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  • 201. Carlsson, Jenny
    et al.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Sundström, Jens
    Teixeira, Rita
    Wellmer, Frank
    Meyerowitz, Elliot M.
    Glimelius, Kristina
    Microarray analysis reveals altered expression of a large number of nuclear genes in developing cytoplasmic male sterile Brassica napus flowers2007In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 49, no 3, p. 452-462Article in journal (Refereed)
    Abstract [en]

    To gain new insights into the mechanism underlying cytoplasmic male sterility (CMS), we compared the nuclear gene expression profiles of flowers of a Brassica napus CMS line with that of the fertile B. napus maintainer line using Arabidopsis thaliana flower-specific cDNA microarrays. The CMS line used has a B. napus nuclear genome, but has a rearranged mitochondrial (mt) genome consisting of both B. napus and A. thaliana DNA. Gene expression profiling revealed that a large number of genes differed in expression between the two lines. For example, nuclear genes coding for proteins that are involved in protein import into organelles, genes expressed in stamens and pollen, as well as genes implicated in either cell-wall remodeling or architecture, were repressed in the CMS line compared with B. napus. These results show that the mt genome of the CMS line strongly influences nuclear gene expression, and thus reveal the importance of retrograde signalling between the mitochondria and the nucleus. Furthermore, flowers of the CMS line are characterized by a replacement of stamens with carpelloid organs, and thus partially resemble the APETALA3 (AP3) and PISTILLATA (PI) mutants. In accordance with this phenotype, AP3 expression was downregulated in the stamens, shortly before these organs developed carpelloid characteristics, even though it was initiated correctly. Repression of PI succeeded that of AP3 and might be a consequence of a loss of AP3 activity. These results suggest that AP3 expression in stamens depends on proper mt function and a correct nuclear-mt interaction, and that mt alterations cause the male sterility phenotype of the CMS line.

  • 202. Carr, Martin
    et al.
    Leadbeater, Barry S C
    Baldauf, Sandra L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Conserved Meiotic Genes Point to Sex in the Choanoflagellates2010In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 57, no 1, p. 56-62Article in journal (Refereed)
    Abstract [en]

    The choanoflagellates are a widespread group of heterotrophic aquatic nanoflagellates, which have recently been confirmed as the sister-group to Metazoa. Asexual reproduction is the only mode of cell division that has been observed within the group; at present the range of reproductive modes, as well as the ploidy level, within choanoflagellates are unknown. The recent discovery of long terminal repeat retrotransposons within the genome of Monosiga brevicollis suggests that this species also has sexual stages in its life cycle because asexual organisms cannot tolerate retrotransposons due to the rapid accumulation of deleterious mutations caused by their transposition. We screened the M. brevicollis genome for known eukaryotic meiotic genes, using a recently established "meiosis detection toolkit" of 19 genes. Eighteen of these genes were identified, none of which appears to be a pseudogene. Four of the genes were also identified in expressed sequence tag data from the distantly related Monosiga ovata. The presence of these meiosis-specific genes provides evidence for meiosis, and by implication sex, within this important group of protists.

  • 203. Carrasco, Claudio
    et al.
    Holliday, Scott D.
    Hansel, Alfred
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik.
    Lindblad, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik.
    Golden, James W.
    Heterocyst-Specific Excision of the Anabaena sp. Strain PCC 7120 hupL Element requires xisC2005In: Journal of Bacteriology, Vol. 187, no 17, p. 6031-6038Article in journal (Refereed)
    Abstract [en]

    In nitrogen-limiting conditions, approximately 10% of the vegetative cells in filaments of the cyanobacterium Anabaena (Nostoc) sp. strain PCC7120 differentiate into nitrogen-fixing heterocysts. During the late stages of heterocyst differentiation, three DNA-elements, each embedded within an open reading frame, are programmed to excise from chromosome by site-specific recombination. The DNA elements are named after the genes that they interrupt: nifD, fdxN, and hupL. The nifD and fdxN elements each contain a gene, xisA or xisF, respectively, that encodes the site-specific recombinase required for programmed excision of the element. Here, we show that the xisC gene (alr0677), which is present at one end of the 9,435-bp hupL element, is required for excision of the hupL element. A strain in which the xisC gene was inactivated showed no detactable excision of the hupL element. hupL encodes the large subunit of uptake of hydrogenase. The xisC mutant forms heterocysts and grows diazotrophically, but unlike the wild type, it evolved hydrogen gas under nitrogen-fixing conditions. Overexpression of xisC from a plasmid in the wild-type background caused a low level of hupL rearrangement even in nitrogen-replete conditions. Expression of xisC in Escherichia coli was sufficient to produce rearrangement of an artificial substrate plasmid bearing the hupL elemenat recombination sites. Sequence analysis indicated that XisC is a divergent member of the phage integrase family of recombinases. Site-directed mutagenesis of xisC showed that the XisC recombinase has functional silmilarity to the phage integrase family.

  • 204.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Emilsson, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Preece, Paul
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies2000In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 10, no 8, p. 1219-29Article in journal (Refereed)
    Abstract [en]

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

  • 205.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Emilsson, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Sundberg, Rolf
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Decrease of serotonin receptor 2C in schizophrenia brains identified by high-resolution mRNA expression analysis2003In: Biological Psychiatry, ISSN 0006-3223, E-ISSN 1873-2402, Vol. 54, no 11, p. 1212-1221Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: RNA expression profiling can provide hints for the selection of candidate susceptibility genes, for formulation of hypotheses about the development of a disease, and/or for selection of candidate gene targets for novel drug development. We measured messenger RNA expression levels of 16 candidate genes in brain samples from 55 schizophrenia patients and 55 controls. This is the largest sample so far used to identify genes differentially expressed in schizophrenia brains. METHODS: We used a sensitive real-time polymerase chain reaction methodology and a novel statistical approach, including the development of a linear model of analysis of covariance type. RESULTS: We found two genes differentially expressed: monoamine oxidase B was significantly increased in schizophrenia brain (p =.001), whereas one of the serotonin receptor genes, serotonin receptor 2C, was significantly decreased (p =.001). Other genes, previously proposed to be differentially expressed in schizophrenia brain, were invariant in our analysis. CONCLUSIONS:The differential expression of serotonin receptor 2C is particularly relevant for the development of new atypical antipsychotic drugs. The strategy presented here is useful to evaluate hypothesizes for the development of the disease proposed by other investigators.

  • 206.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Åberg, Karolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    McCarthy, Shane
    Andersson, Björn
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Serotonin receptor 2C (HTR2C) and schizophrenia: effect of medication and genetic variants on expression levelsManuscript (Other academic)
  • 207.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Åberg, Karolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    McCarthy, Shane
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Andersson, Björn
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Serotonin Receptor 2C (HTR2C) and Schizophrenia: Examination of Possible Medication and Genetic Influences on Expression Levels2005In: American Journal of Medical Genetics, ISSN 0148-7299, E-ISSN 1096-8628, Vol. 134B, p. 84-89Article in journal (Refereed)
    Abstract [en]

    The serotonin receptor 2C (HTR2C) gene is of interest in schizophrenia due to its involvement in regulation of dopamine activity in the prefrontal cortex. We have previously reported a decreased expression of HTR2C mRNA levels in the prefrontal cortex of schizophrenia patients. The variability in mRNA expression levels is evaluated here more closely in relation to promoter haplotypes and neuroleptic treatment received by the patients. The decrease in HTR2C mRNA was present in neuroleptic treated individuals and in patients untreated at death, indicating that the lower expression is not a short-term medication effect. Three promoter polymorphisms were used to construct haplotypes. No SNP displayed genotypic or haplotypic association with the disease. Gene expression of HTR2C was not affected by haplotype and the expression decrease in schizophrenia patients was similar in all haplotype combinations (diplotypes). We conclude that the decrease in HTR2C expression in schizophrenia may be related to the disease mechanism rather than to drug treatment. The disease related changes in HTR2C expression are not related to the promoter variants typed in our sample, but could be due to other regulatory variants or trans-acting factors.

  • 208.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Species Limits, and Evolutionary History of Glassfrogs2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Recognizing the mechanisms of speciation and the limits of species is essential to understand the origin of biodiversity and how to conserve it. The general aims of my investigations during my doctoral studies were two-fold: to study evolutionary patterns and processes, and to provide specific and superspecific taxonomic classifications that try to reflect evolutionary history. I have focused my research on anurans in their biodiversity hotspot, the American Tropics.

    I have used morphological, behavioral (mating calls), and genetic (DNA sequences) characters to study species boundaries between frogs of the genus Pristimantis and the family Centrolenidae (glassfrogs). The results show that the exclusive use of single lines of evidence or the application of arbitrary thresholds impair and bias our ability to recognize new species and limit the possibility to understand evolutionary processes. Only an integrative approach combining every source of evidence provides the necessary feedback to discover all species and test their identity by comparing independent sets of data. This approach further allows identifying those species that probably represent stable comparative units (well supported species hypotheses) and to flag taxa that require further assessment.

    Phylogenetic reconstructions based on seven nuclear and mitochondrial genes for about 100 species of glassfrogs revealed that previous hypotheses of relationships were mislead by rampant convergent evolution at the phenotypic level. None of the previously suggested classifications fit with the reconstructed evolutionary history. Consequently, we proposed a new classification consistent with this phylogeny.

    I also studied the tempo and mode of diversification among glassfrogs. Based on sequences from ten genes in 87 species, I estimated species divergence times, age-range correlation between sister species, and reconstructed ancestral areas and dispersal/vicariance events. The results revealed a complex model of diversification where geographical isolation seems to be the dominant scenario for speciation and only clades of altitudinal generalists have been able to spread across the Neotropical rainforests.

    List of papers
    1. Deciphering the products of evolution at the species level: the need for an integrative taxonomy
    Open this publication in new window or tab >>Deciphering the products of evolution at the species level: the need for an integrative taxonomy
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    2009 (English)In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 38, no 4, p. 431-447Article in journal (Refereed) Published
    Abstract [en]

    Progress in molecular techniques together with the incorporation of phylogenetic analyses of DNA into taxonomy have caused an increase in the number of species' discoveries in groups with morphological characters that are difficult to study or in those containing polytypic species. But some emerged criticisms plead for a taxonomic conservatism grounded either on the requirement of providing evidences of morphological distinctiveness or reproductive barriers to erect new species names. In a case study of taxonomic research on Neotropical frogs, we combine several lines of evidence (morphological characters, prezygotic reproductive isolation and phylogenetic analyses of mitochondrial DNA) to test the status of 15 nominal species and to assess the degree of agreement of the different lines of evidence. Our study reveals that morphology alone is not sufficient to uncover all species, as there is no other single line of evidence independently. Full congruence between lines of evidence is restricted to only four out of the 15 species. Five species show congruence of two lines of evidence, whereas the remaining six are supported by only one. The use of divergence in morphological characters seems to be the most conservative approach to delineate species boundaries because it does not allow the identification of some sibling reciprocally monophyletic species differing in their advertisement calls. The separate analysis of differences in advertisement calls (evidence of reproductive isolation) or of phylogenetic data alone also shows limitations, because they do not support some morphological species. Our study shows that only an integrative approach combining all sources of evidence provides the necessary feedback to evaluate the taxonomic status of existing species and to detect putative new ones. Furthermore, the application of integrative taxonomy enables the identification of hypotheses about the existence of species that will probably be rejected or changed, and those that can be expected to persist.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100912 (URN)10.1111/j.1463-6409.2008.00381.x (DOI)000267130400005 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    2. Delimiting species boundaries using different criteria: taxonomy of Hyalinobatrachium Glassfrogs (Amphibia: Centrolenidae) from the Guiana Shield
    Open this publication in new window or tab >>Delimiting species boundaries using different criteria: taxonomy of Hyalinobatrachium Glassfrogs (Amphibia: Centrolenidae) from the Guiana Shield
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-100913 (URN)
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2010-01-14
    3. Phylogenetic relationships of glassfrogs (Centrolenidae) based on mitochondrial and nuclear genes
    Open this publication in new window or tab >>Phylogenetic relationships of glassfrogs (Centrolenidae) based on mitochondrial and nuclear genes
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    2008 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 2, p. 574-595Article, review/survey (Refereed) Published
    Abstract [en]

    Glassfrogs (family Centrolenidae) represent an exceptionally diverse group among Neotropical anurans, but their evolutionary relationships never have been assessed from a molecular perspective. Mitochondrial and nuclear markers were used to develop a novel hypothesis of centrolenid phylogeny. Ingroup sampling included 100 terminals, with 78 (53%) of the named species in the family, representing most of the phenotypic diversity described for the group. Thirty-five species representing taxa traditionally associated with glassfrogs were used as outgroups. Gene sampling consisted of complete or partial sequences of three mitochondrial (12S, 16S, ND1) and three nuclear markers (c-myc exon 2, RAG1, POMC) for a total of ∼4362 bp. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analyses for individual genes and combined datasets. The separate analysis of mitochondrial and nuclear datasets allowed us to clarify the relationships within glassfrogs; also, we corroborate the sister-group relationship between Allophryne ruthveni and glassfrogs. The new phylogeny differs significantly from all previous morphology-based hypotheses of relationships, and shows that hypotheses based on few traits are likely to misrepresent evolutionary history. Traits previously hypothesized as unambiguous synapomorphies are shown to be homoplastic, and all genera in the current taxonomy (Centrolene, Cochranella, Hyalinobatrachium, Nymphargus) are found to be poly- or paraphyletic. The new topology implies a South American origin of glassfrogs and reveals allopatric speciation as the most important speciation mechanism. The phylogeny profoundly affects the traditional interpretations of glassfrog taxonomy, character evolution, and biogeography-topics that now require more extensive evaluation in future studies.

    Keywords
    Anura, Biogeography, Centrolenidae, Evolution, Homoplasy, Monophyly, Neotropics, Phylogeny, Speciation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100914 (URN)10.1016/j.ympev.2008.04.012 (DOI)000258556100016 ()18515151 (PubMedID)
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    4. Phylogenetic systematics of Glassfrogs (Amphibia: Centrolenidae) and their sister taxon Allophryne ruthveni
    Open this publication in new window or tab >>Phylogenetic systematics of Glassfrogs (Amphibia: Centrolenidae) and their sister taxon Allophryne ruthveni
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    2009 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 2100, p. 1-97Article, review/survey (Refereed) Published
    Abstract [en]

    Based on a molecular phylogeny, a new phylogenetic taxonomy that is compatible with both the International Code of Zoological Nomenclature (ICZN) and the PhyloCode is proposed for Glassfrogs and their sister taxon, Allophryne ruthveni. The arrangement presented herein emphasizes the recognition of clades having (i) significant statistical support and congruence among phylogenetic estimation methods (i.e., parsimony, maximum likelihood, and Bayesian inference criteria), (ii) congruence among genetic markers, and (iii) morphological and/or behavioral distinctiveness. Also, when previously recognized groups are recovered as monophyletic or nearly monophyletic, we propose taxa that minimize the number of name changes required to make these groups monophyletic, preserving the names and contents of previous classifications (i.e., nomenclatural stability). The evolutionary proximity of Centrolenidae and Allophrynidae is recognized by combining these families into an unraked taxon, Allocentroleniae-a proposal that maintains the traditional names and species contents of Centrolenidae and Allophrynidae. We arrange centrolenid diversity in two subfamilies: Centroleninae and Hyalinobatrachinae. Within Centroleninae, the diagnosis and species content of the genera Centrolene, Cochranella, and Nymphargus are modified; Teratohyla is resurrected and modified, and Chimerella, Espadarana, Rulyrana, Sachatamia, and Vitreorana are proposed as new genera. The other subfamily, Hyalinobatrachinae, contains the new genus Celsiella and a modified Hyalinobatrachium that fully corresponds to the former fleischmanni Group. Additionally, the genus Ikakogi is described. Ikakogi could not be assigned with confidence to either subfamily and it is placed as incertae sedis in Centrolenidae. The data at hand suggest that Ikakogi tayrona is a lineage as old as the subfamilies Hyalinobatrachinae and Centroleninae. The revised taxonomy differs markedly from previous arrangements, which were based on phenetics and few morphological characters. Most of the genera defined herein are confined to distinct biogeographic regions, highlighting the importance of geography in the speciation of Glassfrogs. The principal limitation of this proposal is that it is based on an incomplete sampling of taxa (54% of the recognized Glassfrogs). Although diagnoses are based on phenotypic traits, there are several cases (16% of all species) in which the allocation of species is ambiguous because of morphological homoplasy and the lack of molecular data. Finally, in an attempt to facilitate species identification, comparison, and generic placement, we provide photographs for most (similar to 96%) of the recognized centrolenid species.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100915 (URN)000266232500001 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    5. Biogeography and diversification of Neotropical glassfrogs (Anura: Centrolenidae)
    Open this publication in new window or tab >>Biogeography and diversification of Neotropical glassfrogs (Anura: Centrolenidae)
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-100916 (URN)
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2010-01-14
    6. A new species of Hyalinobatrachium (Centrolenidae : Anura) from Serrania de Perija, Venezuela
    Open this publication in new window or tab >>A new species of Hyalinobatrachium (Centrolenidae : Anura) from Serrania de Perija, Venezuela
    2007 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 1441, p. 51-62Article in journal (Refereed) Published
    Abstract [en]

    We describe a new species of Hyalinobatrachium from Serran a de Perija, Estado de Zulia, Venezuela. The new species is placed in the Hyalinobatrachium fleischmanni group and can be differentiated from all other species of Hyalinobatrachium by having small enamelled glands on the lower part of the upper lip and on the skin covering the jaw, iris with a horizontal dark band that connects the pupil with the lateral edges of the eye, marked ulnar and tarsal white enamelled folds, extensive webbing between fingers and between toes, white pericardium and an advertisement call formed by a high-pitched single note composed of two parts: a group of modulated pulses increasing in frequency followed by a long and modulated sound at a constant frequency.

    Keywords
    Andes, biogeography, colombia, glass frogs, hyalinobatrachium tatayoi, taxonomy
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-15723 (URN)000245487700004 ()
    Available from: 2008-05-19 Created: 2008-05-19 Last updated: 2017-12-08Bibliographically approved
    7. Glassfrogs (Anura: Centrolenidae) of Kaieteur National Park, Guyana, with notes on the distribution and taxonomy of some species of the family in the Guiana Shield
    Open this publication in new window or tab >>Glassfrogs (Anura: Centrolenidae) of Kaieteur National Park, Guyana, with notes on the distribution and taxonomy of some species of the family in the Guiana Shield
    2008 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 1680, p. 25-53Article in journal (Refereed) Published
    Abstract [en]

    We provide new distribution records and discuss the taxonomy of three species of Glassfrogs from the Guiana Shield: Centrolene gorzulai, Cochranella helenae, and Hyalinobatrachium taylori. These three species were collected in Kaieteur National Park in west-central Guyana. Taxonomic changes were based on morphological, bioacoustic and genetic ( a fragment of the mitochondrial ribosomal gene 16S) comparisons. We consider Centrolene papillahallicum to be a junior synonym of C. gorzulai. We assign the Venezuelan population of Cochranella oyampiensis to Co. helenae and describe the phenotypic variation of this taxon. We refine the description of Cochranella oyampiensis and transfer it to the Co. spinosa species group. We propose the new name Cochranella helenae Group for those species of Cochranella assigned to the former Co. oyampiensis Group. We report the first record of Cochranella midas for French Guiana, and the first record of Hyalinobatrachium nouraguense, new emendation, for Suriname.

    Keywords
    Centrolenid frogs, Centrolene gorzulai, Centrolene papillahallicum, Cochranella ametarsia, Cochranella helenae, Cochranella midas, Cochranella oyampiensis, French Guiana, Hyalinobatrachium mondolfii, Hyalinobatrachium ouraguense, Hyalinobatrachium taylori, mitochondrial DNA, Suriname
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100917 (URN)000252281700002 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    8. Comments on the distribution, taxonomy and advertisement call of the Guyanan glass frog Hyalinobatrachium ignioculus (Anura: Centrolenidae)
    Open this publication in new window or tab >>Comments on the distribution, taxonomy and advertisement call of the Guyanan glass frog Hyalinobatrachium ignioculus (Anura: Centrolenidae)
    2008 (English)In: Salamandra, ISSN 0036-3375, Vol. 44, no 4, p. 235-240Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-100918 (URN)
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2009-09-18Bibliographically approved
    9. Taxonomic identity of Cochranella petersi Goin, 1961 and Centrolenella ametarsia Flores, 1987
    Open this publication in new window or tab >>Taxonomic identity of Cochranella petersi Goin, 1961 and Centrolenella ametarsia Flores, 1987
    2008 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 1815, p. 25-34Article in journal (Refereed) Published
    Abstract [en]

    We assess the taxonomic status of Hyalinobatrachium petersi and Cochranella ametarsia based on the examination oftype material and recently collected specimens. We conclude that the material assigned to them is morphologically undistinguishablefrom two previously described species (Cochranella pulverata and Cochranella oyampiensis, respectively) and, therefore, are junior synonyms.

    Keywords
    Centrolenidae, ametarsia, Cochranella, Hyalinobatrachium, oyampiensis, petersi, pulverata, Synonymy
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100919 (URN)000257321200002 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    10. Resurrection of Hyalinobatrachium orocostale and notes on the Hyalinobatrachium orientale species complex (Anura: Centrolenidae)
    Open this publication in new window or tab >>Resurrection of Hyalinobatrachium orocostale and notes on the Hyalinobatrachium orientale species complex (Anura: Centrolenidae)
    2008 (English)In: Herpetologica, ISSN 0018-0831, E-ISSN 1938-5099, Vol. 64, no 4, p. 472-484Article in journal (Refereed) Published
    Abstract [en]

    Hyalinobatrachium orientale has a complex taxonomic history suggesting that more than one species could be under this name. In this review, we try to clarify the current taxonomic status of this species by means of morphological, bioacoustic, and mitochondrial DNA sequence comparisons of specimens from Tobago Island and the Venezuelan Cordillera de la Costa (Oriental Sector, Cordillera del Litoral and Cordillera del Interior). Our data support the resurrection of Hyalinobatrachium orocostale, restricted to the Cordillera del Interior. Additionally, specimens from Cordillera del Litoral and Oriental Sector do not form a monophyletic group; hence, we define as Hyalinobatrachium sp. the populations from Cordillera del Litoral and H. orientale sensu stricto the populations from the Oriental Sector. Preliminary bioacoustic and morphological analyses indicate that the populations from Tobago are conspecific with Hyalinobatrachium orientale sensu stricto.

    Keywords
    Cordillera de la Costa, Cryptic species, Glassfrogs, Mitochondrial DNA, Taxonomy, Tobago, Venezuela
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100920 (URN)10.1655/07-049R2.1 (DOI)000264060900007 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    11. Species status of Centrolene lema Duellman & Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy
    Open this publication in new window or tab >>Species status of Centrolene lema Duellman & Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy
    2009 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, Vol. 1980, p. 16-28Article in journal (Refereed) Published
    Abstract [en]

    We evaluate the hypothesis of Centrolene lema as a species distinct from C. gorzulae using morphological, bioacousticand genetic comparisons. Our results show that there are no consistent differences in any of these three areas; hence, wepresent C. lema as a synonym of C. gorzulae. Additionally we provide new data on the distribution and ecology of thespecies.

    Keywords
    Bioacoustics, Centrolene gorzulae, Centrolenid frogs, Distribution, Glassfrogs, Guiana Shield, Guyana, mitochondrial DNA, Synonym, Venezuela
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100921 (URN)000262632400002 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    12. A new species of Hyalinobatrachium (Anura: Centrolenidae) from the Amazonian slopes of the central Andes with comments on the diversity of the genus in the area
    Open this publication in new window or tab >>A new species of Hyalinobatrachium (Anura: Centrolenidae) from the Amazonian slopes of the central Andes with comments on the diversity of the genus in the area
    Show others...
    2009 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 2143, p. 24-44Article in journal (Refereed) Published
    Abstract [en]

    We describe a new species of Hyalinobatrachium from the Amazonian   slopes of the Andes in Peru and Bolivia on the basis of morphological,   bioacoustic and genetic characteristics. Hyalinobatrachium carlesvilai   sp. nov. can be distinguished from other species of Hyalinobatrachium   by the combination of the following characters: (1) truncate snout in   dorsal and lateral view; (2) white pericardium; (3) enameled dorsal,   tarsal and cloacal folds; (4) hand webbing formula III 2(-) -1(+) IV;   (5) iris cream; (6) advertisement call consisting of a single,   frequency-modulated note with a pulsed section followed by a tonal   section. The new species had been previously identified as   Hyalinobatrachium munozorum and H. bergeri. The advertisement call of   the new species was previously assigned to H. bergeri. Here we describe   the previously unknown call of Hyalinobatrachium bergeri. Additionally,   we study the taxonomic status of H. lemur and H. pellucidum and place   the former as synonym of the later. We extend the distribution of H. pellucidum to Departamento Cusco in southern Peru.

    Keywords
    Bioacoustics, Centrolenid frogs, Cryptic species, Glassfrogs, Hyalinobatrachium bergeri, Hyalinobatrachium lemur, Hyalinobatrachium munozorum, Hyalinobatrachium pellucidum, mitochondrial DNA, Synonymy, Taxonomy
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100922 (URN)000267615900002 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
  • 209.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ayarzaguena, J.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    A new species of Hyalinobatrachium (Centrolenidae : Anura) from Serrania de Perija, Venezuela2007In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 1441, p. 51-62Article in journal (Refereed)
    Abstract [en]

    We describe a new species of Hyalinobatrachium from Serran a de Perija, Estado de Zulia, Venezuela. The new species is placed in the Hyalinobatrachium fleischmanni group and can be differentiated from all other species of Hyalinobatrachium by having small enamelled glands on the lower part of the upper lip and on the skin covering the jaw, iris with a horizontal dark band that connects the pupil with the lateral edges of the eye, marked ulnar and tarsal white enamelled folds, extensive webbing between fingers and between toes, white pericardium and an advertisement call formed by a high-pitched single note composed of two parts: a group of modulated pulses increasing in frequency followed by a long and modulated sound at a constant frequency.

  • 210.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Guayasamin, Juan M.
    Ayarzagüena, José
    Trueb, Linda
    Vilà, Carles
    Biogeography and diversification of Neotropical glassfrogs (Anura: Centrolenidae)Manuscript (Other (popular science, discussion, etc.))
  • 211.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Guayasamin, Juan M.
    Kok, Philippe J. R.
    Species status of Centrolene lema Duellman & Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy2009In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, Vol. 1980, p. 16-28Article in journal (Refereed)
    Abstract [en]

    We evaluate the hypothesis of Centrolene lema as a species distinct from C. gorzulae using morphological, bioacousticand genetic comparisons. Our results show that there are no consistent differences in any of these three areas; hence, wepresent C. lema as a synonym of C. gorzulae. Additionally we provide new data on the distribution and ecology of thespecies.

  • 212.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Padial, José M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Chaparro, Juan C.
    Aguayo, Rodrigo
    de la Riva, Ignacio
    A new species of Hyalinobatrachium (Anura: Centrolenidae) from the Amazonian slopes of the central Andes with comments on the diversity of the genus in the area2009In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 2143, p. 24-44Article in journal (Refereed)
    Abstract [en]

    We describe a new species of Hyalinobatrachium from the Amazonian   slopes of the Andes in Peru and Bolivia on the basis of morphological,   bioacoustic and genetic characteristics. Hyalinobatrachium carlesvilai   sp. nov. can be distinguished from other species of Hyalinobatrachium   by the combination of the following characters: (1) truncate snout in   dorsal and lateral view; (2) white pericardium; (3) enameled dorsal,   tarsal and cloacal folds; (4) hand webbing formula III 2(-) -1(+) IV;   (5) iris cream; (6) advertisement call consisting of a single,   frequency-modulated note with a pulsed section followed by a tonal   section. The new species had been previously identified as   Hyalinobatrachium munozorum and H. bergeri. The advertisement call of   the new species was previously assigned to H. bergeri. Here we describe   the previously unknown call of Hyalinobatrachium bergeri. Additionally,   we study the taxonomic status of H. lemur and H. pellucidum and place   the former as synonym of the later. We extend the distribution of H. pellucidum to Departamento Cusco in southern Peru.

  • 213.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Señaris, J. Celsa
    Ayarzagüena, José
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Resurrection of Hyalinobatrachium orocostale and notes on the Hyalinobatrachium orientale species complex (Anura: Centrolenidae)2008In: Herpetologica, ISSN 0018-0831, E-ISSN 1938-5099, Vol. 64, no 4, p. 472-484Article in journal (Refereed)
    Abstract [en]

    Hyalinobatrachium orientale has a complex taxonomic history suggesting that more than one species could be under this name. In this review, we try to clarify the current taxonomic status of this species by means of morphological, bioacoustic, and mitochondrial DNA sequence comparisons of specimens from Tobago Island and the Venezuelan Cordillera de la Costa (Oriental Sector, Cordillera del Litoral and Cordillera del Interior). Our data support the resurrection of Hyalinobatrachium orocostale, restricted to the Cordillera del Interior. Additionally, specimens from Cordillera del Litoral and Oriental Sector do not form a monophyletic group; hence, we define as Hyalinobatrachium sp. the populations from Cordillera del Litoral and H. orientale sensu stricto the populations from the Oriental Sector. Preliminary bioacoustic and morphological analyses indicate that the populations from Tobago are conspecific with Hyalinobatrachium orientale sensu stricto.

  • 214.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Vilà, Carles
    Ayarzagüena, José
    Blanc, Michel
    Ernst, Raffael
    Delimiting species boundaries using different criteria: taxonomy of Hyalinobatrachium Glassfrogs (Amphibia: Centrolenidae) from the Guiana ShieldManuscript (Other (popular science, discussion, etc.))
  • 215. Cavelier, L
    et al.
    Erikson, I
    Tammi, M
    Jalonen, P
    Lindholm, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Smith, P
    Luthman, H
    Gyllensten, U
    MtDNA mutations in maternally inherited diabetes: presence of the 3397 ND1 mutation previously associated with Alzheimer's and Parkinson's disease2001In: Hereditas, ISSN 0018-0661, E-ISSN 1601-5223, Vol. 135, no 1, p. 65-70Article in journal (Refereed)
    Abstract [en]

    Mutations in the mitochondrial tRNA(leu) (UUR) gene have been associated with diabetes mellitus and deafness. We screened for the presence of mtDNA mutations in the tRNA(leu) (UUR) gene and adjacent ND1 sequences in 12 diabetes mellitus pedigrees with a possible maternal inheritance of the disease. One patient carried a G to A substitution at nt 3243 (tRNA(leu) (UUR) gene) in heteroplasmic state. In a second pedigree a patient had an A to G substitution at nt 3397 in the ND1 gene. All maternal relatives of the proband had the 3397 substitution in homoplasmic state. This substitution was not present in 246 nonsymptomatic Caucasian controls. The 3397 substitution changes a highly conserved methionine to a valine at aa 31 and has previously been found in Alzheimer's (AD) and Parkinson's (PD) disease patients. Substitutions in the mitochondrial ND1 gene at aa 30 and 31 have associated with a number of different diseases (e.g. AD/PD, MELAS, cardiomyopathy and diabetes mellitus, LHON, Wolfram-syndrome and maternal inherited diabetes) suggesting that changes at these two codons may be associated with very diverse pathogenic processes. In a further attempt to search for mtDNA mutations outside the tRNAleu gene associated with diabetes, the whole mtDNA genome sequence was determined for two patients with maternally inherited diabetes and deafness. Except for substitutions previously reported as polymorphisms, none of the two patients showed any non-synonymous substitutions either in homoplasmic or heteroplasmic state. These results imply that the maternal inherited diabetes and deafness in these patients must result from alterations of nuclear genes and/or environmental factors.

  • 216. Ceplitis, Alf
    et al.
    Slotte, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Neuffer, Barbara
    Linde, Marcus
    Kraft, Thomas
    Lascoux, Martin
    QTL mapping of flowering time using AFLP and candidate gene markers in the tetraploid Capsella bursa-pastoris (Brassicaceae).Manuscript (Other (popular science, discussion, etc.))
  • 217.
    Ceplitis, Alf
    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.
    Su, Yingtao
    Lascoux, Martin
    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.
    Bayesian inference of evolutionary history from chloroplast microsatellites in the cosmopolitan weed Capsella bursa-pastoris (Brassicaceae).2005In: Mol Ecol, ISSN 0962-1083, Vol. 14, no 14, p. 4221-33Article in journal (Other scientific)
  • 218.
    Ceplitis, H.
    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.
    Ellegren, H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Adaptive molecula evolution in HINTW, a female-specific gene in birds.2004In: Molecular Biology and Evolution, no 21, p. 249-254Article in journal (Refereed)
  • 219. Ceresini, Paulo C.
    et al.
    Shew, H David.
    James, Timothy
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Vilgalys, Rytas J.
    Cubeta, Marc A.
    Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci.2007In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 7, p. 163-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The soil fungus Rhizoctonia solani anastomosis group 3 (AG-3) is an important pathogen of cultivated plants in the family Solanaceae. Isolates of R. solani AG-3 are taxonomically related based on the composition of cellular fatty acids, phylogenetic analysis of nuclear ribosomal DNA (rDNA) and beta-tubulin gene sequences, and somatic hyphal interactions. Despite the close genetic relationship among isolates of R. solani AG-3, field populations from potato and tobacco exhibit comparative differences in their disease biology, dispersal ecology, host specialization, genetic diversity and population structure. However, little information is available on how field populations of R. solani AG-3 on potato and tobacco are shaped by population genetic processes. In this study, two field populations of R. solani AG-3 from potato in North Carolina (NC) and the Northern USA; and two field populations from tobacco in NC and Southern Brazil were examined using sequence analysis of two cloned regions of nuclear DNA (pP42F and pP89). RESULTS: Populations of R. solani AG-3 from potato were genetically diverse with a high frequency of heterozygosity, while limited or no genetic diversity was observed within the highly homozygous tobacco populations from NC and Brazil. Except for one isolate (TBR24), all NC and Brazilian isolates from tobacco shared the same alleles. No alleles were shared between potato and tobacco populations of R. solani AG-3, indicating no gene flow between them. To infer historical events that influenced current geographical patterns observed for populations of R. solani AG-3 from potato, we performed an analysis of molecular variance (AMOVA) and a nested clade analysis (NCA). Population differentiation was detected for locus pP89 (Phi ST = 0.257, significant at P < 0.05) but not for locus pP42F (Phi ST = 0.034, not significant). Results based on NCA of the pP89 locus suggest that historical restricted gene flow is a plausible explanation for the geographical association of clades. Coalescent-based simulations of genealogical relationships between populations of R. solani AG-3 from potato and tobacco were used to estimate the amount and directionality of historical migration patterns in time, and the ages of mutations of populations. Low rates of historical movement of genes were observed between the potato and tobacco populations of R. solani AG-3. CONCLUSION: The two sisters populations of the basidiomycete fungus R. solani AG-3 from potato and tobacco represent two genetically distinct and historically divergent lineages that have probably evolved within the range of their particular related Solanaceae hosts as sympatric species.

  • 220.
    Chen, J
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Kallman, T
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Gyllenstrand, N
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Lascoux, M
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict2010In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 104, no 1, p. 3-14Article in journal (Refereed)
    Abstract [en]

    In all, 10 nuclear loci were re-sequenced in four spruce species. Three of the species are boreal species with very large natural ranges: Picea mariana and P. glauca are North American, and P. abies, is Eurasian. The fourth species, P. breweriana, is a Tertiary relict from Northern California, with a very small natural range. Although the boreal species population sizes have fluctuated through the Ice Ages, P. breweriana is believed to have had a rather stable population size through the Quaternary. Indeed, the average Tajima’s D was close to zero in this species and negative in the three boreal ones. Reflecting differences in current population sizes, nucleotide diversity was an order of magnitude lower in P. breweriana than in the boreal species. This is in contrast to the similar and high levels of heterozygosity observed in previous studies at allozyme loci across species. As the species have very different histories and effective population sizes, selection at allozyme loci rather than demography appears to be a better explanation for this discrepancy. Parameters of Isolation-with-Migration (IM) models were also estimated for pairs of species. Shared polymorphisms were extensive and fixed polymorphisms few. Divergence times were much shorter than those previously reported. There was also evidence of historical gene flow between P. abies and P. glauca. The latter was more closely related to P. abies than to its sympatric relative P. mariana. This last result suggests that North American and Eurasian species might have been geographically much closer in the recent past than they are today.

  • 221. Cho, Nam-Hyuk
    et al.
    Kim, Hang-Rae
    Lee, Jung-Hee
    Kim, Se-Yoon
    Kim, Jaejong
    Cha, Sunho
    Kim, Sang-Yoon
    Darby, Alistair C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Fuxelius, Hans-Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Yin, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Kim, Ju Han
    Kim, Jihun
    Lee, Sang Joo
    Koh, Young-Sang
    Jang, Won-Jong
    Park, Kyung-Hee
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Choi, Myung-Sik
    Kim, Ik-Sang
    The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host–cell interaction genes2007In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 104, no 19, p. 7981-7986Article in journal (Refereed)
    Abstract [en]

    Scrub typhus is caused by the obligate intracellular rickettsia Orientia tsutsugamushi (previously called Rickettsia tsutsugamushi). The bacterium is maternally inherited in trombicuid mites and transmitted to humans by feeding larvae. We report here the 2,127,051-bp genome of the Boryong strain, which represents the most highly repeated bacterial genome sequenced to date. The repeat density of the scrub typhus pathogen is 200-fold higher than that of its close relative Rickettsia prowazekii, the agent of epidemic typhus. A total of 359 tra genes for components of conjugative type IV secretion systems were identified at 79 sites in the genome. Associated with these are >200 genes for signaling and host–cell interaction proteins, such as histidine kinases, ankyrin-repeat proteins, and tetratrico peptide-repeat proteins. Additionally, the O. tsutsugamushi genome contains >400 transposases, 60 phage integrases, and 70 reverse transcriptases. Deletions and rearrangements have yielded unique gene combinations as well as frequent pseudogenization in the tra clusters. A comparative analysis of the tra clusters within the genome and across strains indicates sequence homogenization by gene conversion, whereas complexity, diversity, and pseudogenization are acquired by duplications, deletions, and transposon integrations into the amplified segments. The results suggest intragenomic duplications or multiple integrations of a massively proliferating conjugative transfer system. Diversifying selection on host–cell interaction genes along with repeated population bottlenecks may drive rare genome variants to fixation, thereby short-circuiting selection for low complexity in bacterial genomes.

  • 222.
    Constantinescu, O.
    et al.
    Uppsala University, Museums etc., Museum of Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Mel'nik, V.A.
    Verkley, G.J.M.
    Two parasitic fungi on a new host, Syringa (Oleaceae)2006In: Mycotaxon, Vol. 94, p. 175-179Article in journal (Refereed)
    Abstract [en]

    Thedgonia ligustrina, the agent of Ligustrum leaf-spot, and Gloeosporidiella turgida, known as a parasite of Fraxinus, are reported for the first time on Syringa spp. Both fungi were found in Sweden, the first in a tree nursery in the south, and the second on plants cultivated in Uppsala. Brief descriptions and illustration are provided and the distribution of T. ligustrina is reviewed.

  • 223.
    Constantinescu, Ovidiu
    et al.
    Uppsala University, Museums etc., Museum of Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Thines, Marco
    Dimorphism of sporangia in Albuginaceae (Chromista, Peronosporomycetes)2006In: Sydowia, ISSN 0082-0598, Vol. 58, no 2, p. 178-190Article in journal (Refereed)
    Abstract [en]

    By using light- and scanning electron microscopy, the dimorphism of sporangia in Albuginales is demonstrated in 220 specimens of Albugo, Pustula and Wilsoniana, parasitic on plants belonging to 13 families. The presence of two kinds of sporangia is due to the sporangiogenesis and considered to be present in all representatives of the Albuginales. Primary and secondary sporangia are the term recommended to be used for these dissemination organs.

  • 224.
    Corl, Ammon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Davis, Alison R.
    Kuchta, Shawn R.
    Sinervo, Barry
    Selective loss of polymorphic mating types is associated with rapid phenotypic evolution during morphic speciation2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 9, p. 4254-4259Article in journal (Refereed)
    Abstract [en]

    Polymorphism may play an important role in speciation because new species could originate from the distinctive morphs observed in polymorphic populations. However, much remains to be understood about the process by which morphs found new species. To detail the steps of this mode of speciation, we studied the geographic variation and evolutionary history of a throat color polymorphism that distinguishes the "rock-paper-scissors" mating strategies of the side-blotched lizard, Uta stansburiana. We found that the polymorphism is geographically widespread and has been maintained for millions of years. However, there are many populations with reduced numbers of throat color morphs. Phylogenetic reconstruction showed that the polymorphism is ancestral, but it has been independently lost eight times, often giving rise to morphologically distinct subspecies/species. Changes to the polymorphism likely involved selection because the allele for one particular male strategy, the "sneaker" morph, has been lost in all cases. Polymorphism loss was associated with accelerated evolution of male size, female size, and sexual dimorphism, which suggests that polymorphism loss can promote rapid divergence among populations and aid species formation.

  • 225.
    Costa, José Luis
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    The tRNALeu (UAA) Intron of Cyanobacteria: Towards Understanding a Genetic Marker2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The tRNALeu (UAA) intron has been recorded in the plastid genome of many algae and land plants and was the first intron to be discovered in cyanobacteria. In all known cases it interrupts the tRNALeu anticodon loop at a conserved position (U-intron-AA). Cyanobacteria are a diverse group of photosynthetic prokaryotes, some involved in symbiotic associations with a wide range of organisms. The most studied associations are those with plants, where strains of Nostoc are the common cyanobacterial partner. In this thesis two aspects of the biology of the cyanobacterial tRNALeu (UAA) intron are focused: first, the use of the intron as a genetic marker for studying the diversity and specificity of two cyanobacterial symbiosis (bryophytes and cycads) and second, the evolutionary patterns of the intron by using the unique data set generated from the diversity analysis.

    From the studies, many different Nostoc strains are involved in the two symbiotic associations, although no variation was observed within a single bryophyte cavity or cycad coralloid root. Furthermore, a certain level of temporal stability in the cyanobiont composition of the bryophyte population was found and, in the cycad association different coralloid roots from a single specimen may harbor different cyanobacteria. That a minor cyanobiont could have avoided detection is still possible but unlikely. The sequence alignment of the Nostoc tRNALeu (UAA) introns reveals great sequence similarity with size variation only found in the structural element P6b. This element was found to consist of heptanucleotide repeats and of other non-repetitive genetic elements (NIS elements). The sporadic occurrence of the NIS elements indicates recent origins and a mechanism for its dispersal is proposed.

    In this thesis new insights are given concerning cyanobacterial symbioses and also on the mechanisms involved in the evolution of an old genetic element: the tRNALeu (UAA) intron in cyanobacteria.

    List of papers
    1. Cyanobiont diversity within coralloid roots of selected cycad species
    Open this publication in new window or tab >>Cyanobiont diversity within coralloid roots of selected cycad species
    1999 (English)In: FEMS Microbiology Ecology, ISSN 0168-6496, Vol. 28, p. 85-91Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92108 (URN)
    Available from: 2004-09-23 Created: 2004-09-23 Last updated: 2012-08-22
    2. Sequenced based data supports a single Nostoc strain in coralloid roots of cycads
    Open this publication in new window or tab >>Sequenced based data supports a single Nostoc strain in coralloid roots of cycads
    2004 (English)In: FEMS Microbiology Ecology, ISSN 0168-6496, Vol. 49, p. 481-487Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92109 (URN)
    Available from: 2004-09-23 Created: 2004-09-23 Last updated: 2012-08-22
    3. Genetic diversity of Nostoc symbionts endophytically associated with two bryophyte species
    Open this publication in new window or tab >>Genetic diversity of Nostoc symbionts endophytically associated with two bryophyte species
    2001 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, Vol. 67, p. 4393-4396Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92110 (URN)
    Available from: 2004-09-23 Created: 2004-09-23 Last updated: 2012-08-22
    4. The cyanobacterial tRNA(Leu) (UAA) intron: Evolutionary patterns in a genetic marker
    Open this publication in new window or tab >>The cyanobacterial tRNA(Leu) (UAA) intron: Evolutionary patterns in a genetic marker
    2002 (English)In: Molecular Biology and Evolution, ISSN 0737-4038, Vol. 19, p. 850-857Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92111 (URN)
    Available from: 2004-09-23 Created: 2004-09-23 Last updated: 2012-08-22
    5. Dispersal of iterated sequences in the genome of the cyanobacterium Nostoc punctiforme
    Open this publication in new window or tab >>Dispersal of iterated sequences in the genome of the cyanobacterium Nostoc punctiforme
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92112 (URN)
    Available from: 2004-09-23 Created: 2004-09-23 Last updated: 2010-01-14Bibliographically approved
  • 226.
    Costa, José Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Elhai, Jeff
    Cousins, Sarah
    Lindblad, Peter
    Dispersal of iterated sequences in the genome of the cyanobacterium Nostoc punctiformeManuscript (Other (popular science, discussion, etc.))
  • 227.
    Costa, José Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Martínez-Romero, Esperanza
    Lindblad, Peter
    Sequenced based data supports a single Nostoc strain in coralloid roots of cycads2004In: FEMS Microbiology Ecology, ISSN 0168-6496, Vol. 49, p. 481-487Article in journal (Refereed)
  • 228.
    Costa, José Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Paulsrud, Per
    Lindblad, Peter
    Cyanobiont diversity within coralloid roots of selected cycad species1999In: FEMS Microbiology Ecology, ISSN 0168-6496, Vol. 28, p. 85-91Article in journal (Refereed)
  • 229.
    Costa, José Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Paulsrud, Per
    Lindblad, Peter
    The cyanobacterial tRNA(Leu) (UAA) intron: Evolutionary patterns in a genetic marker2002In: Molecular Biology and Evolution, ISSN 0737-4038, Vol. 19, p. 850-857Article in journal (Refereed)
  • 230.
    Costa, José Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Paulsrud, Per
    Rikkinen, Jouko
    Lindblad, Peter
    Genetic diversity of Nostoc symbionts endophytically associated with two bryophyte species2001In: Applied and Environmental Microbiology, ISSN 0099-2240, Vol. 67, p. 4393-4396Article in journal (Refereed)
  • 231.
    Costa, José-Luis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Martínez Romero, Esperanza
    Lindblad, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Sequence based data supports a single Nostoc strain in individual coralloid roots of cycads2004In: FEMS Microbiology: Ecology, Vol. 49, p. 481-487Article in journal (Refereed)
    Abstract [en]

    The genertic diversity of cyanobacteria associated with cycads was examined using the tRNA Leu (UAA) intron as a genetic marker. Coralloid roots of both natural populations of the cycad Macrozamia riedlei (Fischer ex Gaudichaud-Beaupré) C.A. Gardner growing in Perth, Australia and cycads growing in greenhouses, also in Perth, were used and their respective cyanobionts analyzed. Several Nostoc strains were found to be involved in this symbiosis, both in natural populations and greenhouse-orginated cycads. However, only one strain was present in individual coralloid roots and in individual plants, even when analyzing different coralloid roots from the same plant. Moreover, when examining plants growing close to each other (female plants and their respective offspring) the same cyanobacterium was consistently present in the different coralloid roots. Whether this reflects a selective mechanism or merely the availability of Nostoc strains remains to be ascertained. The high cyanobacterial diversity in coralloid roots of cycads revealed by PCR fingerprinting is, therefore, contested. In this study, the potential probems of using different methods (e.g. PCR fingerprinting) to study the genetic diversity of symbiotic cyanobacteria, is also addressed.

  • 232. Crespo, Ana
    et al.
    Lumbsch, H. Thorsten
    Mattsson, Jan-Eric
    Blanco, Oscar
    Divakar, Pradeep K.
    Articus, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Wiklund, Elisabeth
    Bawingan, Paulina A.
    Wedin, Mats
    Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 44, no 2, p. 812-824Article in journal (Refereed)
    Abstract [en]

    Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 1.20 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.

  • 233. Cruz, F.
    et al.
    Vilà, C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Webster, Matthew T.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    The legacy of domestication: Accumulation of deleterious mutations in the dog genome2008In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 25, no 11, p. 2331-2336Article in journal (Refereed)
    Abstract [en]

    Dogs exhibit more phenotypic variation than any other mammal and are affected by a wide variety of genetic diseases. However, the origin and genetic basis of this variation is still poorly understood. We examined the effect of domestication on the dog genome by comparison with its wild ancestor, the gray wolf. We compared variation in dog and wolf genes using whole-genome single nucleotide polymorphism (SNP) data. The d(N)/d(S) ratio (omega) was around 50% greater for SNPs found in dogs than in wolves, indicating that a higher proportion of nonsynonymous alleles segregate in dogs compared with nonfunctional genetic variation. We suggest that the majority of these alleles are slightly deleterious and that two main factors may have contributed to their increase. The first is a relaxation of selective constraint due to a population bottleneck and altered breeding patterns accompanying domestication. The second is a reduction of effective population size at loci linked to those under positive selection due to Hill-Robertson interference. An increase in slightly deleterious genetic variation could contribute to the prevalence of disease in modern dog breeds.

  • 234. Dacks, JB
    et al.
    Davis, LAM
    Sjögren, ÅM
    Andersson, Jan O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Roger, AJ
    Doolittle, WF
    Evidence for cryptic Golgi in putatively ‘Golgi-lacking’ lineages2003In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 270, p. S168-71Article in journal (Refereed)
    Abstract [en]

    Golgi bodies are nearly ubiquitous in eukaryotic cells. The apparent lack of such structures in certain eukaryotic lineages might be taken to mean that these protists evolved prior to the acquisition of the Golgi, and it raises questions of how these orga

  • 235. Dalén, L.
    et al.
    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.
    Angerbjörn, A.
    Identifying species from pieces of faeces.2004In: Conservation Genetics, ISSN 1566-0621, no 5, p. 105-111Article in journal (Refereed)
  • 236. Dalén, Love
    et al.
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Meijer, Tomas
    Shapiro, Beth
    Recovery of DNA from Footprints in the Snow2007In: Canadian field-naturalist, ISSN 0008-3550, Vol. 121, no 3, p. 321-324Article in journal (Refereed)
    Abstract [en]

    The recovery of trace amounts of DNA has been demonstrated to be a reliable tool in conservation genetics and has become a key component of modern forensic casework. To date, genetic data have been successfully recovered from a variety of sources, including biological fluids, faeces, clothing, and even directly from fingerprints. However, to our knowledge and despite their widespread occurrence and clear potential as a source of DNA, genetic information has not previously been recovered directly from footprints. Here, we extract and amplify mitochondrial DNA from a snow footprint, <48-hours old, made by a Swedish Arctic Fox (Alopex lagopus). Our results demonstrate that it is possible to recover Sufficient DNA from recent footprints to accurately type the source of the print, with implications for conservation biology and forensic science.

  • 237. Dalén, Love
    et al.
    Nyström, Veronica
    Valdiosera, Cristina
    Germonpré, Mietje
    Sablin, Mikhail
    Turner, Elaine
    Angerbjörn, Anders
    Arsuaga, Juan Luis
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox2007In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 104, no 16, p. 6726-6729Article in journal (Refereed)
    Abstract [en]

    How species respond to an increased availability of habitat, for example at the end of the last glaciation, has been well established. In contrast, little is known about the opposite process, when the amount of habitat decreases. The hypothesis of habitat tracking predicts that species should be able to track both increases and decreases in habitat availability. The alternative hypothesis is that populations outside refugia become extinct during periods of unsuitable climate. To test these hypotheses, we used ancient DNA techniques to examine genetic variation in the arctic fox (Alopex lagopus) through an expansion/contraction cycle. The results show that the arctic fox in midlatitude Europe became extinct at the end of the Pleistocene and did not track the habitat when it shifted to the north. Instead, a high genetic similarity between the extant populations in Scandinavia and Siberia suggests an eastern origin for the Scandinavian population at the end of the last glaciation. These results provide new insights into how species respond to climate change, since they suggest that populations are unable to track decreases in habitat avaliability. This implies that arctic species may be particularly vulnerable to increases in global temperatures.

  • 238. Dani, FR
    et al.
    Foster, KR
    Zacchi, F
    Seppä, P
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics.
    Can cuticular lipids provide sufficient information for within-colony nepotism in wasps?2004In: Proceedings of the Royal Soc. B, Vol. 271, p. 745-753Article in journal (Other (popular scientific, debate etc.))
  • 239. Daniel, Thomas F.
    et al.
    McDade, Lucinda A.
    Manktelow, Mariette
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Kiel, Carrie A.
    The "Tetramerium Lineage" (Acanthaceae : Acanthoideae : Justicieae): Delimitation and intra-lineage relationships based on cp and nrITS sequence data2008In: Systematic Botany, ISSN 0363-6445, E-ISSN 1548-2324, Vol. 33, no 2, p. 416-436Article in journal (Refereed)
    Abstract [en]

    We used DNA sequence data from five genic regions (nrITS; chloroplast trnL-F, trnT-L, rps16, trnS-G) to study phylogenetic relationships of the Tetramerium lineage (Acanthaceae: Justicieae). From a sample of 70 species (representing 25 genera) previously affiliated with the Tetramerium lineage, 68 are included therein. Our analyses excluded Papuasian Calycacanthus and Neotropical Streblacanthus monospermus from the Tetramerium lineage; however, two species described in Justicia (J. gonzalezii and J. medranoi) and a Malagasy species of uncertain generic affinities are nested within the lineage. A monophyletic Tetramerium lineage consists of 23 currently recognized genera with at least 168 species, more than 70% of which occur in the New World. Old World Chlamydocardia and Clinacanthus are serially sister to all other members of the lineage. Other Old World taxa consist of: Ecbolium clade (all sampled species of Ecbolium plus Malagasy Populina richardii), Megalochlamys clade (Megalochlamys, Trichaulax and the unidentified Malagasy species), and two isolated taxa (Angkalanthus and Chorisochora). All analyses strongly support monophyly of the New World Tetramerium lineage. The basal clades of New World plants, all with nototribic flowers, are: 1) the taxonomically heterogeneous but palynologically consistent Mirandea clade, and 2) the Pachystachys clade + the South American Anisacanthus clade. The second is sister to all other NW plants, referred to here as the core Tetramerium lineage. We recognize five clades within the core Tetramerium lineage related as follows: (Henrya clade (Carlowrightia parviflora clade (North American Anisacanthus clade (core Carlowrightia clade + Tetramerium)))). Macromorphological synapomorphies are unknown for the Tetramerium lineage and for many of its constituent clades. However, we propose sternotribic flowers as synapomorphic for the core Tetramerium lineage, and flowers with the lower-central lobe of the corolla modified into a keel as a synapomorphy for a lineage consisting of Tetramerium and the core Carlowrightia clade. Palynological characters provide putative synapomorphies for some clades (e.g. Ecbolium clade, Mirandea clade) and autapomorphies for several species (e.g. Mexacanthus mcvaughii, Trichalux mwasumbii). An Old World origin is postulated for the Tetramerium lineage, and we posit a single dispersal event to America and subsequent extensive radiation there, especially in arid zones of Mexico and adjacent regions. Taxonomic implications of our results are extensive. Notably, many traditionally recognized genera (e.g. Anisacanthus, Carlowrightia, Mirandea) are not monophyletic and emphasis on floral form often has been phylogenetically misleading; for example, floral adaptations to pollination by hummingbirds have evolved at least eight times in the New World Tetramerium lineage.

  • 240.
    Darby, Alistair C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Cho, N. H.
    Fuxelius, Hans-Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Westberg, Joakim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv G.E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Intracellular pathogens go extreme: genome evolution in the Rickettsiales2007In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 23, no 10, p. 511-520Article, review/survey (Refereed)
    Abstract [en]

    The Rickettsiales, a genetically diverse group of the α-Proteobacteria, include major mammalian pathogens, such as the agents of epidemic typhus, scrub typhus, ehrlichioses and heartwater disease. Sequenced genomes of this bacterial order have provided exciting insights into reductive genome evolution, antigenic variation and host cell manipulation. Recent results suggest that human pathogens emerged relatively late in the evolution of the Rickettsiales. Surprisingly, there is no association between pathogenicity and the acquisition of novel virulence genes. Here, we explore the genomic differences between members of the Rickettsiales and ask what are the changes that enable infectious agents to emerge from seemingly harmless bacteria.

  • 241. Das, S
    et al.
    Lagercrantz, Ulf
    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.
    Lascoux, Martin
    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.
    Black mustard2006In: Genome mapping and molecular breeding in plants: Oilseeds, Springer, , 2006Chapter in book (Refereed)
  • 242. Davids, W.
    et al.
    Fuxelius, H. H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, S. G. E.
    The journey to smORF-land2003In: Comparative and Functional Genomics, Vol. 4, p. 537-541Article in journal (Refereed)
  • 243.
    Davids, Wagied
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Causes of Substitution Frequency Variation in Pathogenic Bacteria2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Estimating substitution frequencies at sites that influence (Ka) and do not influence (Ks) the amino acid sequence is important for understanding the dynamics of molecular sequence evolution and the selective pressures that have shaped genetic variation.

    The aim of this work was to gain a deeper understanding of the driving forces of substitution frequency variation in human pathogens. Rickettsia prowazekii, the causative agent of epidemic typhus and Helicobacter pylori, which has been implicated in gastric diseases were used as model systems. A specific focus was on the evolution of orphan genes in Rickettsia. Additionally, adaptive sequence evolution and factors influencing protein evolutionary rates in H. pylori were studied.

    The comparative sequence analyses of orphan genes using Typhus Group (TG) and Spotted Fever Group (SFG) Rickettsia, indicate that orphan genes in the SFG correspond to pseudogenes in the TG and that pseudogenes in the SFG correspond to extensively degraded gene remnants in the TG. The analysis also showed that ancestral gene sequences could be reconstructed from extant gene remnants of closely related species. The studies of split genes in R. conorii indicate that many of the small fragmented ORFs are probably pseudogenes. Analysis of the H. pylori carbamoyl phosphate synthetase provided an opportunity to understand natural selection acting on a protein undergoing adaptive evolution. Factors such as network properties, protein-protein interactions, gene essentiality and chromosomal position on protein evolutionary rates in H. pylori were studied, of which antigenicity and gene location were identified as the strongest factors.

    In conclusion, high Ka/Ks ratios in human pathogens may reflect either adaptive sequence evolution or gene deterioration. Distinguishing between the two is an important task in molecular evolution and also of great relevance for medical microbiology and functional genomics research.

    List of papers
    1. Small RNAs in Rickettsia: are they functional?
    Open this publication in new window or tab >>Small RNAs in Rickettsia: are they functional?
    2002 In: Trends in Genetics, ISSN 0168-9525, Vol. 18, no 7, p. 331-334Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92753 (URN)
    Available from: 2005-03-23 Created: 2005-03-23Bibliographically approved
    2. Birth and death of orphan genes in Rickettsia
    Open this publication in new window or tab >>Birth and death of orphan genes in Rickettsia
    2003 In: Molecular Biology and Evolution, ISSN 0737-4038, Vol. 20, no 10, p. 1575-1587Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92754 (URN)
    Available from: 2005-03-23 Created: 2005-03-23Bibliographically approved
    3. The journey to smORFland
    Open this publication in new window or tab >>The journey to smORFland
    2003 In: Comparative and Functional Genomics, ISSN 1532-6268, Vol. 4, no 5, p. 537-541Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92755 (URN)
    Available from: 2005-03-23 Created: 2005-03-23Bibliographically approved
    4. To code or not to code: Sequence evolution in Rickettsia
    Open this publication in new window or tab >>To code or not to code: Sequence evolution in Rickettsia
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-92756 (URN)
    Available from: 2005-03-23 Created: 2005-03-23 Last updated: 2010-01-13Bibliographically approved
    5. Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori
    Open this publication in new window or tab >>Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori
    2002 In: Journal of Molecular Evolution, ISSN 1432-1432, Vol. 54, no 4, p. 458-464Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92757 (URN)
    Available from: 2005-03-23 Created: 2005-03-23Bibliographically approved
    6. Sources of substitution frequency variation in Helicobacter pylori
    Open this publication in new window or tab >>Sources of substitution frequency variation in Helicobacter pylori
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-92758 (URN)
    Available from: 2005-03-23 Created: 2005-03-23 Last updated: 2010-01-13Bibliographically approved
  • 244.
    Davids, Wagied
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Amiri, Haleh
    Andersson, Siv
    Small RNAs in Rickettsia: are they functional?2002In: Trends in Genetics, ISSN 0168-9525, Vol. 18, no 7, p. 331-334Article in journal (Refereed)
  • 245.
    Davids, Wagied
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Fuxelius, Hans-Henrik
    Andersson, Siv
    The journey to smORFland2003In: Comparative and Functional Genomics, ISSN 1532-6268, Vol. 4, no 5, p. 537-541Article in journal (Refereed)
  • 246.
    Davids, Wagied
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Gamieldien, Junaid
    Liberles, David
    Hide, Winston
    Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori2002In: Journal of Molecular Evolution, ISSN 1432-1432, Vol. 54, no 4, p. 458-464Article in journal (Refereed)
  • 247.
    Davids, Wagied
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Sällström, Björn
    Arnaout, Ramy
    Andersson, Siv
    Sources of substitution frequency variation in Helicobacter pyloriManuscript (Other academic)
  • 248.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Hagemann, Ulrich
    Bate, Jenny
    Meyboom, Ronald H. B.
    Allergic reactions to medicines derived from Pelargonium species2007In: Drug Safety, ISSN 0114-5916, E-ISSN 1179-1942, Vol. 30, no 8, p. 677-680Article in journal (Refereed)
    Abstract [en]

    Pelargonium (Pelargonium sidoides DC and P. reniforme Curtis) is reported to have immune modulating properties and antibacterial activity, and Pelargonium extracts have been used for the treatment of respiratory tract and gastrointestinal infections. Introduced in the early 1980s in Germany, Umckaloabo® (ISO Arzneimittel), an ethanolic extract of the roots of P. sidoides and P. reniforme, was the first Pelargonium-derived product to be commonly used in a country in the EU. According to the Umckaloabo® product information, this extract has no known adverse effects. However, there is a theoretical risk of interactions with anticoagulants such as warfarin, and antiplatelet drugs, such as aspirin (acetylsalicylic acid). To date, the Uppsala Monitoring Centre has, through the WHO international pharmacovigilance programme, received 34 case reports of allergic reactions suspected to be associated with the use of Pelargonium extract, all originating from Germany. In a number of these reports, the description and timing of the event was indicative of an acute Coombs and Gell Type I hypersensitivity reaction; two of these patients needed treatment for circulatory failure. So far, the experience of such reactions is limited to Germany. Since Pelargonium-containing herbal products have recently been approved in a number of other countries, the possibility of the occurrence of allergic reactions has become of more general interest and further information regarding these products is needed.

  • 249.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kool, Anneleen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Björk, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Ethnobotanical research and teaching: A Case in Bulgaria2006In: Program of the Society for Economic Botany 47th Annual Meeting, 2006Conference paper (Other (popular science, discussion, etc.))
    Abstract [en]

    Introduction

    Bulgarian people in rural areas have a tradition of using herbal medicine as household remedies,

    due partly to the scarcity of pharmaceuticals during the Soviet era. As part of a fieldwork exercise

    in the ethnobotany course taught at Uppsala University students carried out ethnobotanical

    research in different areas in Bulgaria to study and describe these traditions.

    Objectives

    To study: Plants used to treat fevers and cold; plants used to treat wounds and for pain-relief;

    plants grown in home gardens; plants used for magical purposes; and awareness of endangerment

    of medicinally used plants.

    Methods

    Our group of 16 students was divided in groups of two-three students. Each group had written a

    project proposal focusing on one of the study objectives, and carried out this research with the help

    of a Bulgarian translator, who was knowledgeable about the local flora. Three field sites had been

    selected to spread the students throughout the country and to prevent informant fatigue. Interviews

    were semi-structured and if necessary, walks were made with the informants to point out plants and

    collect herbarium vouchers.

    Results

    The students as a whole managed to collect an enormous amount of data in a very short time, and

    some groups carried out as many as 18 interviews during the 8-day field period. Results were

    analyzed per group and presented during a one-day seminar at Ruse University, Bulgaria.

    Conclusion

    Bulgarian villagers, mainly ederly people, rely to a great extent on the use of medicinal plants to

    treat common and non-threatening chronic diseases. These plants are often grown in home

    gardens, and less so collected in the wild. Knowledge is often based on books, and less so on

    maternal or paternal transmission. The people living in Roussenski Lom national park experience

    that most medicinally used wild plants have stayed equal or increased in abundance over the last

    decennium. Carrying out ethnobotanical field research can be effective and efficiently done as part

    of a course training ethnobotany students.

  • 250.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Kool, Anneleen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Broberg, Anders
    Department of Chemistry, Swedish University of Agricultural Sciences.
    Mziray, William R
    National Herbarium of Tanzania, Tropical Pesticide Research Institute.
    Hedberg, Inga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Levenfors, Jolanta J
    Agrivir AB, Uppsala.
    Anti-fungal and anti-bacterial activity of some herbal remedies from Tanzania2005In: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 96, no 3, p. 461-469Article in journal (Refereed)
    Abstract [en]

    Plants are not only important to the millions of people to whom traditional medicine serves as the only opportunity for health care and to those who use plants for various purposes in their daily lives, but also as a source of new pharmaceuticals. During interviews with the Pare people from Northeastern Tanzania, 29 plants that are used for medicinal purposes as well as 41 plants used for non-medicinal purposes were reported. Six medicinally used plants were selected for bioactivity analysis. Extracts of Coccinia adoensis, Cineraria grandiflora, Pavonia urens, Marattia fraxinea, Clutia abyssinica var. usambarica, and Vangueria infausta were made using ethyl acetate, methanol, cold water and boiling water. The antimicrobial activity was tested on Candida albicans, Aspergillus fumigatus, Fusarium culmorum, Staphylococcus aureus, Pseudomonas syringae, and Erwinia amylovora. All plants showed activity against several test organisms.

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