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  • 1.
    Aagaard, Sunniva M. D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Greilhuber, Johann
    University of Vienna, Department of Systematic and Evolutionary Botany.
    Zhang, Xian-Chun
    Institute of Botany,Chinese Academy of Sciences .
    Wikström, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Occurrence and evolutionary origins of polyploids in the club moss genus Diphasiastrum (Lycopodiaceae)2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 52, no 3, p. 746-754Article in journal (Refereed)
    Abstract [en]

    Two polyploid taxa are commonly recognized in the genus Diphasiastrum, D. wightianum from Asia and D. zanclophyllum from South Africa and Madagascar. Here we present results from Feulgen DNA image densitometry analyses providing the first evidence for the polyploid origin of D. zanclophyllum. Reported for the first time is also data confirming that D. multispicatum and D. veitchii, representing putative parent lineages for D. wightianum, are diploids. Phylogenetic analyses of nuclear regions RPB2, LEAFY and LAMB4 reveal that putative tetraploid accessions are of allopolyploid origin. Diphasiastrum zanclophyllum shows close relationships to the North American taxon D. digitatum on the maternal side, but the paternal relationship is less clear. Two accessions from Asia, both found to be polyploid, have D. veitchii as maternal parent, whereas the paternal paralogs show relationships to D. multispicatum and D. tristachyum, respectively. None of these parental combinations have previously been hypothesized.

  • 2.
    Aagaard, Sunniva Margrethe Due
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Reticulate Evolution in Diphasiastrum (Lycopodiaceae)2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis relationships and the occurrence of reticulate evolutionary events in the club moss genus Diphasiastrum are investigated. Diphasiastrum is initially established as a monophyletic group within Lycopodiaceae using non recombinant chloroplast sequence data. Support is obtained for eight distinct parental lineages in Diphasiastrum, and relationships among the putative parent taxa in the hypothesized hybrid complexes; D. alpinum, D. complanatum, D. digitatum, D. multispicatum, D. sitchense, D. tristachyum and D. veitchii are presented.

    Feulgen DNA image densitometry data and sequence data obtained from three nuclear regions, RPB2, LEAFY and LAMB4, were used to infer the origins of three different taxa confirmed to be allopolyploid; D. zanclophyllum from South Africa, D. wightianum from Malaysia and an undescribed taxon from China. The two Asian polyploids have originated from two different hybrid combinations, D. multispicatum x D. veitchii and D. tristachyum x D. veitchii. Diphasiastrum zanclophyllum originates from a cross between D. digitatum and an unidentified diploid taxon.

    The occurrence of three homoploid hybrid combinations commonly recognized in Europe, D. alpinum x D. complanatum, D. alpinum x D. tristachyum and D. complanatum x D. tristachyum, are verified using the same three nuclear regions. Two of the three hybrid combinations are also shown to have originated from reciprocal crosses. Admixture analyses performed on an extended, dataset similarly identified predominately F1 hybrids and backcrosses. The observations and common recognition of hybrid species in the included populations are hence most likely due to frequent observations of neohybrids in hybrid zones. Reticulate patterns are, however, prominent in the presented dataset. Hence future studies addressing evolutionary and ecological questions in Diphasiastrum should emphasize the impact of gene flow between parent lineages rather than speciation as the result of hybridization.

    List of papers
    1. Resolving maternal relationships in the clubmoss genus Diphasiastrum (Lycopodiaceae)
    Open this publication in new window or tab >>Resolving maternal relationships in the clubmoss genus Diphasiastrum (Lycopodiaceae)
    2009 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 58, no 3, p. 835-848Article in journal (Refereed) Published
    Abstract [en]

    Diphasiastrum comprises 20-30 species. In addition to a number of species with a circumboreal distribution, several island endemics and putative diploid hybrid species contribute to the diversity of the group. To assess the integrity and relationships of the recognized species, a global phylogeny of Diphasiastrum is constructed using five chloroplast regions comprising ~9000 bp. Six monophyletic groups are identified. Accessions identified as hybrid species cluster in all but one case together with one of its putative parents. Two microsatellite loci are identified, and allelic information combined with sequence information is found diagnostic for the three putative parental taxa in the Central Europe hybrid complexes. Haplotype screening is performed on six Central European populations, from where one or more putative diploid hybrid species have been reported to grow in sympatry with their parent species. The most common parental haplotypes are identified in all populations. Additional intraspecific variation, restricted to single populations, is identified in all sympatric populations at very low frequencies. Taking the low degree of sequence and microsatellite variation into consideration, the acknowledged morphological diversity in Central Europe is probably best explained by phenotypic plasticity, ancestral polymorphisms or relatively recent events of reticulate evolution.

    Keywords
    Chloroplast microsatellites, Diphasiastrum, Diploid hybrid species, Lycopodium, Lycopodiaceae, Plastid phylogeny
    National Category
    Biological Sciences
    Research subject
    Systematic Botany
    Identifiers
    urn:nbn:se:uu:diva-99576 (URN)000269774900012 ()
    Available from: 2009-03-16 Created: 2009-03-16 Last updated: 2017-12-13Bibliographically approved
    2. Occurrence and evolutionary origins of polyploids in the club moss genus Diphasiastrum (Lycopodiaceae)
    Open this publication in new window or tab >>Occurrence and evolutionary origins of polyploids in the club moss genus Diphasiastrum (Lycopodiaceae)
    2009 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 52, no 3, p. 746-754Article in journal (Refereed) Published
    Abstract [en]

    Two polyploid taxa are commonly recognized in the genus Diphasiastrum, D. wightianum from Asia and D. zanclophyllum from South Africa and Madagascar. Here we present results from Feulgen DNA image densitometry analyses providing the first evidence for the polyploid origin of D. zanclophyllum. Reported for the first time is also data confirming that D. multispicatum and D. veitchii, representing putative parent lineages for D. wightianum, are diploids. Phylogenetic analyses of nuclear regions RPB2, LEAFY and LAMB4 reveal that putative tetraploid accessions are of allopolyploid origin. Diphasiastrum zanclophyllum shows close relationships to the North American taxon D. digitatum on the maternal side, but the paternal relationship is less clear. Two accessions from Asia, both found to be polyploid, have D. veitchii as maternal parent, whereas the paternal paralogs show relationships to D. multispicatum and D. tristachyum, respectively. None of these parental combinations have previously been hypothesized.

    Keywords
    Diphasiastrum, Feulgen DNA image densitometry, Lycopodium, Lycopodiaceae, low-copy nuclear genes, phylogenies, polyploidy
    National Category
    Biological Sciences
    Research subject
    Systematic Botany
    Identifiers
    urn:nbn:se:uu:diva-99577 (URN)10.1016/j.ympev.2009.05.004 (DOI)000268265800016 ()
    Available from: 2009-03-16 Created: 2009-03-16 Last updated: 2017-12-13Bibliographically approved
    3. Reticulate phylogenetic patterns in diploid European Diphasiastrum (Lycopodiaceae).
    Open this publication in new window or tab >>Reticulate phylogenetic patterns in diploid European Diphasiastrum (Lycopodiaceae).
    (English)Manuscript (Other academic)
    Abstract [en]

    In Central Europe, three species belonging to Diphasiastrum are considered to be of homoploid hybrid origin. Diphasiastrum issleri is suggested to have originated from a cross between D. alpinum and D. complanatum, D. oellgaardii from D. alpinum and D. tristachyum, and D. zeilleri from D. complanatum and D. tristachyum. Variation at three nuclear regions and two chloroplast microsatellites verify the presence of all three putative parental combinations in Europe. Data obtained with Feulgen DNA image densitometry confirms that all specimens displaying such pattern are diploid. Also, two of three parental combinations have probably arisen repeatedly, implied by the occurrence of chloroplast haplotypes associated with different parents. The presented dataset cannot be used as argument for the existence of independent evolutionary entities hybrid origin. This is nonetheless an important first step in order to address the influence of reticulate evolutionary events in European Diphasiastrum

    Keywords
    Keywords – Diphasiastrum, homoploid hybridization, Lycopodiaceae, Lycopodium, low copy nuclear genes, phylogenies, Feulgen DNA image densitometry
    Identifiers
    urn:nbn:se:uu:diva-99578 (URN)
    Available from: 2009-03-16 Created: 2009-03-16 Last updated: 2010-01-14
    4. Homoploid hybridization in Central European Diphasiastrum (Lycopodiaceae).
    Open this publication in new window or tab >>Homoploid hybridization in Central European Diphasiastrum (Lycopodiaceae).
    (English)Manuscript (Other academic)
    Abstract [en]

    Three species of homoploid hybrid origin are commonly recognized among Central European Diphasiastrum, and reticulate evolutionary events have for a long time been acknowledged as an important factor contributing to the species count in the genus. Presented evidence obtained from molecular data has until recently been scarce and inconclusive. Recent studies have, however, documented reticulate phylogenetic patterns involving all putative parental combinations reported from Central Europe. Reciprocal crosses involving the same parental combinations have also been confirmed. In order to further explore these putative reticulate events, admixture analyses using a Bayesian approach as implemented in the program NewHybrids are conducted on an expanded dataset obtained from six Central European populations from where putative hybrid taxa are reported. A majority of the accessions included in the analyses were inferred to represent pure bred D. alpinum, D. complanatum, D. tristachyum, F1 hybrids, F2 hybrids or backcrosses with one of the parent species. Accessions displaying ambiguous classification were found in both allopatric parent populations as well as in Central European hybrid populations. Presented results indicate the presence of frequently occurring hybrid zones with first and second generation hybrids as well as backcrosses.

    Keywords
    admixture analysis, Bayesian clustering, Diphasiastrum, homoploid hybridization, Lycopodiaceae, Lycopodium, NewHybrids.
    National Category
    Biological Systematics
    Research subject
    Systematic Botany; Population Biology
    Identifiers
    urn:nbn:se:uu:diva-99579 (URN)
    Available from: 2009-03-16 Created: 2009-03-16 Last updated: 2010-01-14
    5. Revised lectotypification of Lycopodium complanatum L. (Lycopodiaceae)
    Open this publication in new window or tab >>Revised lectotypification of Lycopodium complanatum L. (Lycopodiaceae)
    2009 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 58, no 3, p. 974-976Article in journal (Refereed) Published
    Abstract [en]

    The currently accepted lectotype of the circumboreal species Lycopodium complanatum L., or Diphasiastrum complanatum (L.) Holub, is a specimen of the related species L. tristachyum Pursh, or D. tristachyum (Pursh) Holub, mainly distributed in eastern North America and Europe. This lectotype, in LINN, is here superseded in favour of an alternative original element in the Celsius herbarium in Uppsala, supported by an epitype, on the grounds of conflict with the protologue. Thereby the traditional usage of the well-known name L. complanatum can be maintained.

    Keywords
    Diphasiastrum, nomenclature, Lycopodium, Lycopodiaceae, typification.
    National Category
    Biological Systematics
    Research subject
    Systematic Botany; Biology with specialization in Systematics
    Identifiers
    urn:nbn:se:uu:diva-99572 (URN)000269774900026 ()
    Available from: 2009-03-16 Created: 2009-03-16 Last updated: 2017-12-13Bibliographically approved
  • 3.
    Aagaard, Sunniva M.D.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Greilhuber, Johann
    Vogel, Johannes C.
    Wikström, Niklas
    Reticulate phylogenetic patterns in diploid European Diphasiastrum (Lycopodiaceae).Manuscript (Other academic)
    Abstract [en]

    In Central Europe, three species belonging to Diphasiastrum are considered to be of homoploid hybrid origin. Diphasiastrum issleri is suggested to have originated from a cross between D. alpinum and D. complanatum, D. oellgaardii from D. alpinum and D. tristachyum, and D. zeilleri from D. complanatum and D. tristachyum. Variation at three nuclear regions and two chloroplast microsatellites verify the presence of all three putative parental combinations in Europe. Data obtained with Feulgen DNA image densitometry confirms that all specimens displaying such pattern are diploid. Also, two of three parental combinations have probably arisen repeatedly, implied by the occurrence of chloroplast haplotypes associated with different parents. The presented dataset cannot be used as argument for the existence of independent evolutionary entities hybrid origin. This is nonetheless an important first step in order to address the influence of reticulate evolutionary events in European Diphasiastrum

  • 4.
    Aagaard, Sunniva M.D.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Gyllenstrand, Niclas
    Wikström, Niklas
    Homoploid hybridization in Central European Diphasiastrum (Lycopodiaceae).Manuscript (Other academic)
    Abstract [en]

    Three species of homoploid hybrid origin are commonly recognized among Central European Diphasiastrum, and reticulate evolutionary events have for a long time been acknowledged as an important factor contributing to the species count in the genus. Presented evidence obtained from molecular data has until recently been scarce and inconclusive. Recent studies have, however, documented reticulate phylogenetic patterns involving all putative parental combinations reported from Central Europe. Reciprocal crosses involving the same parental combinations have also been confirmed. In order to further explore these putative reticulate events, admixture analyses using a Bayesian approach as implemented in the program NewHybrids are conducted on an expanded dataset obtained from six Central European populations from where putative hybrid taxa are reported. A majority of the accessions included in the analyses were inferred to represent pure bred D. alpinum, D. complanatum, D. tristachyum, F1 hybrids, F2 hybrids or backcrosses with one of the parent species. Accessions displaying ambiguous classification were found in both allopatric parent populations as well as in Central European hybrid populations. Presented results indicate the presence of frequently occurring hybrid zones with first and second generation hybrids as well as backcrosses.

  • 5.
    Aagaard, Sunniva MD
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Såstad, Sigurd M
    Greilhuber, J
    Moen, A
    A secondary hybrid zone between diploid Dactylorhiza incarnata ssp cruenta and allotetraploid D-lapponica (Orchidaceae)2005In: Heredity, Vol. 94, p. 488-496Article in journal (Refereed)
  • 6.
    Aagaard, Sunniva M.D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Vogel, Johannes C.
    Wikström, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Resolving maternal relationships in the clubmoss genus Diphasiastrum (Lycopodiaceae)2009In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 58, no 3, p. 835-848Article in journal (Refereed)
    Abstract [en]

    Diphasiastrum comprises 20-30 species. In addition to a number of species with a circumboreal distribution, several island endemics and putative diploid hybrid species contribute to the diversity of the group. To assess the integrity and relationships of the recognized species, a global phylogeny of Diphasiastrum is constructed using five chloroplast regions comprising ~9000 bp. Six monophyletic groups are identified. Accessions identified as hybrid species cluster in all but one case together with one of its putative parents. Two microsatellite loci are identified, and allelic information combined with sequence information is found diagnostic for the three putative parental taxa in the Central Europe hybrid complexes. Haplotype screening is performed on six Central European populations, from where one or more putative diploid hybrid species have been reported to grow in sympatry with their parent species. The most common parental haplotypes are identified in all populations. Additional intraspecific variation, restricted to single populations, is identified in all sympatric populations at very low frequencies. Taking the low degree of sequence and microsatellite variation into consideration, the acknowledged morphological diversity in Central Europe is probably best explained by phenotypic plasticity, ancestral polymorphisms or relatively recent events of reticulate evolution.

  • 7. Achatz, Johannes Georg
    et al.
    Hooge, Matthew
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Jondelius, Ulf
    Tyler, Seth
    Systematic revision of acoels with 9+0 sperm ultrastructure (Convolutida) and the influence of sexual conflict on morphology2010In: Journal of Zoological Systematics and Evolutionary Research, ISSN 0947-5745, E-ISSN 1439-0469, Vol. 48, no 1, p. 9-32Article, review/survey (Refereed)
    Abstract [en]

    We have used newly discerned morphological characters as well as molecular-sequence data from 18S and 28S rDNA to revise the families recently designated as the '9+0' acoels - what we call Convolutida. Characters from the ultrastructure of sperm, with their '9+0' axonemes, are useful in delineating the Convolutida, but are either species-specific or too conserved within the group to be used to infer relationships within it. Male genital organs, prostatoid organs, and sagittocysts, on the other hand, give a good phylogenetic signal for reconstructing relationships of such genera as Conaperta, Anaperus, and Achoerus; some features of the reproductive organs correlate with habitat and show how the Convolutida probably originated as epiphytic predators and radiated into the mesopsammon, pelagic, and coral-associated realms. In this revision of the Convolutida we provide revised synopses of its families - which we restrict to the Anaperidae, Convolutidae, and Sagittiferidae - and describe a new species, Polychoerus gordoni, from New Zealand. We transfer the genus Adenopea from the Antroposthiidae to the Convolutidae; Conaperta, Neochildia, and Oxyposthia from the Convolutidae to the Anaperidae; Paranaperus and Praeanaperus from the Anaperidae to the Haploposthiidae. Convoluta aegyptica is synonymized with Convoluta boehmigi, Convoluta lacazii with Convoluta sordida, and the genus Picola (Convolutidae) with Deuterogonaria (Haploposthiidae). Amphiscolops blumi, A. carvalhoi, and A. langerhansi, all of which possess a cellular seminal bursa, are transferred to the genus Heterochaerus. Convoluta elegans and Pseudanaperus tinctus are classified as nomina nuda. We use our findings on the ultrastructure of female genital organs and spermatozoa to show that sexual conflict plays a major role in the evolution of diversity of these structures and that the phylogeny of the Acoela would comprise early forms without female genital organs and hyper- or hypodermal transfer of sperm through advanced forms with ever longer and narrower bursal nozzles and sperm with axial microtubules. Moreover, our results show that the acquisition of endosymbiotic algae happened at least twice within the Acoela.

  • 8. Agalou, Adamantia
    et al.
    Purwantomo, Sigit
    Övernäs, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Johannesson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Zhu, Xiaoyi
    Estiati, Amy
    de Kam, Rolf J.
    Engström, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Slamet-Loedin, Inez H.
    Zhu, Zhen
    Wang, Mei
    Xiong, Lizhong
    Meijer, Annemarie H.
    Ouwerkerk, Pieter B. F.
    A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members2008In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 66, no 1-2, p. 87-103Article in journal (Refereed)
    Abstract [en]

    The homeodomain leucine zipper (HD-Zip) genes encode transcription factors that have diverse functions in plant development and have often been implicated in stress adaptation. The HD-Zip genes are the most abundant group of homeobox (HB) genes in plants and do not occur in other eukaryotes. This paper describes the complete annotation of the HD-Zip families I, II and III from rice and compares these gene families with Arabidopsis in a phylogeny reconstruction. Orthologous pairs of rice and Arabidopsis HD-Zip genes were predicted based on neighbour joining and maximum parsimony (MP) trees with support of conserved intron-exon organization. Additionally, a number of HD-Zip genes appeared to be unique to rice. Searching of EST and cDNA databases and expression analysis using RT-PCR showed that 30 out of 31 predicted rice HD-Zip genes are expressed. Most HD-Zip genes were broadly expressed in mature plants and seedlings, but others showed more organ specific patterns. Like in Arabidopsis and other dicots, a subset of the rice HD-Zip I and II genes was found to be regulated by drought stress. We identified both drought-induced and drought-repressed HD-Zip genes and demonstrate that these genes are differentially regulated in drought-sensitive versus drought-tolerant rice cultivars. The drought-repressed HD-Zip family I gene, Oshox4, was selected for promoter-GUS analysis, showing that drought-responsiveness of Oshox4 is controlled by the promoter and that Oshox4 expression is predominantly vascular-specific. Loss-of-function analysis of Oshox4 revealed no specific phenotype, but overexpression analysis suggested a role for Oshox4 in elongation and maturation processes.

  • 9. Aguirre-Hudson, B.
    et al.
    Kokubun, T.
    Spooner, B.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Taxonomy of Calicium victorianum (F. Wilson) Tibell (Caliciaceae, Lecanorales), a lichenized ascomycete new to Europe2007In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 39, no 5, p. 401-407Article in journal (Refereed)
    Abstract [en]

    The morphological features and chemical compounds found in the first European collection of Calicium victorianum are compared with type material from Australia of C. piperatum F. Wilson. The phylogenetic relationships of the species are discussed by comparing its nuclear rDNA ITS 1-5.8S-ITS2 with that of other species of Calicium.

  • 10. Akkoc, Nurullah
    et al.
    Sari, Ismail
    Akar, Servet
    Binicier, Omer
    Thomas, Mark G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Weale, Michael E.
    Birlik, Merih
    Savran, Yusuf
    Onen, Fatos
    Bradman, Neil
    Plaster, Christopher A.
    Increased Prevalence of M694V in Patients With Ankylosing Spondylitis: Additional Evidence for a Link With Familial Mediterranean Fever2010In: Arthritis and Rheumatism, ISSN 0004-3591, E-ISSN 1529-0131, Vol. 62, no 10, p. 3059-3063Article in journal (Refereed)
    Abstract [en]

    Objective. To assess whether there is a statistically significant difference in the frequency of common MEFV allele variants in patients with ankylosing spondylitis (AS) as compared with control patients with rheumatoid arthritis (RA) and with healthy control subjects. Methods. Sixty-two patients with AS, 50 healthy control subjects, and 46 patients with RA were assessed for the presence of MEFV variants. Exon 10 was analyzed by direct sequencing. E148Q was analyzed by restriction endonuclease enzyme digestion (REED) or by direct sequencing when REED analysis failed. Results. The allele frequency of all MEFV variants in the AS group was significantly higher than that in the pooled control group of healthy subjects plus RA patients (15.3% versus 6.8%; P = 0.021). M694V was the only variant that was significantly more common in the AS group than in the combined or individual control groups (P = 0.026 for AS patients versus healthy controls, P = 0.046 for AS patients versus RA patient controls, and P = 0.008 for AS patients versus healthy and RA patient control groups). The carriage rate of M694V was also significantly higher in the AS patient group than in the combined control group (odds ratio 7.0, P = 0.014). Neither M694V nor any other MEFV variant showed a correlation with most of the disease-related measures examined. Conclusion. We found an increased frequency of MEFV variants in AS patients as compared with healthy controls and with RA patient controls. This was primarily due to the presence of M694V. The roles of other exon 10 variants, as well as the relationship between the variant status and the severity and clinical course of the disease, need to be explored in further studies that include sufficiently large sample sizes.

  • 11. Ala-Poikela, M.
    et al.
    Svensson, E.
    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.
    Rojas, A.
    Horko, T.
    Paulin, L.
    Valkonen, J.
    Kvarnheden, A.
    Genetic diversity and mixed infections of begomoviruses in tomato, pepper and cucurbit crops in Nicaragua2005In: Plant Pathology, no 54, p. 448-459Article in journal (Refereed)
  • 12. Albach, Dirk
    et al.
    Meudt, Heidi
    Oxelman, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk Botanik.
    Piecing together the "new" Plantaginaceae.2005In: American Journal of Botany, Vol. 92, p. 297-315Article in journal (Refereed)
  • 13.
    Alsmark, Cecilia M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Frank, A. Carolin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Karlberg, E. Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Legault, Boris-Antoine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Ardell, David H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Canbäck, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Eriksson, Ann-Sofie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Näslund, A. Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Handley, Scott A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Huvet, Maxime
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    La Scola, Bernard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Holmberg, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae2004In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 101, no 26, p. 9716-9721Article in journal (Refereed)
    Abstract [en]

    We present the complete genomes of two human pathogens, Bartonella quintana (1,581,384 bp) and Bartonella henselae (1,931,047 bp). The two pathogens maintain several similarities in being transmitted by insect vectors, using mammalian reservoirs, infecting similar cell types (endothelial cells and erythrocytes) and causing vasculoproliferative changes in immunocompromised hosts. A primary difference between the two pathogens is their reservoir ecology. Whereas B. quintana is a specialist, using only the human as a reservoir, B. henselae is more promiscuous and is frequently isolated from both cats and humans. Genome comparison elucidated a high degree of overall similarity with major differences being B. henselae specific genomic islands coding for filamentous hemagglutinin, and evidence of extensive genome reduction in B. quintana, reminiscent of that found in Rickettsia prowazekii. Both genomes are reduced versions of chromosome I from the highly related pathogen Brucella melitensis. Flanked by two rRNA operons is a segment with similarity to genes located on chromosome II of B. melitensis, suggesting that it was acquired by integration of megareplicon DNA in a common ancestor of the two Bartonella species. Comparisons of the vector-host ecology of these organisms suggest that the utilization of host-restricted vectors is associated with accelerated rates of genome degradation and may explain why human pathogens transmitted by specialist vectors are outnumbered by zoonotic agents, which use vectors of broad host ranges.

  • 14.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Olsson, Urban
    Lei, Fumin
    Wang, Hai-tao
    Gao, Wei
    Sundberg, Per
    Phylogeny and classification of the Old World Emberizini (Aves, Passeriformes)2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 47, no 3, p. 960-973Article in journal (Refereed)
    Abstract [en]

    The phylogeny of the avian genus Emberiza and the monotypic genera Latoucheornis, Melophus and Miliaria (collectively the Old World Emberizini), as well as representatives for the New World Emberizini, the circumpolar genera Calcarius and Plectrophertax and the four other generally recognized tribes in the subfamily Emberizinae was estimated based on the mitochondrial cytochrome b gene and introns 6-7 of the nuclear ornithine decarboxylase (ODC) gene. Our results support monophyly of the Old World Emberizini, but do not corroborate a sister relationship to the New World Emberizini. Calcarius and Plectrophenax form a clade separated from the other Emberizini. This agrees with previous studies, and we recommend the use of the name Calcariini. Latoucheornis, Melophus and Miliaria are nested within Emberiza, and we therefore propose they be synonymized with Emberiza. Emberiza is divided into four main clades, whose relative positions are uncertain, although a sister relation between a clade with six African species and one comprising the rest of the species (30, all Palearctic) is most likely. Most clades agree with traditional, morphology-based, classifications. However, four sister relationships within Emberiza, three of which involve the previously recognized Latoucheornis, Melophus and Miliaria, are unpredicted, and reveal cases of strong morphological divergence. In contrast, the plumage similarity between adult male Emberiza (formerly Latoucheornis) siemsseni and the nominate subspecies of the New World Junco hyemalis is shown to be the result of parallel evolution. A further case of parallel plumage evolution, between African and Eurasian taxa, is pointed out. Two cases of discordance between the mitochondrial and nuclear data with respect to branch lengths and genetic divergences are considered to be the result of introgressive hybridization.

  • 15.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Olsson, Urban
    Rasmussen, Pamela C.
    Yao, Cheng-Te
    Ericson, Per G. P.
    Sundberg, Per
    Morphological, vocal and genetic divergence in the Cettia acanthizoides complex (Aves : Cettiidae)2007In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 149, no 3, p. 437-452Article in journal (Refereed)
    Abstract [en]

    We used morphological, vocal and molecular (one mitochondrial and two nuclear loci) data to re-evaluate the taxonomic status of the taxa acanthizoides, concolor, and brunnescens in the Cettia acanthizoides (J. Verreaux, 1871) complex. We conclude that all three are valid taxa, and that acanthizoides of China and concolor of Taiwan are best treated as conspecific, whereas brunnescens of the Himalayas is better considered as a separate species. The degree of morphological, vocal, and genetic differentiation is variably congruent among all taxa; the recently separated acanthizoides and concolor differ slightly in plumage and structure but are indistinguishable in vocalizations, whereas the earlier diverged brunnescens and acanthizoides/concolor differ only slightly more in morphology but to a much greater degree in vocalizations. We stress the essential nature of taxonomic revisions as a prerequisite for the biodiversity estimates required for conservation planning.

  • 16.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Rasmussen, Pamela C.
    Olsson, Urban
    Sundberg, Per
    Species delimitation based on multiple criteria: the Spotted Bush Warbler Bradypterus thoracicus complex (Aves : Megaluridae)2008In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 154, no 2, p. 291-307Article in journal (Refereed)
    Abstract [en]

    We demonstrate the importance of using multiple criteria in species delimitations, whatever the conceptual base for species delimitation. We do this by studying plumage, biometrics, egg coloration, song, mitochondrial DNA and habitat/altitudinal distribution in the Spotted Bush Warbler Bradypterus thoracicus (Blyth) complex, and by conducting playback experiments. Taxa that we suggest are best treated as separate species [B. thoracicus (Blyth), B. davidi (La Touche) and B. kashmirensis (Sushkin)] differ in most or all of these aspects, particularly in song and mitochondrial DNA, while those that we treat as subspecies (suschkini) or synonyms (przevalskii) differ slightly and only in morphology.

  • 17. Alström-Rapaport, Cecilia
    et al.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Wallén, Johan
    Lascoux, Martin
    Phylogeographic structure in Brassica nigra, a signal of early agricultural spread in Europe?Manuscript (Other (popular science, discussion, etc.))
  • 18. Altekar, G
    et al.
    Dwarkadas, S
    Huelsenbeck, John
    Ronquist, Fredrik
    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.
    Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference2004In: Bioinformatics, Vol. 20, p. 407-415Article in journal (Refereed)
  • 19. Amiri, Haleh
    et al.
    Davids, Wagied
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Birth and death of orphan genes in Rickettsia2003In: Molecular Biology and Evolution, ISSN 0737-4038, Vol. 20, no 10, p. 1575-1587Article in journal (Refereed)
  • 20. Amiri, Haleh
    et al.
    Karlberg, Olof
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv G.E.
    Deep origin of plastid/parasite ATP/ADP translocases2003In: J Mol Evol, Vol. 56, p. 137-150Article in journal (Refereed)
  • 21. An, Junghwa
    et al.
    Bechet, Arnaud
    Berggren, Åsa
    Brown, Sarah K.
    Bruford, Michael W.
    Cai, Qingui
    Cassel-Lundhagen, Anna
    Cezilly, Frank
    Chen, Song-Lin
    Cheng, Wei
    Choi, Sung-Kyoung
    Ding, X.Y.
    Fan, Yong
    Feldheim, Kevin A.
    Feng, Z.Y.
    Friesen, Vicki L.
    Gaillard, Maria
    Galaraza, Juan A.
    Gallo, Leonardo
    Ganeshaiah, K. N.
    Geraci, Julia
    Gibbons, John G.
    Grant, William S.
    Grauvogel, Zac
    Gustafsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Guyon, Jeffrey R.
    Han, L.
    Heath, Daniel D.
    Hemmilä, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Hogan, Derek
    Hou, B. W.
    Jakse, Jernej
    Javornik, Branka
    Kanuch, Peter
    Kim, Kyung-Kil
    Kim, Kyung-Seok
    Kim, Sang-Gyu
    Kim, Sang-In
    Kim, Woo-Jin
    Kim, Yi-Kyung
    Klich, Maren A.
    Kreiser, Brian R.
    Kwan, Ye-Seul
    Lam, Athena W.
    Lasater, Kelly
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Lee, Hang
    Lee, Yun-Sun
    Li, D. L.
    Li, Shao-Jing
    Li, W. Y.
    Liao, Xiaolin
    Liber, Zlatko
    Lin, Lin
    Liu, Shaoying
    Luo, Xin-Hui
    Ma, Y. H.
    Ma, Yajun
    Marchelli, Paula
    Min, Mi-Sook
    Moccia, Maria Domenica
    Mohana, Kumara P.
    Moore, Marcelle
    Morris-Pocock, James A.
    Park, Han-Chan
    Pfunder, Monika
    Ivan, Radosavljevic
    Ravikanth, G.
    Roderick, George K.
    Rokas, Antonis
    Sacks, Benjamin N.
    Saski, Christopher A.
    Satovic, Zlatko
    Schoville, Sean D.
    Sebastiani, Federico
    Sha, Zhen-Xia
    Shin, Eun-Ha
    Soliani, Carolina
    Sreejayan, N.
    Sun, Zhengxin
    Tao, Yong
    Taylor, Scott A.
    Templin, William D.
    Shaanker, R. Uma
    Vasudeva, R.
    Vendramin, Giovanni G.
    Walter, Ryan P.
    Wang, Gui-Zhong
    Wang, Ke-Jian
    Wang, Y. Q.
    Wattier, Rémi A.
    Wei, Fuwen
    Widmer, Alex
    Woltmann, Stefan
    Won, Yong-Jin
    Wu, Jing
    Xie, M. L.
    Xu, Genbo
    Xu, Xiao-Jun
    Ye, Hai-Hui
    Zhan, Xiangjiang
    Zhang, F.
    Zhong, J.
    Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 20092010In: Molecular Ecology Resources, ISSN 1755-098X, Vol. 10, no 2, p. 404-408Article in journal (Refereed)
    Abstract [en]

    This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.

  • 22.
    Anderson, Cajsa Lisa
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Systematisk botanik.
    All we need now is fossils; a new phylogenetic dating method (PATHd8) allowing thousands of taxa and multiple fossil constraints.2006In: Ancient life and modern approaches: Abstracts of the second International Paleontological Congress, 2006, p. 45-Conference paper (Refereed)
    Abstract [en]

    Estimation of divergence times in phylogenetic trees using sequence data

    becomes increasingly popular, but so far dating studies have given widely different results,

    and especially datings of the lower nodes within the angiosperms and metazoans, have given

    much older ages than those obtained from the fossil record. It has been concluded in different

    studies that more taxa, and more fossils are needed for more reliable age estimates. For this

    reason, a dating method that can handle very large data sets with multiple fossil constraints is

    necessary.

    Chronograms obtained by e.g. penalized likelihood and Bayesian methods, often

    adds a large "ghost range" to the fossil record, and produces chronograms with a more or less

    smooth appearance, even if the corresponding phylograms have apparently very

    heterogeneous rates. Compared to the other methods, our recently developed method,

    PATHd8, gives the results with the best agreement with the fossil record, which coincides

    with the least smooth appearance of the chronograms. When other programs often run into

    computational problems when analysing trees with hundreds of leaves, PATHd8 has no

    problems analysing thousands of taxa instantaneously. An arbitrary number of fossil age

    constraints can be specified, either as fixed-, minimum or maximum age.

    With our new method, the biggest problem in dating studies is that we need

    more fossils, and these fossils must be well dated and assigned to the correct branches of the

    phylogeny. Therefore, to accomplish divergence time estimates, which hopefully approximate

    the real ages, biologists now need to cooperate with palaeontologists.

  • 23.
    Anderson, Cajsa Lisa
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Dating Divergence Times in Phylogenies2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis concerns different aspects of dating divergence times in phylogenetic trees, using molecular data and multiple fossil age constraints.

    Datings of phylogenetically basal eudicots, monocots and modern birds (Neoaves) are presented. Large phylograms and multiple fossil constraints were used in all these studies. Eudicots and monocots are suggested to be part of a rapid divergence of angiosperms in the Early Cretaceous, with most families present at the Cretaceous/Tertiary boundary. Stem lineages of Neoaves were present in the Late Cretaceous, but the main divergence of extant families took place around the Cre-taceous/Tertiary boundary.

    A novel method and computer software for dating large phylogenetic trees, PATHd8, is presented. PATHd8 is a nonparametric smoothing method that smoothes one pair of sister groups at a time, by taking the mean of the added branch lengths from a terminal taxon to a node. Because of the local smoothing, the algorithm is simple, hence providing stable and very fast analyses, allowing for thousands of taxa and an arbitrary number of age constraints.

    The importance of fossil constraints and their placement are discussed, and concluded to be the most important factor for obtaining reasonable age estimates.

    Different dating methods are compared, and it is concluded that differences in age estimates are obtained from penalized likelihood, PATHd8, and the Bayesian autocorrelation method implemented in the multidivtime program. In the Bayesian method, prior assumptions about evolutionary rate at the root, rate variance and the level of rate smoothing between internal edges, are suggested to influence the results.

    List of papers
    1. Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil constraints.
    Open this publication in new window or tab >>Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil constraints.
    2005 In: American Journal of Botany, Vol. 92, no 10, p. 1737–1748-Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-96058 (URN)
    Available from: 2007-09-03 Created: 2007-09-03Bibliographically approved
    2. Diversification of Neoaves through time: Integration of molecular sequence data and fossils
    Open this publication in new window or tab >>Diversification of Neoaves through time: Integration of molecular sequence data and fossils
    Show others...
    2006 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, no 4, p. 543-547Article in journal (Refereed) Published
    Abstract [en]

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

    Keywords
    Divergence times, Fossils, Molecular clock, Neoaves, Nuclear DNA, Phylogeny
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96059 (URN)10.1098/rsbl.2006.0523 (DOI)000242686500018 ()17148284 (PubMedID)
    Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2017-12-14Bibliographically approved
    3. Hangin’ on to our rocks ’n clocks: a reply to Brown et al.
    Open this publication in new window or tab >>Hangin’ on to our rocks ’n clocks: a reply to Brown et al.
    2007 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 3, no 3, p. 260-261Article in journal (Refereed) Published
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96060 (URN)10.1098/rsbl.2007.0103. (DOI)
    Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2017-12-14Bibliographically approved
    4. Estimating divergence times in large phylogenetic trees
    Open this publication in new window or tab >>Estimating divergence times in large phylogenetic trees
    Show others...
    2007 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 5, p. 741-752Article in journal (Refereed) Published
    Abstract [en]

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

    Keywords
    Divergence times, estimation, molecular clock, phylogenetic trees, substitution rates
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96061 (URN)10.1080/10635150701613783 (DOI)000250959000004 ()17886144 (PubMedID)
    Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2017-12-14Bibliographically approved
    5. Monocots
    Open this publication in new window or tab >>Monocots
    2009 (English)In: Timetree of life / [ed] S. Blair Hedges and Sudhir Kumar, Oxford University Press, 2009Chapter in book (Other academic)
    Place, publisher, year, edition, pages
    Oxford University Press, 2009
    Series
    Oxford biology
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-96062 (URN)978-0-19-953503-3 (ISBN)
    Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2013-06-18Bibliographically approved
    6. Dating phylogenies: an evaluation of three methods based on the lycopod family Selaginellaceae.
    Open this publication in new window or tab >>Dating phylogenies: an evaluation of three methods based on the lycopod family Selaginellaceae.
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-96063 (URN)
    Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2010-01-13Bibliographically approved
  • 24.
    Anderson, Cajsa Lisa
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Dating phylogenies: an evaluation of three methods based on the lycopod family Selaginellaceae.Manuscript (Other academic)
  • 25.
    Anderson, Cajsa Lisa
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Systematisk botanik.
    PATHd8 - a new phylogenetic dating method allowing thousands of taxa and multiple fossil constraints2006In: 7th european paleobotany-palynology: program and abstracts, 2006, p. 6-Conference paper (Refereed)
    Abstract [en]

    Estimation of divergence times in phylogenetic trees using DNA sequence data becomes increasingly popular, but so far dating studies have given widely different results, and especially datings of the lower nodes within the angiosperms and metazoans, have given much older ages than those obtained from the fossil record. It has been concluded in different studies that more taxa, and more fossils are needed for more reliable age estimates. For this reason, a dating method that can handle very large data sets with multiple fossil constraints is necessary.

    Chronograms obtained by the currently most used methods often adds a large "ghost range" to the fossil record. Compared to the other methods, our recently developed method, PATHd8, gives the most reasonable results, with the best agreement with the fossil record, in all studies performed so far.

    The only way to improve the datings further, and hopefully obtain divergence time estimates which approximate the real ages, is to include more fossils. The combination of allowing an arbitrary number of fossil age constraints with the capability to analyse thousands of taxa instantaneously, makes PATHd8 a strong alternative to other methods. All we need now to accomplish better studies, is cooperation between biologists and paleontologists.

  • 26.
    Anderson, Cajsa Lisa
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Bremer, Kåre
    Friis, Else Marie
    Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil constraints.2005In: American Journal of Botany, Vol. 92, no 10, p. 1737–1748-Article in journal (Refereed)
  • 27.
    Anderson, Cajsa Lisa
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk botanik.
    Bremer, Kåre
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Friis, Else Marie
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points2005In: American Journal of Botany, Vol. 92, p. 1737-1748Article in journal (Refereed)
    Abstract [en]

    A molecular dating of the phylogenetically basal eudicots (Ranunculales, Proteales, Sabiales, Buxales and Trochodendrales sensu

    Angiosperm Phylogeny Group II) has been performed using several fossils as minimum age constraints. All rbcL sequences available

    in GenBank were sampled for the taxa in focus. Dating was performed using penalized likelihood, and results were compared with

    nonparametric rate smoothing. Fourteen eudicot fossils, all with a Cretaceous record, were included in this study for age constraints.

    Nine of these are assigned to basal eudicots and the remaining five taxa represent core eudicots. Our study shows that the choice of

    methods and fossil constraints has a great impact on the age estimates, and that removing one single fossil change the results in the

    magnitude of tens of million years. The use of several fossil constraints increase the probability of approaching the true ages. Our

    results suggest a rapid diversification during the late Early Cretaceous, with all the lineages of basal eudicots emerging during the

    latest part of the Early Cretaceous. The age of Ranunculales was estimated to 120 my, Proteales to 119 my, Sabiales to 118 my,

    Buxales to 117 my, and Trochodendrales to 116 my.

  • 28.
    Anderson, Cajsa Lisa
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Bremer, Kåre
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Friis, Else Marie
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Divergence times of phylogenetically basal eudicots2005In: XVII International Botanical Congress: Vienna, Austria, Europe 17-23 July 2005, 2005, p. 728-Conference paper (Refereed)
    Abstract [en]

    A molecular dating of the phylogenetically basal eudicots (Ranunculales, Proteales, Sabiales, Buxales and Trochodendrales sensu APGII) has been performed using several fossils as minimum age constraints. We have sampled all rbcL sequences available in GenBank for the taxa in focus. Dating was done using Penalized Likelihood, and compared with NonParametric Rate Smoothing. We show that choice of method and fossil constraints has a great impact on the age estimates, and that it is important to use several fossil constraints to yield good age estimates. We discuss the 14 fossils we have chosen to include in this study and present a critical review of other fossils potentially useful in dating studies within the basal eudicots. Our results suggest a rapid diversification during the Early-mid Cretaceous, with all the lineages of basal eudicots emerging during the latest part of the Early Cretaceous. The age of Ranunculales was estimated to 120 myr, Proteales to 119 myr, Sabiales to 118 myr, Buxales to 117 myr and Trochodendrales to 116 myr.

  • 29.
    Anderson, Cajsa Lisa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Janssen, Thomas
    Monocots2009In: Timetree of life / [ed] S. Blair Hedges and Sudhir Kumar, Oxford University Press, 2009Chapter in book (Other academic)
  • 30. Anderson, Frank E.
    et al.
    Córdoba, Alonso J.
    Thollesson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Bilaterian phylogeny based on analyses of a region of the sodium-potassium ATPase alpha-subunit gene2004In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 58, no 3, p. 252-268Article in journal (Refereed)
    Abstract [en]

    Molecular investigations of deep-level relationships within and among the animal phyla have been hampered by a lack of slowly evolving genes that are amenable to study by molecular systematists. To provide new data for use in deep-level metazoan phylogenetic studies, primers were developed to amplify a 1.3-kb region of the subunit of the nuclear-encoded sodium–potassium ATPase gene from 31 bilaterians representing several phyla. Maximum parsimony, maximum likelihood, and Bayesian analyses of these sequences (combined with ATPase sequences for 23 taxa downloaded from GenBank) yield congruent trees that corroborate recent findings based on analyses of other data sets (e.g., the 18S ribosomal RNA gene). The ATPase-based trees support monophyly for several clades (including Lophotrochozoa, a form of Ecdysozoa, Vertebrata, Mollusca, Bivalvia, Gastropoda, Arachnida, Hexapoda, Coleoptera, and Diptera) but do not support monophyly for Deuterostomia, Arthropoda, or Nemertea. Parametric bootstrapping tests reject monophyly for Arthropoda and Nemertea but are unable to reject deuterostome monophyly. Overall, the sodium–potassium ATPase -subunit gene appears to be useful for deep-level studies of metazoan phylogeny.

  • 31.
    Andersson, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Nilsson, Peter
    Dual-genome primer design for construction of DNA microarrays2005In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 21, no 3, p. 325-332Article in journal (Refereed)
    Abstract [en]

    Motivation: Microarray experiments using probes covering a whole transcriptome are expensive to initiate, and a major part of the costs derives from synthesizing gene-specific PCR primers or hybridization probes. The high costs may force researchers to limit their studies to a single organism, although comparing gene expression in different species would yield valuable information.

    Results: We have developed a method, implemented in the software DualPrime, that reduces the number of primers required to amplify the genes of two different genomes. The software identifies regions of high sequence similarity, and from these regions selects PCR primers shared between the genomes, such that either one or, preferentially, both primers in a given PCR can be used for amplification from both genomes. To assure high microarray probe specificity, the software selects primer pairs that generate products of low sequence similarity to other genes within the same genome. We used the software to design PCR primers for 2182 and 1960 genes from the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. Primer pairs were shared among 705 pairs of genes, and single primers were shared among 1184 pairs of genes, resulting in a saving of 31% compared to using only unique primers. We also present an alternative primer design method, in which each gene shares primers with two different genes of the other genome, enabling further savings.

  • 32. Andersson, Anders F.
    et al.
    Lundgren, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Eriksson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Rosenlund, Magnus
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Nilsson, Peter
    Global analysis of mRNA stability in the archaeon Sulfolobus2006In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 7, no 10, p. R99-Article in journal (Refereed)
    Abstract [en]

    Background: Transcript half-lives differ between organisms, and between groups of genes within the same organism. The mechanisms underlying these differences are not clear, nor are the biochemical properties that determine the stability of a transcript. To address these issues, genome-wide mRNA decay studies have been conducted in eukaryotes and bacteria. In contrast, relatively little is known about RNA stability in the third domain of life, Archaea. Here, we present a microarray-based analysis of mRNA half-lives in the hyperthermophilic crenarchaea Sulfolobus solfatoricus and Sulfolobus acidocaldarius, constituting the first genome-wide study of RNA decay in archaea. Results: The two transcriptomes displayed similar half-life distributions, with medians of about five minutes. Growth-related genes, such as those involved in transcription, translation and energy production, were over-represented among unstable transcripts, whereas uncharacterized genes were over-represented among the most stable. Half-life was negatively correlated with transcript abundance and, unlike the situation in other organisms, also negatively correlated with transcript length. Conclusion: The mRNA half-life distribution of Sulfolobus species is similar to those of much faster growing bacteria, contrasting with the earlier observation that median mRNA half-life is proportional to the minimal length of the cell cycle. Instead, short half-lives may be a general feature of prokaryotic transcriptomes, possibly related to the absence of a nucleus and/or more limited post-transcriptional regulatory mechanisms. The pattern of growth-related transcripts being among the least stable in Sulfolobus may also indicate that the short half-lives reflect a necessity to rapidly reprogram gene expression upon sudden changes in environmental conditions.

  • 33.
    Andersson, Anders F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Pelve, Erik A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Lindeberg, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Lundgren, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Nilsson, Peter
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Replication-biased genome organisation in the crenarchaeon Sulfolobus2010In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, p. 454-Article in journal (Refereed)
    Abstract [en]

    Background: Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. Results: We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more highly expressed at all three origins. The bias by far exceeds what would be anticipated by gene dosage effects alone. In addition, early replicating regions are denser in archaeal core genes (enriched in essential functions), display lower intergenic distances, and are devoid of mobile genetic elements. Conclusion: The strong replication-biased structuring of the Sulfolobus chromosome implies that the multiple replication origins serve purposes other than simply shortening the time required for replication. The higher-level chromosomal organisation could be of importance for minimizing the impact of DNA damage, and may also be linked to transcriptional regulation.

  • 34.
    Andersson, Anna-Carin
    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 Functional Genomics. Evolutionär funktionsgenomik.
    Alström-Rapaport, Cecilia
    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.
    Fredga, Karl
    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.
    Lack of mitochondrial DNA divergence between chromosome races of the common shrew, Sorex araneus, in Sweden. Implications for interpreting chromosomal evolution and colonization history.2005In: Mol Ecol, ISSN 0962-1083, Vol. 14, no 9, p. 2703-16Article in journal (Refereed)
  • 35.
    Andersson, Anna-Carin
    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. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Narain, Y
    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.
    Tegelström, 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 Functional Genomics. evolutionär funktionsgenomik.
    Fredga, 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 Functional Genomics. evolutionär funktionsgenomik.
    No apparent reduction of gene flow in a hybrid zone between the West and North European karyotypic groups of the common shrew, Sorex araneus.2004In: Mol Ecol, ISSN 0962-1083, Vol. 13, no 5, p. 1205-15Article in journal (Refereed)
    Abstract [en]

    The common shrew, Sorex araneus, exhibits an unusually high level of karyotypic variation. Populations with identical or similar karyotypes are defined as chromosome races, which are, in turn, grouped into larger evolutionary units, karyotypic groups. Using six microsatellite markers, we investigated the genetic structure of a hybrid zone between the Sidensjo and Abisko chromosome races, representatives of two distinct karyotypic groups believed to have been separated during the last glacial maximum, the West European karyotypic group (western group) and the North European karyotypic group (northern group), respectively. Significant FST values among populations suggest some weak genetic structure. All hierarchical levels show similar levels of genetic differentiation, equivalent to levels of genetic structure in several intraracial studies of common shrew populations from central Europe. Notably, genetic differentiation was of the same order of magnitude between and within karyotypic groups. Although the genetic differentiation was weak, the correlation between genetic and geographical distance was positive and significant, suggesting that the genetic variation observed between populations is a function of geographical distance rather than racial origin. Hence, considerable chromosomal differences do not seem to prevent extensive gene flow.

  • 36.
    Andersson, Anna-Carin
    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 Functional Genomics. Evolutionär funktionsgenomik.
    Thulin, CG
    Tegelstrom, 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 Functional Genomics. evolutionär funktionsgenomik.
    Applicability of rabbit microsatellite primers for studies of hybridisation between an introduced and a native hare species1999In: HEREDITAS, ISSN 0018-0661, Vol. 130, no 3, p. 309-315Article in journal (Refereed)
    Abstract [en]

    Introduced species may hybridise with relatives in the native Fauna or flora and thereby compete for matings and transmit alien DNA. Such interference may contaminate unique genepools, disturb existing ecological balances and may ultimately result in the

  • 37.
    Andersson, Jan O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Eukaryotic gene transfer: adaptation and replacements2008In: Horizontal Gene Transfer in the Evolution of Pathogenesis / [ed] Michael Hensel, Herbert Schmidt, Cambridge: Cambridge University Press , 2008, p. 293-316Chapter in book (Other academic)
  • 38.
    Andersson, Jan O
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv GE
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Genome degradation is an ongoing process in Rickettsia1999In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, ISSN 0737-403, Vol. 16, no 9, p. 1178-1191Article in journal (Other academic)
    Abstract [en]

    To study reductive evolutionary processes in bacterial genomes, we examine sequences in the Rickettsia genomes which are unconstrained by selection and evolve as pseudogenes, one of which is the metK gene, which codes for AdoMet synthetase. Here, we sequenced the metK gene and three surrounding genes in eight different species of the genus Rickettsia. The metK gene was found to contain a high incidence of deletions in six lineages, while the three genes in its surroundings were functionally conserved in all eight lineages. A more drastic example of gene degradation was identified in the metK downstream region, which contained an open reading frame in Rickettsia felis. Remnants of this open reading frame could be reconstructed in five additional species by eliminating sites of frameshift mutations and termination codons. A detailed examination of the two reconstructed genes revealed that deletions strongly predominate over insertions and that there is a strong transition bias for point mutations which is coupled to an excess of GC-to-AT substitutions. Since the molecular evolution of these inactive genes should reflect the rates and patterns of neutral mutations, our results strongly suggest that there is a high spontaneous rate of deletions as well as a strong mutation bias toward AT pairs in the Rickettsia genomes. This may explain the low genomic G + C content (29%), the small genome size (1.1 Mb), and the high noncoding content (24%), as well as the presence of several pseudogenes in the Rickettsia prowazekii genome.

  • 39.
    Andersson, Jan O
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv GE
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Insights into the evolutionary process of genome degradation1999In: Current Opinion in Genetics and Development, ISSN 0959-437X, E-ISSN 1879-0380, Vol. 9, no 6, p. 664-671Article in journal (Refereed)
    Abstract [en]

    Studies of noncoding and pseudogene sequence diversity, particularly in Rickettsia, have begun to reveal the basic principles of genome degradation in microorganisms. Increasingly, studies of genes and genomes suggest that there has been an extensive amount of horizontal gene transfer among microorganisms. As this inflow of genetic material does not seem generally to have resulted in genome size expansions, however, degenerative processes must be at the very least as widespread as horizontal gene transfer. The basic principles of gene degradation and elimination that are being explored in Rickettsia are likely to be of major importance for our understanding of how microbial genomes evolve.

  • 40.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    The bacterial world gets smaller2006In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 314, no 5797, p. 259-260Article, review/survey (Other academic)
  • 41.
    Andersson, Siv G.E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Deterioration of alpha-Proteobacterial human pathogen genomes2005In: Threat of Infection: Microbes of High Pathogenic Potential – Strategies for Detection, Control and Eradication, Internationales Symposium vom 25. bis 28. Juli 2004 in Würzburg / [ed] Jörg Hacker, Hans-Dieter Klenk, 2005, Vol. 92, no 344, p. 81-86Conference paper (Other academic)
  • 42.
    Anderung, C
    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. Evolutionsbiolgoi.
    Baubliene, J
    Daugnora, L
    Götherström, A
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Mitochondrial DNA from medieval wisent remains indicates loss of genetic variation in the modern population.2006In: Molecular Ecology, Vol. 15, p. 2083-Article in journal (Refereed)
  • 43.
    Anderung, C
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hellborg, L
    Seddon, J
    Hanotte, O
    Götherström, A
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Investigation of X- and Y-specific single nucleotide polymorphisms in taurine (Bos taurus) and indicine (Bos indicus) cattle2007In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 38, no 6, p. 595-600Article in journal (Refereed)
    Abstract [en]

    Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossbreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle breeds (four Sanga breeds, including Raya Azebu, Danakil, Caprivi, Nguni; and two Zebu breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X-chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX) and ZFX genes, and five previously identified Y-chromosomal markers in the DDX3Y (previously DBY) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X-chromosome individuals, recombinant X-chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle breeds.

  • 44.
    Anderung, Cecilia
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Genetic Analyses of Bovid Remains and the Origin of Early European Cattle2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The aurochs Bos primigenius, extinct since 1627, was the wild progenitor of cattle. It is believed that all European cattle originate from one domestication event in the Near East 10 000 years ago. However, it is evident from the archaeological record that the aurochs survived into historic time and spent many years existing alongside domestic cattle. Thus, a question posed is whether aurochsen were locally domesticated or incorporated into early domestic cattle stock.

    In this thesis, genetic techniques are applied to ancient and modern DNA from bovids in order to study questions relating to the origin of early European cattle. DNA from ancient specimens is fragmented and in greatly reduced quantity. Therefore mitochondrial DNA, present in many copies in the living cell, has long been dominating the ancient DNA research field. Analyses of ancient DNA presented in this work are based on both mitochondrial DNA and nuclear DNA, through the study of Single Nuclear Polymorohism (SNPs). A method for typing ancient SNPs was developed and applied to ancient cattle bones.

    Mitochondrial DNA of cattle is structured into five geographically distributed lineages, the dominant lineage in Europe is also found in the Near East where additional lineages are found. This pattern has been attributed to the proposed domestication event in the Near East from where cattle carrying the single lineage were brought to Europe. However, the results presented here show that cattle domestication was more complicated than previously suggested. SNP data from extant cattle and bones from cattle and aurochs point towards a hybridisation event. European cattle appear indeed to have been domesticated in the Near East and brought in to the European continent from there. However, once in Europe, hybridisation with local aurochsen took place. It appears therefore that today’s cattle descend both from both Anatolian and European aurochsen.

    List of papers
    1. Prehistoric contacts over the Straits of Gibraltar indicated by genetic analysis of Iberian Bronze Age cattle
    Open this publication in new window or tab >>Prehistoric contacts over the Straits of Gibraltar indicated by genetic analysis of Iberian Bronze Age cattle
    Show others...
    2005 In: Proceedings of the National Academy of Science, Vol. 102, no 14, p. 8431-8435Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95018 (URN)
    Available from: 2006-10-20 Created: 2006-10-20Bibliographically approved
    2. Tracing genetic change over time with SNPs in ancient and modern cattle
    Open this publication in new window or tab >>Tracing genetic change over time with SNPs in ancient and modern cattle
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-95019 (URN)
    Available from: 2006-10-20 Created: 2006-10-20 Last updated: 2010-01-13Bibliographically approved
    3. Cattle domestication in the near east was followed by hybridization with aurochs bulls in Europe
    Open this publication in new window or tab >>Cattle domestication in the near east was followed by hybridization with aurochs bulls in Europe
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    2005 In: Proc. R. Soc. B, Vol. 272, no 1579, p. 2345-2350Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95020 (URN)
    Available from: 2006-10-20 Created: 2006-10-20Bibliographically approved
    4. Identification of X and Y specific single nucleotide polymorphisms (SNPs) and insertion/deletions diagnostic of taurine Bos taurus and indicine Bos indicus cattle
    Open this publication in new window or tab >>Identification of X and Y specific single nucleotide polymorphisms (SNPs) and insertion/deletions diagnostic of taurine Bos taurus and indicine Bos indicus cattle
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-95021 (URN)
    Available from: 2006-10-20 Created: 2006-10-20 Last updated: 2010-01-13Bibliographically approved
    5. Mitochondrial DNA variation in ancient European cattle: tracing the introduction routes of domestic cattle
    Open this publication in new window or tab >>Mitochondrial DNA variation in ancient European cattle: tracing the introduction routes of domestic cattle
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-95022 (URN)
    Available from: 2006-10-20 Created: 2006-10-20 Last updated: 2010-01-13Bibliographically approved
    6. Medieval remains from Lithuania indicate loss of a mitochondrial haplotype in Bison bonasus
    Open this publication in new window or tab >>Medieval remains from Lithuania indicate loss of a mitochondrial haplotype in Bison bonasus
    2006 In: Molecular Ecology Comment, Vol. 15, no 10, p. 3083-Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95023 (URN)
    Available from: 2006-10-20 Created: 2006-10-20Bibliographically approved
  • 45.
    Anderung, Cecilia
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Baubliene, Jurgita
    Bouwman, Abigail
    Brandström, Mikael
    Carretero, José Miguel
    Ortega, Ana Isabel
    Buckley, Michael
    Daugnora, Linas
    Elburg, Rengert
    Collins, Matthew J
    Mitochondrial DNA variation in ancient European cattle: tracing the introduction routes of domestic cattleManuscript (Other academic)
  • 46.
    Anderung, Cecilia
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Baubliene, Jurgita
    Daugnora, Linas
    Götherström, Anders
    Medieval remains from Lithuania indicate loss of a mitochondrial haplotype in Bison bonasus2006In: Molecular Ecology Comment, Vol. 15, no 10, p. 3083-Article in journal (Refereed)
  • 47.
    Anderung, Cecilia
    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.
    Baubliene, Jurgita
    Daugnora, Linas
    Götherström, Anders
    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.
    Medieval remains from Lithuania indicate loss of a mitochondrial haplotype in Bison bonasus.2006In: Mol Ecol, ISSN 0962-1083, Vol. 15, no 10, p. 3083-Article in journal (Refereed)
  • 48.
    Anderung, Cecilia
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Bouwman, Abigail
    Persson, Per
    Carretero, José Miguel
    Ortega, Ana Isabel
    Elburg, Rengert
    Smith, Colin
    Arsuaga, Juan Luis
    Ellegren, Hans
    Göthertröm, Anders
    Prehistoric contacts over the Straits of Gibraltar indicated by genetic analysis of Iberian Bronze Age cattle2005In: Proceedings of the National Academy of Science, Vol. 102, no 14, p. 8431-8435Article in journal (Refereed)
  • 49.
    Anderung, Cecilia
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Hellborg, Linda
    Seddon, Jennifer
    Hanotte, Olivier
    Götherström, Anders
    Identification of X and Y specific single nucleotide polymorphisms (SNPs) and insertion/deletions diagnostic of taurine Bos taurus and indicine Bos indicus cattleManuscript (Other academic)
  • 50.
    Anderung, Cecilia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Persson, P.
    Bouwman, A.
    Elburg, R.
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Fishing for ancient DNA2008In: Forensic Science International: Genetics, Vol. 2, no 2, p. 104-107Article in journal (Refereed)
    Abstract [en]

    The major problems concerning ancient DNA studies are related to the amount of extractable DNA and the precautions needed to avoid contamination. From the very first step of the analyses, the DNA extraction, these problems must be confronted. There are several extraction methods available for DNA in ancient tissue; several of them are complicated and time consuming. and none of the methods have reached an acceptance level such that they are routinely used on a widespread basis. Here we investigate the efficiency of two methods. one based on magnetic separation of the targeted molecules. and one based oil silica binding. The efficiency rate of these two on the material studied seems to be identical. The silica binding method has the benefit of relative simplicity, but the magnetic separation technique also hits advantages. For example, it is possible to reuse the extract several times for different loci, and it is possible to concentrate all extracted DNA from one locus into one PCR.

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