 6803.2006In: International Journal of Hydrogen Energy, Vol. 31, p. 1439-1444Article in journal (Refereed)
  • 57.
    Ardell, David H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics. 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.
    TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA sythetase2006In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 34, no 3, p. 893-904Article in journal (Refereed)
    Abstract [en]

    We present TFAM, an automated, statistical method to classify the identity of tRNAs. TFAM, currently optimized for bacteria, classifies initiator tRNAs and predicts the charging identity of both typical and atypical tRNAs such as suppressors with high confidence. We show statistical evidence for extensive variation in tRNA identity determinants among bacterial genomes due to variation in overall tDNA base content. With TFAM we have detected the first case of eukaryotic-like tRNA identity rules in bacteria. An alpha-proteobacterial clade encompassing Rhizobiales, Caulobacter crescentus and Silicibacter pomeroyi, unlike a sister clade containing the Rickettsiales, Zymomonas mobilis and Gluconobacter oxydans, uses the eukaryotic identity element A73 instead of the highly conserved prokaryotic element C73. We confirm divergence of bacterial histidylation rules by demonstrating perfect covariation of alpha-proteobacterial tRNA(His) acceptor stems and residues in the motif IIb tRNA-binding pocket of their histidyl-tRNA synthetases (HisRS). Phylogenomic analysis supports lateral transfer of a eukaryotic-like HisRS into the alpha-proteobacteria followed by in situ adaptation of the bacterial tDNA(His) and identity rule divergence. Our results demonstrate that TFAM is an effective tool for the bioinformatics, comparative genomics and evolutionary study of tRNA identity.

  • 58.
    Arez, Anna
    et al.
    Lisbon, Portugal.
    Pålsson, Katinka
    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 Zoology. Systematisk zoologi.
    Snounou, G
    UK.
    Jaenson, Thomas
    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 Zoology. Systematisk zoologi.
    doRosario, Virgilio
    Lisbon, Portugal.
    Transmission of mixed Plasmodium species and Plasmodium falciparum genotypes2003In: American Journal of Tropical Medicine and Hygiene, Vol. 68, p. 161-168Article in journal (Refereed)
  • 59.
    Arrendal, Johanna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Björklund, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Reliability of noninvasive genetic census of otters compared to field censuses2007In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, no 5, p. 1097-1107Article in journal (Refereed)
    Abstract [en]

    Conservation and management actions are often highly dependent on accurate estimations of population sizes. However, these estimates are difficult to obtain for elusive and rare species. We compared two census methods for Eurasian otter: snow tracking and noninvasive genetic census based on the genotyping of faecal samples. With the noninvasive genetic census we detected the presence of almost twice as many otters as with snow tracking (23 and 10–15, respectively), and mark-recapture estimates based on the genetic census indicated that the real number of otters could be even higher. Our results indicate that snow tracking tends to underestimate the number of individuals and also that it is more susceptible to subjective assessment. We compared the strengths and weaknesses of the two methods.

  • 60.
    Arrendal, Johanna
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology. Zooekologi.
    Walker, CF
    Sundqvist, AK
    Hellborg, L
    Vila, Carles
    Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Genetic evaluation of an otter transocation program2004In: Conservation Genetics, Vol. 5, p. 79-88Article in journal (Refereed)
  • 61. Arrendal, J.S.E.
    et al.
    Walker, C.W.
    Sundqvist, A.-K.
    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.
    Hellborg, L.C.
    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.
    Vilà, Carles
    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.
    Genetic assessment of a demographically successful translocation program.2004In: Conservation Genetics, no 5, p. 79-88Article in journal (Other scientific)
  • 62.
    Articus, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Neuropogon and the phylogeny of Usnea s. lat. (Parmeliaceae, Ascomycetes)In: TAXONArticle in journal (Refereed)
  • 63.
    Articus, Kristina
    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.
    Neuropogon and the phylogeny of Usnea s.l. (Parmeliaceae, Lichenized Ascomycetes)2004In: TAXON, Vol. 53, no 4, p. 925-934Article in journal (Refereed)
  • 64.
    Articus, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Phylogenetic Studies in Usnea (Parmeliaceae) and Allied Genera2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis deals with the phylogeny of the lichen genus Usnea (Parmeliaceae, Ascomycetes). The relationships and the morphological variation among Usnea species has been studied, as well as the relationship of Usnea to allied genera.

    Two species, U. florida and U. subfloridana, which earlier were regarded to form two separate species have been synonymized. In an analysis based on sequence data these two taxa formed a monophyletic group of intermixed specimens. Usnea florida and U. subfloridana have earlier been regarded to form a species pair, but the species pairs concept cannot be applied in this case.

    The morphological characters traditionally used for species recognition of a number of European Usnea species have been analyzed regarding their reliability. The evolution and distribution of the morphological characters was studied in relation to a phylogeny based on sequence data. Most characters proved to be homoplastic in relation to the phylogeny. Few characters were consistent in a clade, and the same character could be inconsistent in another clade. Therefore a combination of several characters is recommended for species recognition.

    The relationship of Neuropogon to Usnea was investigated based on sequence data. Neuropogon showed to be closely related to Usnea subg. Usnea. The subgenera Eumitria and Dolichousnea formed the sister group to the clade comprising subg. Usnea and Neuropogon. Usnea is paraphyletic in this investigation. Eumitria is treated as a genus and the subgenus Dolichousnea is elevated to generic rank.

    The position of Usnea, Neuropogon, Eumitria, and Dolichousnea in the family Parmeliaceae was investigated based on a phylogeny obtained by sequence data. Protousnea probably forms the sister group to the clade of Usnea, Neuropogon, Eumitria, and Dolichousnea. Several monophyletic groups in the family Parmeliaceae were identified.

    List of papers
    1. Ribosomal DNA and β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species
    Open this publication in new window or tab >>Ribosomal DNA and β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species
    Show others...
    2002 (English)In: Mycological Research, no 4, p. 412-418Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91304 (URN)
    Available from: 2004-02-04 Created: 2004-02-04 Last updated: 2009-04-02Bibliographically approved
    2. Morphology and sequence data - conflict and concordance in a phylogeny of some European Usnea species
    Open this publication in new window or tab >>Morphology and sequence data - conflict and concordance in a phylogeny of some European Usnea species
    (English)In: Botanical Journal of the Linnean SocietyArticle in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-91305 (URN)
    Available from: 2004-02-04 Created: 2004-02-04 Last updated: 2018-03-29Bibliographically approved
    3. Neuropogon and the phylogeny of Usnea s. lat. (Parmeliaceae, Ascomycetes)
    Open this publication in new window or tab >>Neuropogon and the phylogeny of Usnea s. lat. (Parmeliaceae, Ascomycetes)
    (English)In: TAXONArticle in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-91306 (URN)
    Available from: 2004-02-04 Created: 2004-02-04 Last updated: 2009-04-02Bibliographically approved
    4. The monophyletic groups in the Parmeliaceae
    Open this publication in new window or tab >>The monophyletic groups in the Parmeliaceae
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-91307 (URN)
    Available from: 2004-02-04 Created: 2004-02-04 Last updated: 2010-01-14Bibliographically approved
  • 65.
    Articus, Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Mattsson, Jan-Eric
    Tibell, Leif
    Grube, Martin
    Wedin, Mats
    Ribosomal DNA and β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species2002In: Mycological Research, no 4, p. 412-418Article in journal (Refereed)
  • 66.
    Articus, Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Mattsson, Jan-Eric
    Wedin, Mats
    Tibell, Leif
    Morphology and sequence data - conflict and concordance in a phylogeny of some European Usnea speciesIn: Botanical Journal of the Linnean SocietyArticle in journal (Refereed)
  • 67.
    Ashitani, Tatsuya
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Garboui, Samira
    Pålsson, Katinka
    Vongsombath, Chanda
    Jaenson, Thomas
    Borg-Karlson, Anna-Karin
    Hyptis suaveolens a source for arthropod repellent compounds.: Repellency of sesquiterpene oxides and sulfides to Ixodes ricinusManuscript (Other (popular science, discussion, etc.))
  • 68. Aspi, J
    et al.
    Roininen, E
    Ruokonen, M
    Kojola, I
    Vila, C
    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. Evoutionary biology.
    Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population.2006In: Mol Ecol, ISSN 0962-1083, Vol. 15, no 6, p. 1561-76Article in journal (Refereed)
    Abstract [en]

    The Finnish wolf population (Canis lupus) was sampled during three different periods (1996-1998, 1999-2001 and 2002-2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long-term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period.

  • 69.
    Ast, Jennifer C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Urbanczyk, Henryk
    Dunlap, Paul V.
    Multi-gene analysis reveals previously unrecognized phylogenetic diversity in Aliivibrio2009In: Systematic and Applied Microbiology, ISSN 0723-2020, E-ISSN 1618-0984, Vol. 32, no 6, p. 379-386Article in journal (Refereed)
    Abstract [en]

    The "Vibrio fischeri species group" recently was reclassified as a new genus, Aliivibrio, comprising four species, Aliivibrio fischeri, Aliivibrio logei, Aliivibrio salmonicida, and Aliivibrio wodanis. Only limited phylogenetic analysis of strains within Aliivibrio has been carried out, however, and taxonomic ambiguity is evident within this group, especially for phenotypically unusual strains and certain strains isolated from bioluminescent symbioses. Therefore, to examine in depth the evolutionary relationships within Aliivibrio and redefine the host affiliations of symbiotic species, we examined several previously identified and newly isolated strains using phylogenetic analysis based on multiple independent loci, gapA, gyrB, pyrH, recA, rpoA, the luxABE region, and the 16S rRNA gene. The analysis resolved Aliivibrio as distinct from Vibrio, Photobacterium, and other genera of Vibrionaceae, and resolved A. fischeri, A. salmonicida, A. logei, and A. wodanis as distinct, well-supported clades. However, it also revealed that several previously reported strains are incorrectly identified and that substantial unrecognized diversity exists in this genus. Specifically, strain ATCC 33715 (Y-1) and several other strains having a yellow-shifted luminescence were not members of A. fischeri. Furthermore, no strain previously identified as A. logei grouped with the type strain (ATCC 29985(T)), and no bona-fide strain of A, logei was identified as a bioluminescent symbiont. Several additional strains identified previously as A. logei group instead with the type strain of A. wodanis (ATCC BAA-104(T)), or are members of a new clade. Two strongly supported clades were evident within A. fischeri, a phylogenetic structure that might reflect differences in the host species or differences in the ecological incidence of strains. The results of this study highlight the importance of basing taxonomic conclusions on examination of type strains. (C) 2009 Elsevier GmbH. All rights reserved.

  • 70.
    Atkinson, Gemma C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Hauryliuk, Vasili
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components2008In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 8, p. 290-Article in journal (Refereed)
    Abstract [en]

    Background: Members of the eukaryote/archaea specific eRF1 and eRF3 protein families have central roles in translation termination. They are also central to various mRNA surveillance mechanisms, together with the eRF1 paralogue Dom34p and the eRF3 paralogues Hbs1p and Ski7p. We have examined the evolution of eRF1 and eRF3 families using sequence similarity searching, multiple sequence alignment and phylogenetic analysis. Results: Extensive BLAST searches confirm that Hbs1p and eRF3 are limited to eukaryotes, while Dom34p and eRF1 (a/eRF1) are universal in eukaryotes and archaea. Ski7p appears to be restricted to a subset of Saccharomyces species. Alignments show that Dom34p does not possess the characteristic class-1 RF minidomains GGQ, NIKS and YXCXXXF, in line with recent crystallographic analysis of Dom34p. Phylogenetic trees of the protein families allow us to reconstruct the evolution of mRNA surveillance mechanisms mediated by these proteins in eukaryotes and archaea. Conclusion: We propose that the last common ancestor of eukaryotes and archaea possessed Dom34p-mediated no-go decay (NGD). This ancestral Dom34p may or may not have required a trGTPase, mostly like a/eEF1A, for its delivery to the ribosome. At an early stage in eukaryotic evolution, eEF1A was duplicated, giving rise to eRF3, which was recruited for translation termination, interacting with eRF1. eRF3 evolved nonsense-mediated decay (NMD) activity either before or after it was again duplicated, giving rise to Hbs1p, which we propose was recruited to assist eDom34p in eukaryotic NGD. Finally, a third duplication within ascomycete yeast gave rise to Ski7p, which may have become specialised for a subset of existing Hbs1p functions in non-stop decay (NSD). We suggest Ski7p-mediated NSD may be a specialised mechanism for counteracting the effects of increased stop codon read-through caused by prion-domain [ PSI+] mediated eRF3 precipitation.

  • 71.
    Attitalla, Idress H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Biological and Molecular Characteristics of Microorganism-Stimulated Defence Response in Lycopersicon esculentum –L2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Microorganisms, including two fungi, Phytophthora cryptogea and Fusarium oxysporum strain Fo-(IMI 386351), and one bacterium, Pesudomonas sp. strain MF30, were tested for their abilities to stimulate plant defence responses in tomato (Lycopersicon esculentum –L.) and to serve as effective biocontrol agents (Bs). The study included in vivo and in vitro characterization of biological attributes of the microorganisms, pertaining to their abilities to stimulate plant immunity against a fungal pathogen, Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato wilt disease. Using Lycopersicon esculentum –L. as a model plant for examining some fundamental elements of the plant-microorganism interaction, the study reveals and clarifies some aspects of the close association and the complexity of such systems.

    For each B, the results revealed a B-distinct plant-microorganism interaction, which included systemic induced resistance (SIR). A phylogenetic analyses of the partial sequences of two Fo-(IMI 386351) genes, a mitochondrial small subunit ribosomal DNA (mtSSU rDNA) and the nuclear translation elongation factor 1α (EF-1α), provided phylogenetic trees confirming that Fo-(IMI 386351) might be a member of Fol or of F. oxysporum f. sp. melonis, which have polyphyletic evolutionary origins. RFLP analysis (mtDNA), suggested that Fo-(IMI 386351) probably belongs to Fol. For routine and accurate differentiation between two morphologically indistinguishable F. oxysporum formae speciales strains, F. oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici, a molecular method (mtDNA RFLP analysis) was developed, and its usefulness for such differentiation was compared with that of two other methods: isozyme analysis and an osmotic method, revealed with high performance liquid chromatography (HPLC). The HPLC-spectra of Fo-(IMI 386351) had an extra peak for the two tested fractions, indicating that activation of the observed plant defence mechanism could have been at least partially the result of one of the products of the eliciting microbe. Preliminary results obtained by nuclear magnetic resonance spectrometry of those fractions suggest that the extra peak probably represents an oligosaccharide, which may have acted as a mobile signal and triggered the plant defence mechanisms.

    We concluded that (1) our three tested microorganisms are able to stimulate plant defence mechanisms by triggering SIR (plant immunity), (2) the complexity and elaborateness of evolved plant-microbe interactions involving plant defence can, at least in some cases, be observed and studied in the laboratory, and (3) molecular tools can be a powerful means for identifying fungal strains and for clarifying their taxonomical relationships.

    List of papers
    1. A rapid molecular method for differentiating two special forms (lycopersici and radicis-lycopersici) of Fusarium oxysporum
    Open this publication in new window or tab >>A rapid molecular method for differentiating two special forms (lycopersici and radicis-lycopersici) of Fusarium oxysporum
    2004 (English)In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 108, no 7, p. 787-794Article in journal (Refereed) Published
    Abstract [en]

    Two pathogenic special forms (f. sp.) of the Fusarium oxysporum species complex f. sp. lycopersici (Fol) and f. sp. radicis-lycopersici (Forl) are morphologically indistinguishable. Although they are pathogenic to the same host genus Lycopersicon (tomato), and infect the same tomato cultivar, they form distinct diseases; Fol causes wilt and Forl causes crown rot and root rot. These two special forms apparently exist as genetically isolated populations, based on vegetative compatibility and molecular variation at the DNA level. In seeking efficient diagnostic tools for differentiating Fol and Forl isolates, we examined three techniques: isozyme analysis, mitochondrial DNA (mtDNA) RFLP by HaeIII-digestion of total genomic DNA, and an osmotic method using high performance liquid chromatography (HPLC) to detect fungal pigments. The isolates were collected from geographically widespread locations. Distinct HPLC-profile differences were found between an endophytic non-pathogenic isolate and the other pathogenic isolates. However, the direct mtDNA RFLP technique proved to be an efficient diagnostic tool for routine differentiation of Fol and Forl isolates.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-91409 (URN)10.1017/S0953756204000322 (DOI)
    Available from: 2004-02-19 Created: 2004-02-19 Last updated: 2017-12-14Bibliographically approved
    2. Biology and partial sequencing of an endophytic Fusarium oxysporum and plant defense complex
    Open this publication in new window or tab >>Biology and partial sequencing of an endophytic Fusarium oxysporum and plant defense complex
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-91410 (URN)
    Available from: 2004-02-19 Created: 2004-02-19 Last updated: 2010-01-13Bibliographically approved
    3. Systemic resistance to Fusarium wilt in tomato induced by Phytophthora cryptogea
    Open this publication in new window or tab >>Systemic resistance to Fusarium wilt in tomato induced by Phytophthora cryptogea
    2001 In: Journal of Phytopathology, ISSN 0931-1785, Vol. 149, no 7-8, p. 373-380Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91411 (URN)
    Available from: 2004-02-19 Created: 2004-02-19Bibliographically approved
    4. Pseudomonas sp. strain MF30 suppresses Fusarium wilt of tomato in vivo
    Open this publication in new window or tab >>Pseudomonas sp. strain MF30 suppresses Fusarium wilt of tomato in vivo
    2001 In: Phytopathologia Mediterranea, ISSN 0031-9465, Vol. 40, no 3, p. 234-239Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91412 (URN)
    Available from: 2004-02-19 Created: 2004-02-19Bibliographically approved
  • 72.
    Attitalla, Idress Hamad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, Jamshid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Levenfors, Jens
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Brishammar, Sture
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    A rapid molecular method for differentiating two special forms (lycopersici and radicis-lycopersici) of Fusarium oxysporum2004In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 108, no 7, p. 787-794Article in journal (Refereed)
    Abstract [en]

    Two pathogenic special forms (f. sp.) of the Fusarium oxysporum species complex f. sp. lycopersici (Fol) and f. sp. radicis-lycopersici (Forl) are morphologically indistinguishable. Although they are pathogenic to the same host genus Lycopersicon (tomato), and infect the same tomato cultivar, they form distinct diseases; Fol causes wilt and Forl causes crown rot and root rot. These two special forms apparently exist as genetically isolated populations, based on vegetative compatibility and molecular variation at the DNA level. In seeking efficient diagnostic tools for differentiating Fol and Forl isolates, we examined three techniques: isozyme analysis, mitochondrial DNA (mtDNA) RFLP by HaeIII-digestion of total genomic DNA, and an osmotic method using high performance liquid chromatography (HPLC) to detect fungal pigments. The isolates were collected from geographically widespread locations. Distinct HPLC-profile differences were found between an endophytic non-pathogenic isolate and the other pathogenic isolates. However, the direct mtDNA RFLP technique proved to be an efficient diagnostic tool for routine differentiation of Fol and Forl isolates.

  • 73. Axeisson, T
    et al.
    Shavorskaya, O
    Lagercrantz, U
    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.
    Multiple flowering time QTLs within several Brassica species could be the result of duplicated copies of one ancestral gene.2001In: Genome, ISSN 0831-2796, Vol. 44, no 5, p. 856-64Article in journal (Refereed)
  • 74.
    Axelsson, E.
    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.
    Smith, N.G.C.
    Sundström, H.
    Berlin, S.
    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.
    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.
    Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey.2004In: Molecular Biology and Evolution, no 21, p. 1538-1547Article in journal (Refereed)
  • 75.
    Axelsson, Erik
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Comparative Genomics in Birds2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    To shed light on forces that shape the molecular evolution of bird genomes, and in turn avian adaptations, comparative analyses of avian DNA sequences are important. Moreover, contrasting findings in birds to those of other organisms will lend a clearer view on general aspects of molecular evolution. However, few such analyses have been conducted in birds. Progress is presented in this thesis.

    Theories predict a reduction in the mutation rate of the Z chromosome as the harmful effects of recessive mutations are exposed in female birds. We find no evidence for this. Instead, the substitution rates of sex chromosomes and autosomes are largely compatible with expectations from male-biased mutation. This suggests that a majority of mutations arise during DNA replication.

    Substitution rates also vary across chicken autosomes. For instance, microchromosomes accumulate ~20% more substitutions than macrochromosomes. We show that a majority of the autosomal variation in substitution rate can be accounted for by GC content, mainly due to the incidence of mutable CpG-dinucleotides.

    Sequence comparisons also show that the pattern of nucleotide substitution varies in the chicken genome and this reinforces regional differences in base composition.

    The level of selective constraint in at least some avian lineages is higher than in mammalian lineages as indicated by low dN/dS – ratios. Larger historical population sizes of birds relative to mammals could explain this observation. Within the avian genome, the dN/dS is lower for genes on micro- than macrochromosomes, potentially owing to a higher incidence of house-keeping genes in the former category.

    Contrasting data on non-synonymous and synonymous substitution for divergence and polymorphism shows that positive selection has contributed more to the evolution of Z-linked than autosomal genes. This is likely explained by the full exposure of beneficial recessive mutations on Z when in female birds.

    List of papers
    1. Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey
    Open this publication in new window or tab >>Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey
    Show others...
    2004 In: Mol. Biol. Evol., ISSN 0737-4038, Vol. 21, no 8, p. 1538−1547-Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95327 (URN)
    Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2016-04-08Bibliographically approved
    2. Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosmes then on macrochromosomes
    Open this publication in new window or tab >>Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosmes then on macrochromosomes
    Show others...
    2005 In: Genome Res., ISSN 1088-9051, Vol. 15, p. 120-125Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95328 (URN)
    Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2016-04-08Bibliographically approved
    3. Strong regional biases in nucleotide substitution in the chicken genome
    Open this publication in new window or tab >>Strong regional biases in nucleotide substitution in the chicken genome
    2006 In: Mol. Biol. Evol., ISSN 0737-4038, Vol. 23, no 6, p. 1203-1216Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95329 (URN)
    Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2016-04-08Bibliographically approved
    4. Fast-X on the Z: Rapid evolution of sex-linked genes in birds
    Open this publication in new window or tab >>Fast-X on the Z: Rapid evolution of sex-linked genes in birds
    2007 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 17, no 5, p. 618-624Article in journal (Refereed) Published
    Abstract [en]

    Theoretical work predicts natural selection to be more efficient in the fixation of beneficial mutations in X-linked genes than in autosomal genes. This “fast-X effect” should be evident by an increased ratio of nonsynonymous to synonymous substitutions (dN/dS) for sex-linked genes; however, recent studies have produced mixed support for this expectation. To make an independent test of the idea of fast-X evolution, we focused on birds, which have female heterogamety (males ZZ, females ZW), where analogous arguments would predict a fast-Z effect. We aligned 2.8 Mb of orthologous protein-coding sequence of zebra finch and chicken from 172 Z-linked and 4848 autosomal genes. Zebra finch data were in the form of EST sequences from brain cDNA libraries, while chicken genes were from the draft genome sequence. The dN/dS ratio was significantly higher for Z-linked (0.110) than for all autosomal genes (0.085; P = 0.002), as well as for genes linked to similarly sized autosomes 1–10 (0.0948; P = 0.04). This pattern of fast-Z was evident even after we accounted for the nonrandom distribution of male-biased genes. We also examined the nature of standing variation in the chicken protein-coding regions. The ratio of nonsynonymous to synonymous polymorphism (pN/pS) did not differ significantly between genes on the Z chromosome (0.104) and on the autosomes (0.0908). In conjunction, these results suggest that evolution proceeds more quickly on the Z chromosome, where hemizygous exposure of beneficial nondominant mutations increases the rate of fixation.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95330 (URN)10.1101/gr.6031907 (DOI)000246297900009 ()17416747 (PubMedID)
    Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2018-02-22Bibliographically approved
    5. Natural selection in protein-coding genes expressed in avian brain
    Open this publication in new window or tab >>Natural selection in protein-coding genes expressed in avian brain
    Show others...
    2008 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 12, p. 3008-3017Article in journal (Refereed) Published
    Abstract [en]

    The evolution of birds from theropod dinosaurs took place approximately 150 million years ago, and was associated with a number of specific adaptations that are still evident among extant birds, including feathers, song and extravagant secondary sexual characteristics. Knowledge about the molecular evolutionary background to such adaptations is lacking. Here, we analyse the evolution of > 5000 protein-coding gene sequences expressed in zebra finch brain by comparison to orthologous sequences in chicken. Mean d(N)/d(S) is 0.085 and genes with their maximal expression in the eye and central nervous system have the lowest mean d(N)/d(S) value, while those expressed in digestive and reproductive tissues exhibit the highest. We find that fast-evolving genes (those which have higher than expected rate of nonsynonymous substitution, indicative of adaptive evolution) are enriched for biological functions such as fertilization, muscle contraction, defence response, response to stress, wounding and endogenous stimulus, and cell death. After alignment to mammalian orthologues, we identify a catalogue of 228 genes that show a significantly higher rate of protein evolution in the two bird lineages than in mammals. These accelerated bird genes, representing candidates for avian-specific adaptations, include genes implicated in vocal learning and other cognitive processes. Moreover, colouration genes evolve faster in birds than in mammals, which may have been driven by sexual selection for extravagant plumage characteristics.

    Keywords
    adaptive evolution, chicken, comparative genomics, positive selection, zebra finch
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95331 (URN)10.1111/j.1365-294X.2008.03795.x (DOI)000256494700018 ()
    Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2018-02-22Bibliographically approved
  • 76.
    Axelsson, Erik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hultin-Rosenberg, Lina
    Brandström, Mikael
    Zwalen, Martin
    Clayton, David F.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Natural selection in protein-coding genes expressed in avian brain2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 12, p. 3008-3017Article in journal (Refereed)
    Abstract [en]

    The evolution of birds from theropod dinosaurs took place approximately 150 million years ago, and was associated with a number of specific adaptations that are still evident among extant birds, including feathers, song and extravagant secondary sexual characteristics. Knowledge about the molecular evolutionary background to such adaptations is lacking. Here, we analyse the evolution of > 5000 protein-coding gene sequences expressed in zebra finch brain by comparison to orthologous sequences in chicken. Mean d(N)/d(S) is 0.085 and genes with their maximal expression in the eye and central nervous system have the lowest mean d(N)/d(S) value, while those expressed in digestive and reproductive tissues exhibit the highest. We find that fast-evolving genes (those which have higher than expected rate of nonsynonymous substitution, indicative of adaptive evolution) are enriched for biological functions such as fertilization, muscle contraction, defence response, response to stress, wounding and endogenous stimulus, and cell death. After alignment to mammalian orthologues, we identify a catalogue of 228 genes that show a significantly higher rate of protein evolution in the two bird lineages than in mammals. These accelerated bird genes, representing candidates for avian-specific adaptations, include genes implicated in vocal learning and other cognitive processes. Moreover, colouration genes evolve faster in birds than in mammals, which may have been driven by sexual selection for extravagant plumage characteristics.

  • 77.
    Axelsson, Erik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Smith, Nick G.C.
    Sundström, Hannah
    Berlin, Sofia
    Ellegren, Hans
    Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey2004In: Mol. Biol. Evol., ISSN 0737-4038, Vol. 21, no 8, p. 1538−1547-Article in journal (Refereed)
  • 78.
    Axelsson, Erik
    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.
    Webster, Matthew T
    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.
    Smith, Nick G C
    Burt, David W
    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.
    Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes.2005In: Genome Res, ISSN 1088-9051, Vol. 15, no 1, p. 120-5Article in journal (Refereed)
    Abstract [en]

    A distinctive feature of the avian genome is the large heterogeneity in the size of chromosomes, which are usually classified into a small number of macrochromosomes and numerous microchromosomes. These chromosome classes show characteristic differences in a number of interrelated features that could potentially affect the rate of sequence evolution, such as GC content, gene density, and recombination rate. We studied the effects of these factors by analyzing patterns of nucleotide substitution in two sets of chicken-turkey sequence alignments. First, in a set of 67 orthologous introns, divergence was significantly higher in microchromosomes (chromosomes 11-38; 11.7% divergence) than in both macrochromosomes (chromosomes 1-5; 9.9% divergence; P = 0.016) and intermediate-sized chromosomes (chromosomes 6-10; 9.5% divergence; P = 0.026). At least part of this difference was due to the higher incidence of CpG sites on microchromosomes. Second, using 155 orthologous coding sequences we noted a similar pattern, in which synonymous substitution rates on microchromosomes (13.1%) were significantly higher than were rates on macrochromosomes (10.3%; P = 0.024). Broadly assuming neutrality of introns and synonymous sites, or constraints on such sequences do not differ between chromosomal classes, these observations imply that microchromosomal genes are exposed to more germ line mutations than those on other chromosomes. We also find that dN/dS ratios for genes located on microchromosomes (average, 0.094) are significantly lower than those of macrochromosomes (average, 0.185; P = 0.025), suggesting that the proteins of genes on microchromosomes are under greater evolutionary constraint.

  • 79.
    Axelsson, Erik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Webster, Matthew T.
    Smith, Nick G.C.
    Burt, David W.
    Ellegren, Hans
    Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosmes then on macrochromosomes2005In: Genome Res., ISSN 1088-9051, Vol. 15, p. 120-125Article in journal (Refereed)
  • 80.
    Axelsson, T
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Bowman, C M
    Sharpe, A G
    Lydiate, D J
    Lagercrantz, U
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Amphidiploid Brassica juncea contains conserved progenitor genomes.2000In: Genome, ISSN 0831-2796, Vol. 43, no 4, p. 679-88Article in journal (Refereed)
  • 81.
    Backlund, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Nilsson, Siwert
    Naturhistoriska Riksmuséet.
    Pollen morphology and the systematic position of Triplostegia (Dipsacales)1997In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 46, no 1, p. 21-31Article in journal (Refereed)
    Abstract [en]

    Triplostegia comprises two species of perennial herbs from southeast Asia, T. glandulifera and T. grandiflora. The systematic position of the genus has been debated ever since it was described, and it has been placed in either Dipsacaceae or Valerianaceae, or in a family of its own Triplo-stegiaceae. Pollen of Triplostegia, investigated by light microscopy and scanning electron micro-scopy, is similar to that of both Dipsacaceae and Valerianaceae. Presence of numerous branched and bent columellae as well as an aperturem argins tructurer esemblingt he halo found in Valeria-naceae indicates a closer relationship to the Valerianaceae. A sister-group relationship between Triplostegia and the Valerianaceae is furthermore supported by other studies of molecular and morphological data. In order to maximize information content in the framework of mandatory classificational ranks, Triplostegia is best included in the family Valerianaceae, as the sole mem-ber of a subfamily Triplostegioideae.

  • 82.
    Backlund, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Phylogenetic Studies in the Gentianales – Approaches at Different Taxonomic Levels2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis deals with phylogenetic relationships at different taxonomic levels. All the plants studied are or have been included in the order Gentianales, which comprises about 17 200 species. The phylogenies are based on parsimony analyses of nucleotide sequence data (DNA) from different regions in the chloroplast genome, but morphological characteristics have also been studied.

    Analyses of sequence data from the genes rbcL and ndhF provide the interfamilial structure of the order Gentianales, shown to comprise the families Apocynaceae (incl. Asclepiadaceae), Gelsemiaceae, Gentianaceae, Loganiaceae, and Rubiaceae. Exclusion of certain genera from the Loganiaceae is confirmed and their phylogenetic positions are clarified. Some of these genera remain within the Gentianales, while others belong to other orders. Exclusion of the tribe Buddlejeae from the Loganiaceae is confirmed, and a monophyletic group formed by Buddleja, Emorya, Gomphostigma, and Nicodemia is recognized and placed in the Lamiales. The Loganiaceae s.str. forms, after these exclusions, a strongly supported monophyletic group comprising 13 genera.

    The tribe Paederieae in the family Rubiaceae is analysed using sequence data from the regions rbcL gene, rps16 intron, and the regions trnT-F, and is shown to be paraphyletic. These results lead to a new circumscription of Paederieae comprising the genera Leptodermis, Paederia, Serissa, and Spermadictyon. The tribe Putorieae is reestablished with the single genus Plocama, including 34 species. Aitchisonia, Choulettia, Crocyllis, Gaillonia, Jaubertia, Pseudogaillonia, Pterogaillonia, and Putoria are reduced to synonyms of Plocama based on the molecular analyses and morphological studies.

    The Mediterranean species of the re-circumscribed Plocama, previously segregated as the genus Putoria, are revised. Two species, Plocama calabrica and P. brevifolia, are recognized, their synonymics are established, and seven lectotypes are selected.

    List of papers
    1. Relationships of the Buddlejaceae s.l. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF andrbcL sequence data
    Open this publication in new window or tab >>Relationships of the Buddlejaceae s.l. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF andrbcL sequence data
    1999 (English)In: Systematic Botany, Vol. 24, no 2, p. 164-182Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93714 (URN)
    Available from: 2005-11-10 Created: 2005-11-10 Last updated: 2009-04-02Bibliographically approved
    2. Phylogenetic relationships within the order Gentianales based on ndhF and rbcL sequences, with particular reference to the Loganiaceae
    Open this publication in new window or tab >>Phylogenetic relationships within the order Gentianales based on ndhF and rbcL sequences, with particular reference to the Loganiaceae
    2000 (English)In: American Journal of Botany, Vol. 87, no 7, p. 1029-1043Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93715 (URN)
    Available from: 2005-11-10 Created: 2005-11-10 Last updated: 2009-04-02Bibliographically approved
    3. Paraphyly of Paederieae, recognition of Putorieae and expansion of Plocama (Rubiaceae-Rubioideae)
    Open this publication in new window or tab >>Paraphyly of Paederieae, recognition of Putorieae and expansion of Plocama (Rubiaceae-Rubioideae)
    2007 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 2, p. 315-328Article in journal (Refereed) Published
    Abstract [en]

    Phylogenetic analyses of taxa that have been included in the tribe Paederieae are performed on the basis of a molecular dataset of plastid DNA sequences (the rbcL gene, rps16 intron, and the regions trnT-F). The paraphyly of Paederieae as currently circumscribed is confirmed. A clade comprising Paederia, Spermadictyon, Leptodermis, and Serissa is retrieved and the circumscription of Paederieae is proposed to be restricted to this clade. Paederia is sister to a clade with Spermadictyon, Leptodermis, and Serissa. Paederia is subdivided into an Asian and an African clade, and within the African clade seven species endemic to Madagascar are sister to P. pospischilii in north-eastern Africa. The position of Kelloggia as sister to Rubieae is confirmed and a position of Saprosma in the Spermacoceae alliance is supported. The genera Putoria, Gaillonia (with segregates), Plocama, and Aitchisonia form a clade that is sister to Theligoneae/Kelloggia/Rubieae. The name Putorieae is resurrected for the members of this clade. A synopsis of Putorieae is provided, where all species are placed in an expanded Plocama with 34 species. Thirty-one new combinations in Plocama are proposed. Plocama pendula on the Canary Islands is strongly supported as sister to a clade with P. crocyllis (former Crocyllis) in southern Africa and P. yemenensis and P. tinctoria (former Gaillonia) in southern Arabia/Horn of Africa.

    Keywords
    Gaillonia, molecular phylogenetics, Paederieae, Plocama, Putorieae, rbcL, rps16, Rubiaceae, trnT-F
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-93716 (URN)000247420000006 ()
    Available from: 2005-11-10 Created: 2005-11-10 Last updated: 2017-12-14Bibliographically approved
    4. Revision of the Mediterranean species of Plocama (Rubiaceae)
    Open this publication in new window or tab >>Revision of the Mediterranean species of Plocama (Rubiaceae)
    2007 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 2, p. 516-520Article in journal (Refereed) Published
    Abstract [en]

    The Mediterranean species of Plocama (incl. Putoria) are revised and two species, the widespread P. calabrica, comb. nov., and P. brevifolia, comb. nov., in Morocco and Algeria, are recognized. The variation and circumscription of the species are discussed and distribution maps are provided. Several names are reduced to synonymy and seven lectotypes are designated.

    Keywords
    distribution maps; Mediterranean region; Plocama; Putoria; Putorieae; Rubiaceae; taxonomy; typification
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-93717 (URN)000247420000022 ()
    Available from: 2005-11-10 Created: 2005-11-10 Last updated: 2017-12-14Bibliographically approved
  • 83.
    Backlund, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Bremer, Birgitta
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Paraphyly of Paederieae, recognition of Putorieae and expansion of Plocama (Rubiaceae-Rubioideae)2007In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 2, p. 315-328Article in journal (Refereed)
    Abstract [en]

    Phylogenetic analyses of taxa that have been included in the tribe Paederieae are performed on the basis of a molecular dataset of plastid DNA sequences (the rbcL gene, rps16 intron, and the regions trnT-F). The paraphyly of Paederieae as currently circumscribed is confirmed. A clade comprising Paederia, Spermadictyon, Leptodermis, and Serissa is retrieved and the circumscription of Paederieae is proposed to be restricted to this clade. Paederia is sister to a clade with Spermadictyon, Leptodermis, and Serissa. Paederia is subdivided into an Asian and an African clade, and within the African clade seven species endemic to Madagascar are sister to P. pospischilii in north-eastern Africa. The position of Kelloggia as sister to Rubieae is confirmed and a position of Saprosma in the Spermacoceae alliance is supported. The genera Putoria, Gaillonia (with segregates), Plocama, and Aitchisonia form a clade that is sister to Theligoneae/Kelloggia/Rubieae. The name Putorieae is resurrected for the members of this clade. A synopsis of Putorieae is provided, where all species are placed in an expanded Plocama with 34 species. Thirty-one new combinations in Plocama are proposed. Plocama pendula on the Canary Islands is strongly supported as sister to a clade with P. crocyllis (former Crocyllis) in southern Africa and P. yemenensis and P. tinctoria (former Gaillonia) in southern Arabia/Horn of Africa.

  • 84.
    Backlund, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Bremer, Birgitta
    Phylogenetic relationships within the order Gentianales based on ndhF and rbcL sequences, with particular reference to the Loganiaceae2000In: American Journal of Botany, Vol. 87, no 7, p. 1029-1043Article in journal (Refereed)
  • 85.
    Backlund, Maria
    et al.
    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.
    Revision of the Mediterranean species of Plocama (Rubiaceae)2007In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 2, p. 516-520Article in journal (Refereed)
    Abstract [en]

    The Mediterranean species of Plocama (incl. Putoria) are revised and two species, the widespread P. calabrica, comb. nov., and P. brevifolia, comb. nov., in Morocco and Algeria, are recognized. The variation and circumscription of the species are discussed and distribution maps are provided. Several names are reduced to synonymy and seven lectotypes are designated.

  • 86.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Gene Mapping in Ficedula Flycatchers2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within < 50 kb indicating that > 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.

    List of papers
    1. Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): Conserved synteny but gene order rearrangements on the avian Z chromosome
    Open this publication in new window or tab >>Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): Conserved synteny but gene order rearrangements on the avian Z chromosome
    Show others...
    2006 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 174, no 1, p. 377-386Article in journal (Refereed) Published
    Abstract [en]

    Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher-one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of) the chicken Z chromosome. All genes were also found to be located on the Z chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X chromosome and may thus be a general feature in sex chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only similar to 50% that of chicken, challenging the widely held view that birds generally have high recombination rates.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-97940 (URN)10.1534/genetics.106.058917 (DOI)000241134400033 ()
    Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2018-02-22Bibliographically approved
    2. Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome
    Open this publication in new window or tab >>Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome
    2008 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 4, p. 964-980Article in journal (Refereed) Published
    Abstract [en]

    Although there is growing interest to take genomics into the complex realms of natural populations, there is a general shortage of genomic resources and tools available for wild species. This applies not at least to birds, for which genomic approaches should be helpful to questions such as adaptation, speciation and population genetics. In this study, we describe a genome-wide reference set of conserved avian gene markers, broadly applicable across birds. By aligning protein-coding sequences from the recently assembled chicken genome with orthologous sequences in zebra finch, we identified particularly conserved exonic regions flanking introns of suitable size for subsequent amplification and sequencing. Primers were designed for 242 gene markers evenly distributed across the chicken genome, with a mean inter-marker interval of 4.2 Mb. Between 78% and 93% of the markers amplified a specific product in five species tested (chicken, peregrine falcon, collared flycatcher, great reed warbler and blue tit). Two hundred markers were sequenced in collared flycatcher, yielding a total of 122.41 kb of genomic DNA sequence (12096 bp coding sequence and 110 314 bp noncoding). Intron size of collared flycatcher and chicken was highly correlated, as was GC content. A polymorphism screening using these markers in a panel of 10 unrelated collared flycatchers identified 871 single nucleotide polymorphisms (pi = 0.0029) and 33 indels (mainly very short). Avian genome characteristics such as uniform genome size and low rate of syntenic rearrangements suggest that this marker set will find broad utility as a genome-wide reference resource for molecular ecological and population genomic analysis of birds. We envision that it will be particularly useful for obtaining large-scale orthologous targets in different species--important in, for instance, phylogenetics--and for large-scale identification of evenly distributed single nucleotide polymorphisms needed in linkage mapping or in studies of gene flow and hybridization.

    Keywords
    chicken, collared flycatcher, comparative anchored tagged sequences, linkage mapping, QTL analysis, single nucleotide polymorphism
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-97941 (URN)10.1111/j.1365-294X.2007.03551.x (DOI)000252900200003 ()17927703 (PubMedID)
    Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2018-02-22
    3. A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution
    Open this publication in new window or tab >>A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution
    Show others...
    2008 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 179, p. 1479-1495Article in journal (Refereed) Published
    Abstract [en]

    By taking advantage of a recently developed reference markerset for avian genome analysis we have constructed a gene-basedgenetic map of the collared flycatcher, an important "ecologicalmodel" for studies of life-history evolution, sexual selection,speciation, and quantitative genetics. A pedigree of 322 birdsfrom a natural population was genotyped for 384 single nucleotidepolymorphisms (SNPs) from 170 protein-coding genes and 71 microsatellites.Altogether, 147 gene markers and 64 microsatellites form 33linkage groups with a total genetic distance of 1787 cM. Malerecombination rates are, on average, 22% higher than femalerates (total distance 1982 vs. 1627 cM). The ability to anchorthe collared flycatcher map with the chicken genome via thegene-based SNPs revealed an extraordinary degree of both syntenyand gene-order conservation during avian evolution. The greatmajority of chicken chromosomes correspond to a single linkagegroup in collared flycatchers, with only a few cases of inter-and intrachromosomal rearrangements. The rate of chromosomaldiversification, fissions/fusions, and inversions combined isthus considerably lower in birds (0.05/MY) than in mammals (0.6–2.0/MY).A dearth of repeat elements, known to promote chromosomal breakage,in avian genomes may contribute to their stability. The degreeof genome stability is likely to have important consequencesfor general evolutionary patterns and may explain, for example,the comparatively slow rate by which genetic incompatibilityamong lineages of birds evolves.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-97942 (URN)10.1534/genetics.108.088195 (DOI)000258313400028 ()
    Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2018-02-22
    4. Levels of linkage disequilibrium in a wild bird population
    Open this publication in new window or tab >>Levels of linkage disequilibrium in a wild bird population
    2006 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, no 3, p. 435-438Article in journal (Refereed) Published
    Abstract [en]

    Population-based mapping approaches are attractive for tracing the genetic background to phenotypic traits in wild species, given that it is often difficult to gather extensive and well-defined pedigrees needed for quantitative trait locus analysis. However, the feasibility of association or hitch-hiking mapping is dependent on the degree of linkage disequilibrium. (LD) in the population, on which there is yet limited information for wild species. Here we use single nucleotide polymorphism (SNP) markers from 23 genes in a recently established linkage map of the Z chromosome of the collared flycatcher, to study the extent of LD in a natural bird population. In most but not all cases we find SNPs within the same intron (less than 500 bp) to be in perfect LD. However, LD then decays to background level at a distance 1 cM or 400-500 kb. Although LD seems more extensive than in other species, if the observed pattern is representative for other regions of the genome and turns out to be a general feature of natural bird populations, dense marker maps might be needed for genome scans aimed at identifying association between marker and trait loci.

    Keywords
    collared flycatcher, recombination, Z chromosome
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-97943 (URN)10.1098/rsbl.2006.0507 (DOI)000241863400032 ()17148424 (PubMedID)
    Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2018-02-22
    5. A high-density scan of the Z chromosome in ficedula flycatchers reveals candidate loci for diversifying selection
    Open this publication in new window or tab >>A high-density scan of the Z chromosome in ficedula flycatchers reveals candidate loci for diversifying selection
    Show others...
    2010 (English)In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 64, no 12, p. 3461-3475Article in journal (Refereed) Published
    Abstract [en]

    Theoretical and empirical data suggest that genes located on sex chromosomes may play an important role both for sexually selected traits and for traits involved in the build-up of hybrid incompatibilities. We investigated patterns of genetic variation in 73 genes located on the Z chromosomes of two species of the flycatcher genus Ficedula, the pied flycatcher and the collared flycatcher. Sequence data were evaluated for signs of selection potentially related to genomic differentiation in these young sister species, which hybridize despite reduced fitness of hybrids. Seven loci were significantly more divergent between the two species than expected under neutrality and they also displayed reduced nucleotide diversity, consistent with having been influenced by directional selection. Two of the detected candidate regions contain genes that are associated with plumage coloration in birds. Plumage characteristics play an important role in species recognition in these flycatchers suggesting that the detected genes may have been involved in the evolution of sexual isolation between the species.

    Keywords
    FST peak, Nucleotide diversity, Selection, Sex chromosomes, Speciation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-97944 (URN)10.1111/j.1558-5646.2010.01082.x (DOI)000284850100010 ()20629730 (PubMedID)
    Available from: 2008-12-22 Created: 2008-12-22 Last updated: 2018-02-22
  • 87.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Brandström, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Cheng, Hans
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): Conserved synteny but gene order rearrangements on the avian Z chromosome2006In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 174, no 1, p. 377-386Article in journal (Refereed)
    Abstract [en]

    Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher-one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of) the chicken Z chromosome. All genes were also found to be located on the Z chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X chromosome and may thus be a general feature in sex chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only similar to 50% that of chicken, challenging the widely held view that birds generally have high recombination rates.

  • 88.
    Backström, Niclas
    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.
    Ceplitis, Helene
    Berlin, Sofia
    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.
    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.
    Gene conversion drives the evolution of HINTW, an ampliconic gene on the female-specific avian W chromosome.2005In: Mol Biol Evol, ISSN 0737-4038, Vol. 22, no 10, p. 1992-9Article in journal (Refereed)
    Abstract [en]

    The HINTW gene on the female-specific W chromosome of chicken and other birds is amplified and present in numerous copies. Moreover, as HINTW is distinctly different from its homolog on the Z chromosome (HINTZ), is a candidate gene in avian sex determination, and evolves rapidly under positive selection, it shows several common features to ampliconic and testis-specific genes on the mammalian Y chromosome. A phylogenetic analysis within galliform birds (chicken, turkey, quail, and pheasant) shows that individual HINTW copies within each species are more similar to each other than to gene copies of related species. Such convergent evolution is most easily explained by recurrent events of gene conversion, the rate of which we estimated at 10(-6)-10(-5) per site and generation. A significantly higher GC content of HINTW than of other W-linked genes is consistent with biased gene conversion increasing the fixation probability of mutations involving G and C nucleotides. Furthermore, and as a likely consequence, the neutral substitution rate is almost twice as high in HINTW as in other W-linked genes. The region on W encompassing the HINTW gene cluster is not covered in the initial assembly of the chicken genome, but analysis of raw sequence reads indicates that gene copy number is significantly higher than a previous estimate of 40. While sexual selection is one of several factors that potentially affect the evolution of ampliconic, male-specific genes on the mammalian Y chromosome, data from HINTW provide evidence that gene amplification followed by gene conversion can evolve in female-specific chromosomes in the absence of sexual selection. The presence of multiple and highly similar copies of HINTW may be related to protein function, but, more generally, amplification and conversion offers a means to the avoidance of accumulation of deleterious mutations in nonrecombining chromosomes.

  • 89.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Fagerberg, Sofie
    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.
    Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 4, p. 964-980Article in journal (Refereed)
    Abstract [en]

    Although there is growing interest to take genomics into the complex realms of natural populations, there is a general shortage of genomic resources and tools available for wild species. This applies not at least to birds, for which genomic approaches should be helpful to questions such as adaptation, speciation and population genetics. In this study, we describe a genome-wide reference set of conserved avian gene markers, broadly applicable across birds. By aligning protein-coding sequences from the recently assembled chicken genome with orthologous sequences in zebra finch, we identified particularly conserved exonic regions flanking introns of suitable size for subsequent amplification and sequencing. Primers were designed for 242 gene markers evenly distributed across the chicken genome, with a mean inter-marker interval of 4.2 Mb. Between 78% and 93% of the markers amplified a specific product in five species tested (chicken, peregrine falcon, collared flycatcher, great reed warbler and blue tit). Two hundred markers were sequenced in collared flycatcher, yielding a total of 122.41 kb of genomic DNA sequence (12096 bp coding sequence and 110 314 bp noncoding). Intron size of collared flycatcher and chicken was highly correlated, as was GC content. A polymorphism screening using these markers in a panel of 10 unrelated collared flycatchers identified 871 single nucleotide polymorphisms (pi = 0.0029) and 33 indels (mainly very short). Avian genome characteristics such as uniform genome size and low rate of syntenic rearrangements suggest that this marker set will find broad utility as a genome-wide reference resource for molecular ecological and population genomic analysis of birds. We envision that it will be particularly useful for obtaining large-scale orthologous targets in different species--important in, for instance, phylogenetics--and for large-scale identification of evenly distributed single nucleotide polymorphisms needed in linkage mapping or in studies of gene flow and hybridization.

  • 90.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Forstmeier, Wolfgang
    Schielzeth, Holger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mellenius, Harriet
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nam, Kiwoong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bolund, Elisabeth
    Webster, Matthew T.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Öst, Torbjörn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Schneider, Melanie
    Kempenaers, Bart
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The recombination landscape of the zebra finch Taeniopygia guttata genome2010In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 20, no 4, p. 485-495Article in journal (Refereed)
    Abstract [en]

    Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single nucleotide polymorphisms in a multigeneration pedigree of more than 1000 zebra finches (Taeniopygia guttata) to develop a genetic linkage map, and then we used these map data together with the recently available draft genome sequence of the zebra finch to estimate recombination rates in 1 Mb intervals across the genome. The average zebra finch recombination rate (1.5 cM/Mb) is higher than in humans, but significantly lower than in chicken. The local rates of recombination in chicken and zebra finch were only weakly correlated, demonstrating evolutionary turnover of the recombination landscape in birds. The distribution of recombination events was heavily biased toward ends of chromosomes, with a stronger telomere effect than so far seen in any organism. In fact, the recombination rate was as low as 0.1 cM/Mb in intervals up to 100 Mb long in the middle of the larger chromosomes. We found a positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs. Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.

  • 91.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Karaiskou, Nikoletta
    Leder, Erica H.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Primmer, Craig R.
    Qvarnström, Anna
    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, Animal ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution2008In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 179, p. 1479-1495Article in journal (Refereed)
    Abstract [en]

    By taking advantage of a recently developed reference markerset for avian genome analysis we have constructed a gene-basedgenetic map of the collared flycatcher, an important "ecologicalmodel" for studies of life-history evolution, sexual selection,speciation, and quantitative genetics. A pedigree of 322 birdsfrom a natural population was genotyped for 384 single nucleotidepolymorphisms (SNPs) from 170 protein-coding genes and 71 microsatellites.Altogether, 147 gene markers and 64 microsatellites form 33linkage groups with a total genetic distance of 1787 cM. Malerecombination rates are, on average, 22% higher than femalerates (total distance 1982 vs. 1627 cM). The ability to anchorthe collared flycatcher map with the chicken genome via thegene-based SNPs revealed an extraordinary degree of both syntenyand gene-order conservation during avian evolution. The greatmajority of chicken chromosomes correspond to a single linkagegroup in collared flycatchers, with only a few cases of inter-and intrachromosomal rearrangements. The rate of chromosomaldiversification, fissions/fusions, and inversions combined isthus considerably lower in birds (0.05/MY) than in mammals (0.6–2.0/MY).A dearth of repeat elements, known to promote chromosomal breakage,in avian genomes may contribute to their stability. The degreeof genome stability is likely to have important consequencesfor general evolutionary patterns and may explain, for example,the comparatively slow rate by which genetic incompatibilityamong lineages of birds evolves.

  • 92.
    Backström, Niclas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Gustafsson, Lars
    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.
    Levels of linkage disequilibrium in a wild bird population2006In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, no 3, p. 435-438Article in journal (Refereed)
    Abstract [en]

    Population-based mapping approaches are attractive for tracing the genetic background to phenotypic traits in wild species, given that it is often difficult to gather extensive and well-defined pedigrees needed for quantitative trait locus analysis. However, the feasibility of association or hitch-hiking mapping is dependent on the degree of linkage disequilibrium. (LD) in the population, on which there is yet limited information for wild species. Here we use single nucleotide polymorphism (SNP) markers from 23 genes in a recently established linkage map of the Z chromosome of the collared flycatcher, to study the extent of LD in a natural bird population. In most but not all cases we find SNPs within the same intron (less than 500 bp) to be in perfect LD. However, LD then decays to background level at a distance 1 cM or 400-500 kb. Although LD seems more extensive than in other species, if the observed pattern is representative for other regions of the genome and turns out to be a general feature of natural bird populations, dense marker maps might be needed for genome scans aimed at identifying association between marker and trait loci.

  • 93. Bai, Shi
    et al.
    Jain, Mahendra K.
    Berg, Otto G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Contiguous binding of decylsulfate on the interface-binding surface of pancreatic phospholipase A22008In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 47, no 9, p. 2899-2907Article in journal (Refereed)
    Abstract [en]

    Pig pancreatic IB phospholipase A(2) (PLA2) forms three distinguishable premicellar E-i(#) (i = 1, 2, and 3) complexes at successively higher decylsulfate concentrations. The Hill coefficient for E-1(#) is n(1) = 1.6, and n(2) and n(3) for E-2(#) and E-3(#) are about 8 each. Saturation-transfer difference nuclear magnetic resonance (NMR) and other complementary results with PLA2 show that decylsulfate molecules in E-2(#) and E-3(#) are contiguously and cooperatively clustered on the interface-binding surface or i-face that makes contact with the substrate interface. In these complexes, the saturation-transfer difference NMR signatures of H-1 in decylsulfate are different. The decylsulfate epitope for the successive E, complexes increasingly resembles the micellar complex formed by the binding of PLA2 to preformed micelles. Contiguous cooperative amphiphile binding is predominantly driven by the hydrophobic effect with a modest electrostatic shielding of the sulfate head group in contact with PLA2. The formation of the complexes is also associated with structural change in the enzyme. Calcium affinity of E-2(#) appears to be modestly lower than that of the free enzyme and Ell. Binding of decylsulfate to the i-face does not require the catalytic calcium required for the substrate binding to the active site and for the chemical step. These results show that E-i(#) complexes are useful to structurally characterize the cooperative sequential and contiguous binding of amphiphiles on the i-face. We suggest that the allosteric changes associated with the formation of discrete E-i(#) complexes are surrogates for the catalytic and allosteric states of the interface activated PLA2.

  • 94.
    Balciuniene, J
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Emilsson, L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Oreland, L
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Pettersson, U
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Investigation of the functional effect of monoamine oxidase polymorphisms in human brain2002In: Human Genetics, ISSN 0340-6717, E-ISSN 1432-1203, Vol. 110, no 1, p. 1-7Article in journal (Refereed)
  • 95. Balciuniene, J
    et al.
    Syvänen, A-C
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Sciences. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    McLeod, H L
    Pettersson, U
    Jazin, E E
    Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    The geographic distribution of monoamine oxidase haplotypes supports a bottleneck during the dispersion of modern humans from Africa.2001In: J Mol Evol, ISSN 0022-2844, Vol. 52, no 2, p. 157-63Article in journal (Other scientific)
  • 96.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    An overview of the phylogeny and diversity of eukaryotes2008In: Journal of systematics and evolution, ISSN 1674-4918, Vol. 46, no 3, p. 263-273Article in journal (Refereed)
    Abstract [en]

    Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eukaryotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predominantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the proposed relationships of these groups to each other.

  • 97. Barnett, Ross
    et al.
    Barnes, Ian
    Phillips, Matthew J
    Martin, Larry D
    Harington, C Richard
    Leonard, Jennifer 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.
    Cooper, Alan
    Evolution of the extinct Sabretooths and the American cheetah-like cat.2005In: Curr Biol, ISSN 0960-9822, Vol. 15, no 15, p. R589-90Article in journal (Other scientific)
  • 98. Barrio-Amorós, Cesar L.
    et al.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Comments on the distribution, taxonomy and advertisement call of the Guyanan glass frog Hyalinobatrachium ignioculus (Anura: Centrolenidae)2008In: Salamandra, ISSN 0036-3375, Vol. 44, no 4, p. 235-240Article in journal (Refereed)
  • 99. Barrio-Amorós, César L.
    et al.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    The taxonomic status of Rhaebo anderssoni (Melin, 1941)(Anura:Bufonidae)2008In: Salamandra, ISSN 0036-3375, Vol. 44, no 1, p. 59-62Article in journal (Refereed)
  • 100. Bartosch-Härlid, Anna
    et al.
    Berlin, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Smith, Nick G.C.
    Moller, Anders P.
    Ellegren, Hans
    Life history and the male mutation bias.2003In: Evolution, ISSN 0014-3820, Vol. 57, no 10, p. 2398-2406Article in journal (Refereed)
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